Structure-functional studies have recently revealed a spectrum of diverse high-affinity nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this study, we combine atomistic simulations with the ensemble-based mutational profiling of binding for the SARS-CoV-2 S-RBD complexes with a wide range of nanobodies to identify dynamic and binding affinity fingerprints and characterize the energetic determinants of nanobody-escaping mutations. Using an in silico mutational profiling approach for probing the protein stability and binding, we examine dynamics and energetics of the SARS-CoV-2 complexes with single nanobodies Nb6 and Nb20, VHH E, a pair combination VHH E + U, a biparatopic nanobody VHH VE, and a combination of the CC12.3 antibody and VHH V/W nanobodies. This study characterizes the binding energy hotspots in the SARS-CoV-2 protein and complexes with nanobodies providing a quantitative analysis of the effects of circulating variants and escaping mutations on binding that is consistent with a broad range of biochemical experiments. The results suggest that mutational escape may be controlled through structurally adaptable binding hotspots in the receptor-accessible binding epitope that are dynamically coupled to the stability centers in the distant binding epitope targeted by VHH U/V/W nanobodies. This study offers a plausible mechanism in which through cooperative dynamic changes, nanobody combinations and biparatopic nanobodies can elicit the increased binding affinity response and yield resilience to common escape mutants.
Verkhivker, G. M.; Agajanian, S.; Oztas, D. Y.; Gupta, G. Atomistic simulations and in silico mutational profiling of protein stability and binding in the SARS-CoV-2 spike protein complexes with nanobodies: Molecular determinants of mutational escape mechanisms. ACS Omega. 2021. https://doi.org/10.1021/acsomega.1c03558
Domains in the full-length SARS-CoV-2 S protein and a detailed structural organization of the S-RBD, cysteine residues that form disulfide linkages in the S-RBD protein, structural organization of cysteine clusters in the S2 subdomain of the SARS-CoV-2 spike prefusion structure, covariance matrices of residue fluctuations in the S-RBD complexes with nanobodies, and structural mapping of protein stability hotspots for the panel of studied nanobodies (PDF)
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