SARS-CoV-2 and MERS-CoV spike protein binding studies support stable mimic of bound 9-O-acetylated sialic acids

Many disease-causing viruses target sialic acids (Sias), a class of nine-carbon sugars known to coat the surface of many cells including those in the lungs. Human beta coronaviradae, known for causing respiratory tract diseases, often bind Sias, some preferentially bind to those with 9-O-Ac-modification. Currently, co-binding of SARS-CoV-2, a beta coronavirus responsible for the COVID-19 pandemic, to human Sias has been reported and its preference towards α2-3-linked Neu5Ac shown. Nevertheless, O-acetylated Sias-protein binding studies are difficult, due to the ester lability. We studied the binding free energy differences between Neu5,9Ac2α2-3GalβpNP and its more stable 9-NAc mimics binding to SARS-CoV-2 spike protein using molecular dynamics and alchemical free energy simulations. We identified multiple Sias-binding pockets, including two novel sites, with similar binding affinities to those of MERS-CoV, a known co-binder of sialic acid. In our binding poses, 9-NAc and 9-OAc Sias bind similarly, suggesting an experimentally reasonable mimic to probe viral mechanisms.