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 .
Claims 209-210, 213-214, 234, 249 and 354-374 are pending.
Applicant's election with traverse of Group III that read on (A) lenalidomide as the particular compound (I) wherein X is O, R1 is piperidine-2,6-dionyl, R2a hydrogen, R2b is hydrogen, R3 is -NH2, and n is 1 as the species of compound, (B) Amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) as the particular COF1/CRBN-binding polypeptide, (C) A chimeric antigen receptor (CAR) as the particular heterologous polypeptide, (D) the COF1/CRBN-binding polypeptide is operatively linked to the heterologous polypeptide or CAR via a linker as the species of whether the COF1/CRBN (cereblon)-binding polypeptide is fused or linked directly or indirectly via linker, (E) Lenalidomide as the particular immunomodulatory imide drug (IMiD), (F) An estrogen receptor (ER) domain" as the particular degradation domain, (G) Furin and furin cleavage site of GTGAEDPRPSRKRR (SEQ ID NO: 127) as the particular protease having a particular sequence, (H) CAR comprising an antigen binding domain that binds CD19 as the particular chimeric antigen receptor
is in the reply filed on Oct 16, 2025 is acknowledged. The traversal is on the ground(s) that there would be no serious burden if all of the species were searched and examined together, and therefore the species election requirement should be withdrawn.
This is not found persuasive because of the reasons set forth in the restriction mailed July 16, 2025; there would be a serious search and examination burden if restriction were not required because: (a) the species of nucleic acid molecule encoding structurally different fusion protein comprising different compound of Formula I (COF1)/CRBN (cereblon)-binding polypeptide that comprises different combination of IKZF polypeptide, heterologous polypeptide, distinct degradation domain, e.g., estrogen receptor domain (ER), FKB protein (FKBP) domain, or dihydrofolate reductase (DHFR) domain, distinct heterologous protease cleavage site by different protease, e.g., furin, PCSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, and heterologous polypeptide, e.g., chimeric antigen receptor that binds to different target are not obvious variant of each other based on the record; (b) the inventions have acquired a separate status in the art in view of their different classification; (c) the inventions have acquired a separate status in the art due to their recognized divergent subject matter; (d) the inventions require a different field of search (for example, searching different classes/subclasses or electronic resources, or employing different search queries); (e) the prior art applicable to one invention would not likely be applicable to another invention; and/or (f) the inventions are likely to raise different non-prior art issues under 35 U.S.C. 101 and/or 35 U.S.C. 112, first paragraph.
The requirement is still deemed proper and is therefore made FINAL.
Claims 368 and 369 are withdrawn from further consideration by the examiner, 37 C.F.R. 1.142(b) as being drawn to non-elected inventions.
Claims 209-210, 213-214, 234, 249 and 354-367, 370 and 374, drawn to nucleic acid molecule encoding a particular fusion polypeptide, vector, viral particle, cell comprising said fusion polypeptide, and method of making said cell that read on that read on (A) lenalidomide as the particular compound (I) wherein X is O, R1 is piperidine-2,6-dionyl, R2a hydrogen, R2b is hydrogen, R3 is -NH2, and n is 1 as the species of compound, (B) Amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) as the particular COF1/CRBN-binding polypeptide, (C) A chimeric antigen receptor (CAR) as the particular heterologous polypeptide, (D) the COF1/CRBN-binding polypeptide is operatively linked to the heterologous polypeptide or CAR via a linker" as the species of whether the COF1/CRBN (cereblon)-binding polypeptide is fused or linked directly or indirectly via linker, (E) Lenalidomide as the particular immunomodulatory imide drug (IMiD), (F) An estrogen receptor (ER) domain" as the particular degradation domain, (G) Furin and furin cleavage site of GTGAEDPRPSRKRR (SEQ ID NO: 127) as the particular protease having a particular sequence, (H) CAR comprising an antigen binding domain that binds CD19, are being acted upon in this Office Action.
Priority
Applicant’ claim priority to provisional application 62/574,188, filed Oct 18, 2017, is acknowledged.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on Oct 16, 2025 and July 18, 2024 have been considered by the examiner and an initialed copy of the IDS is included with this Office Action.
Drawings
The drawings filed on April 8, 2024 are acceptable.
Specification
The amendment to the specification filed on July 18, 2024 has been entered.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant's cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objection
Claims 1, 359, 360 are objected to because of the following informalities: the claims use theabbreviation (COF1) without first defining it. To clarify the claim, applicant should first spell out thefull term before using an abbreviation. Appropriate correction is required.
Claim 372 is objected to because of the following informality: duplicate “a component of a CRISPR/Cas system” in (d) should be deleted.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 362, 363, 364, 366, 370, 371, 372 are 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 362 recites a broad range or limitation, e.g., IKZF polypeptide together with a narrow range or limitation, e.g., IKZF1, IKZF2, IKZF3, IKZF4, IKZF5, IKZF2 polypeptide having H141Q substitution (numbered according to SEQ ID NO 21), IKZF4 polypeptide having H188Q (numbered according to SEQ ID NO: 22) or a structural motif thereof that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
Claim 364 recites a broad range or limitation, e.g., immunomodulatory imide drug (IMiD) together with a narrow range or limitation, e.g., lenalidomide, pomalidomide, thalidomide, and 2-(4-(tert- butyl)phenyl)-N-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-5-yl)methyl)acetamide that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
Claim 364 contains the trademark/trade name “IMiD”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112, second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name “IMiD®” is used to identify/describe immunomodulatory imide drug accordingly, the identification/description is indefinite.
Claim 366 is rejected on the judicially-created basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature. The members of the improper Markush grouping do not share a substantial feature and a common use that flows from the substantial structural feature for the following reasons: estrogen receptor (ER) domain, FKB protein (FKBP) domain, dihydrofolate reductase (DHFR) domain do not share a substantial feature and common use that flows from such structures. In response to this rejection, Applicant should either amend the claim(s) to recite only individual species or grouping of species that share a substantial structural feature as well as a common use that flows from the substantial structural feature, or present a sufficient showing that the species recited in the alternative of the claims(s) in fact share a substantial structural feature as well as a common use that flows from the substantial structural feature. This is a rejection on the merits and may be appealed to the Board of Patent Appeals and Interferences in accordance with 35 U.S.C. §134 and 37 CFR 41.31(a)(1) (emphasis provided).
Claim 371 recites a broad range or limitation, e.g., mammalian intracellular protease together with a narrow range or limitation, e.g., furin, PCSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV proteas, and elastase 1 that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
Claim 371 is rejected on the judicially-created basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature. The members of the improper Markush grouping do not share a substantial feature and/or a common use that flows from the substantial structural feature for the following reasons: (a) the heterologous protease cleavage site cleaved by any mammalian intracellular protease such as furin, PCSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, or elastase 1 or any mammalian extracellular protease such as Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, or elastase 1 do not share a common structure or sequence.
Claim 372 (a) recites heterologous polypeptide in Table 2. Note that MPEP 2173.05(s) states that where possible, claims are to be complete in themselves. Incorporation by reference to a specific table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a table into the claim. Incorporation by reference is a necessity doctrine, not for applicant's convenience.” Exparte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).
Claim 372 (b), (d) recites “a component of the apoptosis pathway, a component of a CRISPR/Cas system, a component of a CRISPR/Cas system, CD8, CD19 and CD22” is ambiguous and indefinite because the specification does not define the “component” of the apoptosis pathway, CRISPR/Cas system, CD8, CD19 or CD19. One of ordinary skill in the art cannot determine the metes and bounds to avoid infringing on the claim.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 365-371 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claims 365-371 fail to limit the parent claim from which claims 365-371 depend as the parent claim 214 is drawn to a cell comprising a fusion polypeptide that comprises a compound of Formula (I) (COF1)/CRBN (cereblon)-binding polypeptide and a heterologous polypeptide, whereas claim 365 further comprises a degradation domain and any heterologous protease cleavage site, wherein the degradation domain is estrogen receptor (ER) domain, FKB protein (FKBP) domain or dihydrofolate reductase (DHFR) recited in claim 366 and wherein the heterologous protease cleavage site such as the ones recited in claim 371 wherein the fusion polypeptide comprises degradation domain, heterologous protease cleavage site, heterologous polypeptide and the COF1/CRBN-binding polypeptide in any order from N-terminus to C-terminus set forth in claim 370. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim rejections under - 35 U.S.C. 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 209-210, 213-214, 234, 249 and 354-367, 370 and 374 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The MPEP § 2163 lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the Application. These include: the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
For claims drawn to a genus, MPEP §2163 states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus, See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406, M.P.E.P. § 2163, II, A, 3, (a), (ii).
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210. (Original) A vector comprising the nucleic acid molecule of claim 209.
213. (Previously Presented) A viral particle comprising the vector of claim 210.
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234. (Currently Amended) A method of making a cell, said method comprising providing a cell with the nucleic acid molecule encoding the fusion polypeptide of claim 209.
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354. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 1.
355. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3.
356. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 1.
357. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 1 or 3.
358. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide is:(a) fused to the heterologous polypeptide;(b) linked to the heterologous polypeptide by a peptide bond;(c) linked to the heterologous polypeptide by a bond other than a peptide bond;(d) linked directly to the COF1/CRBN-binding polypeptide;(e) linked indirectly to the COF1/CRBN-binding polypeptide; or (f) operatively linked to the heterologous polypeptide via a linker, a glycine serine linker, or a linker comprising the amino acid sequence of SEQ ID NO: 28.
359. (New) The cell of claim 214, wherein the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with cereblon (CRBN) in the absence of COF1 is no more than 0.01%,0.1%, 1%, 5%,10%, 15%, or 20% of the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with CRBN in the presence of COF 1.
360. (New) The cell of claim 214, wherein the degradation or ubiquitination of the fusion polypeptide in the absence of COF1 is no more than 0.01%, 0.1%, 1%,10%, 20%, 30%, 40%,50%,60%, or 70% of the degradation or ubiquitination of the fusion polypeptide in the presence of COF1.
361. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide:(a) is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between 20 and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length, or between 55 and 65 amino acid residues in length; (b) comprises a beta turn, a beta hairpin, a beta strand, or an alpha helix; (c) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, and a first alpha helix; or (d) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, a first alpha helix, and a second alpha helix.
362. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:(a) a naturally occurring IKZF polypeptide or a COF 1/CRBN-binding variant thereof, or a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4, IKZF5, or a COF1/CRBN-binding variant thereof, or at least one less lysine than the corresponding native sequence;(b) two or more discontinuous sequences from a naturally occurring IKZF polypeptide, or a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4, or IKZF5; or (c) an IKZF polypeptide, an IKZF 1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide having H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide having H188Q substitution (numbered according to SEQ ID NO: 22), or a structural motif thereof.
363. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:
(a) amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19), or the amino acid sequence of SEQ ID NO: 5, or a sequence that differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues;
(b) amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19) or a sequence that differs from amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues;
(c) amino acid residues 136-139 of IKZF3 (numbered according to SEQ ID NO: 19);
(d) amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19), or the amino acid sequence of SEQ ID NO: 11, or a sequence that differs from amino acid residues 236- 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues;
(e) the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91);
(f) a first sequence comprising amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) or a first sequence that differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues; and a second sequence comprising amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19) or a second sequence that differs from amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues;
(g) a first sequence comprising amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91);
(h) an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41, 42, and 43; or
(i) the amino acid sequence of SEQ ID NO: 2 or 4.
364. (New) The cell of claim 214, wherein the COF1 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof, or is selected from the group consisting of lenalidomide, pomalidomide, thalidomide, and 2-(4-(tert-butyl)phenyl)-N-((2-(2,6-dioxopiperidin- 3-yl)-1-oxoisoindolin-5-yl)methyl)acetamide, or a pharmaceutically acceptable salt thereof.
365. (New) The cell of claim 214, wherein the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF1/CRBN-binding polypeptide and the heterologous polypeptide by a heterologous protease cleavage site.
366. (New) The cell of claim 365, wherein the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain, or a dihydrofolate reductase (DHFR) domain.
367. (New) The cell of claim 366, wherein the degradation domain is an ER domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 46 or 48.
368. (New) The cell of claim 366, wherein the degradation domain is an FKBP domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 50.
369. (New) The cell of claim 366, wherein the degradation domain is a DHFR domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 51.
370. (New) The cell of claim 365, wherein the fusion polypeptide comprises, from N-terminus to C- terminus:
i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide, and the COF 1/CRBN-binding polypeptide;
ii) the degradation domain, the heterologous protease cleavage site, the COF 1/CRBN- binding polypeptide, and the heterologous polypeptide;
iii) the COF 1/CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site, and the degradation domain; or iv) the heterologous polypeptide, the COF1/CRBN-binding polypeptide, the heterologous protease cleavage site, and the degradation domain.
371. (New) The cell of claim 365, wherein the heterologous protease cleavage site:
(a) is cleaved by a mammalian intracellular protease or by a protease selected from the group consisting of furin, PCSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, and elastase 1;
(b) comprises a sequence comprising a cleavage motif selected from the group consisting of Arg-X-Lys/Arg-Arg consensus motif (X can be any amino acid; SEQ ID NO: 52), Arg-X-X-X- Lys/Arg-Arg consensus motif (X can be any amino acid; SEQ ID NO: 53), Arg-Arg-X consensus motif (SEQ ID NO : 54), Ile-Glu-Pro-Asp-X consensus motif (SEQ ID NO: 55), Ile-Glu/Asp-Gly- Arg (SEQ ID NO: 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58), Leu-Pro-X-Thr-Gly/Ala consensus motif (SEQ ID NO: 59), Leu-Glu-Val-Phe-Gln- Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), Glu-Asn-Leu-Tyr-Phe- Gln-Gly (SEQ ID NO: 62), and [Ala/Gly/Ser/Val]-X (X can be any amino acid; SEQ ID NO: 63);
(c) is cleaved by furin or comprises a furin cleavage site selected from the group consisting of RTKR (SEQ ID NO: 123); GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125);GTGAEDPRPSRKRR (SEQ ID NO: 127); LQWLEQQVAKRRTKR (SEQ ID NO: 129); GTGAEDPRPSRKRRSLGG (SEQ ID NO: 131); GTGAEDPRPSRKRRSLG (SEQ ID NO: 133); SLNLTESHNSRKKR (SEQ ID NO: 135); CKINGYPKRGRKRR (SEQ ID NO: 137); and SARNRQKR (SEQ ID NO: 34);
(d) is cleaved by a mammalian extracellular protease or by a protease selected from the group consisting of Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, and elastase 1; or
(e) comprises an amino acid sequence selected from the group consisting of Ile-Glu/Asp- Gly-Arg (SEQ ID NO : 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58), Leu-Pro-X-Thr-Gly/Ala consensus motif (SEQ ID NO: 59), Leu-Glu-Val-Phe- Gln-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), Glu-Asn-Leu-Tyr- Phe-Gln-Gly (SEQ ID NO: 62), and [Ala/Gly/Ser/Val]-X (X can be any amino acid; SEQ ID NO:63).
372. (New) The cell of claim 214, wherein the heterologous polypeptide:
(a) is chosen from a cytoplasmic and/or nuclear polypeptide, a transmembrane polypeptide, or a heterologous polypeptide in Table 2;
(b) is a cytoplasmic and/or nuclear polypeptide selected from the group consisting of a component of the apoptosis pathway, a component of a CRISPR/Cas system, a transcription factor, Tet methylcytosine dioxygenase 2 (TET2), FKBP, and Tau;
(c) is a transmembrane polypeptide selected from the group consisting of CD62L, CCR1, CCR2, CCR5, CCR7, CCR10, CXCR2, CXCR3, CXCR4, CXCR6, CTLA4, PD1, BTLA, VISTA, CD137L, CD80, CD86, TIGIT, CD3, CD8, CD19, CD22, CD20, BCMA, and a chimeric antigen receptor (CAR); or
(d) is selected from the group consisting of a chimeric antigen receptor (CAR), a component of a CRISPR/Cas system, CD8, CD19, and CD22.
373. (New) The cell of claim 214, wherein the cell is a mammalian cell.
374. (New) The cell of claim 214, wherein the cell is a human T cell or a human NK cell.
The claims do not recite sufficient structure and thus do not meet the written description requirement.
Regarding “compound of Formula (I) (COF1)/CRBN-binding polypeptide”, the specification defines:
[0668] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. As used herein, the term “compound of Formula (I) (COF1)/CRBN-binding polypeptide” refers to a polypeptide that binds to COF1, a polypeptide that binds to a complex of COF1 and CRBN, or a polypeptide that binds to CRBN in the presence of COF1. In some embodiments, the COF1/CRBN-binding polypeptide binds to COF1 with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−5, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide binds to the complex of COF1 and CRBN with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−5, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide binds to CRBN in the presence of COF1 with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−1, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide, when present in a fusion polypeptide (e.g., operably linked to a heterologous polypeptide (e.g., a fusion polypeptide as described herein)), can result in an increase in ubiquitination of the fusion polypeptide. In some embodiments, the COF1/CRBN-binding polypeptide, when present in a fusion polypeptide (e.g., operably linked to a heterologous polypeptide (e.g., a fusion polypeptide as described herein)), can result in an increase in degradation of the fusion polypeptide.
Regarding the term “CRBN”, the specification defines as follow:
[0672] As used herein, the term “CRBN” refers to a protein that in humans is encoded by the CRBN gene, or fragment or variant thereof (e.g., an amino acid sequence substantially identical thereto, e.g., least 85, 87, 90, 95, 97, 98, 99, or 100% identical thereto). Swiss-Prot accession number Q96SW2 provides exemplary human CRBN amino acid sequences.
The specification exemplifies:
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However, the specification does not describe the structure, e.g., nucleic acid sequences of all fusion protein comprising any compound of formula (I) (COF1)/CRBN (cereblon)-binding polypeptide, including any variant or any fragment thereof, e.g., least 85, 87, 90, 95, 97, 98, 99, or 100% identical thereto) and any and all heterologous polypeptide (claims 209-210, 213-214, 234), such as any chimeric antigen receptor (claim 249) to enable one of skill in the art to "visualize or recognize" most members of the genus encompassed by the claimed nucleic acid molecules for making any cell (claim 234).
Regarding any compound of formula I, the specification discloses just lenalidomide, much less nucleic acid molecule encoding such.
For example, Mori et al (Scientific Reports 8: 1294, 2018; PTO 1449) teaches binding to cereblon (CRBN) is primarily mediated by the glutarimide ring. Correspondingly, glutarimide alone is able to bind CRBN and inhibit ubiquitylation to a similar extent as (R)-thalidomide (Fig. 8a, b and Supplementary Fig. 6), whereas phthalimide and glutaric anhydride, which lack the ring amide of glutarimide, exhibit no binding (Fig. 8, c, d). Both carbonyl groups of glutarimide are important and the absence of one carbonyl group results in loss of binding (δ-valerolactam in Fig. 8d). Bulky modification of the glutarimide C4-carbon atom also results in loss of CRBN binding due to steric clashes (cycloheximide in Fig. 8d), see Fig. 8a-d, p. 9, last paragraph, in particular. As such, it is unpredictable which compound of formula I with bulky modification of the glutarimide ring (aka R1) other than thalidomide, lenalidomide maintains binding to cereblon (CRBN).
Regarding COF1 is any immunomodulatory imide drug (IMiD) or any pharmaceutically acceptable salt thereof (claim 364), the specification discloses just lenalidomide as the compound that mediate degradation of IKZF3 tag binding to CRBN.
However, it is not clear other undisclosed compound, e.g., other than lenalidomide, pomalidomide, and thalidomide, is capable of degrading any COF1/CRBN-binding polypeptide such as IKZF2, IKZF4 and IKZF5 (claim 362) in any given cell type. There are no working examples.
For example, Kronke (Oncoimmunology 3(7): e914742, 2014; PTO 1449) teaches that lenalidomide binding to CRBN induces degradation of IKZF1 (aka Ikaros) and IKZF3 (aka Aiolos) but not other Ikaros family members, e.g., KIZF2, IKZF4 and IKZF5, see p. e941742-1, in particular.
Further, Sperling (Blood 134(2): 160-170, 2019; PTO 892) teaches that the activity of molecules that induce protein degradation depends on the strength of ligase-substrate interaction in the presence of drug, the levels of the ubiquitin ligase, and the expression level of competing substrates, see abstract, in particular. The efficacy of a thalidomide analog may be influenced by both the level of CRBN expression and the levels of alternative substrates; also different cell lines vary in their sensitivity to lenalidomide, see p. 163-165, Fig. 3A, in particular. Thus, compound of formula I (COF1) such as lenalidomide, pomalidomide, and thalidomide binding to CRBN do not degrade KIZF2, IKZF4 and IKZF5 and different cell lines have different sensitivity.
Regarding claim 361, the specification does not describe the structure, e.g., nucleic acid sequence encoding any and all COF1/CRBN binding polypeptide having (a) any such length set forth in claim 361 (a) or (b) comprises a beta turn, a beta hairpin, a beta strand, or an alpha helix; (c) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, and a first alpha helix; or (d) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, a first alpha helix, and a second alpha helix to enable one of skill in the art to recognize most members of the genus of nucleic acid molecule encoding such.
Regarding COF1/CRBN variant thereof (claim 362), the specification discloses IKZF3 136-180 comprising the amino acid sequence of SEQ ID NO: 5, IKZF3 145-170 comprising the amino acid sequence of SEQ ID NO: 9, IKZF3 149-169 comprising SEQ ID NO: 24, IKZF3 residues 136-180 and 236-249 comprises the amino acid sequence of SEQ ID NO: 2 or 3 binds to cereblon (CRBN) in the presence of lenalidomide and facilitate degradation of IKZF3. Replacing amino acid residues 236-249, which correspond to an alpha-helix of IKZF3 with the amino acid sequence of SEQ ID NO: 91, substituting lysine residue at position of SEQ ID NO: 19 to arginine (SEQ ID NO: 84) or serine (SEQ ID NO: 100) did not impact the ability of the IKZF3 tag mediate degradation.
However, the specification does not describe random substitution, deletion, addition or a combination thereof within any IKZF, IKZF1(aka Ikaros), IK2F2, IKZF3 (aka Aiolos), IKZF4, IKZF5, the corresponding nucleic acid molecule, still maintains 3-D structure and degradation function in the presence of any COF1.
Regarding any sequence differs from animo acid residues 136-180 of IKZF3 numbered according to SEQ ID NO: 19 by any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 amino acid residues (claim 363 (a), (b)) or differs from amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO 19) by no more than 1, 2, 3, 4, 5, 6 or 7 amino acid residues (claim 363 (d), (f)) or differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 residues (claim 363 (f)), the specification discloses just human IKZF3-based degradation tag comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 3 (residues 136-180 and 236-249) with or without N-terminus Methionine residue or substituting K245 for R (K245R, SEQ ID NO 91).
However, the specification does not teach which amino acid within residues 136-180 of IKZF3 numbered according to SEQ ID NO: 19 having any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 amino acid substitutions, deletions, additions or a combination thereof such that the modified IKZF3 still maintains 3-D structure and binding to cereblon/compound of formula I and the corresponding nucleic acid molecule. Likewise, the specification does not teach which animo acid within 236-249 of IKZF3 (numbered according to SEQ ID NO 19) having 1, 2, 3, 4, 5, 6 or 7 substitutions, deletions, addition or a combination thereof such that the modified IKZF3 still maintains 3-D structure and binding to cereblon/compound of formula I.
Regarding heterologous protease cleavage is cleaved by any mammalian intracellular protease (claim 371(a), (d)), the specification does not describe the structure, e.g., nucleic acid sequence encoding the cleavage motif shared by members of genus of “mammalian intracellular protease”. The specification does not describe a sufficient number of mammalian intracellular proteases or structure common to members of the genus, sufficient to show possession of the claimed genus at the time of filing.
Regarding heterologous polypeptide is any component of any apoptotic pathway, CRISPR/Cas system (claim 372), the specification does not describe the structure, amino acid sequence of the “component” of any apoptotic pathway, CRISPR/Cas system fused to Formula (I) (COF1)/CRBN (cereblon) binding polypeptide, the corresponding nucleic acid molecule encompassed by the cell.
Regarding heterologous polypeptide is any chimeric antigen receptor (claim 249), Guedan et al (Engineering and Design of Chimeric Antigen Receptors" Molecular Therapy Methods & Clinical Development; Vol. 12: 145-156, March 2019; PTO 892) teaches that despite intensive research efforts to define optimal CAR design, a universally improved CAR structure has not yet been discovered. As of now, each CAR construct needs empirical testing for evaluation and several studies indicate that small modifications can have major consequences on the therapeutic outcomes (p. 146, 1st col.). Therefore, CARs exemplified in the instant specification is not sufficient since the state of the art teaches that there is great diversity and small changes or modifications can greatly affect the function of the CARs.
The genus of polynucleotides encoding COF1/cereblon (BRCN) binding polypeptide such as beta turn, beta hairpin, alpha helix or variant of IKZF3 fused to a heterologous polypeptide such as CARs, further comprises any degradation domain is enormous and the examples provided in the specification are small in number.
The specification does not disclose a representative number of species that reflect on the variation within each subgenus or structure common to members of the genus. One of skill in the art cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus. Thus, one of skill in the art cannot "visualize or recognize" most members of the genus of nucleic acid molecules for making any cell to show possession of the claimed genus at the time of filing. Thus, the claims lack written description.
“When a patent claims a genus using functional language to define a desired result, the specification must demonstrate that the applicant has made a generic invention that achieves the claimed result and do so by showing that the applicant has invented species sufficient to support a claim to the functionally-defined genus.” See Capon v. Eshhar, 418 F.3d 1349 (Fed. Cir. 2005).
A “patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.”), see Noelle v. Lederman, 69 USPQ2d 1508 1514 (CAFC 2004), (citing Enzo Biochem II, 323 F. 3d at 965; Regents, 119 F.3d at 1568), MPEP 2163.IIAii
Section 112 states that “[t]he specification shall contain a written description of the invention . . . in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains . . . to make and use the same . . . .” This requirement ensures “that the inventor actually invented the invention claimed.” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (en banc). To show invention, a patentee must convey in its disclosure that it “had possession of the claimed subject matter as of the filing date.” Id. at 1350. Demonstrating possession “requires a precise definition” of the invention. Id. To provide this “precise definition” for a claim to a genus, a patentee must disclose “a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can ‘visualize or recognize’ the members of the genus.” Id.
When there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. A description of what a material does, rather than of what it is, usually does not suffice. Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (see page 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (see Vas-Cath at page 1116).
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
One cannot describe what one has not conceived. See Fiddles v. Baird, 30 USPQ2d 1481, 1483. In Fiddles v. Baird, claims directed to mammalian FGF’s were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence.
Therefore, only (1) a nucleic acid molecule encoding a fusion polypeptide comprising a cereblon (CRBN)-binding polypeptide, a linker and a heterologous polypeptide wherein the CRBN-binding polypeptide is IKZF3 comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO 1, wherein the heterologous polypeptide is a chimeric antigen receptor comprising a CD19 binding scFv, a CD8 transmembrane domain, a 4-1BB and a CD3 zeta domain, wherein the ubiquitination or degradation of the fusion polypeptide is mediated by the presence of a compound selected from the group consisting of lenalidomide, pomalidomide and thalidomide binding to CRBN, (2) a nucleic acid molecule encoding a fusion protein comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 92, 93, 32, 94, 30, 31, 95, 96, 97 and 98, (3) a vector comprising said nucleic acid molecule, (4) a host cell comprising said vector, (5) a method of decreasing the expression of a fusion polypeptide on a T cell, comprising i) providing a T cell comprising said nucleic acid molecule, ii) contacting said cell ex vivo with a compound selected from the group consisting of lenalidomide, pomalidomide and thalidomide, wherein the presence of lenalidomide, pomalidomide or thalidomide decreased the expression level of the fusion polypeptide, (6) the nucleic acid molecule wherein the linker is SEQ ID NO 28, SEQ ID NO: 37, SEQ ID NO: 38 or SEQ ID NO: 39, but not the full breadth of the claims meets the written description provision of 35 U.S.C. § 112, first paragraph.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. § 112 is severable from its enablement provision (see page 1115).
Claims 209-210, 213-214, 234, 249 and 354-367, 370 and 374 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for (1) a nucleic acid molecule encoding a fusion polypeptide comprising a cereblon (CRBN)-binding polypeptide, a linker and a heterologous polypeptide wherein the CRBN-binding polypeptide is IKZF3 comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO 1, wherein the heterologous polypeptide is a chimeric antigen receptor comprising a CD19 binding scFv, a CD8 transmembrane domain, a 4-1BB and a CD3 zeta domain, wherein the ubiquitination or degradation of the fusion polypeptide is mediated by the presence of a compound selected from the group consisting of lenalidomide, pomalidomide and thalidomide binding to CRBN, (2) a nucleic acid molecule encoding a fusion protein comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 92, 93, 32, 94, 30, 31, 95, 96, 97 and 98, (3) a vector comprising said nucleic acid molecule, (4) a host cell comprising said vector, (5) a method of decreasing the expression of a fusion polypeptide on a T cell, comprising i) providing a T cell comprising said nucleic acid molecule, ii) contacting said cell ex vivo with a compound selected from the group consisting of lenalidomide, pomalidomide and thalidomide, wherein the presence of lenalidomide, pomalidomide or thalidomide decreased the expression level of the fusion polypeptide, (6) the nucleic acid molecule wherein the linker is SEQ ID NO 28, SEQ ID NO: 37, SEQ ID NO: 38 or SEQ ID NO: 39, does not reasonably provide enablement for any nucleic acid molecule as set forth in claims 209-210, 213-214, 234, 249 and 354-367, 370 and 374. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make/use the invention commensurate in scope with these claims.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). These factors include, but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. . In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
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210. (Original) A vector comprising the nucleic acid molecule of claim 209.
213. (Previously Presented) A viral particle comprising the vector of claim 210.
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234. (Currently Amended) A method of making a cell, said method comprising providing a cell with the nucleic acid molecule encoding the fusion polypeptide of claim 209.
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354. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3 or SEQ ID NO: 1.
355. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3.
356. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 1.
357. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 1 or 3.
358. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide is:(a) fused to the heterologous polypeptide;(b) linked to the heterologous polypeptide by a peptide bond;(c) linked to the heterologous polypeptide by a bond other than a peptide bond;(d) linked directly to the COF1/CRBN-binding polypeptide;(e) linked indirectly to the COF1/CRBN-binding polypeptide; or (f) operatively linked to the heterologous polypeptide via a linker, a glycine serine linker, or a linker comprising the amino acid sequence of SEQ ID NO: 28.
359. (New) The cell of claim 214, wherein the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with cereblon (CRBN) in the absence of COF1 is no more than 0.01%,0.1%, 1%, 5%,10%, 15%, or 20% of the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with CRBN in the presence of COF 1.
360. (New) The cell of claim 214, wherein the degradation or ubiquitination of the fusion polypeptide in the absence of COF1 is no more than 0.01%, 0.1%, 1%,10%, 20%, 30%, 40%,50%,60%, or 70% of the degradation or ubiquitination of the fusion polypeptide in the presence of COF1.
361. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide:(a) is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between 20 and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length, or between 55 and 65 amino acid residues in length;(b) comprises a beta turn, a beta hairpin, a beta strand, or an alpha helix;(c) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, and a first alpha helix; or (d) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, a first alpha helix, and a second alpha helix.
362. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:(a) a naturally occurring IKZF polypeptide or a COF 1/CRBN-binding variant thereof, or a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4, IKZF5, or a COF1/CRBN-binding variant thereof, or at least one less lysine than the corresponding native sequence;(b) two or more discontinuous sequences from a naturally occurring IKZF polypeptide, or a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4, or IKZF5; or (c) an IKZF polypeptide, an IKZF 1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide having H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide having H188Q substitution (numbered according to SEQ ID NO: 22), or a structural motif thereof.
363. (New) The cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:
(a) amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19), or the amino acid sequence of SEQ ID NO: 5, or a sequence that differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues;
(b) amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19) or a sequence that differs from amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues;
(c) amino acid residues 136-139 of IKZF3 (numbered according to SEQ ID NO: 19);
(d) amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19), or the amino acid sequence of SEQ ID NO: 11, or a sequence that differs from amino acid residues 236- 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues;
(e) the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91);
(f) a first sequence comprising amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) or a first sequence that differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues; and a second sequence comprising amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19) or a second sequence that differs from amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues;
(g) a first sequence comprising amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91);
(h) an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41, 42, and 43; or
(i) the amino acid sequence of SEQ ID NO: 2 or 4.
364. (New) The cell of claim 214, wherein the COF1 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof, or is selected from the group consisting of lenalidomide, pomalidomide, thalidomide, and 2-(4-(tert-butyl)phenyl)-N-((2-(2,6-dioxopiperidin- 3-yl)-1-oxoisoindolin-5-yl)methyl)acetamide, or a pharmaceutically acceptable salt thereof.
365. (New) The cell of claim 214, wherein the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF1/CRBN-binding polypeptide and the heterologous polypeptide by a heterologous protease cleavage site.
366. (New) The cell of claim 365, wherein the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain, or a dihydrofolate reductase (DHFR) domain.
367. (New) The cell of claim 366, wherein the degradation domain is an ER domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 46 or 48.
368. (New) The cell of claim 366, wherein the degradation domain is an FKBP domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 50.
369. (New) The cell of claim 366, wherein the degradation domain is a DHFR domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 51.
370. (New) The cell of claim 365, wherein the fusion polypeptide comprises, from N-terminus to C- terminus:
i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide, and the COF 1/CRBN-binding polypeptide;
ii) the degradation domain, the heterologous protease cleavage site, the COF 1/CRBN- binding polypeptide, and the heterologous polypeptide;
iii) the COF 1/CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site, and the degradation domain; or iv) the heterologous polypeptide, the COF1/CRBN-binding polypeptide, the heterologous protease cleavage site, and the degradation domain.
371. (New) The cell of claim 365, wherein the heterologous protease cleavage site:
(a) is cleaved by a mammalian intracellular protease or by a protease selected from the group consisting of furin, PCSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, and elastase 1;
(b) comprises a sequence comprising a cleavage motif selected from the group consisting of Arg-X-Lys/Arg-Arg consensus motif (X can be any amino acid; SEQ ID NO: 52), Arg-X-X-X- Lys/Arg-Arg consensus motif (X can be any amino acid; SEQ ID NO: 53), Arg-Arg-X consensus motif (SEQ ID NO : 54), Ile-Glu-Pro-Asp-X consensus motif (SEQ ID NO: 55), Ile-Glu/Asp-Gly- Arg (SEQ ID NO: 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58), Leu-Pro-X-Thr-Gly/Ala consensus motif (SEQ ID NO: 59), Leu-Glu-Val-Phe-Gln- Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), Glu-Asn-Leu-Tyr-Phe- Gln-Gly (SEQ ID NO: 62), and [Ala/Gly/Ser/Val]-X (X can be any amino acid; SEQ ID NO: 63);
(c) is cleaved by furin or comprises a furin cleavage site selected from the group consisting of RTKR (SEQ ID NO: 123); GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125);GTGAEDPRPSRKRR (SEQ ID NO: 127); LQWLEQQVAKRRTKR (SEQ ID NO: 129); GTGAEDPRPSRKRRSLGG (SEQ ID NO: 131); GTGAEDPRPSRKRRSLG (SEQ ID NO: 133); SLNLTESHNSRKKR (SEQ ID NO: 135); CKINGYPKRGRKRR (SEQ ID NO: 137); and SARNRQKR (SEQ ID NO: 34);
(d) is cleaved by a mammalian extracellular protease or by a protease selected from the group consisting of Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease, and elastase 1; or
(e) comprises an amino acid sequence selected from the group consisting of Ile-Glu/Asp- Gly-Arg (SEQ ID NO : 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58), Leu-Pro-X-Thr-Gly/Ala consensus motif (SEQ ID NO: 59), Leu-Glu-Val-Phe- Gln-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), Glu-Asn-Leu-Tyr- Phe-Gln-Gly (SEQ ID NO: 62), and [Ala/Gly/Ser/Val]-X (X can be any amino acid; SEQ ID NO:63).
372. (New) The cell of claim 214, wherein the heterologous polypeptide:(a) is chosen from a cytoplasmic and/or nuclear polypeptide, a transmembrane polypeptide, or a heterologous polypeptide in Table 2;(b) is a cytoplasmic and/or nuclear polypeptide selected from the group consisting of a component of the apoptosis pathway, a component of a CRISPR/Cas system, a transcription factor, Tet methylcytosine dioxygenase 2 (TET2), FKBP, and Tau;(c) is a transmembrane polypeptide selected from the group consisting of CD62L, CCR1, CCR2, CCR5, CCR7, CCR10, CXCR2, CXCR3, CXCR4, CXCR6, CTLA4, PD1, BTLA, VISTA, CD137L, CD80, CD86, TIGIT, CD3, CD8, CD19, CD22, CD20, BCMA, and a chimeric antigen receptor (CAR); or (d) is selected from the group consisting of a chimeric antigen receptor (CAR), a component of a CRISPR/Cas system, CD8, CD19, and CD22.
373. (New) The cell of claim 214, wherein the cell is a mammalian cell.
374. (New) The cell of claim 214, wherein the cell is a human T cell or a human NK cell.
Regarding “compound of Formula (I) (COF1)/CRBN-binding polypeptide”, the specification defines:
[0668] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. As used herein, the term “compound of Formula (I) (COF1)/CRBN-binding polypeptide” refers to a polypeptide that binds to COF1, a polypeptide that binds to a complex of COF1 and CRBN, or a polypeptide that binds to CRBN in the presence of COF1. In some embodiments, the COF1/CRBN-binding polypeptide binds to COF1 with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−5, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide binds to the complex of COF1 and CRBN with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−5, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide binds to CRBN in the presence of COF1 with an affinity (K.sub.D) that is lower than 10.sup.−3, 10.sup.−4, 10.sup.−1, 10.sup.−6, 10.sup.−7, or 10.sup.−8 M, e.g., as measured by a method recognized in the art, e.g., Biacore. In some embodiments, the COF1/CRBN-binding polypeptide, when present in a fusion polypeptide (e.g., operably linked to a heterologous polypeptide (e.g., a fusion polypeptide as described herein)), can result in an increase in ubiquitination of the fusion polypeptide. In some embodiments, the COF1/CRBN-binding polypeptide, when present in a fusion polypeptide (e.g., operably linked to a heterologous polypeptide (e.g., a fusion polypeptide as described herein)), can result in an increase in degradation of the fusion polypeptide.
Thus, the term compound of Formula (I) (COF1)/CRBN-binding polypeptide is unlimited.
Regarding the term “CRBN”, the specification defines as follow:
[0672] As used herein, the term “CRBN” refers to a protein that in humans is encoded by the CRBN gene, or fragment or variant thereof (e.g., an amino acid sequence substantially identical thereto, e.g., least 85, 87, 90, 95, 97, 98, 99, or 100% identical thereto). Swiss-Prot accession number Q96SW2 provides exemplary human CRBN amino acid sequences.
The specification exemplifies:
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340
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279
807
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348
805
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585
833
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77
792
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395
805
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523
818
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472
813
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578
823
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485
818
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587
812
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578
828
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However, the specification does not teach the structure, e.g., nucleic acid sequences of all fusion protein comprising any compound of formula (I) (COF1)/CRBN (cereblon)-binding polypeptide, including any variant or any fragment thereof, e.g., least 85, 87, 90, 95, 97, 98, 99, or 100% identical thereto) and any and all heterologous polypeptide (claims 209-210, 213-214, 234), such as any chimeric antigen receptor (claim 249) to enable one of skill in the art to make and use without undue experimentation.
Regarding compound of formula I, the specification discloses just lenalidomide, much less nucleic acid molecule encoding such.
Regarding COF1 is any immunomodulatory imide drug (IMiD) or any pharmaceutically acceptable salt thereof (claim 364), the specification discloses just lenalidomide as the compound that mediate degradation of IKZF3 (aka HILD tag) when binds to cereblon (CRBN).
However, it is not clear other undisclosed compound, other than lenalidomide, pomalidomide, and thalidomide, is capable of degrading any fusion protein comprising COF1/CRBN-binding polypeptide such as IKZF2, IKZF4 and IKZF5 (claim 362) in any given cell type. There are no working examples.
For example, Kronke (Oncoimmunology 3(7): e914742, 2014; PTO 1449) teaches that lenalidomide binding to CRBN induces degradation of IKZF1 (aka Ikaros) and IKZF3 (aka Aiolos) but NOT other Ikaros family members, e.g., KIZF2, IKZF4 and IKZF5, see p. e941742-1, in particular.
Further, Sperling (Blood 134(2): 160-170, 2019; PTO 892) teaches that the activity of molecules that induce protein degradation depends on the strength of ligase-substrate interaction in the presence of drug, the levels of the ubiquitin ligase, and the expression level of competing substrates, see abstract, in particular. The efficacy of a thalidomide analog may be influenced by both the level of CRBN expression and the levels of alternative substrates; also different cell lines vary in their sensitivity to lenalidomide, see p. 163-165, Fig. 3A, in particular. Thus, compound of formula I (COF1) such as lenalidomide, pomalidomide, and thalidomide binding to CRBN do not degrade KIZF2, IKZF4 and IKZF5 and different cell lines have different sensitivity.
Regarding claim 361, the specification does not teach the structure, e.g., nucleic acid sequence encoding any and all COF1/CRBN binding polypeptide having (a) any such length set forth in claim 361 (a) or (b) comprises a beta turn, a beta hairpin, a beta strand, or an alpha helix; (c) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, and a first alpha helix; or (d) comprises, from N-terminus to C-terminus, a first beta strand, a beta hairpin, a second beta strand, a first alpha helix, and a second alpha helix to enable one of skill in the art to make and use without undue experimentation.
Regarding COF1/CRBN-binding variant thereof (claim 362), the specification discloses IKZF3 136-180 comprising the amino acid sequence of SEQ ID NO: 5, IKZF3 145-170 comprising the amino acid sequence of SEQ ID NO: 9, IKZF3 149-169 comprising SEQ ID NO: 24, IKZF3 residues 136-180 and 236-249 comprises the amino acid sequence of SEQ ID NO: 2 or 3 maintains lenalidomide compound binding to cereblon (CRBN) and facilitate degradation of IKZF3. Replacing amino acid residues 236-249, which correspond to an alpha-helix of IKZF3 with the amino acid sequence of SEQ ID NO: 91, substituting lysine residue at position of SEQ ID NO: 19 to arginine (SEQ ID NO: 84) or serine (SEQ ID NO: 100) did not impact the ability of the IKZF3 tag mediate degradation.
However, the specification does not teach random substitution, deletion, addition or a combination thereof within any IKZF, IKZF1(aka Ikaros), IK2F2, IKZF3 (aka Aiolos), IKZF4, IKZF5, the corresponding nucleic acid molecule, still maintains 3-D structure and degradation function.
Regarding any sequence differs from animo acid residues 136-180 of IKZF3 numbered according to SEQ ID NO: 19 by any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 amino acid residues (claim 363 (a), (b)) or differs from amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO 19) by no more than 1, 2, 3, 4, 5, 6 or 7 amino acid residues (claim 363 (d), (f)) or differs from amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19) by any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 residues (claim 363 (f)), the specification discloses just human IKZF3-based degradation tag comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 3 (residues 136-180 and 236-249) with or without N-terminus Methionine residue or substituting K245 for R (K245R, SEQ ID NO 91).
However, the specification does not teach which amino acid within residues 136-180 of IKZF3 numbered according to SEQ ID NO: 19 having any 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35 or 40 amino acid substitutions, deletions, additions or a combination thereof such that the modified IKZF3 still maintains 3-D structure and binding to cereblon/compound of formula I and degradation of IKZF3. Likewise, the specification does not teach which animo acid within 236-249 of IKZF3 (numbered according to SEQ ID NO 19) having 1, 2, 3, 4, 5, 6 or 7 substitutions, deletions, addition or a combination thereof such that the modified IKZF3 still maintains 3-D structure and binding to cereblon/compound of formula I. There are no working examples.
Regarding heterologous protease cleavage is cleaved by any mammalian intracellular protease (claim 371(a), (d)), the specification does not teach the structure, e.g., nucleic acid sequence encoding the cleavage motif shared by members of genus of “mammalian intracellular protease” to enable one of skilled in the art to make and use without undue experimentation.
Regarding heterologous polypeptide is any component of any apoptotic pathway, CRISPR/Cas system (claim 372), the specification does not teach the structure, amino acid sequence of the “component” of any apoptotic pathway, CRISPR/Cas system fused to Formula (I) (COF1)/CRBN (cereblon) binding polypeptide, the corresponding nucleic acid molecule encompassed by the cell.
Regarding heterologous polypeptide is any chimeric antigen receptor (claim 249), Guedan et al (Engineering and Design of Chimeric Antigen Receptors" Molecular Therapy Methods & Clinical Development; Vol. 12: 145-156, March 2019; PTO 892) teaches that despite intensive research efforts to define optimal CAR design, a universally improved CAR structure has not yet been discovered. As of now, each CAR construct needs empirical testing for evaluation and several studies indicate that small modifications can have major consequences on the therapeutic outcomes (p. 146, 1st col.). Therefore, CARs exemplified in the instant specification is not sufficient since the state of the art teaches that there is great diversity and small changes or modifications can greatly affect the function of the CARs.
As such, it is unpredictable which undisclosed nucleic acid encoding which COF1/CRBN (cereblon) binding polypeptide comprises component of any apoptotic pathway or CRISPR/Cas system in the presence of any compound of formula I is effective for CRBN binding mediated degradation of the fusion polypeptide. There are insufficient working examples. As such, undue experimentation would be required of one skilled in the art to practice the claimed invention, commensurate in scope with the claims. See page 1338, footnote 7 of Ex parte Aggarwal, 23 USPQ2d 1334 (PTO Bd. Pat App. & Inter. 1992).
The scope of the claims must bear a reasonable correlation with the scope of enablement. See In re Fisher, 166 USPQ 19 24 (CCPA 1970).
In re wands, 858 F.2d at 737, 8 USPQ2d at 1404 (Fed. Cir. 1988), the decision of the court indicates that the more unpredictable the area is, the more specific enablement is necessary.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 209-210, 214, 234, 362-364, 373 and 374 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by WO2015077058 (Fink hereafter, published May 28, 2015; PTO 1449).
Claim 209 encompasses a nucleic acid molecule encoding a fusion polypeptide that comprises a compound of formula (I) (COF1)/CRBN (Cereblon)-binding polypeptide and a heterologous polypeptide wherein the compound is lenalidomide.
Claim 210 recites a vector comprising the nucleic acid molecule of claim 209.
Claim 213 recites a viral particle comprising the vector of claim 210.
Claim 214 recites a cell comprising a fusion polypeptide of claim 209.
Claim 234 recites a method of making a cell, said method comprising providing a cell with the nucleic acid molecule encoding the fusion polypeptide of claim 209.
Claim 362 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:(a) a naturally occurring IKZF polypeptide or a COF 1/CRBN-binding variant thereof, or a naturally occurring IKZF1, IKZF2, IKZF3 (elected species), IKZF4, IKZF5.
Claim 363 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:
(a) amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19),
(b) amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19);
(c) amino acid residues 136-139 of IKZF3 (numbered according to SEQ ID NO: 19);
(d) the amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19).
Claim 364 recites the cell of claim 214, wherein the COF1 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof, or is selected from the group consisting of lenalidomide, pomalidomide, thalidomide , and 2-(4-(tert-butyl)phenyl)-N-((2-(2,6-dioxopiperidin- 3-yl)-1-oxoisoindolin-5-yl)methyl)acetamide, or a pharmaceutically acceptable salt thereof.
Claim 373 recites the cell of claim 214, wherein the cell is a mammalian cell.
Claim 374 recites the cell of claim 214, wherein the cell is a human T cell or a human NK cell.
Regarding claim 209, Fink teaches nucleic acid molecules (p 18, p. 20) that encodes fusion protein, e.g., HA-IKZF3 or FLAG-tagged IKZF3 (see p. 23, lines 27-33) comprising a IKZF3 or IKZF1 (instant COF1)/CRBN (cereblon)-binding polypeptide, p. 7-8) fused to a heterologous polypeptide, e.g., hemagglutinin (HA) or FLAG, see HA-1KZF1 or HA-IKZF3 (Figure 9B, 9C, p. 47, line 19); and Ftuc-fused IKZF3 in 293T cells, see p. 23, p. 46, line 17-20, Example 3. The binding of IKZF3 to CRBN in the presence of a compound of formula I (COF1) such as lenalidomide caused a dose-dependent reduction of fusion proteins (Figure 6B). In the presence of a compound, e.g., thalidomide or lenalidomide (instant compound of formula I), lenalidomide binds to CRBN causes selective ubiquitination and degradation of IFZF1 or IKZF3 fusion polypeptide, see p. 27, line 32-33, p. 29, p. 45-47, p. 47, line 26-62, in particular.
The reference lenalidomide has the claimed structure below:
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137
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where the claimed compound of formula (I)
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wherein X is O, R1 is piperidine-2,6-dionyl, R2a is hydrogen, R2b is hydrogen, R3 is -NH2, and n is 1, see p. 28, in particular.
Regarding claim 210, Fink teaches vectors expressing the indicated cDNA, see p. 23, line 4-5, p. 36, line 9-10.
Regarding claim 213, Fink teaches viral construct packaged into a viral particle can be used to accomplish both efficient introduction of an expression and transcription of the encoded protein into the cell, see p. 36, line 1-2.
Regarding claim 214, Fink teaches cells, e.g., 293T cells were transfected with 40 ng of CMY-IRES-RenillaLUC-IRBS-IKZF3-FireflyLUC reporter plasmid (vector) comprising nucleic acid encoding fusion protein comprising IKZF3 (instant COF1)/CRBN (cereblon)-binding polypeptide) fused to a heterologous polypeptide, e.g., firefly LUC reporter. Examples of cell include MM1 S multiple myeloma cells stably expressing (aka providing a cell with the nucleic acid molecule encoding) a fusion protein comprising a heterologous polypeptide fused to a CRBN-binding polypeptide, e.g., HA-1KZF1 or HA-IKZF3; and FFtuc-fused IKZF3 in 293T cells, see Example 3.
Regarding claim 362(a), (b), Fink teaches various variant of IKZF1 isoform 2 (NP001207694, sequence at p. 5), IKZF1 isoform 1 (NCB1 NP_006051, sequence at p. 6), and IKZF3 (NCBI Accession No. NP_036613.2, sequence at p. 7).
Regarding claim 363(a), Fink teaches the human IKZF3 (aka COF1/CRBN-binding polypeptide comprising SEQ ID NO: 4) which comprises the claimed amino acids 136-180 of IKZF3. The term “comprising” is open ended. It expands the claimed amino acid residues 136-180 of IKZF3 to include additional amino acids at both ends to read on the reference human IKZF3. The reference SEQ ID NO: 4 is identical to the claimed SEQ ID NO: 19, see sequence alignment below:
ALIGNMENT:
Query Match 100.0%; Score 2717; Length 509;
Best Local Similarity 100.0%;
Matches 509; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEDIQTNAELKSTQEQSVPAESAAVLNDYSLTKSHEMENVDSGEGPANEDEDIGDDSMKV 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEDIQTNAELKSTQEQSVPAESAAVLNDYSLTKSHEMENVDSGEGPANEDEDIGDDSMKV 60
Qy 61 KDEYSERDENVLKSEPMGNAEEPEIPYSYSREYNEYENIKLERHVVSFDSSRPTSGKMNC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 KDEYSERDENVLKSEPMGNAEEPEIPYSYSREYNEYENIKLERHVVSFDSSRPTSGKMNC 120
Qy 121 DVCGLSCISFNVLMVHKRSHTGERPFQCNQCGASFTQKGNLLRHIKLHTGEKPFKCHLCN 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 DVCGLSCISFNVLMVHKRSHTGERPFQCNQCGASFTQKGNLLRHIKLHTGEKPFKCHLCN 180
Qy 181 YACQRRDALTGHLRTHSVEKPYKCEFCGRSYKQRSSLEEHKERCRTFLQSTDPGDTASAE 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 YACQRRDALTGHLRTHSVEKPYKCEFCGRSYKQRSSLEEHKERCRTFLQSTDPGDTASAE 240
Qy 241 ARHIKAEMGSERALVLDRLASNVAKRKSSMPQKFIGEKRHCFDVNYNSSYMYEKESELIQ 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ARHIKAEMGSERALVLDRLASNVAKRKSSMPQKFIGEKRHCFDVNYNSSYMYEKESELIQ 300
Qy 301 TRMMDQAINNAISYLGAEALRPLVQTPPAPTSEMVPVISSMYPIALTRAEMSNGAPQELE 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 TRMMDQAINNAISYLGAEALRPLVQTPPAPTSEMVPVISSMYPIALTRAEMSNGAPQELE 360
Qy 361 KKSIHLPEKSVPSERGLSPNNSGHDSTDTDSNHEERQNHIYQQNHMVLSRARNGMPLLKE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 KKSIHLPEKSVPSERGLSPNNSGHDSTDTDSNHEERQNHIYQQNHMVLSRARNGMPLLKE 420
Qy 421 VPRSYELLKPPPICPRDSVKVINKEGEVMDVYRCDHCRVLFLDYVMFTIHMGCHGFRDPF 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 VPRSYELLKPPPICPRDSVKVINKEGEVMDVYRCDHCRVLFLDYVMFTIHMGCHGFRDPF 480
Qy 481 ECNMCGYRSHDRYEFSSHIARGEHRALLK 509
|||||||||||||||||||||||||||||
Db 481 ECNMCGYRSHDRYEFSSHIARGEHRALLK 509
Regarding claim 364, the reference compound is lenalidomide, thalidomide, and pomalidomide, which are known immunomodulatory imide drug (IMiD), see p. 28, line 21-26.
Regarding claims 373 and 374, Fink teaches human T cells (see Example 6 at p. 49), 293T cells (p. 47, line 19) which are mammalian cells, see p. 66, cell lines.
Thus, the reference teachings anticipate the claimed invention.
Claims 209-210, 213-214, 234, 249, 358-364, 373 and 374 are rejected under 35 U.S.C. 102 (a)(2) as being anticipated by US Patent No. 10,683,360 (Brayshaw hereafter, published May 28, 2015; PTO 1449) as evidenced by WO2015077058 (Fink hereafter, published May 28, 2015; PTO 1449).
Claim 209 encompasses a nucleic acid molecule encoding a fusion polypeptide that comprises a compound of formula (I) (COF1)/CRBN (Cereblon)-binding polypeptide and a heterologous polypeptide wherein the compound is lenalidomide.
Claim 210 recites a vector comprising the nucleic acid molecule of claim 209.
Claim 213 recites a viral particle comprising the vector of claim 210.
Claim 214 recites a cell comprising a fusion polypeptide of claim 209.
Claim 234 recites a method of making a cell, said method comprising providing a cell with the nucleic acid molecule encoding the fusion polypeptide of claim 209.
Claim 358 recites the e cell of claim 214, wherein the COF1/CRBN-binding polypeptide is:(a) fused to the heterologous polypeptide; or (b) operatively linked to the heterologous polypeptide via a linker, a glycine serine linker.
Claim 359 recites the cell of claim 214, wherein the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with cereblon (CRBN) in the absence of COF1 is no more than 0.01%,0.1%, 1%, 5%,10%, 15%, or 20% of the association of the COF1/CRBN-binding polypeptide or the fusion polypeptide with CRBN in the presence of COF1.
Claim 360 recites the cell of claim 214, wherein the degradation or ubiquitination of the fusion polypeptide in the absence of COF1 is no more than 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the degradation or ubiquitination of the fusion polypeptide in the presence of COF1.
Claim 361 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide: (a) is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between 20 and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length, or between 55 and 65 amino acid residues in length.
Claim 362 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:(a) a naturally occurring IKZF polypeptide or a COF 1/CRBN-binding variant thereof, or a naturally occurring IKZF1, IKZF2, IKZF3 (elected species).
Claim 363 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:
(a) amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19) or
(b) amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19).
Claim 364 recites the e cell of claim 214, wherein the COF1 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof, or is selected from the group consisting of lenalidomide (elected species), pomalidomide, and thalidomide.
Claim 372 recites the cell of claim 214, wherein the heterologous polypeptide: a chimeric antigen receptor (CAR).
Claim 362 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:(a) a naturally occurring IKZF polypeptide or a naturally occurring IKZF3 (elected species).
Claim 363 recites the cell of claim 214, wherein the COF1/CRBN-binding polypeptide comprises:
(a) amino acid residues 136-180 of IKZF3 (numbered according to SEQ ID NO: 19),
(b) amino acid residues 136-170 of IKZF3 (numbered according to SEQ ID NO: 19);
(c) amino acid residues 136-139 of IKZF3 (numbered according to SEQ ID NO: 19);
(d) the amino acid residues 236-249 of IKZF3 (numbered according to SEQ ID NO: 19).
Claim 364 recites the cell of claim 214, wherein the COF1 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof, or is selected from the group consisting of lenalidomide (elected species), pomalidomide, thalidomide.
Claim 373 recites the cell of claim 214, wherein the cell is a mammalian cell.
Claim 374 recites the cell of claim 214, wherein the cell is a human T cell or a human NK cell.
Regarding claim 209, Brayshaw teaches a polynucleotide of SEQ ID NO: 39, which encodes a fusion protein, e.g., construct 5 comprising heterologous polypeptide, e.g., anti-BCMA anti-BCMA chimeric antigen receptor (CAR), fused to a linker of SEQ ID NO: 25, follows by a cereblon (CRBN) binding polypeptide or degron, e.g., Ikaros residues 131-175, and residues 231-249 see col., 1, line 30, Fig. 7, col. 34, line 21-in particular. In the presence of a compound of formula 1 (COF1), e.g., Lenalidomide, Lenalidomide binds to CRBN and induces degradation of CAR, see col. 37, in particular. Brayshaw further teaches the degradation domain comprises TASAEARHIKAEMG of SEQ ID NO: 28. The term “comprising” is open ended.
The reference lenalidomide inherently has the chemical structure of
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wherein X is O, R1 is piperidine-2,6-dionyl, R2a is hydrogen, R2b is hydrogen, R3 is -NH2, and n is 1 as evidenced by Fink et al, see p. 28, in particular.
Regarding claim 210, Brayshaw teaches vector, such as viral vector, plasmid, see col. 20, lines 47-50, in particular.
Regarding claim 213, Brayshaw teaches vector can be viral vector, e.g., lentivirus, see col. 20, lines 52-67, in particular.
Regarding claims 214, 249, Brayshaw teaches a method of making a cell and controlling the protein levels of the expressed fusion protein by providing a cell, e.g., T cell (col. 25, line 63-65), transducing or transfecting polynucleotide or expression vector into said cell (col. 25, lines 66-67), wherein the polynucleotide or DNA sequence encodes a fusion polypeptide comprising fusing a ubiquitin targeting protein (which may also be referred to as a ubiquitin targeting domain), e.g., Ikaros 3, or the conserved structural motif thereof (instant CRBN-binding polypeptide, see col. 27, lines 11-12, Table 3) directly to the protein, e.g., a chimeric antigen receptor to be turned off by addition of an external compound (contacting cell ex vivo or externally via administration from outside of the cell, see col. 4, lines 54-55) with a compound, e.g., thalidomide, lenalidomide and pomalidomide or a functional derivative or analog thereof can simply be added in order to induce binding to ubiquitin ligase which results in ubiquitination, see entire document, Figs. 1, 6, col. 15, lines 1-34, col. 19, line 23-46, col. 27, line 12-16, Example 3, in particular. The term “optionally” does not require the expression level to be decreased by at least about 1 to 100 percent.
Regarding claim 358 (a) or (f), Brayshaw teaches that the IMiD dependent cereblon substrates (aka instant CRBN-binding polypeptide), e.g., Ikaros 1, Ikaros 3, or the conserved structural motif thereof (instant CRBN-binding polypeptide) genetically fused directly to the protein, e.g., a chimeric antigen receptor (see col. 15, line 1) or via a linker comprises G, S or GS residues, e.g., (GGGGS)n = 1-3, see col. 19, lines 14-22.
Regarding claim 359, Brayshaw teaches that in the presence of 10 nM lenalidomide, the construct 1 is decreased by no more than 20% compared to in the absence of lenalidomide, see Figure 3 (18216-15778/18216 x 100 = 13.4 %), in particular.
Regarding claim 360, Brayshaw teaches that in the presence of 10,000 nM lenalidomide, the construct 3 is decreased by no more than 60% compared to in the absence of lenalidomide, see Figure 3 (40043-19521/42043 x 100 = 53.5 %), in particular.
Regarding claim 361(a), Brayshaw teaches that Ikaros 3, or the conserved structural motif thereof (instant CRBN-binding polypeptide) can be less than 135 amino acids in length, for example 25, 50, 75, 80, 90 in length, see col. 6, line 51-53, col. 9, line 9-11, in particular. Minimizing the size of the motif required for effective ubiquitination has advantages, especially if the heterologous protein is introduced via a viral vector where space is a premium, see col. 4, lines 13-17, in particular. The reference Ikaros 3 family of zinc finger 3 (IKZF3, 141-173) is 31 amino acids in length, which is with the claimed range of between 10 and 95 residues in length, between 15 and 90 amino acids in length, between 20 and 85 amino acid residues in length, between 25 and 80 amino acid residues in length or between 30 and 75 amino acid residues in length or between 35 and 70 amino acid residues in length as per claim 361, see col. 38, reference SEQ ID NO: 6.
Regarding claim 362 (a), Brayshaw teaches that BCBN-binding polypeptide is Ikaros 3 (aka IKZF3), see col. 27, line 10-11, col. 27, lines 40-42, in particular.
Regarding claim 363 (b), Brayshaw teaches that BCBN-binding polypeptide is Ikaros 3 comprises residues 131-175 (SEQ ID NO 8), which is within the claimed range of amino acid residues 136-170, see col. 34, in particular. The term “comprises” is open-ended. It expands the claimed CRBN-binding polypeptide to include additional amino acid residues at both ends.
Regarding claim 363 (d), Brayshaw further teaches that BCBN-binding polypeptide is Ikaros 3 residues 231-249 (SEQ ID NO: 28), see col. 34, in particular. Again, the term “comprises” is open-ended. It expands the claimed CRBN-binding polypeptide to include additional amino acid residues at both ends.
Regarding claim 364, Brayshaw further teaches that the compound of formula I is an immunomodulatory imide drug (IMiD), e.g., thalidomide, lenalidomide and pomalidomide or a functional derivative or analog thereof, see col. 15, lines 15-50, col. 19, line 14 to col. 20, in particular.
Regarding claims 373, 374, Brayshaw teaches host cell, e.g., T cell, NK-cell (see col. 21, lines 1-30), human T lymphocytes (col. 22, lines 34-35) which are mammalian cells, in particular.
Thus, the reference teachings anticipate the claimed invention.
Claim Rejections - 35 USC § 103
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 of this title, 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
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 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.
Claims 214 and 365-367, 370 and 371 are rejected under 35 U.S.C. 103 as being unpatentable over US Patent No. 10,683,360 (Brayshaw hereafter, published May 28, 2015; PTO 1449) in view of Miyazaki (J American Chemical Society 134: 3942-3945, 2012; PTO 1449) and WO0023602 publication (Clackson hereafter, published April 27, 2000; PTO 1449).
Claim 365 recites the cell of claim 214, wherein the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF1/CRBN-binding polypeptide and the heterologous polypeptide by a heterologous protease cleavage site.
Claim 366 recites the cell of claim 365, wherein the degradation domain is an estrogen receptor (ER) domain.
Claim 367 recites the cell of claim 366, wherein the degradation domain is an ER domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 46 or 48.
Claim 370 recites the cell of claim 365, wherein the fusion polypeptide comprises, from N-terminus to C- terminus:
the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide, and the COF 1/CRBN-binding polypeptide;
the degradation domain, the heterologous protease cleavage site, the COF 1/CRBN- binding polypeptide, and the heterologous polypeptide;
the COF 1/CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site, and the degradation domain; or
the heterologous polypeptide, the COF1/CRBN-binding polypeptide, the heterologous protease cleavage site, and the degradation domain.
The teachings of Brayshaw have been discussed supra.
Brayshaw not teach the cell further comprises a degradation domain, wherein the degradation domain is separated from the COF1/CRBN-binding polypeptide and the heterologous polypeptide by a heterologous protease cleavage site as per claim 365, wherein the fusion polypeptide, from N-terminus to C-terminus: i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF1/CRBN-binding polypeptide, wherein the degradation domain is estrogen receptor (ER) domain as per claim 366, wherein the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF1/CRBN-binding polypeptide and the heterologous polypeptide by a heterologous protease cleavage site as per claim 365 wherein the fusion protein from N-terminus to C-terminus: i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide, and the COF 1/CRBN-binding polypeptide; or ii) the heterologous polypeptide, the COF1/CRBN-binding polypeptide, the heterologous protease cleavage site, and the degradation domain as per claim 370.
However, Clackson teaches a method of conditionally regulate the expression of a membrane protein of interest, see entire document, Example 7, in particular. Typically, the fusion protein contains a secretory signal sequence to target the fusion protein to a secretory compartment such as the ER or any part of the Golgi apparatus. Clackson teaches the fusion protein is designed to contain at least one conditional retention domain (CRD) and a secretory signal sequence. Proteins containing one or more CRDs are, as a rule, retained in the secretory machinery except in the presence of a ligand which binds to the protein. Examples of conditional retention domain (CRDs or aggregation domain) include retinol binding proteins such as human FKBP12 mutants, F36M hFKBP12, see p. 2, p. 11-12. The degradation compound is AP21998 (example 7). A typical fusion protein comprises a signal sequence, a conditional retention domain, a furin or protease cleavage site, and a polypeptide sequence comprising a selected target protein sequence, see p. 2.
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When the fusion protein exits the endoplasmic reticulum (ER) following addition of ligand, the enzymatic cleavage site allows the protein to be released from the CRD and secreted. Ideally, the cleavage site should be specific to an enzyme which resides in a cellular compartment between the ER and the plasma membrane, e.g., the Golgi apparatus. An exemplary cleavage enzyme is furin, also known as PACE, see p. 19. The consensus cleavage sequence of furin is RX(K/R)R wherein X is any amino acid as per claims 371 (a), or (b), see p. 20, in particular. Additional furin cleavage site comprises the sequence SARNRQKR, see p. 2, lines 18-20 and example 7. One particular advantage of having furin cleavage site as the cleavage enzyme is that its recognition sequence is located exclusively N-terminal to the cleavage site. This allows the portion of the protein that encodes the target protein to be released from the cell unaltered by the presence of additional amino acids, see p. 20, lines 10-13.
Clackson does not teach the degradation domain is from an estrogen receptor (ER) domain as per claim 366.
However, Miyazaki teaches the use of estrogen receptor ligand binding domain (ERLBD, residues 305−549 of ERS1) as a degradation domain (aka destabilizing domain or DD) to regulate the stability of specific proteins in a rapid, reversible, and tunable manner using a small molecule, e.g., CMP8 or 4OHT. When this destabilizing domain (DD) is fused to a protein of interest, its instability is conferred to the protein of interest, resulting in rapid degradation of the entire fusion protein. CMP8 or 4OHT are high-affinity ligands for mutant ERLBD that stabilizes fusion proteins in a dose-dependent manner, and protein levels in the absence of ligands are negligible. This ERLBD-derived DD system is orthogonal to the existing FKBP- and DHFR-based DD systems, in the sense that the stabilizing ligands do not affect the stability of their noncognate DDs. This novel DD system will enable researchers to simultaneously and independently regulate three proteins in biological studies, see entire document, Figure 1, p. 3944, in particular.
In view of the combined teachings of the references, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the claimed invention to produce a cell expressing a chimeric antigen receptor fusion protein of Brayshaw by further includes a conditional degradation domain from estrogen receptor of Miyazaki, with a furin cleavage site at the N-terminus to C-terminus of the therapeutic protein as taught by Clackson to arrive at the claimed invention with a reasonable expectation success, e.g., conditional induced CAR expression on T cells.
The person of ordinary skill would have had a reasonable expectation of success in putting Miyazaki’s estrogen receptor destabilized domain in Brayshaw’ Chimeric antigen receptor (CAR) for conditional control expression of CAR on T cells; the fusion protein is degraded in the absence of the small molecule e.g., CMP8 or 4OHT for estrogen receptor, and in the presence of the small molecule, e.g., CMP8 or 4OHT, the fusion protein is not degraded and the degradation domain (DD) is removed by intracellular protease furin having a consensus cleavage sequence of Arg-X-Lys/Arg motif.
One of ordinary skill in the art would have been motivated to do so Clackson teaches one particular advantage of having furin as the cleavage enzyme is that its recognition sequence is located exclusively N-terminal to the cleavage site. This allows the portion of the protein that encodes the target protein to be released from the cell unaltered by the presence of additional amino acids, see p. 20, lines 10-13.
One of ordinary skill in the art would have been motivated to do so because Miyazaki teaches the estrogen receptor ERLBD-derived DD system will enable researchers to simultaneously and independently regulate three proteins in biological studies, see entire document, Figure 1, p. 3944, in particular.
Claim 370 is included as it is within the purview of one of ordinary skill in the art would have arranged the fusion polypeptide, from N-terminus to C-terminus, by having the drug inducible degradation domain either N-terminus of Brayshaw’s fusion protein to arrive at i) degradation domain, cleavable linker having furin cleavage site, the heterologous polypeptide (CAR) and the COF1/CRBN-binding polypeptide IKZF3 as per claim 370 (ii). One of ordinary skill in the art would have arranged the fusion polypeptide, from N-terminus to C-terminus, by having the degradation domain at the C-terminus of Brayshaw’s fusion protein to arrive at i) the heterologous polypeptide (CAR), the COF1/CRBN-binding polypeptide IKZF3, a linker comprising a furin protease cleavage site linked to the degradation domain as per claim 370 (iv), as it is an obvious variation of the references teachings.
“The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results."' KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 {2007).
‘'The test of obviousness is not express suggestion of the cl aimed invention in any or all of the references but rather what the references taken collectively would suggest to those of ordinary skill in the art presumed to be familiar with them."' See In re Rosselet 146 USPQ 183, 186 (CCPA 1965).
“There is no requirement (under 35 USC 103(a)) that the prior art contain an express suggestion to combine known elements to achieve the claimed invention. Rather, the suggestion to combine may come from the prior art, as filtered through the knowledge of one skilled in the art.,” Motorola, Inc, v. Interdigital Tech. Corn., 43 USPQ2d 1481, 1489 (Fed. Cir. 1997).
Accordingly, the claimed invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filling date of the claimed invention especially in the absence of evidence to the contrary.
Claim 367 is rejected under 35 U.S.C. 103 as being unpatentable over US Patent No. 10,683,360 (Brayshaw hereafter, published May 28, 2015; PTO 1449) in view of Miyazaki (J American Chemical Society 134: 3942-3945, 2012; PTO 892) and WO0023602 publication (Clackson hereafter, published April 27, 2000; PTO 1449) as applied to claims 214 and 365-366 and 370 mentioned above and further in view of Zhang (WO2016106244, published June 30, 2016; PTO 892).
367. (New) The cell of claim 366, wherein the degradation domain is an ER domain and comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 46.
The combine teachings of Brayshaw, Miyazaki and Clackson have been discussed supra.
The references above do not teach the estrogen receptor (ER) domain comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 46 as per claim 367.
However, Zhang teaches estrogen receptor ligand binding domain (ERLBD, residues 305-549 of ERS1) can be engineered as a destabilizing domain, since numerous agonist and antagonist of estrogen receptor, e.g., 4-hydroxytamoxifen (4HT) and CMP8 are known (see p. 72, p. 301, para [00736]) and widely available and typically not expensive, see p. 74. By using one of these ERLBD, it is possible to regulate the stability of an ERLB-derived DD using a ligand that does not perturb endogenous estrogen-sensitive networks, see p. 73, in particular. Example of the ERLBD (aka ER50) comprises the amino acid sequence shown in example 1, which is 100% identical to the claimed SEQ ID NO: 46, para. [00724], sequence alignment below.
Query Match 100.0%; Score 1250; Length 245;
Best Local Similarity 100.0%;
Matches 245; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRV 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRV 60
Qy 61 PGFVDLALHDQVHLLECAWMEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGGVEI 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PGFVDLALHDQVHLLECAWMEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGGVEI 120
Qy 121 FDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITD 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 FDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITD 180
Qy 181 TLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSSKRMEHLYSMKCKNVVPLSDLLLEML 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSSKRMEHLYSMKCKNVVPLSDLLLEML 240
Qy 241 DAHRL 245
|||||
Db 241 DAHRL 245
Zhang teaches the advantage of tandem fusion of more than one DD at the N or C-term may enhance degradation, see p. 6, para. [0014], lowest overall activity and least background (see para. [0012], [0016]).
In view of the combined teachings of the references, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the claimed invention to substitute a known estrogen receptor ligand binding domain (ERLBD) in the fusion protein of Brayshaw, Miyazaki and Clackson for another, e.g., Zhang’s estrogen receptor ligand binding domain (ERLBD comprising the claimed amino acid sequence of SEQ ID NO: 46 to arrive at the claimed invention with a reasonable expectation of success, e.g., degradation domain from estrogen receptor comprising SEQ ID NO: 46 of Zhang and Miyazaki, with a furin cleavage site at the N-terminus to C-terminus of the therapeutic protein as taught by Clackson with a reasonable expectation of success, e.g., conditional inducible CAR expression on T cells. In this case, simple substitution of one known element for another to obtain predictable results is obvious, see KSR International Co. V. Teleflex Inc. 82 USPQ2d 1385 (2007).
One of ordinary skill in the art would have had an expectation of success at the time the invention was made to substitute a known estrogen receptor ligand binding domain (ERLBD) for another because
Zhang teaches the advantage of tandem fusion of more than one destabilizing domain (DD) at the N or C-terminus of fusion protein may enhance degradation (see p. 6, para. [0014]) in the presence of 4-hydroxytamoxifen (4HT) as the 4-hydroxytamoxifen (4HT) binding to estrogen receptor are known (see p. 72, p. 301, para [00736]), widely available and typically not expensive, see p. 74.
One of ordinary skill in the art would have been motivated to have made and used a fusion protein to include additional degradation domain represented by SEQ ID NO: 46 for additional control of protein expression because Zhang teaches that the advantage of tandem fusion of more than one DD at the N or C-term may enhance degradation, see p. 6, para. [0014], lowest overall activity and least background (see para. [0012], [0016]).
A person of ordinary skill in the art is always motivated to pursue the known options within her or his technical grasp. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense.
“The test of obviousness is not express suggestion of the cl aimed invention in any or all of the references but rather what the references taken collectively would suggest to those of ordinary skill in the art presumed to be familiar with them.” See In re Rosselet 146 USPQ 183, 186 (CCPA 1965).
“There is no requirement (under 35 USC 103(a)) that the prior art contain an express suggestion to combine known elements to achieve the claimed invention. Rather, the suggestion to combine may come from the prior art, as filtered through the knowledge of one skilled in the art.,” Motorola, Inc, v. Interdigital Tech. Corn., 43 USPQ2d 1481, 1489 (Fed. Cir. 1997).
Accordingly, the claimed invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filling date of the claimed invention especially in the absence of evidence to the contrary.
Conclusion
Nucleic acid molecules encoding an amino acid sequence selected from the group consisting of SEQ ID NO: 1, 3, 92, 93, 94, 95, 96, 97 and 98 are free of prior art.
Claims 354-357 are free of prior art.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PHUONG HUYNH whose telephone number is (571)272-0846. The examiner can normally be reached on 9:00 a.m. to 6:30 p.m. The examiner can also be reached on alternate alternative Friday from 9:00 a.m. to 5:30 p.m.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Misook Yu, can be reached at 571-270-3497. The fax phone number for the organization where this application or proceeding is assigned is 571-272-0839.
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/PHUONG HUYNH/ Primary Examiner, Art Unit 1641