Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

Abstract Remdesivir is the only FDA-approved drug for treatment of COVID-19 patients. The active form remdesivir acts as a nucleoside analog and inhibits RNA-dependent RNA polymerase (RdRp) coronaviruses including SARS-CoV-2. incorporated by RdRp into growing product allows addition three more nucleotides before synthesis stalls. Here we use synthetic chemistry, biochemistry cryo-electron microscopy to establish molecular mechanism remdesivir-induced stalling. We show that fourth nucleotide following incorporation impaired barrier further translocation. This translocation causes retention 3ʹ-nucleotide in substrate-binding site interferes with entry next triphosphate, thereby stalling RdRp. In structure remdesivir-stalled state, matched located template base center, this may impair proofreading viral 3ʹ-exonuclease. These mechanistic insights should facilitate quest improved antivirals target coronavirus replication.