Diketo acid inhibitors of nsp13 of SARS-CoV-2 block viral replication
Angela Corona, Valentina Noemi Madia, Riccardo De Santis, Candida Manelfi, Roberta Emmolo, Davide Ialongo, Elisa Patacchini, Antonella Messore, Donatella Amatore, Giovanni Faggioni, Marco Artico, Daniela Iaconis, Carmine Talarico, Roberto Di Santo, Florigio Lista, Roberta Costi, Enzo Tramontano
Abstract
For RNA viruses, RNA helicases have long been recognized to play critical roles during virus replication cycles, facilitating proper folding and replication of viral RNAs, therefore representing an ideal target for drug discovery. SARS-CoV-2 helicase, the non-structural protein 13 (nsp13) is a highly conserved protein among all known coronaviruses, and, at the moment, is one of the most explored viral targets to identify new possible antiviral agents. In the present study, we present six diketo acids (DKAs) as nsp13 inhibitors able to block both SARS-CoV-2 nsp13 enzymatic functions. Among them four compounds were able to inhibit viral replication in the low micromolar range, being active also on other human coronaviruses such as HCoV229E and MERS CoV. The experimental investigation of the binding mode revealed ATP-non-competitive kinetics of inhibition, not affected by substrate-displacement effect, suggesting an allosteric binding mode that was further supported by molecular modelling calculations predicting the binding into an allosteric conserved site located in the RecA2 domain.