Highly potent antiviral drug candidates targeting SARS-CoV-2 nsp3 and nsp5

ABSTRACT Faced with the emergence of three epidemics linked to a virus from the coronaviridæ family over the last 20 years (SARS-CoV in China in 2002, MERS-CoV in Arabia in 2012, and SARS- CoV-2 worldwide in 2019), the identification of new antiviral treatments is of major public health concern. As part of the development of new drugs, several molecular modeling tools such as docking, virtual screening and molecular dynamics were combined with databases to decipher potential inhibitors of coronavirus targets. We performed a structure-based design of antiviral drugs targeting SARS-CoV-2 non-structural proteins 3 and 5 (nsp3 and nsp5) based on a high-throughput virtual screening of the ZINC15 database tranches for ligand docking followed by click chemistry with a particular attention paid to relaxed structures mimicking potential in vivo interactions. Based on the above in silico approaches, we selected two small molecules with high affinity binding for nsp3 and nsp5 named Amb929 and Amb701, respectively. We then assessed the antiviral activity of both the Amb929 and Amb701 against SARS-CoV-2 infection taking into account their potential cytotoxicity. Although both compounds inhibited SARS-CoV-2 replication in vitro , Amb929 displayed the most efficient anti-SARS-CoV-2 activity. Among these two drugs, Amb929 was less cytotoxic compared to Amb701, demonstrating an optimal anti-SARS-CoV-2 response with a high selectivity index in cell culture and a high inhibition of SARS-CoV-2 replication compared to untreated condition on a model of human airway epithelium (HAE), paving the way for the development of drugs with very potent anti-coronavirus activity.