A mechanistic understanding of the modes of Ca ion binding to the SARS-CoV-1 fusion peptide and their role in the dynamics of host membrane penetration

Abstract

Viral envelope fusion with the host cell membrane is dependent on a specific viral fusion peptide (FP) or loop, which becomes exposed during virus entry to drive the process of membrane fusion. In coronaviruses, the FP is a highly conserved domain that sits in the center of spike protein and in SARS-CoV, is adjacent to the S2’ proteolytic cleavage site. This peptide contains a hydrophobic LLF motif, as well as several conserved negatively charged amino acids that interact with Ca2+ ions to promote membrane fusion. In this work we perform a systematic mutagenesis study of the negatively charged amino acids within the SARS-CoV fusion peptide (FP1/FP2) and combine this with molecular dynamics simulations to define the membrane interactions that regulate virus infectivity. We show that the E801/D802 amino acid pair in the SARS-CoV FP is predicted to bind to one Ca2+ ion to promote FP-membrane interaction, with a second Ca2+ ion likely pairing residue D812 with either E821 or D825. The D812/D821 residue pair promotes membrane interaction, whereas the D821/D825 is inhibitory to membrane insertion. Taken together, our results demonstrate the dynamic nature of the coronavirus FP region that likely facilitates its interactions with and insertion into the host cell membrane.Author SummaryCoronaviruses have reemerged as a highly pathogenic virus family through the rise of SARS-CoV, MERS-CoV, and more recently, SARS-CoV-2. As more transmissible variants of SARS-CoV-2 arise, it is imperative that we understand the mechanisms of CoV viral entry to enable the development of effective therapeutics. Recent reviews have suggested the repurposing of FDA-approved calcium channel blockers to treat infection by coronaviruses; however, calcium’s method of action on viral-host cell fusion events is unknown. We have found that increased calcium availability leads to increased viral infection across the CoV family, suggesting that calcium is involved in mediating the interaction between the viral fusion peptide and the host cell membrane. As such, we hypothesize that the highly conserved fusion peptide interacts directly with calcium and this interaction is required for viral entry and infection. Through mutagenesis studies of specific negatively charged residues in the fusion peptide, we have identified residues that impact viral infectivity. We have also compared the infectivity of wild-type and mutant CoV pseudoparticles in calcium-rich or -depleted environments using chelating drugs. Our data mirrors the residue coordination observed SARS-CoV-2, as both between SARS-CoV and SARS-CoV-2 FPs bind to two calcium ions. These results demonstrate the importance of Ca2+ for CoV FP function during viral entry and opens the possibility of utilizing FDA-approved calcium-blocking drugs as a treatment for COVID-19.