DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Claims 2, 15, and 17-30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4/2/2026.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) was submitted on 3/27/2026 before the mailing of a first office action. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Status
Claims 1-32 are pending. Claims 2, 15, and 17-30 are withdrawn from further consideration. Claims 1, 3-14, 16, and 31-32 are under examination.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Specifically, hyperlinks occur at para. [0014] in the specification.
Claim Rejections - 35 USC § 112
Claim 14 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 14 recites: “The method according to claim 1 comprising a step of supporting the peptide on the solid phase synthesis resin.”
It is not clear if this is an additional step or meant to replace the steps in claim 1. Because dependent claims must contain all the limitations of the claim from which they depend, this claim shall be interpreted as the former for examination. This can be resolved by adding “further” before “comprising”.
Claim 14 is rejected.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 12, 13, and 31 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
In totality, Yang discloses a process for creating a 2-Cl-trityl resin preloaded with an N-methylated amino acid, which, when used in solid phase peptide synthesis reaction, necessarily results in a peptide that comprises at least one N-substituted amino acid. Because the resin is preloaded, the peptide is supported on the solid phase resin before the first elongation reaction.
Consequently, claim 1 is anticipated by Yang et al. and rejected.
Regarding claim 12, claim 1 is anticipated as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is anticipated by Yang et al. and rejected.
Regarding claim 13, claim 1 is anticipated as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is anticipated by Yang et al. and rejected.
Regarding claim 31, claim 1 is anticipated as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is anticipated by Yang et al. and rejected.
Claim 8 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is anticipated as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is anticipated by Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is anticipated as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is anticipated by Yang et al. as evidenced by Lesarri et al. and rejected.
Regarding claim 10, claim 9 is anticipated as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is anticipated by Yang et al. as evidenced by Lesarri et al. and rejected.
Regarding claim 11, claim 10 is anticipated as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is anticipated by Yang et al. as evidenced by Lesarri et al. and rejected.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 3 and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is anticipated as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over Yang et al. in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is anticipated as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over Yang et al. in view of Holm et al. and rejected.
Claims 4-6 are rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is anticipated as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is anticipated as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is anticipated as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious over Yang et al. in view of Ficht et al. and rejected.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is anticipated as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over Yang et al. in view of Prior et al. and rejected.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is anticipated as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over Yang et al. in view of Angeletti et al. and rejected.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1, 12, 13, and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘379 patent recites:
“A method for producing a peptide compound by a liquid phase method, comprising:
step 1: linking an N-protected amino acid or N-protected peptide to a C-protected amino acid or C-protected peptide;
step 2: removing the N-protecting group after step 1; and
optionally repeating steps 1 and 2 a plurality of times to produce the peptide compound;
wherein the method does not comprise isolating the product of each of steps 1 and 2;
wherein each of the steps comprised in the method for producing the peptide compound is carried out in Solvent B, which is one or more solvents selected independently from the group consisting of toluene, 2-methyltetrahydrofuran (2-MeTHF), methyl tert-butyl ether (MTBE), dimethyl carbonate, anisole, isopropyl acetate, heptane, ethyl acetate, and 4-methyltetrahydropyran;
wherein workup in each of the steps comprised in the method for producing the peptide compound comprises one or more operations selected from the group consisting of a liquid separation operation, a filtration operation, and a concentration operation;
wherein Solvent C is added for the liquid separation operation;
wherein Solvent C is a water-immiscible solvent which comprises one or more solvents selected from the group consisting of 2-MeTHF, dimethyl carbonate, anisole, isopropyl acetate, ethyl acetate, MTBE, cyclopentyl methyl ether (CPME), 4-methyltetrahydropyran, and heptane;
wherein the workup in the steps comprised in the method for producing the peptide compound comprises one or more of the liquid separation operation; and
wherein the peptide compound comprises at least one N-alkyl amino acid residue.” (Emphasis added)
The ‘379 patent does not disclose the case wherein the first peptide is supported on the resin before the first elongation step.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘379 patent to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘379 patent in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘379 patent in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘379 patent in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘379 patent in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘379 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘379 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘379 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘379 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘379 patent in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘379 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘379 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘379 patent in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘379 patent in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘379 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘379 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘379 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘379 patent in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,312,379 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘379 patent in view of Yang et al. and Angeletti et al. and rejected.
Claims 1, 12, 13, and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘299 patent recites:
“A method for producing a peptide compound having an N-substituted-α,α-disubstituted amino acid residue at the N-terminus and comprising a dipeptide residue in which the N-substituted-α,α-disubstituted amino acid residue is linked to an N-substituted amino acid residue, a salt thereof, or a solvate of these, the method comprising the following steps of:
Step A: reacting (1) an N-substituted amino acid, a salt thereof, or a solvate of these, or a peptide compound having an N-substituted amino acid residue at the N-terminus, a salt thereof, or a solvate of these, wherein the main-chain amino group of the N-substituted amino acid or the N-substituted amino acid residue is represented by —NHR, wherein R is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted aralkyl, and optionally substituted cycloalkyl, or R represents a carbon chain bonded to the N atom, which together with the carbon atom at the α-position form an optionally substituted ring,
with (2) an α,α-disubstituted amino acid having an amino group protected with an electron-withdrawing protecting group, a salt thereof, a dehydrated product thereof, or a solvate of these, wherein the amino group is the amino group on the main chain of the α,α-disubstituted amino acid and is represented by the formula —NHR′, wherein R′ is the electron-withdrawing protecting group, wherein the electron-withdrawing protecting group is a protecting group with which the pKa in water of the NH group to which the protecting group is bonded is 6 to 11,
in the presence or absence of a condensing reagent to obtain a peptide compound having an α,α-disubstituted amino acid residue having an amino group protected with an electron-withdrawing protecting group at the N-terminus and comprising a dipeptide residue in which the α,α-disubstituted amino acid residue is linked to an N-substituted amino acid residue, a salt thereof, or a solvate of these; and
Step B: introducing a substituent to the amino group of the α,α-disubstituted amino acid residue protected with the electron-withdrawing protecting group at the N-terminus in the presence of a base and a substituent-introducing agent to obtain a peptide compound having an α,α-disubstituted amino acid residue having an amino group on the main chain of the α,α-disubstituted amino acid substituted with the substituent and protected with the electron-withdrawing protecting group at the N-terminus and comprising a dipeptide residue in which the α,α-disubstituted amino acid residue is linked to the N-substituted amino acid residue, a salt thereof, or a solvate of these.”
The ‘299 patent does not disclose the case wherein the first peptide is supported on the resin before the first elongation step.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘299 patent to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘299 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘299 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘299 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘299 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘299 patent in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘299 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘299 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘299 patent in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘299 patent in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘299 patent in view of Yang et al. and Angeletti et al. and rejected.
Claims 1, 12, 13, and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘836 patent recites:
A method of producing a peptide comprising at least one N-alkylated amino acid or proline, wherein the N-alkyl of the N-alkylated amino acid and the proline are optionally substituted with a substituent independently selected from the group consisting of a halogen group, an ether group, and a hydroxyl group;
wherein the method comprises the steps of:
1) preparing an (Fmoc-protected amino acid comprising at least one each of following functional groups i) and ii), an Fmoc-protected peptide comprising the Fmoc-protected amino acid:
i) a main chain amino group protected by at least one protecting group having an Fmoc skeleton; and
ii) at least one free carboxylic acid group or active esterified carboxylic acid group;
The ‘836 patent does not disclose the case wherein the first peptide is supported on the resin before the first elongation step.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘836 patent to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘836 patent in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘836 patent in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘836 patent in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘836 patent in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘836 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘836 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘836 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘836 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘836 patent in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘836 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘836 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘836 patent in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘836 patent in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘836 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘836 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘836 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘836 patent in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,787,836 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘836 patent in view of Yang et al. and Angeletti et al. and rejected.
Claims 1, 12, 13, and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘141 patent recites:
“A method of producing a peptide comprising at least one N-alkylated amino acid or proline, wherein the N-alkyl of the N-alkylated amino acid and the proline are optionally substituted with a substituent independently selected from the group consisting of a halogen group, an ether group, and a hydroxyl group;
wherein the method comprises the steps of:
1) preparing an Fmoc-protected amino acid comprising at least one each of following functional groups i) and ii), or an Fmoc-protected peptide comprising the Fmoc-protected amino acid:
i) a main chain amino group protected by at least one protecting group having an Fmoc skeleton; and
ii) at least one free carboxylic acid group or active esterified carboxylic acid group;
The ‘141 patent does not disclose the case wherein the first peptide is supported on the resin before the first elongation step.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘141 patent to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘141 patent in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘141 patent in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘141 patent in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘141 patent in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘141 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘141 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘141 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘141 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘141 patent in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘141 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘141 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘141 patent in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘141 patent in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘141 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘141 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘141 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘141 patent in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,281,141 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘141 patent in view of Yang et al. and Angeletti et al. and rejected.
Claims 1, 12, 13, and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘299 patent recites:
“ A method of producing a peptide comprising at least one N-alkylated amino acid or proline, wherein the N-alkyl of the N-alkylated amino acid and the proline are optionally substituted with a substituent independently selected from the group consisting of a halogen group, an ether group, and a hydroxyl group;
wherein the method comprises the steps of:
1) preparing an Fmoc-protected amino acid comprising at least one each of following functional groups i) and ii), or an Fmoc-protected peptide comprising the Fmoc-protected amino acid:
i) a main chain amino group protected by at least one protecting group having an Fmoc skeleton; and
ii) at least one free carboxylic acid group or active esterified carboxylic acid group;
2) making the Fmoc-protected amino acid, or the Fmoc-protected peptide prepared in step 1) to be supported onto a solid phase;
3) deprotecting the protecting group having the Fmoc skeleton of the Fmoc-protected amino acid, or the Fmoc-protected peptide, which is supported onto the solid phase, by using a base to expose its amino group;
4) forming an amide bond by adding a new Fmoc-protected amino acid, or a new Fmoc-protected peptide; and
5) cleaving the peptide obtained in step 4) off from the solid phase under a condition of weaker acidity than TFA;
wherein the condition of weaker acidity than TFA in step 5) is a condition that uses a weakly acidic solution containing a fluoroalcohol.”
The ‘299 patent does not disclose the case wherein the first peptide is supported on the resin before the first elongation step.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘299 patent to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘299 patent in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘299 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘299 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘299 patent and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘299 patent and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘299 patent in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘299 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘299 patent in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘299 patent in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘299 patent in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘299 patent in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,542,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘299 patent in view of Yang et al. and Angeletti et al. and rejected.
Claims 1, 12, 13, and 31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 18/854,568 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)).
This is a provisional nonstatutory double patenting rejection.
Applicant claim 1 recites: “A method for producing a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof by a solid phase process, the method comprising elongating a peptide supported on a solid phase synthesis resin, wherein the peptide is supported on the solid phase synthesis resin before a first elongation reaction in the solid phase process.”
Claim 1 of the ‘568 application recites:
“A method for producing a peptide compound by a solid phase method, the method comprising: a preparation step of preparing a first amino acid having an amino group or a first peptide having an amino group supported on a solid phase; and a condensation step of condensing the first amino acid or first peptide, and a second amino acid having a protected amino group and/or protected hydroxy group and a carboxy group, or a second peptide having a protected amino group and/or protected hydroxy group and a carboxy group in the presence of at least one carbodiimide-based condensing agent represented by the following formula (A): RA-N=C=N-RB (A) wherein RAisC4-C10secondary or tertiary alkyl, and RBisC2-C1o alkyl, C6-C10 aryl, orC7-C14 arylalkyl, and each group in RA and RBisoptionally substituted with one or more groups independently selected from halogen, C1-C6 alkoxy, di-C1-C6 alkylamino, or 4- to 8-membered cyclic amino,and an additive.” (Emphasis added).
The ‘568 application patent does not disclose the case wherein the peptide synthesized is N-substituted.
However, Yang discloses a scheme that is for the production of peptides that contain N-methylated residues: “The incorporation of N-methyl amino acids into biologically active peptides has been widely used to study conformation and biological activity. An N-methylated peptide amide bond often exhibits higher resistance to proteolysis and thus may result in improved oral activity and enhanced duration of action. N-methylated peptides are generally synthesized by incorporation of protected N-methylated amino acids in solution or solid phase.” (Yang et al., page 7307, Abstract).
Specifically, Yang adapts the then recently discovered Fukuyama reaction for the production of a preloaded 2-Cl-trityl resin:
“Recently, a new amine protection/alkylation protocol was introduced by Fukuyama and coworkers, and was found to be effective in the preparation of secondary amines from primary amines without either primary or tertiary amine contamination. They also demonstrated the synthesis of mono alkylated phenylalanines based on this strategy. Adaptation of this method to solid phase peptide synthesis should prove extremely valuable. Herein we report the solid phase synthesis of N-methyl amino acids or their N-Fmoc protected analogs by applying the Fukuyama amine synthesis.
We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7307, para. 1).
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(Yang et al., page 7308, top of page).
“In summary, the Fukuyama amine synthesis is a reliable method for the solid phase conversion of amino acids to their N-methylated forms in high yield and purity. The procedure is especially valuable for the preparation of N-methylated amino acids that are difficult to synthesize by conventional methods. In addition, this methodology can be easily adapted for the preparation of other N-alkyl amino acids providing a good alternative to reductive alkylation.” (Yang et al., page 7309, para. 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the preloaded resin of Yang with the method of the ‘568 application to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use the preloaded scheme of Yang in order to create an N-methylated amino acid at the C-terminus and to avoid reductive alkylation as disclosed by Yang.
A person of ordinary skill in the art would have a reasonable expectation of success because Yang discloses the following yields:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 1 is obvious over the ‘568 application in view of Yang et al. and rejected.
Regarding claim 12, claim 1 is obvious as described above. Claim 12 further recites the case wherein the solid phase synthesis resin is CTC resin, Wang resin, SASRIN resin, Trt resin, Mtt resin, or Mmt resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 12 is obvious over the ‘568 application in view of Yang et al. and rejected.
Regarding claim 13, claim 1 is obvious as described above. Claim 13 further recites the case wherein the solid phase synthesis resin is CTC resin.
Yang discloses the usage of CTC resin:
“We investigated the scope of the reaction by using amino acids preloaded on the 2-CI-trityl resin, since it has been widely used for fully protected peptide fragment synthesis.” (Yang et al, page 7308, para. 1).
Consequently, claim 13 is obvious over the ‘568 application in view of Yang et al. and rejected.
Regarding claim 31, claim 1 is obvious as described above. Claim 31 further recites the case wherein the amino acid residue at the C-terminal of the peptide is represented by the formula A:
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Yang discloses the case where Ala is the N-methylated residue:
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(Yang et al., page 7308, bottom of page).
In this case, L1 is a single bond, Q1 is hydrogen, R1 is C1 alkyl, and P1 is C1 alkyl.
Consequently, claim 31 is obvious over the ‘568 application in view of Yang et al. and rejected.
Claims 3 and 32 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as applied to claim 1 above, further in view of Holm et al. WO 1998/011125 (published 3/19/1998).
Regarding claim 3, claim 1 is obvious as described above. Claim 3 further recites the case wherein the peptide is an oligopeptide containing two or more amino acid residues.
Yang only discloses the case wherein a single residue is present on the resin before elongation.
However, Holm discloses a process wherein solid phase synthesis occurs on a resin with 3 to 9 residues supported on the resin before elongation:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide. (Holm et al., claim 1, emphasis added).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘568 application and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with identical C-termini.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 3 is obvious over the ‘568 application and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Regarding claim 32, claim 1 is obvious as described above. Claim 32 further recites:
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As described above, Yang does not disclose a resin with a dipeptide supported before elongation.
However, Holm discloses a resin with 3 to 9 residues attached, which necessarily encompasses a dipeptide:
“A process for the production of peptides
X-AA!-AA2 AAn-Y
wherein AA is an L- or D-amino acid residue,
X is hydrogen or an amino protective group
Y is OH, NH2 or an amino acid sequence comprising from 3 to 9 amino acid residues and n is an integer greater than 2 by solid phase synthesis wherein the C-terminal amino acid in the form of an N-α- protected, if necessary side chain protected reactive derivative is coupled to a solid support or a polymer optionally by means of a linker, subsequently N-α- deprotected, whereafter the subsequent amino acids forming the peptide sequence are stepwise coupled or coupled as a peptide fragment in the form of suitably protected reactive derivatives or fragments, wherein the N-α-protective group is removed following formation of the desired peptide and the peptide is cleaved from the solid support,
characterized in that the C-terminal part attached to the support or polymer comprises a pre- sequence comprising from 3 to 9 , preferably from 5 to 7 amino acid residues independently selected from native L-amino acids having a side chain functionality which is protected during the coupling steps and having a propensity factor Pα > 0,57 and a propensity factor Pβ > 1,10 or the corresponding D-amino acids and said pre-sequence is optionally cleaved from the formed peptide.” (Holm et al., claim 1, emphasis added).
Furthermore, Hold discloses that:
“L-amino acids meeting the above-mentioned limits for the propensity factors Pα and Pβ are Lys, Glu, Asp, Ser, His, Asn, Arg, Met and Gln.
These amino acids all have a side chain functionality selected from a carboxy, carboxa ido, amino, hydroxy, guanidino, sulphide or imidazole group.
Presently preferred amino acids in the pre-sequence are Lys and Glu and combinations thereof, e.g. ( Glu )q(Lys )p , where p + q is 3 to 9 , preferably 6 to 9, and the order of Lys and Glu is arbitrarily chosen .” (Holm et al., page 16, line 23).
This reads on Applicant formula I in the case where:
L1 is a single bond, Q1 is hydrogen, R1 is C4 alkyl substituted with an amino group (lysine), Q2 is hydrogen, R2 is C2 alkyl substituted with a hydroxyl group (serine) and P2 is hydrogen.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method of the ‘568 application and Yang with the resin disclosed by Holm to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination to reduce synthesis errors for making a set of peptides with lysine and serine at the C-terminal.
A person of ordinary skill in the art has a reasonable expectation of success because the method synthesizing N-substituted amino acids disclosed by Yang:
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(Yang et al., page 7308, top of page).
would reasonably be expected to work in the case where there are additional amino acids between the target residue and “R”.
Consequently, claim 32 is obvious over the ‘568 application and Yang et al. as applied to claim 1, further in view of Holm et al. and rejected.
Claims 4-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Swiss Institute of Bioinformatics (https://swisssidechain.ch/browse/family/table.php?family=all, accessed 5/26/2026, dated to 9/4/2018) and Liu et al. (Liu, et al. Analytical Biochemistry 295.1: 9-16 (2001)).
Regarding claim 4, claim 1 is obvious as described above. Claim 4 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal are non-natural amino acid residues.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to produce a peptide compound such that the initially supported peptide is an N-methylated residue according to Yang and the first elongation residue added is an unnatural amino acid.
A person of ordinary skill in the art would be motivated to use one of the unnatural amino acid side chains as disclosed by the Swiss Institute of Bioinformatics in order to incorporate that unnatural amino acid for any scientific or medicinal purpose.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu discloses that solid phase synthesis involving unnatural amino acids is common place: “It is now routine using automatic Edman microsequencing to determine the primary structure of peptides or proteins containing natural amino acids; however, a deficiency in the ability to readily sequence peptides containing unnatural amino acids remains. With the advent of synthetic peptide chemistry, combinatorial chemistry, and the large number of commercially available unnatural amino acids, there is a need for efficient and accurate structure determination of short peptides containing many unnatural amino acids. In this study, 35 commercially available unnatural amino acids were selected to determine their elution profile on an ABI protein sequencer.” (Liu et al., page 9, col. 1, para. 1).
Consequently, claim 4 is obvious over the ‘568 application in view of Yang et al. in view of Swiss Institute of Bioinformatics and Liu et al. and rejected.
Regarding claim 5, claim 1 is obvious as described above. Claim 5 further recites the case wherein an amino acid residue at the C-terminal of the peptide is a non-natural amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use a CTC resin preloaded with an unnatural amino acid as suggested by Yang, Swiss Institute of Bioinformatics, and Liu and then extend at least once using the N-methylated amino acids of Yang to arrive at the claimed invention.
A person of ordinary skill in the would be motivated to do this in order to create an amino acid with a particular unnatural amnio acid at the C-terminus.
A person of ordinary skill in the art would have a reasonable expectation of success because Liu describes that solid phase synthesis of unnatural amino acids is routine and also this is a case of substituting one Fmoc-protected amino acid for another Fmoc-protected amino acid. Once the resin is preloaded with the unnatural amino acid residue, it is standard solid phase synthesis step to extend with an N-methylated residue of Yang, resulting in the claimed invention.
Consequently, claim 5 is obvious over the ‘568 application in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Regarding claim 6, claim 5 is obvious as described above. Claim 6 further recites the case wherein the non-natural amino acid is an N-substituted amino acid residue.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the N-substitution scheme of Yang on a non-natural amino acid a disclosed by Swiss Institute of Bioinformatics to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to make this combination in order to create a resin with an N-substituted non-natural amino acid at the C-terminal position reliably.
A person of ordinary skill in the art would have a reasonable expectation of success because the process of Yang works with a variety of side chains:
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(Yang et al., page 7308, bottom of page).
In particular, a skilled artisan would expect non-natural amino acids that are similar to these amino acids to work such as 2-Aminobutyric acid in place of alanine or 1-Naphthyl-alanine in place of tryptophan.
Consequently, claim 6 is obvious over the ‘568 application in view of Yang et al., Swiss Institute of Bioinformatics, and Liu et al. and rejected.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) in view of Ficht et al. (Ficht, et al. Chemistry–A European Journal 14.12: 3620-3629. (2008)).
Regarding claim 7, claim 1 is obvious as described above. Claim 7 further recites the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
Yang does not disclose the case wherein an amino acid residue at the C-terminal of the peptide is supported on the solid phase synthesis resin by a carboxyl group bonded to a carbon atom at the β-position or a carbon atom at the γ-position of the amino group.
However, Ficht discloses such a side-chain attachment scheme: “An efficient method for the Fmoc-based synthesis of peptide thioesters involves immobilization of the C-terminal amino acid residue through its side chain.25, 46–48 In this manner, Fmoc-Glu-OAllyl, Fmoc-Asp-OAllyl and Fmoc-Lys-OAllyl have been immobilized onto Wang- or Rink amide resin.49 After the peptide is assembled on the resin, removal of the C-terminal allyl group, on-resin thioester formation and subsequent cleavage yields the corresponding glutamine, asparagine and lysine thioesters.” (Ficht et al., page 3621, col.1, para. 2).
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(Ficht et al., page 3622, Scheme 2).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the side chain attachment scheme of Ficht with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would use such a side chain attachment scheme to create thioesters as described by Ficht above. A person of ordinary skill in the art would have a reasonable expectation of success because Yang shows that carboxyl groups attach to 2-Cl-trityl resin just like the Wang resin used by Ficht.
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(Yang et al., page 7308, top of page).
A person of ordinary skill in the art could then apply the side chain scheme of Ficht and substitute the 2-Cl-Trityl resin in Yang for the Wang resin in Ficht. These resins are both used for solid phase peptide synthesis and both accept carboxyl linker as shown above.
Yang shows that N-methylation scheme is applicable at least to aspartic acid:
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(Yang et al., page 7308, bottom of page).
Consequently, claim 7 is obvious the ‘568 application in view of Yang et al. and Ficht et al. and rejected.
Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Fauchere et al. (Fauchere et al. International journal of peptide and protein research 32.4: 269-278 (1988)).
Regarding claim 8, claim 1 is obvious as described above. Claim 8 further recites the case wherein an amino acid residue at the C-terminal of the peptide and/or an amino acid residue adjacent to the amino acid residue at the C-terminal have a bulky side chain.
Yang discloses the case wherein the C-terminal residue is Trp, a bulky amino acid:
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(Yang et al., page 7308, bottom of page).
Trp is bulky because it has the largest van der Waals radius of the common amino acids as disclosed by Fauchere (Fauchere et al., page 271, Table 1).
Consequently, claim 8 is obvious over the ‘568 application in view of Yang et al. as evidenced by Fauchere et al. and rejected.
Claims 9-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) as evidenced by Lesarri et al. (Lesarri, et al. Angewandte Chemie International Edition 43.5: 605-610 (2004)).
Regarding claim 9, claim 1 is obvious as described above. Claim 9 further recites the case wherein the bulky side chain is an optionally substituted branch-chain alkyl group.
Yang discloses the case wherein the C-terminal residue is Val, which has a bulky branch-chain alkyl group as evidenced by Lesarri: “Additionally, the presence of a bulky lateral isopropyl group in valine could generate much greater steric demands compared to the methyl group of alanine, which could affect the conformation of the amino acid backbone of the molecule.” (Lesarri et al., page 606, col. 2, para. 2).
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(Yang et al., page 7308, bottom of page).
Consequently, claim 9 is obvious over the ‘568 application in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 10, claim 9 is obvious as described above. Claim 10 further recites the case wherein the branched-chain alkyl group is bonded to a carbon atom at the α-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is bonded to the alpha carbon of the carboxyl group.
Consequently, claim 10 is obvious over the ‘568 application in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Regarding claim 11, claim 10 is obvious as described above. Claim 11 further recites the case wherein the branched-chain alkyl group has a branch on a carbon atom at the β-position or a carbon atom at the γ-position of the carboxyl group.
In the case of valine, the branched-chain alkyl group is has a branch on the β-position carbon.
Consequently, claim 11 is obvious over the ‘568 application in view of Yang et al. as evidenced by Fauchere et al. and Lesarri et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Prior et al. (Prior, et al. Molecules 23.6: 1475 (2018)).
Regarding claim 14, claim 1 is obvious as described above. Claim 14 further recites the case wherein the method according to claim 1 comprises a step of supporting the peptide on the solid phase synthesis resin. This claim is interpreted as meaning “further comprising” as described above.
Yang does not explicitly disclose loading the peptide onto the synthesis resin because the resin was purchased preloaded. However, Prior discloses a protocol for doing so: ”
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Scheme 1. Solid-phase synthesis of nocardiamides A (1) and B (2) on 2-chlorotrityl chloride (2-CTC) resin. Reagents and conditions: (a) Fmoc-Tyr(tBu)-OH; (b) HBTU, DIPEA, and DMF (r.t., 1.5 h); (c) MeOH (r.t., 0.5 h); (d) 20% piperidine/DMF (r.t., 20 min); (e) Fmoc-AA-OH, HBTU, DIPEA, and DMF (r.t., 0.5 h); (f) TFA/thioanisole/PhOH/1,2-ethanedithiol/H2O (82.5/5/5/2.5/5) (r.t.; 31.1% yield for 3 and 47.8% for 4 after RP-HPLC purification); (g) HBTU, DIPEA, and DMF (r.t.; 7.2% yield for nocardiamide A (1) and 10.7% for nocardiamide B (2) after RP-HPLC purification).” (Prior et al., page 4, scheme 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the first loading step of Prior to support the peptide disclosed by Wang on the CTC resin.
A person of ordinary skill in the art would be motivated to support the peptide on the CTC resin because at least the first residue must be supported on the resin before peptide synthesis can begin. A person of ordinary skill in the art would have a reasonable expectation of success because both Yang and Prior are using CTC resin and therefore the loading protocol from Prior should work for Yang.
Consequently, claim 14 is obvious over the ‘568 application in view of Yang et al. and Prior et al. and rejected.
Claim 14 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,404,299 in view of Yang et al. (Yang, et al. Tetrahedron letters 38.42: 7307-7310 (1997)) and Angeletti et al. (Angeletti, et al. Techniques in protein chemistry. Vol. 7. Academic Press,. 261-274. (1996)).
Regarding claim 16, claim 1 is obvious as described above. Claim 16 recites: “A method for producing a cyclic peptide, a salt thereof, or a solvate thereof, the method comprising the steps of: obtaining a peptide compound containing at least one N-substituted amino acid residue, a salt thereof or a solvate thereof in accordance with the method according to claim 1; removing a solid phase synthesis resin; and cyclizing a C-terminal-side group and a N-terminal-side group of the peptide compound, a salt thereof or a solvate thereof to form a cyclic portion.
Yang does not disclose removing the synthesis resin and cyclizing the resultant peptide.
However, Angeletti discloses a post-cleavage cyclization protocol:
“The 2 on-resin and 2-off resin procedures were chosen as representative methods, and to some extent, for economy. In protocol I, the cleaved peptide was dissolved in 7g/L ammonium acetate, and stirred for 3 days before lyophilization. Protocol II used direct oxygenation for 24 hr in an ammonium bicarbonate buffer at pH 8.5. In protocol III, the peptide-bound resin was treated with a 1.5 molar excess of 0.4 M thallium trifluoraceetate in dimethylformamide for 1 hr before washing, and cleavage. For protocol IV, the peptide-resin was treated with a 4-fold molar excess of 0.1 M mercuric acetate in dimethylformamide for 1 hr, after which the resin was filtered, treated with a 10-fold molar excess of 2-mercaptoethanol in dimethylformamide for 1 hr, filtered and washed with solvents, and cleaved from the resin with 95% TFA in water.” (Angeletti et al., page 263, para. 3)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the off-resin protocol of Angeletti with the method of Yang to arrive at the claimed invention.
A person of ordinary skill in the art would be motivated to use an off-resin protocol because it is cheaper and would have a reasonable expectation of success because Angeletti discloses that the correct structure can be achieved with off-resin protocols:
“Producing cyclized peptides with the correct structure can be achieved readily by either on-resin or post-cleavage techniques (13). Post-cleavage techniques are less expensive and provide reasonable yields of the desired product. However, on-resin techniques produce greater yields of the final product, but are more expensive to perform.” (Angeletti et al., page 273, para. 3).
Consequently, claim 16 is obvious over the ‘568 application in view of Yang et al. and Angeletti et al. and rejected.
Conclusion
Claims 1-14, 16, 31, and 32 are rejected.
Claims 2, 15, and 17-30 are withdrawn from further consideration.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to David Paul Bowles whose telephone number is (571)272-0919. The examiner can normally be reached Monday-Friday 8:30-5:00.
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/DAVID PAUL BOWLES/ Examiner, Art Unit 1654
/LIANKO G GARYU/Supervisory Patent Examiner, Art Unit 1654
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