Computational design of a broad and potent neutralizing antibody against all circulating SARS-CoV-2 variants

Abstract

Despite an unprecedented global deployment of preventive vaccines, coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) , remains an on-going pandemic. This is in part due to the emergence of highly contagious variants of concern (VOCs) that can “break-through” the protection of the current vaccines and therapeutic monoclonal antibodies (mAbs). Apart from these VOCs, variants of interest (VOIs) and variants under monitoring (VUMs) have also emerged due to antigenic drift. Thus, the discovery of a mAb that broadly and potently neutralizes these variants would be of great value. Using a combined computational and experimental approach, we have discovered and developed a human neutralizing Ab (nAb) that binds to the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein of current VOCs, one VOI (Lambda), and two VUMs (Epsilon and Kappa) with potent affinity (pico- to femto-molar dissociation constants, KDs). Initially, a lead Ab was computationally designed based on related antibody-antigen structures in the protein databank, and crystallographically validated to binds to a highly conserved surface of the RBD of wild-type SARS-CoV-2 (Wuhan strain). Subsequently, a tightly binding Ab (KD = 7.2 nM) was developed through experimental affinity enhancement. This then served as a template for the quick computational discovery of a further improved Ab that binds the RBD of the Alpha variant (with the N501Y mutation) with extremely high affinity (KD < 1 pM). Consistent with its measured affinity, this Ab exhibited strong in vitro neutralization activity against the wild-type virus, as well as the Alpha and Delta variants. All amino acids except the one altered in the neutralization resistant N501Y mutant are offset from the epitope surface, explaining its breadth of RBD-binding and neutralization. Moreover, all but the N501 epitope residues are identically conserved throughout the currently circulating SARS-CoV-2 variants, with three of them showing limited variation among sarbecovirus clades Ia and Ib. Accordingly, this antibody exhibits picomolar affinity for SARS-CoV-1 and pangolin CoV. Thus, this Ab is a promising nAb candidate with broad and potent activity against circulating as well as emerging SARS coronaviruses.