Searching for escape-resistant anti-SARS-CoV-2 neutralizing antibodies

Abstract

A major goal of SARS-CoV-2 vaccination is the induction of neutralizing antibodies (nAbs) capable of blocking infection by preventing interaction of the SARS-CoV-2 Spike protein with ACE2 on target cells. Cocktails of monoclonal nAbs can reduce the risk of severe disease if administered early in infection. However, multiple variants of concern (VOCs) have arisen during the pandemic that may escape from nAbs. In this issue of the JCI, Jia Zou, Li Li, and colleagues used yeast display libraries to identify mAbs that bind to Spike proteins with a vast array of single amino acid substitutions. The authors identified mutation-resistant monoclonal nAbs for potential use as therapeutics. Multimerization further improved the potency of selected nAbs. These findings suggest a way forward in development of better nAb cocktails. However, the emergence of the highly mutated omicron (B.1.1.529) variant heightens the importance of finding effective anti-SARS-CoV-2 nAb therapeutics despite rapid viral evolution.

Figure 1. Development and validation of ultrapotent, mutation-resistant, neutralizing Abs as a multistep process.

(A) Zou, Li, et al. (16) acquired and enriched Spike-specific (S-specific) B cells from subjects using FACS. Immunoglobulin heavy and light chains were cloned and expressed as mAbs. (B) Libraries of mutant S sequences were established for screening mAbs. (C) Potent mAbs bound with most mutants and neutralized pseudoviruses and variants of concern (VOCs) in vitro. mAb polymerization enhanced avidity to overcome some mutations that escaped neutralizing antibodies. (D) Similarly, potent mAbs reduced SARS-CoV-2 infection in vitro and in vivo. Escape mutants were identified by sequencing. (E) Ultrapotent mutation-resistant mAbs need to effectively neutralize emerging VOCs. Search strategies for screening and validation of escape-free mAbs could include the following: (i) Molecular dynamics to estimate binding free energy change, and AI to train and test mutation models, including replacement, insertion, and deletion mutations in the S receptor-binding domain (RBD) and N-terminal domain (NTD), and non-S proteins. These 2 strategies may identify potential escape mutants before they arise and serve as a reference for synthesis and validation of escape-free mAbs. (ii) Engineering of escape-free ACE2-Fc fusion proteins to directly neutralize VOCs while eliciting Fc effector functions. (iii) Sourcing mAbs from superimmune donors (those who had infection and later got vaccinated, or vice versa). Potential mAbs would require validation against complex RBD- and NTD-mutant libraries containing multiple mutations. The Spike protein structure shown was acquired from the Protein Data Bank (10.2210/pdb7LYO/pdb).