Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer

Abstract

Non-structural protein 15 (Nsp15) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) forms a homo hexamer and functions as an endoribonuclease. Here, we propose that Nsp15 activity may be inhibited by preventing its hexamerization through drug binding. We first explored the stable conformation of the Nsp15 monomer as the global free energy minimum conformation in the free energy landscape using a combination of parallel cascade selection molecular dynamics (PaCS-MD) and the Markov state model (MSM), and found that the Nsp15 monomer forms a more open conformation with larger druggable pockets on the surface. Targeting the pockets with high druggability scores, we conducted ligand docking and identified compounds that tightly bind to the Nsp15 monomer. The top poses with Nsp15 were subjected to binding free energy calculations by dissociation PaCS-MD and MSM (dPaCS-MD/MSM), indicating the stability of the complexes. One of the identified pockets, which is distinctively bound by inosine analogues, may be an alternative binding site to stabilize viral RNA binding and/or an alternative catalytic site. We constructed a stable RNA structure model bound to both UTP and alternative binding sites, providing a reasonable proposed model of the Nsp15/RNA complex.

Impact of Reinfection with SARS-CoV-2 Omicron Variants in Previously Infected Hamsters

“…By contrast, this consistency was observed less frequently in viral RNA recovered after homologous and heterologous reinfection with Omicron variants harboring amino acid substitutions in more diverse regions. Nsp 15 of SARS-CoV-2 functions as an endoribonuclease ( 36 ). Nsp15 and several other SARS-CoV-2 proteins inhibit primary interferon production and interferon signaling and may, thus, interfere with the body's defense against infection ( 36 – 38 ).…”

“…Nsp 15 of SARS-CoV-2 functions as an endoribonuclease ( 36 ). Nsp15 and several other SARS-CoV-2 proteins inhibit primary interferon production and interferon signaling and may, thus, interfere with the body's defense against infection ( 36 – 38 ). Compared with SARS-CoV and other nidoviruses, the Orf10 protein of SARS-CoV-2 is a unique 38-aa protein ( 39 ).…”

Impact of reinfection with SARS-CoV-2 Omicron variants in previously infected hamsters

“…By contrast, this consistency was less observed in viral RNA recovered after homologous and heterologous reinfection of Omicron variants, with amino acid substitutions occurring in more diverse regions. Nsp 15 of SARS-CoV-2 functions as an endoribonuclease (36). Nsp15 and several other SARS-CoV-2 proteins inhibit primary interferon production and interferon signaling and thus may interfere with the body's defense against infection (36)(37)(38).…”

“…Nsp 15 of SARS-CoV-2 functions as an endoribonuclease (36). Nsp15 and several other SARS-CoV-2 proteins inhibit primary interferon production and interferon signaling and thus may interfere with the body's defense against infection (36)(37)(38). Compared with SARS-CoV and other nidoviruses, the Orf10 protein of SARS-CoV-2 is a unique 38 aa protein (39).…”

Recent insights into the structure and function of coronavirus ribonucleases

“…Another recent study identified additional FDA‐approved drugs that can inhibit Nsp15 activity in vitro [ 86 ]. Using high‐resolution structures as the starting point, in silico screening approaches have also identified numerous putative Nsp15 inhibitors [ 87 , 88 , 89 , 90 , 91 , 92 ].…”