Prosecution Insights
Last updated: April 19, 2026
Application No. 18/551,851

CYSTEINE ENGINEERED ANTIBODY CONSTRUCTS, CONJUGATES AND METHODS OF USE

Non-Final OA §112§DP
Filed
Sep 21, 2023
Examiner
HOLTZMAN, KATHERINE ANN
Art Unit
1646
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Zymeworks, Inc.
OA Round
1 (Non-Final)
64%
Grant Probability
Moderate
1-2
OA Rounds
3y 7m
To Grant
99%
With Interview

Examiner Intelligence

Grants 64% of resolved cases
64%
Career Allow Rate
35 granted / 55 resolved
+3.6% vs TC avg
Strong +62% interview lift
Without
With
+62.4%
Interview Lift
resolved cases with interview
Typical timeline
3y 7m
Avg Prosecution
34 currently pending
Career history
89
Total Applications
across all art units

Statute-Specific Performance

§101
5.6%
-34.4% vs TC avg
§103
27.1%
-12.9% vs TC avg
§102
11.7%
-28.3% vs TC avg
§112
28.8%
-11.2% vs TC avg
Black line = Tech Center average estimate • Based on career data from 55 resolved cases

Office Action

§112 §DP
DETAILED ACTION Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Claim Interpretation Claim 1 recites a cysteine engineered antibody construct comprising one or more cysteine insertion mutations wherein a cysteine is inserted between positions denoted by Kabat numbering for VH, VL, CH1, or VL domains or EU numbering for the CH2 domain. Insertion is interpreted in line with the Specification to mean that the cysteine residue is incorporated into the polypeptide chain between the two number positions – not that one of the residue at one of the number positions is substituted with a cysteine n or that the residue at one of the number positions is thiolated ; see paragraphs 0005 and 0038. This language is repeated in claims 23 and 32 . Claim 5 recites symmetrical mutations and is interpreted as comprising the same position insertion on both the heavy chains or on both light chains; see paragraph 0076. Claim Rejections - 35 USC § 112(b) 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 appl icant regards as his invention. Claim s 1-5, 7-11, 13-28, 31-34, and 38-40 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 s 1 , 23, and 32 recite an antibody construct which Specification paragraph 0044 defines as encompassing full-length antibodies, functional fragments of full-length antibodies, and Fc fusion proteins. Claims 1, 23, and 32 also recite that the antibody construct is based on an immunoglobulin G (IgG). Specification paragraph 0049 states that the limitation “based on” is “used herein to describe an amino acid sequence, mean[s] that the subject amino acid sequence is substantially identical to the stated.” Paragraph 0050 defined “substantially identical” as “the amino acid sequence shares at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with its reference amino acid sequence. […] In general, for peptides, the length of comparison sequences will be at least 10 amino acids, but one skilled in the art will understand that the actual length will depend on the overall length of the sequences being compared. In certain embodiments, the length of comparison sequences may be the full-length of the protein or peptide sequence . ” Similarly, claim 18 recites the phrase “based on an IgG1”. The combination of antibody construct which encompasses fragments and Fc fusion proteins and “based on” an IgG, wherein the construct may have as little as 9 residues over a 10 amino acid sequence comparison identical, makes unclear how much of the IgG sequence is actually required. Is merel y a 10 amino acid subs equence of at least 85% identity to IgG within the cysteine engineered antibody construct required? Is at least 85% identity over the length of the cysteine engineered antibody construct required? The claims encompass constructs which comprise full-length antibodies, antibody fragments, or Fc fusion proteins. Antibody fragments do not require the IgG Fc domain and Fc fusion proteins do not require the antigen binding domains of the IgG. It is unclear how much of the IgG is required to be present in the cysteine engineered antibody construct given that the various construct embodiments seem to encompass distant parts of the IgG. More specifically, which domains (e.g. VH, VL, CH1, CL, CH2, or CH3) are required to have the amino acid sequence of an IgG? The Fc domain and antigen binding domains have implied functions. It is unclear if the cysteine engineered antibody construct is required to retain any single implicit IgG function. Further, the use of open language “comprising” allows for additional mutations, not limited to cysteine mutations, but includes any number of insertions, substitutions, or deletions. Given indefiniteness of the language “based on an IgG” in combination with “comprising”, it is unclear how much of the resulting construct must comprise the sequence of an IgG. The amount of IgG sequence in this construct is critical to recognizing the Kabat and EU number positions of the recited cysteine insertion mutations. For example, if the segment of amino acids preceding Kabat position 237 and following Kabat position 238 are altered, then how would one recognize the cysteine insertion mutation between positions 237 and 238? Especially when the construct is not in the context of a full-length antibody. For the purpose of compact prosecution, the claims have been interpreted as requiring 85% identity to IgG over a 10 amino acid segment of a full-length IgG antibody , fragment, or Fc fusion protein. Claims 2-5, 7-11, 13-22, 24-28, 31, 33, 34, and 38-40 are rejected for depending from claims 1, 23, or 32 and failing to remedy the indefiniteness. Claim Rejections - 35 USC § 112(a) 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 1-5, 7-11, 13-28, 31-34, and 38-40 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 : an antibody construct which is a full-length IgG antibody and comprises one to three of the cysteine insertion mutations recited in claims 1, 23, and 32 and wherein the total number of cysteine insertion mutations may be six ( ie . three symmetrical mutations) and, optionally, wherein the construct comprises the HetFc CH3 mutations in paragraphs 0161-0163 , a conjugate comprising the antibody construct, the method of preparing the antibody construct, and the method of treating a disease or disorder comprising administering the antibody construct , does not reasonably provide enablement for : an antibody construct which comprises at least 85% identity over a 10 amino acid subsequence to IgG, is an antibody fragment or Fc fusion protein, or comprises a combination of more than three of the cysteine insertion mutations recited in claims 1, 23, and 32 or additional unrecited mutations . 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 or use the invention commensurate in scope with these claims. Claims 1, 23, and 32 encompass antibody constructs which comprise one to all ten recited cysteine insertion mutations. Moreover, the use of the open l anguage “comprising” allows for any additional mutations, not merely cysteine insertion mutations. The claims encompass constructs which comprise full-length antibodies, antibody fragments, and Fc fusion proteins. The nature of the invention is to generate cysteine inserted engineered antibodies to which drugs can be conjugated . Dimasi et al. (Molecular Pharmaceutics. 14: 1501-1516; Published: February 28, 2017) teaches an antibody comprising an insertion of cysteine at positions commonly used for cysteine- substitution mutagenesis: A114 of the CH1 domain by Kabat numbering, S239 in the CH2 domain by EU numbering, or V205 in the CL domain by Kabat numbering for site-specific drug conjugation. Dimasi et al. demonstrated that the efficacy of drug conjugation was reduced in the cysteine-inserted antibodies compared to the cysteine-substituted antibodies and, for the C238i and C239i cysteine-inserted antibodies , the Tm was reduced by 10 degrees Celsius compared to the cysteine-substituted and parent antibody ; see Table 3 and Figure 3 . The antibodies C113i, C114i, C204i, nor C205i did not demonstrate the same destabilization and Tm difference compared to the cysteine-substituted equivalents (A114C or V205C) or the native parent antibody; see Figure 3. Additionally, Dimasi et al. demonstrated that only the C239i antibody had the same linker stability in serum as the cysteine -239 -substituted antibody ; see Figure 10. The C238i antibody demonstrated greater linker loss compared to the S239C antibody. The C113i, C114i, C204i, and C205i antibodies also demonstrated greater linker loss than the cysteine-substituted equivalents ( ie . A114C and V205C). Interestingly, Dimasi et al. teache s that the C238i and C239i antibodies resulted in complete elimination of binding to Fc γ R in contrast to the cysteine-substituted antibody at position 239 which only demonstrated reduced Fc γ R binding . The antibodies C113i, C114i, C204i, and C205i maintained similar FcγR binding as the native parent antibody; see page 1510 left column. Orozco et al. (Bioconjugate Chemistry. 32(8): 1834–1844; Published: August 9, 2021 ) teaches that the cysteine insertion at position 239 destabilized the CH2 domain, but the CH3 domain was unaffected; see page 4. In contrast, a cysteine substitution at position 239 did not destabilize the CH2 domain. Orozco et al. teaches that “[t]he insertion of a cysteine at position 239 of the heavy chain (Fc-C239i) changes the structure and/or conformational dynamics of the CH2 domain, which is further, and substantially, disrupted by subsequent formation of an interchain disulfide bond.” Orozco et al. states that “[ i ]n previous studies[26,27], it had been observed that the β-strand G in the CH2 domain was the most destabilized by other mutations in the CH2 domain, demonstrating a lower stability in that specific β-strand. Our data suggest that the additional disulfide bridge at the beginning of the CH2 domain applies strain to a larger region, i.e. across the CH2 domain, distorting it and opening it up compared to the wild type.” In short, the C239i antibody demonstrated altered conformation which likely caused the elimination of binding to FcγR . The C238i and the cysteine-239-substituted antibody did not exhibit the same FcγR binding deficiency or CH2 destabilization. While the level of one of ordinary skill in the art is high, the level of unpredictability is also high. For antibodies, including fragments, the three-dimensional structure is critical for stability and antigen binding function; see Ito et al. (Cellular and Molecular Life Sciences. 53(1): 51-60; Published: January 1997) . Mutations, including insertions, to polypeptide chain of the h eavy and/or light chains can perturb the three-dimensional structure and alter antigen binding; see Segal et al. (PNAS. 71(11): 4298-4302: Published: November 15, 1974). Thus, even when a site is a known cysteine-substitution site, it is unpredictable how cysteine insertion will alter the structure and function of the antibody construct. Further, it is unpredictable how multiple cysteine insertion mutations will alter the function and structure of the antibody construct. The amount of direction provided by the inventor falls short of the potentially enormous scope of an antibody construct, including full-length, fragments, and Fc fusion proteins, comprising one to ten of the recited insertion mutations and at least 85% identity of a 10 amino acid subsequence to IgG – the amount of IgG sequence required is indefinite . By contrast, the inventors have reduced to practice antibody constructs, limited to full-length IgG antibodies, comprising one to three of the recited insertion mutations. There is no reduction to practice of the cysteine insertion mutations in antibody fragments, including VHH or single-domain antibody fragments (see claim 13), or Fc fusion proteins. The claims allow for limitless additional mutations outside of the cysteine insertion mutations of claims 1, 23, and 32, but Applicants have only evaluated the effect of combining up to three of the recited cysteine insertion mutations with the limited heterodimeric Fc mutations listed in paragraphs 0161-0163. Given that Orozco et al. teaches that an insertion mutation after a known cysteine substitution site results in destabilization of the CH2 and altered binding not demonstrated in the cysteine substituted antibody, it is unpredictable how combinations of multiple cysteine insertion mutations , optionally with additional mutations, to full-length antibod ies , antibody fragment s , or Fc fusion protein s will impact antigen binding and/or Fc function. In order for the invention to be made or used in accordance with the scope claimed, one would have to evaluate the cysteine insertion mutations, one and/or combinations, in various antibody fragments and Fc fusion proteins to understand how the insertion mutation impacts antigen binding or Fc functions in a fragment or Fc fusion protein context. Additionally, one would have to evaluate various combinations of up to all ten cysteine insertion mutations in the context of a full-length IgG antibody to understand if or how multiple cysteine insertion mutations affect antigen binding and/or Fc function. Because the claims encompass additional unrecited mutations, one would have to evaluate the effect of combining the cysteine insertion mutations and combinations thereof with additional mutations, aside from those taught in paragraphs 0161-0163, such as , for example, mutations to CH2 which alter Fc function. Further, one would have to evaluate the impact of cysteine insertion mutations or combinations thereof in antibodies , antibody fragments, or Fc fusion proteins with at least 85% identity across a 10 amino acid subsequence to IgG antibodies. Considering the high level of skill, the high level of unpredictability, and the limited direction provided in the Specification , it would take more than reasonable experimentation to make or use the invention commensurate in scope with the clai m. Double Patenting The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg , 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman , 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi , 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum , 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel , 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington , 418 F.2d 528, 163 USPQ 644 (CCPA 1969). A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA. A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13. The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA/25, or PTO/AIA/26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer . Claim s 1-5, 7-11, 13, 14, 16-18 , 20-24, 26-28, and 38-40 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 8, 9, 11, 12, 16, 17, 23, 29, 30, 32, 62, 63, and 67-69 of copending Application No. 19/091,242 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other . Regarding instant claims 1-5, 7-11, 13, 14, 17, 18, 20-2 4, and 26 , copending claims 1, 6, 8, 9, 12, 16, 17, 29, 30, a nd 32 teach an antibody-drug conjugate with formula of instant claims 23 and 24 and the cysteine substitution mutations of instant claims 1, 8, 9, 11, and 23 wherein the antibody sequence is of an IgG. Regarding the number of mutations, copending claim 17 recites five different insertion mutations and claim 1 recites up to 8 linkers, therefore, some insertion mutations from those five recited in copending claim 17 must be duplicated in the other heavy or light chain making the mutation a symmetrical mutation. Copending claims 6, 8, and 9 recite a heterodimeric Fc comprising knob-in-hole mutations. Regarding thermal stability, Table 2.2 evidences that that cysteine insertion mutations recited do not alter the Tm by more than 8 degrees Celsius from the parent antibody. Regarding instant claim 16 , copending claims 30 and 32 teach an antibody-drug conjugate where the antibody comprises an antigen binding site binds c-Met, a tumor associated antigen. Regarding instant claims 27 and 28 , copending claims 62 and 63 recite a pharmaceutical composition comprising the antibody-drug conjugate and pharmaceutically acceptable carrier or diluent and the method of treating cancer. Regarding instant claims 38-40 , copending claims 67-69 teach a polynucleotide encoding the antibody construct, a vector comprising the polynucleotide, and a host cell comprising the vector. Claims 1, 6, 8, 9, 11, 12, 16, 17, 23, 29, 30, 32, 62, 63, and 67-69 of copending Application No. 19/091,242 read on instant c laims 1-5, 7-11, 13, 14, 16-18, 20-24, 26-28, and 38-40 in an anticipatory manner. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. Claim s 31-34 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim s 1, 6, 8, 9, 11, 12, 16, 17, 23, 29, 30, 32, 62, 63, and 67-69 of copending Application No. 19/091,242 in view of Katragadda et al. (US 2019/0099499 A1; Published: April 4, 2019) . The teachings of Application No. 19/091,242 as related to claim(s) 1-5, 7-11, 13, 14, 16-18, 20-24, 26-28, and 38-40 , from which these claims depend are given previously in this Office action and are fully incorporated here. The copending claims do not teach the method of preparing the antibody-drug conjugate. Regarding instant claims 31-34 , Example 3 of Katragadda et al. demonstrates preparing an antibody conjugate with by reducing cysteine residues (see TCEP in paragraph 0183) and incubating the antibody with a linker-payload moiety wherein the linker is thiol reactive (mal for maleimide in paragraph 0186). Given that the copending claims teach linker-payload moieties with a maleimide linker (see ADC 001, ADC 003, and ADC 004 in copending claims 29 and 30), it would have been obvious and one would have had a reasonable expectation of success and predictability to combine the antibody and linker-payload moieties recited in the copending claims by the method taught in Katragadda et al. to prepare the antibody-drug conjugate. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filing date of the application, as evidenced by the references. This is a provisional nonstatutory double patenting rejection. Claim 15 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim s 1, 6, 8, 9, 11, 12, 16, 17, 23, 29, 30, 32, 62, 63, and 67-69 of copending Application No. 19/091,242 in view of Dimasi et al. ( WO 2009/092011 A1; Published : July 23, 2009 ). The teachings of Application No. 19/091,242 as related to claim(s) 1-5, 7-11, 13, 14, 16-18, 20-24, 26-28, and 38-40 , from which these claims depend are given previously in this Office action and are fully incorporated here. The copending claims do not teach a bispecific cysteine engineered antibody construct . Regarding instant claim 15 , Dimasi et al. recites a cysteine engineered bispecific antibody construct; see claim 29. Because the copending claims and Dimasi et al. recite cysteine engineered antibodies conjugated to a drug or therapeutic agent and administered in a method of treating cancer, it would have been obvious and one would have had a reasonable expectation of success modifying the copending antibody construct to bind c-Met and another tumor-associated antigen . One would have been motivated to target two tumor associated antigens in a bispecific antibody-drug conjugate in order to improve specificity and avoid resistance by antigen escape. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art before the effective filing date of the application, as evidenced by the references. This is a provisional nonstatutory double patenting rejection. Conclusion The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Vollmar et al. (Bioconjugate Chemistry. 28: 2538-2548; Published: September 8, 2017) teaches that a cysteine-substituted antibody-drug conjugate at position 149 of the CL domain demonstrated favorable in vivo stability and persistent tumor growth inhibition compared to cysteine substitutions at other sites including position 118 of the CH1 domain and 205 of the CL domain. Benjamin et al. (Molecular Pharmaceutics. 16: 2795-2807; Published: May 8, 2019) teaches the thiolation and conjugation of Q295 of the CH2 domain . Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT KATHERINE ANN HOLTZMAN whose telephone number is FILLIN "Phone number" \* MERGEFORMAT (571)270-0252 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT Monday - Friday 8:30am - 5:00pm MT . Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, FILLIN "SPE Name?" \* MERGEFORMAT Gregory Emch can be reached at FILLIN "SPE Phone?" \* MERGEFORMAT (571)272-8149 . The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. 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. /KATHERINE ANN HOLTZMAN/ Examiner, Art Unit 1646 /JULIET C SWITZER/ Primary Examiner, Art Unit 1682
Read full office action

Prosecution Timeline

Sep 21, 2023
Application Filed
Jun 05, 2025
Response after Non-Final Action
Mar 19, 2026
Non-Final Rejection — §112, §DP (current)

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Prosecution Projections

1-2
Expected OA Rounds
64%
Grant Probability
99%
With Interview (+62.4%)
3y 7m
Median Time to Grant
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