Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes.

The HapImmune ^TM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the V _H and V _L domains, binds HLAs in an unconventional, angled way, with V _L making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.
Competing Interests: Competing interests statement:L.M. started his employment at Aethon Therapeutics after the completion of this study. B.G.N. and S.K. hold equity in Aethon Therapeutics that commercializes the technologies described in this paper. HapImmuneTM is a trademark registered to Aethon Therapeutics. B.G.N. holds equity in Northern Biologics, Ltd., Navire Pharma, Lighthouse Therapeutics, Arvinas, Inc., and Recursion Pharma. His spouse holds equity in Revolution Medicines, Inc. and Moderna and during this research, held equity in Mirati Therapeutics. S.K. holds equity in Revalia Bio. L.M., A.K., T.H., B.G.N., and S.K. are listed as inventors of pending patents on technologies described in this paper filed by New York University. B.G.N. and S.K. receives research funding from Aethon Therapeutics. B.G.N. receives research funding from Repare Therapeutics and Mirati Therapeutics. S.K. has received research funding from Puretech Health, Argenx BVBA, and Black Diamond Therapeutics. B.G.N. and S.K. are co-founders of and receive consulting fees from Aethon Therapeutics. B.G.N. is co-founder of Northern Biologics, Ltd., and Navire Pharma; is co-founder of and receives consulting fees from Lighthouse Therapeutics; is an SAB member and receives consulting fees from Arvinas, Inc.; is a SAB member of Recursion Pharma; received consulting fees from GLG group and AlphaSights; is an expert witness for Johnson and Johnson in the Federal Talc Litigation. S.K. is a co-founder of Revalia Bio.