Structural and functional studies of the SARS-CoV2 replication complex and its inhibitors

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Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase (RdRp) for incorporation into the viral RNA genome. Incorporated analogues can either ‘kill’ (terminate) synthesis, or ‘corrupt’ (genetically or chemically) the RNA. We have shown that the SARS-CoV replication-transcription complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of NAs during replication. However, the use of NAs against coronaviruses has been complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities.

Here, I will discuss Cryo-EM structures and biochemical assays demonstrating the mode of action of a promising candidiate inhibitor, Bemnifosbuvir (AT-527), currently in phase III clinical trials for the treatment of COVID-19. Remarkably, this drug targets not only the viral RdRp, but also a second, coronavirus unique nucleotidyltransferase domain known as the NiRAN. We have now introduced subtle modifications to this drug, which significantly modify the mechanism of action of this NA. This single atom modification provides a general approach to potentiate a wide array of nucleotide analogues against RNA viruses carrying natural resistance to nucleotide analogue antivirals, such as highly pathogenic coronaviruses.