DETAILED ACTION
Status of the Application
Claims 1, 6, 9-15, 21-23 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment of claims 1, 6, 11, cancellation of claims 7-8, 16-20, and addition of claims 21-23 as submitted in a communication filed on 1/27/2026 is acknowledged.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/27/2026 has been entered.
As indicated in prior Office actions, in the interest of advancing prosecution, the Examiner rejoined the embodiment of amended claim 1 that is directed to variants of the polypeptide of SEQ ID NO: 18 having at least 95% sequence identity to the polypeptide of SEQ ID NO: 18.
In view of the amendment of claim 1, which is now found allowable, method claims 12-13, which are directed to methods of use of the allowed product, are rejoined for examination on the merits. Claim 11 has been amended to now require a host cell that comprises the proteins of claims 1, 21-23. Therefore, claim 11 is rejoined for examination on the merits.
New claims 21-23 are directed to the elected invention. Claims 6, 9-10, 14-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 9/5/2023. Claims 1, 11-13, 21-23 are at issue and will be examined only to the extent they encompass the elected invention.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Objections
Claim 11 is objected to due to the recitation of “a protein according to claim X”. Since the protein has been previously defined in claim X, the term should be amended to recite “the protein according to claim X”, or in the alternative, “the protein of claim X”. Appropriate correction is required.
Claims 12-13 are objected to due to the recitation of “a protein according to claim 1”. Since the protein has been previously defined in claim 1, the term should be amended to recite “the protein according to claim 1”, or in the alternative, “the protein of claim 1”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 11 and 23 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. New grounds of rejection are necessitated by amendment.
Claim 23 (claim 11 dependent thereon) is indefinite in the recitation of “a protein…wherein the protein comprises the amino acid sequence of SEQ ID NO: 18 wherein a) the amino acid corresponding to position 166 in SEQ ID NO: 18 is a G and the amino acid according to position 327 in SEQ ID NO: 18 is a Q….j) the amino acid corresponding to position 165 in SEQ ID NO: 18 is a K or C” for the following reasons. The limitations in sections a) through j) are substitutions in view of the fact that the amino acids required at the recited positions are not the amino acids present in SEQ ID NO: 18 at those positions. For example, the amino acid at position 166 of SEQ ID NO: 18 is a serine and the amino acid at position 327 of SEQ ID NO: 18 is a threonine. If the preamble states that the protein comprises the amino acid sequence of SEQ ID NO: 18, then it is unclear as to how it can simultaneously have substitutions at the recited positions. In other words, if the protein is required to comprise the recited amino acids at the positions recited, it cannot comprise SEQ ID NO: 18 as recited in the preamble. Therefore, it is unclear if the claim is directed to any variant of the polypeptide of SEQ ID NO: 18 having any structure, wherein said variant comprises any one of the recited substitutions, or if the claim is directed to a variant of the polypeptide of SEQ ID NO: 18 that comprises all of SEQ ID NO: 18 except for any one of the substitutions recited in parts a)-j). For examination purposes, it will be assumed that claim 23 is directed to a protein having ω-transaminase activity, wherein said protein comprises any structure and at least one of the recited substitutions. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1 and 16 were 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 due to the introduction of new matter.
In view of Applicant’s amendment of claim 1 and cancellation of claim 16, this rejection is hereby withdrawn.
Claims 1 and 16 were 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 and enablement requirements.
In view of Applicant’s amendment of claim 1 and cancellation of claim 16, this rejection is hereby withdrawn.
Claims 11 and 23 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. This rejection is necessitated by amendment.
As stated in MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. Claims 11 and 23 as interpreted require a genus of variants of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity having essentially any structure, wherein said variants can have certain amino acids at specific positions corresponding to positions in the polypeptide of SEQ ID NO: 18. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, 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, reduction to drawings, 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 that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that a representative number of species means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
There is essentially no structural limitation with regard to the members of the genus of proteins required by the claims. While the specification in the instant application discloses the structure of a limited number of species of the recited genus of proteins having ω-transaminase activity, it provides no clue as to the structural elements required in any ω-transaminase, nor does it teach which structural elements of the proteins disclosed, including the protein of SEQ ID NO: 18, are required in any ω-transaminase. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which variants of the polypeptide of SEQ ID NO: 18 having the recited amino acids have ω-transaminase activity.
The claims encompass a large genus of proteins which are essentially unrelated in structure in view of the fact that at most only two amino acids are defined. A sufficient written description of a genus of polypeptides may be achieved by a recitation of a representative number of polypeptides defined by their amino acid sequence or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, there is no recited structural feature which is representative of all the members of the genus of proteins with ω-transaminase activity recited in the claims. There is no information as to which are the structural elements within the polypeptide of SEQ ID NO: 18 that are essential for the recited activity. The specification is completely silent as to the remaining structural elements required in those polypeptides such that the desired ω-transaminase activity is displayed, or a correlation between structure and function which would provide those unknown structural features. Furthermore, while one could argue that the few species disclosed are representative of the structure of all the members of the genus, it is noted that the art teaches several examples of how even highly structurally homologous polypeptides can have different enzymatic activities. See the teachings of Witkowski et al. (Biochemistry 38:11643-11650, 1999), Tang et al. (Phil Trans R Soc B 368:20120318, 1-10, 2013) and Seffernick et al. (J. Bacteriol. 183(8):2405-2410, 2001) previously discussed. Therefore, since minor structural differences may result in changes affecting function, and no additional information correlating structure with the desired functional characteristics has been provided, one cannot reasonably conclude that the few species disclosed are representative of the structure of all the ω-transaminases required.
Due to the fact that the specification only discloses a limited number of species of the genus of ω-transaminases required by the claims, and the lack of description of any additional species by any relevant, identifying characteristics or properties, one of skill in the art would not recognize from the disclosure that Applicant was in possession of the claimed invention.
Claims 11 and 23 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 the protein of SEQ ID NO: 18 and variants of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity that comprise all of SEQ ID NO: 18 except for the specific substitutions recited in claim 23 at positions corresponding to positions 166, 326, 327, 384, 164, 409, 271, 329, 414, or 165 in the polypeptide of SEQ ID NO: 18, does not reasonably provide enablement for variants of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity and essentially any structure, wherein said variants have at most two amino acids defined at specific positions corresponding to positions in the polypeptide of SEQ ID NO: 18. 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 and/or use the invention commensurate in scope with these claims. This rejection is necessitated by amendment.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed. Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breadth of the claims. The factors which have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breadth of the claims. Claims 11 and 23 broadly encompass variants of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity having essentially any structure, and host cells comprising said variants, wherein said variants have at most two amino acids defined at specific positions corresponding to positions in the polypeptide of SEQ ID NO: 18. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation. The enablement provided is not commensurate in scope with the claims due to the lack of information regarding the structural features required in any protein having the recited ω-transaminase activity, as well as the structural elements within the polypeptide of SEQ ID NO: 18 that are required and those that can be modified to obtain variants that have the desired ω-transaminase activity. In the instant case, the specification enables the protein of SEQ ID NO: 18 and variants of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity that comprise all of SEQ ID NO: 18 except for the specific substitutions recited in claim 23 at positions corresponding to positions 166, 326, 327, 384, 164, 409, 271, 329, 414, or 165 in the polypeptide of SEQ ID NO: 18.
The amount of direction or guidance presented and the existence of working examples. The specification discloses the amino acid sequence of the protein of SEQ ID NO: 18, as a working example. However, the specification fails to provide any clue as to the structural elements required in any protein having ω-transaminase activity. No correlation between structure and function has been presented. There is no disclosure of those structural elements in the polypeptide of SEQ ID NO: 18 that are required in any variant of the polypeptide of SEQ ID NO: 18 that has ω-transaminase activity.
The state of prior art, the relative skill of those in the art, and the predictability or unpredictability of the art. The amino sequence of a protein determines its structural and functional properties. While the art discloses a limited number of ω-transaminases, neither the specification nor the art provide a correlation between structure and function such that one of skill in the art can envision the structure of any variant of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity. In addition, the art does not provide any teaching or guidance as to which changes can be made to the protein of SEQ ID NO: 18 such that the resulting variant would display the desired functional characteristics, or the general tolerance of ω-transaminases to structural modifications and the extent of such tolerance.
While the argument can be made that the structure of the variants encompassed by the claims can be obtained by structural homology, the art clearly teaches that (i) there is a high level of unpredictability associated with accurate functional annotation of proteins based solely on structural homology, and (ii) modification of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved is highly unpredictable. See the teachings of Singh et al. (Current Protein and Peptide Science 19(1):5-15, 2018) and Sadowski et al. (Current Opinion in Structural Biology 19:357-362, 2009) previously discussed. The teachings of Singh et al. and Sadowski et al. are further supported by the teachings of Witkowski et al., Tang et al. and Seffernick et al. already discussed, where it is shown that even small amino acid changes result in unpredictable enzymatic activity changes.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. While methods of generating or isolating variants of a polypeptide were known in the art, and enzymatic assays were also known in the art at the time of the invention, it was not routine in the art to screen by a trial and error process for an essentially infinite number of proteins to find those that have the desired enzymatic activity. In the absence of a rational and predictable scheme for determining which variants of the polypeptide of SEQ ID NO: 18 are more likely to have the recited enzymatic activity, or a correlation between structure and function, one of skill in the art would have to test an essentially infinite number of proteins to determine which variants of the protein of SEQ ID NO: 18 have ω-transaminase activity.
Therefore, taking into consideration the extremely broad scope of the claim, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims.
Claim Rejections - 35 USC § 102 (AIA )
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claims 11 and 23 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by van Oosterwijk et al. (Biochemistry 55:4422-4431, 2016). Claims 23 and 11 as interpreted is directed in part to a variant of the polypeptide of SEQ ID NO: 18 having ω-transaminase activity, wherein said variant comprises a tyrosine (Y) at a position corresponding to position 164 of the polypeptide of SEQ ID NO: 18, and a host cell that comprises said variant. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation. van Oosterwijk et al. teach a protein having ω-transaminase activity from B. megaterium (Abstract), which comprises a tyrosine at a position corresponding to position 164 of the polypeptide of SEQ ID NO: 18. See alignment below (bold/underlined/italics). van Oosterwijk et al. teach E. coli cells that comprise said protein intracellularly which were passed through a French press to recover said protein (page 4423, right column, third full paragraph). Therefore, the teachings of van Oosterwijk et al. anticipate the instant claims as written/interpreted.
SEQ ID NO: 18
RESULT 2
A0A1C7D190_PRIMG
ID A0A1C7D190_PRIMG Unreviewed; 483 AA.
AC A0A1C7D190;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 22-FEB-2023, entry version 16.
DE SubName: Full=Transaminase {ECO:0000313|PDB:5G09};
DE EC=2.6.1.- {ECO:0000313|PDB:5G09};
OS Priestia megaterium (Bacillus megaterium).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Priestia.
OX NCBI_TaxID=1404 {ECO:0000313|PDB:5G09};
RN [1] {ECO:0000313|PDB:5G09, ECO:0007829|PDB:5G09}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS).
RX PubMed=27428867; DOI=10.1021/ACS.BIOCHEM.6B00370;
RA van Oosterwijk N., Willies S., Hekelaar J., Terwisscha van Scheltinga A.C.,
RA Turner N.J., Dijkstra B.W.;
RT "Structural Basis of the Substrate Range and Enantioselectivity of Two (S)-
RT Selective omega-Transaminases.";
RL Biochemistry 55:4422-4431(2016).
CC -!- SIMILARITY: Belongs to the class-III pyridoxal-phosphate-dependent
CC aminotransferase family. {ECO:0000256|RuleBase:RU003560}.
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DR PDB; 5G09; X-ray; 1.90 A; A/B/C/D=1-483.
DR PDBsum; 5G09; -.
DR AlphaFoldDB; A0A1C7D190; -.
DR SMR; A0A1C7D190; -.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0008483; F:transaminase activity; IEA:InterPro.
DR CDD; cd00610; OAT_like; 1.
DR Gene3D; 3.90.1150.10; Aspartate Aminotransferase, domain 1; 1.
DR Gene3D; 3.40.640.10; Type I PLP-dependent aspartate aminotransferase-like (Major domain); 1.
DR InterPro; IPR005814; Aminotrans_3.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR43094; AMINOTRANSFERASE; 1.
DR PANTHER; PTHR43094:SF1; AMINOTRANSFERASE CLASS-III; 1.
DR Pfam; PF00202; Aminotran_3; 1.
DR SUPFAM; SSF53383; PLP-dependent transferases; 1.
DR PROSITE; PS00600; AA_TRANSFER_CLASS_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0000313|PDB:5G09, ECO:0007829|PDB:5G09};
KW Pyridoxal phosphate {ECO:0000256|ARBA:ARBA00022898,
KW ECO:0000256|RuleBase:RU003560}.
SQ SEQUENCE 483 AA; 54202 MW; 33214D9DEE4D385A CRC64;
Query Match 93.2%; Score 2368; Length 483;
Best Local Similarity 93.4%;
Matches 450; Conservative 12; Mismatches 20; Indels 0; Gaps 0;
Qy 1 MGLTVQKINWEQVKEWDRKYLMRTRSTQNEYQPVPIESTEGDYLIMPGGTRLLDFFNQLY 60
| |||||||||||||||||||||| |||||||||||||||||||||| ||||||||||||
Db 1 MSLTVQKINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLY 60
Qy 61 CVNIGQKNQKVNAAIKEALDRYGFVWDAYATDYKAKAAKIIIEDILGDEDWPGKVRFVST 120
|||:||||||||||||||||||||||| ||||||||||||||||||||||||||||||||
Db 61 CVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVST 120
Qy 121 GSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAAAVTRLRSFQSGLAGENSGSFSAQI 180
|||||||||||||||||||||||||||||||||||| ||||||::||| |||| ||||||
Db 121 GSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQI 180
Qy 181 PGSSYNNAVLMAPSPNAFQDSNGNCLKDENGELLSVKYTRRMIENYGPEQVAAVITEVPQ 240
||||||:||||||||| ||||:|| ||||||||||||||||||||||||||||||||| |
Db 181 PGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQ 240
Qy 241 GVGSTMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGL 300
| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGL 300
Qy 301 SSSSLPAGAVVVSKEIAAFMDKHRWETGSTYAGHPVAMAAVCANLEVMMEENLVEQAKNS 360
||||||||||:|||||||||||||||: |||||||||||||||||||||||| |||||:|
Db 301 SSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDS 360
Qy 361 GEYIRSKLELLQEKHKSIGNFDGCGLLWLVEIVNAETKTPYVKLDRNFTRGMNLNQIPTQ 420
||||||||||||||||||||||| ||||:|:||||:||||||||||||| ||| ||||||
Db 361 GEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQ 420
Qy 421 IIMEKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQQSHHHH 480
|||:|||||||||||||||||||||||||||||||||||||||||||||||||| |||
Db 421 IIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQALEHHH 480
Qy 481 HH 482
||
Db 481 HH 482
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.
Allowable Subject Matter
The subject matter of claims 1, 21 and 22 appears to be allowable over the prior art of record.
Conclusion
No claim is in condition for allowance.
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Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
July 14, 2026
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