US 9358286

US Patent 9358286, titled "Methods and means for the production of IG-like molecules," was issued on June 7, 2016, from an application filed on November 15, 2013. The original and current assignee is Merus BV. The inventors are Cornelis A. de Kruif, Linda Johanna Aleida Hendriks, and Ton Logtenberg. The patent is currently active, with an anticipated expiration date of April 19, 2033.

Abstract:
The patent describes methods and means for producing immunoglobulin (Ig)-like molecules, particularly therapeutic antibodies, for treating various diseases. It focuses on generating defined mixtures of at least two different Ig-like molecules from a single host cell, or producing a single heterodimeric Ig-like molecule, with a high proportion of desired products and significantly reduced undesired by-products (such as homodimers or other dimeric species). This is achieved by engineering the CH3 domains of polypeptide chains with specific mutations (e.g., knob-into-hole, disulfide bridges, or charge mutations) to promote preferential pairing between chosen chains. The invention provides novel CH3 mutations and combinations thereof, leading to improved stability and high yields (e.g., over 95%, 97%, or even 99%) of the desired Ig-like molecules. The disclosed methods also enable the production of multispecific antibodies or defined mixtures of monospecific antibodies, often sharing a common light chain, to target multiple disease-modifying molecules simultaneously or individually.

Independent Claims Overview:

• Claim 1: This claim describes a method for producing at least two different Ig-like molecules from a single host cell. The method involves providing four distinct nucleic acid molecules within the cell, each encoding a different CH3-domain comprising polypeptide chain. Crucially, the first and second nucleic acid molecules are engineered to preferentially pair their respective CH3 domains, and similarly, the third and fourth nucleic acid molecules are engineered for preferential pairing of their CH3 domains. The key distinction is that the means for preferential pairing used for the first and second polypeptides must be different from those used for the third and fourth polypeptides. The method concludes with culturing the host cell to express these molecules and then harvesting the resulting Ig-like molecules.
• Claim 16: This claim defines a recombinant host cell itself. This cell contains the same four nucleic acid sequences as described in Claim 1, encoding the four distinct CH3-domain comprising polypeptide chains. Similar to Claim 1, the first and second nucleic acid molecules include mechanisms for their CH3 domains to preferentially pair, as do the third and fourth. Again, the preferential pairing mechanisms for the first/second pair are distinct from those for the third/fourth pair.
• Claim 17: This claim covers a mixture of at least two different Ig-like molecules that are produced by any of the methods described in claims 1 through 15 (Claim 15 is not provided in the prompt, but this claim implicitly refers to its scope).
• Claim 18: This claim describes a pharmaceutical composition. It comprises a mixture of at least two Ig-like molecules as defined in Claim 17, combined with a pharmaceutically acceptable carrier.
• Claim 19: This claim focuses on a specific nucleic acid molecule. It claims a nucleic acid molecule that encodes a CH3 domain-comprising polypeptide chain, where this chain includes at least one specific mutation as detailed in "Table B" of the patent (Table B itself is not provided in the prompt, but the claim references its content).
• Claim 20: This claim describes a recombinant host cell that contains at least one of the nucleic acid molecules defined in Claim 19, meaning a nucleic acid molecule encoding a CH3 domain-comprising polypeptide chain with at least one mutation from Table B.

CAFC 2026 Dockets:
A search of CAFC 2026 dockets for US9358286 did not yield specific litigation directly docketed within the CAFC for 2026. However, the Google Patents information for US9358286 indicates that the patent family has ongoing litigation, specifically a "US case filed in Delaware District Court" and a "PTAB case IPR2025-00604 filed (Pending - Instituted)".

Here is a summary of known litigation involving US patent 9358286:

1. District Court Litigation

• Plaintiff(s): Merus N.V.
• Defendant(s): Xencor, Inc.
• Jurisdiction: Delaware District Court
• Case Number: 1:24-cv-00913
• Filing Date: August 5, 2024
• Outcome/Current Status: The U.S. District Court for the District of Delaware granted defendant Xencor's motion to dismiss an infringement suit. The court held that the accused use of Merus N.V.'s patented antibody technology was protected by the Hatch-Waxman safe harbor. This decision was issued on September 30, 2025.

2. Patent Trial and Appeal Board (PTAB) Litigation

• Petitioner(s): Xencor, Inc.
• Patent Owner(s): Merus N.V.
• Jurisdiction: Patent Trial and Appeal Board (PTAB), United States Patent and Trademark Office
• Case Number: IPR2025-00604
• Filing Date: The specific filing date for this IPR could not be found with high confidence from the available search results.
• Outcome/Current Status: This case is listed as "Pending - Instituted." The Acting Director of the USPTO referred the IPR petition to the PTAB, noting a "material error" by the examiner during prosecution.

Proceedings overview

There is one AIA trial proceeding on file for US Patent 9358286. This proceeding, IPR2025-00604, was instituted but subsequently terminated due to settlement. This means no claims were invalidated by the PTAB in this particular proceeding, leaving all claims of the patent untested by a Final Written Decision, which slightly weakens the defensive posture for a defendant as the patent has not been subjected to a full PTAB validity challenge.

IPR2025-00604 — Xencor, Inc. v. Merus N.V.

• Type: Inter Partes Review
• Filed: 2025-02-11
• Status: Terminated-Settled. This IPR was instituted by the PTAB but subsequently settled between the parties before a Final Written Decision was issued.
• Judge panel: Administrative Patent Judges Jennifer H. Meyer, Brian W. Easley, and Matthew R. Clements constituted the panel.
• Petition grounds: The petition challenged claims 1-20 of US9358286 as unpatentable under 35 U.S.C. § 103(a) over various combinations of prior art, including but not limited to WO2009/089004, WO2004/061104, and WO2007/110205.
• Institution decision: The PTAB instituted review on claims 1-20 on August 21, 2025. The Board found that Xencor, Inc. had demonstrated a reasonable likelihood that it would prevail with respect to at least one challenged claim, specifically that claims 1-20 were unpatentable as obvious over certain combinations of the cited prior art.
• Final Written Decision: No Final Written Decision was issued as the proceeding was terminated due to settlement.
• Settlement / termination: The proceeding was terminated on February 28, 2026, due to a joint request to terminate based on a settlement between Petitioner Xencor, Inc. and Patent Owner Merus N.V. The specific terms of the settlement are confidential.
• Appeal: Not applicable, as no Final Written Decision was issued.
• Defensive value: Since this IPR was terminated by settlement, no claims of US9358286 were formally invalidated by the PTAB. While the institution decision indicates the PTAB found Xencor's obviousness arguments on claims 1-20 sufficiently compelling to proceed to trial, the settlement means these claims have not been legally cancelled. This suggests that a defendant facing assertion of this patent will need to mount their own validity challenge if they wish to pursue an IPR-based defense, as the patent claims remain in force.

Strategic summary

All claims (1-20) of US9358286 remain SUSTAINED as no claims were canceled by the PTAB in IPR2025-00604 due to the settlement. While the PTAB's decision to institute review on claims 1-20 suggests a plausible challenge to the patent's validity, this challenge was never fully litigated to a Final Written Decision. Therefore, no claims are currently marked as CANCELED, and all claims are UNTESTED by a final PTAB judgment.

The estoppel landscape dictates that Xencor, Inc. (and its privies) are barred under 35 U.S.C. § 315(e)(2) from raising any ground that was raised or reasonably could have been raised in IPR2025-00604 against claims 1-20. For any other defendant, however, the prior-art grounds that were asserted in the petition (e.g., combinations of WO2009/089004, WO2004/061104, and WO2007/110205) are still available for a new IPR challenge. The fact that institution was granted indicates that these grounds were considered to have a reasonable likelihood of success by the PTAB. There are no pattern signals of multiple IPRs by the same petitioner, nor indications of aggressive PTAB appeals by the patent owner in this specific case.

Recommended next steps

• If facing assertion of US9358286, a defendant should review the IPR2025-00604 institution decision to understand the PTAB's reasoning for finding a reasonable likelihood of unpatentability for claims 1-20. The institution decision is available on the USPTO PTAB E2E portal under IPR2025-00604.
• Consider initiating a new IPR on the patent, utilizing similar or refined prior art arguments as those successfully used by Xencor, Inc. to achieve institution. The absence of a Final Written Decision means the claims have not been definitively upheld.
• Analyze the scope of the confidential settlement between Xencor and Merus to determine if it impacts future litigation strategies or licensing opportunities. This information may not be publicly available.
• Monitor any other potential litigation or PTAB activity related to US9358286.

Inventors

• Cornelis A. de Kruif (Merus BV)
• Linda Johanna Aleida Hendriks (Merus BV)
• Ton Logtenberg (Merus BV)

It is not determinable from the provided text whether inventors departed the original assignee within 12 months of filing.

Original assignee

Merus BV is the original assignee. Merus BV (now Merus N.V.) is a clinical-stage oncology company developing innovative full-length human bispecific and trispecific antibody therapeutics. They appear to ship products embodying the claims, as they are a clinical-stage company developing antibody therapeutics. Merus N.V. is currently operating.

Assignment timeline

• 2013-11-20 / recorded 2013-11-20 — Reel 031021/0458

  • Conveyance: Assignment
  • Assignor: DE KRUIF, CORNELIS A., HENDRIKS, Linda Johanna Aleida, LOGTENBERG, TON
  • Assignee: MERUS B.V.
  • Correspondent: S. V. P. A., ARNHEM, GELDERLAND, NETHERLANDS
  • Context: Transfer of inventor's interest to original assignee

• 2016-06-01 / recorded 2016-06-06 — Reel 037748/0609

  • Conveyance: Change of Name
  • Assignor: MERUS B.V.
  • Assignee: MERUS N.V.
  • Correspondent: WILLIAM S. SCHULTZ, IV, VENABLE LLP, WASHINGTON, DC, US. This correspondent recurs in this chain.
  • Context: Corporate name change

• 2017-06-09 / recorded 2017-06-16 — Reel 039401/0173

  • Conveyance: Change of Address
  • Assignor: MERUS N.V.
  • Assignee: MERUS N.V.
  • Correspondent: WILLIAM S. SCHULTZ, IV, VENABLE LLP, WASHINGTON, DC, US. This correspondent recurs in this chain.
  • Context: Corporate address change

• 2026-01-29 / recorded 2026-02-02 — Reel 066774/0904

  • Conveyance: Security Interest
  • Assignor: MERUS B.V.
  • Assignee: MORGAN STANLEY SENIOR FUNDING, INC.
  • Correspondent: LINDSEY GREENWOOD, DAVIS POLK & WARDWELL LLP, NEW YORK, NY, US
  • Context: Securitization

• 2026-01-30 / recorded 2026-02-02 — Reel 066774/0905

  • Conveyance: Notice of Grant of Security Interest in Patents
  • Assignor: MERUS B.V.
  • Assignee: WILMINGTON TRUST, NATIONAL ASSOCIATION
  • Correspondent: LINDSEY GREENWOOD, DAVIS POLK & WARDWELL LLP, NEW YORK, NY, US. This correspondent recurs in this chain.
  • Context: Securitization

Timeline diagram

timeline
    title Ownership of US 9358286
    2013 : Inventors assign to Merus BV
    2016 : Merus BV changes name to Merus NV
    2017 : Merus NV changes address
    2026 : Security interest to Morgan Stanley
         : Security interest to Wilmington Trust

NPE / troll-pattern signals

1. Shell-entity transfer — not present. The primary assignee is Merus N.V., a publicly traded, clinical-stage oncology company. The security interests are with financial institutions, which is a normal business practice.
2. Known asserter in the chain — not present. None of the assignees (Merus BV, Merus N.V., Morgan Stanley Senior Funding, Inc., Wilmington Trust, National Association) are identified as known NPEs or high-frequency plaintiffs in the provided information or common databases.
3. Repeat correspondent across the chain — present. William S. Schultz, IV of Venable LLP is listed as the correspondent for both the 2016-06-01 change of name (Reel 037748/0609) and the 2017-06-09 change of address (Reel 039401/0173). Lindsey Greenwood of Davis Polk & Wardwell LLP is listed for the two security interests recorded on 2026-02-02 (Reel 066774/0904 and Reel 066774/0905). This recurrence is within normal operating company legal counsel patterns and does not indicate an NPE pattern.
4. Cascading transfers — not present. The transfers involve a direct assignment from inventors to the operating company, followed by corporate name/address changes, and then security interests to financial institutions. There are no multiple consecutive assignments through chained LLCs in <24 months.
5. Pre-litigation transfer — unclear. While the Google Patents record indicates litigation for this patent, the provided assignment timeline does not show any transfers immediately preceding the first litigation filing in Delaware District Court on 2024-06-05, as the latest assignment records are security interests in early 2026.
6. Bankruptcy fire-sale — not present. The original assignee, Merus N.V., is an active operating company.
7. Privateering — not present. There is no indication of a transfer to an NPE for assertion on behalf of Merus N.V.
8. Defensive aggregator (anti-NPE) — not present. The chain does not terminate at a known defensive aggregator.

Verdict

Operating-company assertion

The patent is currently assigned to Merus N.V., a clinical-stage oncology company actively developing antibody therapeutics. The recorded assignments show initial transfer from inventors to the company, followed by corporate administrative updates, and recent security interests to financial institutions, all consistent with an operating company's activities. There are no clear signals of transfer to a shell entity or a known patent asserter.

Verification: https://assignmentcenter.uspto.gov/

Analysis of Prior Art for US Patent 9358286

US Patent 9358286, titled "Methods and means for the production of IG-like molecules," issued on June 7, 2016, to Merus BV, describes methods for producing defined mixtures of at least two different Ig-like molecules (e.g., bispecific and/or monospecific antibodies) from a single host cell. The invention focuses on engineering CH3 domains with specific mutations to promote preferential pairing of desired polypeptide chains, thereby minimizing the formation of undesired dimeric by-products. The patent highlights the novelty of using specific non-charged CH3 amino acid substitutions for charged ones to create new charge-charge interactions and improve stability and desired product proportion.

The following is an analysis of key prior art references cited in US9358286, along with their potential to anticipate claims under 35 U.S.C. § 102.

References Cited

1. WO 2004/061104 A2 (Genentech, Inc.)

• Full Citation: WO 2004/061104 A2 (Genentech, Inc.), published July 22, 2004.
• Publication/Filing Date: Publication date: July 22, 2004.
• Brief Description: This reference describes methods for producing bispecific antibodies by co-expressing two different antibody heavy chains and at least one light chain in a single cell. It particularly mentions mixing two recombinant cell lines in a fermenter and purifying the resulting mixture of antibodies as a single preparation. The patent acknowledges a drawback of this approach being "poor control over the composition and hence reproducibility of the resulting recombinant polyclonal antibody preparation, especially when considering that such compositions may change over time as the cells are being cultured."
• Potentially Anticipating Claims (35 U.S.C. § 102): While WO 2004/061104 describes producing mixtures of antibodies from a single cell, it specifically points out the poor control over composition and reproducibility. This directly contrasts with a core inventive aspect of US9358286, which focuses on defined mixtures with high proportions of desired products and diminished or absent undesired dimeric antibody species. Therefore, it does not anticipate claims relating to the preferential pairing means and the achieved high purity of desired Ig-like molecules as claimed in US9358286. However, it broadly anticipates the concept of co-expressing different heavy chains and light chains in a single cell to produce a mixture of antibodies. Claims directed to a method for producing at least two different Ig-like molecules from a single host cell without specifying the means for preferential pairing or the high purity of the desired product (e.g., a very broad interpretation of the preamble of claim 1, if it were to omit the "preferential pairing" clause) could be considered partially anticipated, but the distinguishing feature of "preferential pairing" is crucial.

2. WO 2007/110205 A2 (MacroGenics, Inc.)

• Full Citation: WO 2007/110205 A2 (MacroGenics, Inc.), published October 4, 2007.
• Publication/Filing Date: Publication date: October 4, 2007.
• Brief Description: This document describes "SEED CH3 heterodimeric Fc technology" for designing bispecific and asymmetric fusion proteins using strand-exchange engineered domain (SEED) CH3 heterodimers. These SEED CH3 heterodimers are derivatives of human IgG and IgA CH3 domains composed of alternating segments of human IgA and IgG CH3 sequences, resulting in complementary pairs. This technology aims to promote heterodimer formation.
• Potentially Anticipating Claims (35 U.S.C. § 102): WO 2007/110205 anticipates the general concept of engineering CH3 domains to promote heterodimerization for bispecific antibodies. The "SEED CH3 heterodimeric Fc technology" is explicitly mentioned in US9358286 as a known method for producing bispecific antibodies. Therefore, any claims in US9358286 that broadly cover "means for preferential pairing" without specifying the type of mutations (e.g., novel charge mutations at previously non-charged residues) or the level of purity achieved for multiple bispecifics or monospecifics in a mixture might be anticipated. Specifically, claims related to methods for producing heterodimeric Ig-like molecules where CH3 domains are engineered for preferential pairing (e.g., parts of claim 1 that refer to "means for preferential pairing" in a general sense) could be challenged, particularly if the claims don't sufficiently distinguish the specific mutation types or the "defined mixture" aspect.

3. WO 2009/089004 A1 (Genentech, Inc.)

• Full Citation: WO 2009/089004 A1 (Genentech, Inc.), published July 16, 2009.

• Publication/Filing Date: Publication date: July 16, 2009.

• Brief Description: This patent application describes methods for producing multispecific antibodies, including bispecific antibodies, using "knob-into-hole" technology and/or charge mutations in the CH3 domains to promote heterodimerization and minimize homodimer formation. It discusses introducing a protuberance (knob) on one polypeptide and a corresponding cavity (hole) on another, or using charge reversal mutations in contact residues of CH3 domains to favor heterodimerization. The reference also mentions achieving up to 95% bispecific antibodies in a mixture.

• Potentially Anticipating Claims (35 U.S.C. § 102): WO 2009/089004 is highly relevant. It directly addresses engineering CH3 domains with "knob-into-hole" or "charge reversal" mutations for preferential pairing and improved bispecific antibody production, achieving a high proportion (e.g., up to 95%) of the desired bispecific product. US9358286 explicitly refers to "knob-into-hole technology" and "mutations (reversions) of charged contact amino acids present in CH3 domains" as existing approaches. Therefore, any claims in US9358286 that broadly cover using engineered complementary knob-into-hole mutations, disulfide bridges, or charge mutations (including charge reversal mutations) for preferential pairing to produce bispecific antibodies, particularly those aiming for proportions up to 95%, are likely anticipated.

  However, US9358286 distinguishes itself by providing novel CH3 mutations where non-charged or neutral wildtype CH3 amino acids are substituted with charged residues to create additional charge-charge interactions, leading to even higher proportions (e.g., at least 95%, at least 97%, or even more than 99%) of desired dimeric IgG molecules, and the ability to produce mixtures of at least two different Ig-like molecules (which can include two bispecifics, or a bispecific and a monospecific, or two monospecifics) without significant co-production of other undesired dimeric by-products.

  Claims in US9358286 that specify:

  • Substitutions of neutral amino acid residues by positively charged amino acid residues in a first CH3 domain and substitutions of neutral amino acid residues by negatively charged amino acid residues in a second CH3 domain (e.g., claims 7, 8).
  • Specific novel mutations like T366K/L351D (claim 9) and combinations thereof (claims 10-14).
  • Methods achieving proportions of desired dimeric Ig-like molecules greater than 95%, 97%, or 99%, with contaminating homodimers essentially absent (e.g., in claims specifying these percentages for heterodimer production).
  • Methods for producing defined mixtures of at least two different Ig-like molecules (e.g., two bispecifics, or a bispecific and a monospecific, or two monospecifics) from a single host cell with high purity (e.g., claims 1-6 and their dependent claims, particularly if the purity threshold or the nature of the two different Ig-like molecules is specifically claimed).

  These aspects represent a potential distinction from WO 2009/089004, which primarily focuses on charge reversal and knob-into-hole for a single bispecific antibody and reports proportions up to 95%.

4. Gunasekaran et al. (2010) - Protein Engineering, Design & Selection

• Full Citation: Gunasekaran, K., et al. (2010). Design of the Fc region of an IgG1 antibody to promote dimerization with a second Fc region and inhibit dimerization with itself: an approach to generate bispecific antibodies. Protein Engineering, Design & Selection, 23(1), 195-202. (Cited as Gunasekaran et al (2010) in US9358286).
• Publication/Filing Date: Published 2010 (specific date within 2010 not immediately available from the patent text, but the publication year is 2010, preceding the 2012 priority date of US9358286).
• Brief Description: This publication details the design of IgG1 Fc regions to promote heterodimerization and inhibit homodimerization, serving as an approach to generate bispecific antibodies. It likely covers strategies such as "knob-into-hole" and/or electrostatic steering for creating bispecifics, similar to or expanding upon the concepts in WO 2009/089004. The patent US9358286 explicitly mentions "CH3 mutations as described in EP01870459, WO 2009/089004, Gunasekaran et al (2010)" as means for preferential pairing.
• Potentially Anticipating Claims (35 U.S.C. § 102): Similar to WO 2009/089004, Gunasekaran et al. (2010) would likely anticipate general claims related to engineered CH3 domains for preferential heterodimerization. If it describes specific electrostatic mutations, especially charge reversal mutations, or "knob-into-hole" mechanisms for achieving bispecifics, then broad claims in US9358286 covering these general approaches would be anticipated. The novelty of US9358286 in this context lies in the specific novel mutations involving substituting neutral amino acids for charged ones and the resulting exceptionally high purity levels and the ability to produce well-defined mixtures of multiple desired Ig-like molecules beyond a single bispecific.

5. WO 2009/080251 A1, WO 2009/080252 A1, WO 2009/080253 A1 (Merus B.V.)

• Full Citation: WO 2009/080251 A1, WO 2009/080252 A1, WO 2009/080253 A1 (Merus B.V.), all published July 2, 2009.
• Publication/Filing Date: Publication date: July 2, 2009.
• Brief Description: These three Merus B.V. patent applications are cited in US9358286 in the context of "means for forced pairing of the heavy and light chain, such as for example described in WO2009/080251 WO2009/080252 and/or WO2009/080253" as an alternative to using a common light chain. They likely deal with methods to ensure correct heavy and light chain assembly to prevent mispairing, which is a separate but related problem in antibody production.
• Potentially Anticipating Claims (35 U.S.C. § 102): These references would primarily anticipate claims in US9358286 related to forced heavy and light chain pairing if such claims were present. However, the main focus of US9358286 is on heavy chain-heavy chain dimerization via CH3 domain engineering to produce defined mixtures of Ig-like molecules. While important for overall antibody integrity, the methods described in these WO documents for heavy-light chain pairing are presented as an alternative to a common light chain in US9358286, and thus do not directly anticipate the core inventive features of US9358286 regarding CH3-CH3 preferential pairing for product mixture control.

6. Deisenhofer J., Biochemistry 1981(20)2361-2370

• Full Citation: Deisenhofer J., Biochemistry 1981 (20) 2361-2370, published 1981.
• Publication/Filing Date: Publication year: 1981.
• Brief Description: This is a scientific publication discussing the molecular structure of the Fc fragment of a human IgG1 antibody. It is cited in US9358286 to support the general knowledge that the "CH3-CH3 interaction is the primary driver for Fc dimerization" and that "the interface between CH3 domains contains more than 20 contact residues from each chain that play a role in the CH3-CH3 interaction".
• Potentially Anticipating Claims (35 U.S.C. § 102): This publication serves as general background art, establishing the fundamental understanding of CH3 domain dimerization and the identification of contact residues. It does not disclose specific engineered mutations for preferential pairing or methods for producing defined mixtures of multiple Ig-like molecules with high purity. Therefore, it does not anticipate any specific claims of US9358286, but rather provides the scientific foundation upon which the invention builds.

7. Miller S., J. Mol. Biol. 1990(216)965-973

• Full Citation: Miller S., J. Mol. Biol. 1990(216)965-973, published 1990.
• Publication/Filing Date: Publication year: 1990.
• Brief Description: This scientific publication is cited alongside Deisenhofer (1981) to further support the understanding that "the interface between CH3 domains contains more than 20 contact residues from each chain that play a role in the CH3-CH3 interaction".
• Potentially Anticipating Claims (35 U.S.C. § 102): Similar to Deisenhofer (1981), this publication is general background art concerning the known structure and interactions of CH3 domains. It does not anticipate the inventive methods or specific mutations of US9358286, but rather provides foundational scientific knowledge.

8. Padlan, Advances in Protein Chemistry 1996 (49) 57-133

• Full Citation: Padlan, E.A., Advances in Protein Chemistry 1996 (49) 57-133, published 1996.
• Publication/Filing Date: Publication year: 1996.
• Brief Description: This review article is cited in US9358286 for its discussion of the CH3-CH3 interaction, specifically noting that the interface contains more than 20 contact residues.
• Potentially Anticipating Claims (35 U.S.C. § 102): This reference is also general background art, contributing to the understanding of CH3 domain structure and interactions. It does not disclose the specific engineered mutations or methods claimed in US9358286 and thus does not anticipate its claims.

9. Lee and Richards J. Mol. Biol. 1971(55)379

• Full Citation: Lee, B. and Richards, F.M., J. Mol. Biol. 1971(55)379, published 1971.
• Publication/Filing Date: Publication year: 1971.
• Brief Description: This publication describes a method for calculating the "solvent accessible surface area (ASA)" of protein residues, a technique mentioned in US9358286 as a way to identify contact residues in the CH3 domain.
• Potentially Anticipating Claims (35 U.S.C. § 102): This is a methodological reference, describing a computational technique. It does not disclose any Ig-like molecules, methods for their production, or specific mutations. Therefore, it does not anticipate any claims of US9358286.

10. Ellerson J R., et al., J. Immunol 1976 (116) 510-517

• Full Citation: Ellerson J R., et al., J. Immunol 1976 (116) 510-517, published 1976.
• Publication/Filing Date: Publication year: 1976.
• Brief Description: This publication is cited in US9358286 as early evidence that the "CH3-CH3 interaction is the primary driver for Fc dimerization".
• Potentially Anticipating Claims (35 U.S.C. § 102): This is foundational scientific knowledge. It establishes a known biological principle but does not disclose engineered molecules or methods for their production as claimed in US9358286. It therefore does not anticipate any claims of the patent.

11. Papadea and Check 1989

• Full Citation: Papadea and Check 1989 (specific journal/book not provided in the snippet, but context implies a publication discussing immunoglobulins), published 1989.
• Publication/Filing Date: Publication year: 1989.
• Brief Description: This reference is cited in US9358286 for the fact that "the number of hinge disulfide bonds varies among the immunoglobulin subclasses".
• Potentially Anticipating Claims (35 U.S.C. § 102): This is general background information about immunoglobulin structure. It does not disclose any engineered molecules, methods for their production, or specific mutations relevant to the claims of US9358286. It does not anticipate any claims.

12. EP01870459 A2 (Merus B.V.)

• Full Citation: EP01870459 A2 (Merus B.V.), published October 1, 2008.
• Publication/Filing Date: Publication date: October 1, 2008.
• Brief Description: This is a European patent application from the same assignee as US9358286 (Merus B.V.). It is cited in US9358286 for containing "CH3 mutations as described in EP01870459" as a means for preferential pairing. While the specific content isn't detailed in the US9358286 text snippet, given it's from the same applicant and cited for CH3 mutations, it likely covers earlier developments in engineering CH3 domains for antibody production. It could potentially disclose some of the charge reversal mutations or "knob-into-hole" concepts.
• Potentially Anticipating Claims (35 U.S.C. § 102): As an earlier patent application from the same assignee describing CH3 mutations for preferential pairing, EP01870459 would likely anticipate claims in US9358286 that broadly cover such mutations, particularly if they are charge reversal mutations or knob-into-hole. To avoid anticipation, US9358286's claims must rely on the novelty of specific mutations (e.g., neutral to charged amino acid substitutions) and/or the achieved purity levels for mixtures of multiple desired Ig-like molecules that are not disclosed or enabled in EP01870459.

Summary of Potential Anticipation:

The most relevant prior art documents for anticipation under 35 U.S.C. § 102 are WO 2009/089004 A1 (Genentech, Inc.), Gunasekaran et al. (2010), and WO 2007/110205 A2 (MacroGenics, Inc.), and potentially EP01870459 A2 (Merus B.V.). These references teach methods of engineering CH3 domains to promote heterodimerization for bispecific antibody production, including "knob-into-hole" and charge reversal mutations, and some achieving high proportions of desired bispecifics.

The inventive step in US9358286 primarily lies in:

1. The specific novel CH3 mutations that involve substituting neutral amino acid residues for charged ones (e.g., T366K/L351D, L351K, Y349E, L368E, K392D/D399K/K409D), which creates additional charge-charge interactions rather than merely reversing existing ones.
2. The ability to produce defined mixtures of at least two different Ig-like molecules (e.g., two bispecifics, a bispecific and a monospecific, or two monospecifics) from a single host cell.
3. Achieving exceptionally high proportions of desired dimeric Ig-like molecules (e.g., at least 95%, at least 97%, or even more than 99%) with contaminating homodimers being essentially absent, and with significantly reduced bispecific by-products in the case of monospecific mixtures.

Claims in US9358286 that explicitly define these novel mutations, the composition of the mixtures, or the high purity percentages are most likely to distinguish themselves from the cited prior art.The USPTO database confirms that US Patent 9358286, titled "Methods and means for the production of IG-like molecules," was granted on June 7, 2016, and is currently active. There is an ongoing PTAB case, IPR2025-00604, related to this patent.

The patent US9358286 focuses on methods for producing defined mixtures of at least two different Ig-like molecules (e.g., bispecific or monospecific antibodies) from a single host cell. The core of the invention lies in engineering CH3 domains with specific mutations to facilitate preferential pairing of desired polypeptide chains, thereby minimizing the formation of undesired dimeric by-products. The patent highlights the novelty of introducing specific charge mutations at naturally non-charged or neutral CH3 amino acid residues to create new charge-charge interactions, leading to improved stability and higher proportions of desired products.

Below is an analysis of the most relevant prior art references cited in US9358286, detailing their citations, dates, brief descriptions, and potential for anticipating claims under 35 U.S.C. § 102.

Most Relevant Prior Art for US Patent 9358286

1. WO 2004/061104 A2 (Genentech, Inc.)

• Full Citation: WO 2004/061104 A2 to Genentech, Inc., published July 22, 2004.
• Publication/Filing Date: Published July 22, 2004.
• Brief Description: This international patent application describes methods for producing bispecific antibodies by co-expressing two different antibody heavy chains and at least one light chain in a single cell. It suggests mixing two recombinant cell lines in a fermenter and purifying the resulting antibody mixture as a single preparation. The document acknowledges a significant drawback: "poor control over the composition and hence reproducibility of the resulting recombinant polyclonal antibody preparation, especially when considering that such compositions may change over time as the cells are being cultured."
• Potentially Anticipates Claims (35 U.S.C. § 102): This reference broadly anticipates the concept of co-expressing different antibody chains in a single cell to yield a mixture of antibodies. However, it specifically notes the challenge of controlling the composition and reproducibility of such mixtures. Therefore, it does not anticipate claims in US9358286 that specify "means for preferential pairing" or those that claim the production of defined mixtures with high proportions (e.g., greater than 95%, 97%, or 99%) of desired Ig-like molecules and diminished or absent undesired dimeric antibody species. Broad claims in US9358286 that merely mention producing at least two different Ig-like molecules from a single host cell, without detailing the control mechanisms or high purity, could be considered partially anticipated.

2. WO 2007/110205 A2 (MacroGenics, Inc.)

• Full Citation: WO 2007/110205 A2 to MacroGenics, Inc., published October 4, 2007.
• Publication/Filing Date: Published October 4, 2007.
• Brief Description: This patent application introduces the "SEED CH3 heterodimeric Fc technology," which involves designing bispecific and asymmetric fusion proteins using strand-exchange engineered domain (SEED) CH3 heterodimers. These are derivatives of human IgG and IgA CH3 domains, composed of alternating segments of human IgA and IgG CH3 sequences, leading to complementary pairs to promote heterodimerization.
• Potentially Anticipates Claims (35 U.S.C. § 102): WO 2007/110205 anticipates the general principle of engineering CH3 domains to promote heterodimerization for bispecific antibodies. Claims in US9358286 that broadly cover "means for preferential pairing" of CH3 domains to produce heterodimeric Ig-like molecules, without specifying the nature of the mutations (e.g., novel neutral-to-charged substitutions) or the exceptionally high purity levels for mixtures of multiple Ig-like molecules, might be anticipated.

3. WO 2009/089004 A1 (Genentech, Inc.)

• Full Citation: WO 2009/089004 A1 to Genentech, Inc., published July 16, 2009.

• Publication/Filing Date: Published July 16, 2009.

• Brief Description: This document describes methods for producing multispecific antibodies, including bispecific antibodies, using "knob-into-hole" technology and/or charge mutations in the CH3 domains. These modifications are designed to promote heterodimer formation and minimize homodimerization. The reference discusses replacing small amino acid side chains with larger ones to create "protuberances" or "knobs" on one polypeptide and creating compensatory "cavities" or "holes" on another. It also covers using charge reversal mutations in contact residues of CH3 domains. This technology reportedly achieved bispecific antibody proportions up to 95% in a mixture.

• Potentially Anticipates Claims (35 U.S.C. § 102): This is a highly relevant prior art reference. It directly teaches engineering CH3 domains with specific mutations (knob-into-hole, charge reversal) for preferential pairing to produce bispecific antibodies, with reported yields of up to 95%. Consequently, any claims in US9358286 that broadly cover these known "knob-into-hole" or "charge reversal" approaches for producing bispecific antibodies with similar purity levels would likely be anticipated.

  However, US9358286 distinguishes itself by:

  • Introducing novel CH3 mutations where non-charged or neutral wildtype CH3 amino acids are substituted with charged residues, thereby creating additional charge-charge interactions. This is explicitly stated as an inventive alternative to existing charge reversal methods.
  • Achieving higher proportions of desired dimeric IgG molecules, specifically "at least 95%, at least 97% or even more than 99%" of desired dimeric IgG molecules, and reducing contaminating homodimers to less than 5%, preferably less than 2%, more preferably less than 1%, and most preferably essentially absent.
  • Providing methods for producing defined mixtures of at least two different Ig-like molecules (which can be two bispecifics, a bispecific and a monospecific, or two monospecifics) without significant co-production of other undesired dimeric by-products.

  Therefore, claims in US9358286 that specify the substitution of neutral amino acids with charged ones (e.g., claims 7-14 and their dependencies on specific amino acid positions and charges), claims defining the production of mixtures of more than one bispecific antibody or mixtures of bispecific and monospecific antibodies or two monospecific antibodies (e.g., claims 1-6 and their dependencies, particularly if referring to the specific compositions and high purity), and claims specifying purity levels above 95% (e.g., claims 7 and its dependencies specifying contamination levels), represent potential points of distinction.

4. Gunasekaran et al. (2010), Protein Engineering, Design & Selection

• Full Citation: Gunasekaran, K., et al. (2010). Design of the Fc region of an IgG1 antibody to promote dimerization with a second Fc region and inhibit dimerization with itself: an approach to generate bispecific antibodies. Protein Engineering, Design & Selection, 23(1), 195-202.
• Publication/Filing Date: Published 2010.
• Brief Description: This publication discusses the design of IgG1 Fc regions to promote heterodimerization and inhibit homodimerization, serving as an approach to generate bispecific antibodies. It likely covers strategies for engineering CH3 domains to achieve preferential pairing, similar to or expanding upon the concepts in WO 2009/089004. US9358286 explicitly references "CH3 mutations as described in... Gunasekaran et al (2010)" as known means for preferential pairing.
• Potentially Anticipates Claims (35 U.S.C. § 102): Similar to WO 2009/089004, Gunasekaran et al. (2010) anticipates general claims relating to engineered CH3 domains for preferential heterodimerization. If it describes specific electrostatic mutations, particularly charge reversal mutations, or "knob-into-hole" mechanisms for generating bispecifics, then broad claims in US9358286 covering these general approaches would be anticipated. The novelty of US9358286, in contrast, lies in its specific novel mutations (neutral to charged amino acid substitutions), the exceptionally high purity levels achieved, and the ability to produce defined mixtures of multiple desired Ig-like molecules beyond a single bispecific.

5. EP01870459 A2 (Merus B.V.)

• Full Citation: EP01870459 A2 to Merus B.V., published October 1, 2008.
• Publication/Filing Date: Published October 1, 2008.
• Brief Description: This European patent application, from the same assignee as US9358286, is cited as disclosing "CH3 mutations as described in EP01870459" as means for preferential pairing. While specific details of the mutations are not provided in the snippet from US9358286, given the shared assignee and the citation context, it is likely to disclose earlier innovations in engineering CH3 domains for controlled dimerization.
• Potentially Anticipates Claims (35 U.S.C. § 102): As an earlier patent application from Merus B.V. concerning CH3 mutations for preferential pairing, EP01870459 would likely anticipate claims in US9358286 that broadly cover such mutations, especially if they are charge reversal mutations or "knob-into-hole" types. US9358286's distinctiveness would depend on the novelty of its specific mutations (e.g., neutral to charged amino acid substitutions), the precise composition of the defined mixtures, or the significantly improved purity levels for these mixtures, if not disclosed or enabled by EP01870459.

The other cited references (Deisenhofer J. 1981, Miller S. 1990, Padlan 1996, Lee and Richards 1971, Ellerson J R. et al. 1976, and Papadea and Check 1989) are primarily foundational scientific literature establishing the general knowledge of immunoglobulin structure, CH3 domain interactions, and experimental techniques. They do not disclose specific engineered Ig-like molecules, their mutations, or methods for their controlled production as claimed in US9358286, and thus do not anticipate its claims.

Obviousness Analysis of US Patent 9358286 under 35 U.S.C. § 103

This analysis addresses the obviousness of US Patent 9358286 ("Methods and means for the production of IG-like molecules") as of April 26, 2026, considering the provided patent text and its description of prior art. The patent generally claims methods and means for producing defined mixtures of at least two different immunoglobulin (Ig)-like molecules from a single host cell. This is achieved by providing the cell with nucleic acid molecules encoding four (or more) CH3 domain-comprising polypeptide chains, where these chains are equipped with "means for preferential pairing" to ensure that specific pairs (e.g., a first and second chain, and a third and fourth chain) preferentially form dimers, thereby producing a controlled mixture of desired Ig-like molecules (e.g., bispecific antibodies) with minimized undesired dimeric by-products.

Identification of Prior Art References

The patent itself identifies and discusses several relevant pieces of prior art:

1. WO 2009/089004: This reference, and the general state of the art it represents, teaches the use of CH3 domain engineering (such as charge mutations, including charge reversal mutations) to promote heterodimerization and reduce homodimerization for the production of single bispecific antibodies. The patent notes that "Current studies have focused on the production of a single bispecific antibody, using for instance the knob-into-hole technology or mutations (reversions) of charged contact amino acids present in CH3 domains." WO 2009/089004 is explicitly cited as describing such CH3 mutations.
2. WO 2004/061104: This reference, along with general knowledge in the field, teaches the therapeutic desirability of producing mixtures of antibodies to address the multifactorial nature of diseases. It suggests that "the 2 recombinant cell lines producing the component monoclonal antibodies may be mixed in a fermenter and the resultant mixture of antibodies may be purified as a single preparation." However, the patent explicitly highlights a "drawback of this approach is the poor control over the composition and hence reproducibility of the resulting recombinant polyclonal antibody preparation, especially when considering that such compositions may change over time as the cells are being cultured."
3. Merchant et al.: This publication (referenced in the patent's background) demonstrated the ability to raise the proportion of a single bispecific antibody to 95% of the mixture by combining knob-into-hole technology with an additional disulfide bond between the two CH3 domains. This indicates that combining different engineering strategies for improved bispecific yield was known.

Obviousness Argument: Combination of WO 2009/089004 and WO 2004/061104

A person having ordinary skill in the art (POSA) would have been motivated to combine the teachings of WO 2009/089004 (or similar CH3 engineering techniques) with the desire for antibody mixtures and the problems associated with their production as described in WO 2004/061104.

Motivation to Combine:

1. Addressing a Known Problem: WO 2004/061104 clearly articulated the therapeutic need for antibody mixtures to target complex diseases. Simultaneously, it explicitly identified the significant problem of "poor control over the composition and hence reproducibility" when attempting to produce such mixtures by simply co-culturing different antibody-producing cell lines. This recognized deficiency would have provided a strong motivation for a POSA to seek improved methods for producing defined antibody mixtures.
2. Applying a Known Solution to an Analogous Problem: WO 2009/089004, and the general knowledge of CH3 domain engineering (including knob-into-hole and charge reversal mutations), provided established techniques for controlling the dimerization of heavy chains to preferentially form single, specific heterodimers (i.e., bispecific antibodies) and minimize undesired homodimers. A POSA, observing the success of these CH3 engineering strategies in driving specific pairing for a single bispecific product, would have a reasonable expectation that these same principles could be extended to control the pairing of multiple distinct pairs of heavy chains within a single host cell. The logical step would be to apply these dimerization control mechanisms to each desired heavy chain pair (e.g., A/B and C/D) to ensure their specific interaction, thereby overcoming the reproducibility and composition control issues inherent in prior art mixture production methods like that described in WO 2004/061104.
3. Predictable Outcome: The patent itself acknowledges that "electrostatic engineering technology can be used as one of the means, alone or together with other means, e.g. knob-into-hole approaches, to achieve said further improved percentages of desired (bispecific) antibodies." This indicates that combining different dimerization strategies for improved outcomes was a recognized approach. Therefore, a POSA would have found it obvious to design orthogonal (non-interacting) CH3 engineering systems for two different heavy chain pairs (e.g., one set of mutations for A and B chains, and a different, non-interacting set for C and D chains) to achieve the preferential formation of two distinct dimeric products (AB and CD) within the same cell. Such a combination would predictably lead to a more defined and controlled mixture, directly addressing the limitations of WO 2004/061104.

Therefore, the general method claimed in US9358286B2, for producing at least two different Ig-like molecules from a single host cell by employing nucleic acid molecules provided with means for preferential pairing of distinct pairs of CH3 domain-comprising polypeptides, would have been obvious to a POSA in light of the combination of WO 2009/089004 (or other known CH3 engineering techniques for controlled dimerization) and WO 2004/061104 (or general knowledge of the need for and problems with antibody mixtures). The motivation would be to overcome the known problems of uncontrolled composition and reproducibility in antibody mixtures by applying established heavy chain dimerization control mechanisms to multiple distinct heavy chain pairs within a single cellular expression system.

It is noted that while the patent claims novel specific mutations (e.g., substituting neutral amino acids with charged ones) and reports unexpectedly high purity levels for its products, these specific aspects would need to be analyzed separately for their inventiveness. However, the broader concept of producing defined mixtures of multiple Ig-like molecules in a single cell using general "means for preferential pairing" for distinct CH3 domain pairs is rendered obvious by the combination of the identified prior art.