Viral evolution is a key consideration in developing antiviral therapeutics. Target diversification due to evolution or immune pressure is a common feature of many viruses, and can result in loss of therapeutic efficacy. In this study, we outline an approach towards the development of escape-resistant therapeutics, using coronaviruses as an exemplar system.
A key insight to this process is that the antigenic diversity across a viral species group provides insights into the evolutionary space within which a viral strain can operate. Consequently, resistance to future evolutionary drift of a viral target can be engineered by developing therapeutics that have sufficient breadth to cover other antigenically distant virus targets within the same viral group. This strategy was applied towards discovery and optimization of an ACE2 receptor decoy designed to neutralize all strains of SARS-CoV-2, as well as other ACE2-using alphacoronaviruses and betacoronaviruses.
Key interaction residues and mutations showing favourable binding energetics against multiple coronavirus species using computational homology modeling were selected and synthesized in a mammalian library display format for screening. Hits were identified, and their breadth and potency were confirmed biochemically via biolayer interferometry and functionally via pseudovirus neutralization assays and live virus neutralization assays in vitro.
ACE2 decoys were identified with increased potency across all tested SARS-CoV-2 variants, as well as other human and animal sarbecovirus, merbecovirus, and setracovirus subgenera. These included hits with >10-fold improvement in binding KD and pseudovirus neutralization IC50.
The improved ACE2 decoy molecules not only offer a promising avenue for broad-spectrum coronavirus neutralization but also provide valuable insights into the ACE2-virus interaction dynamics. Our findings highlight the adaptability and efficacy of combining computational and high-throughput screening approaches to identify future-proof therapeutics in response to emerging and diverse viral threats.