Structure of SARS-CoV-2 2′-O-methyltransferase heterodimer with RNA Cap analog and sulfates bound reveals new strategies for structure-based inhibitor design

Abstract

There are currently no antiviral therapies specific against SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an X-ray crystallographic study of the nsp16/nsp10 2'-O-methyltransferase complex that methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. Heterodimer structures are determined with the methyl donor S-adenosylmethionine (SAM), the reaction product S-adenosylhomocysteine (SAH) or the SAH analog sinefungin (SFG). Furthermore, structures of nsp16/nsp10 with the methylated Cap-0 analog (m7GpppA) and SAM or SAH bound were obtained. Comparative analysis revealed flexible loops in open and closed conformations at the m7GpppA binding pocket. Bound sulfates in several structures suggested the location of the phosphates in the ribonucleotide binding groove. Additional nucleotide binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for development of antiviral inhibitors.

Repurposing Multi-Targeting Plant Natural Product Scaffolds In Silico Against SARS-CoV-2 Non-Structural Proteins Implicated in Viral Pathogenesis

“…In this complex, RdRp elongates the daughter strand through the polymerization of nucleotides, while helicase clears RNA secondary structures and RNA-binding proteins [39]. In addition, among those targeted nsps in this study, the complex of SAM-dependent C2'-O-methyltransferase (nsp16)-that is specific to methylguanine-triphosphate-adenosine-and nsp 10 as its cofactor confer host immune evasion properties for SARS-CoV-2 due to the cap methylation of viral mRNAs [40]. Similarly, the endoribonuclease (nsp15) cleaves at the 3' end of uridylates [41] and also antagonizes the activation of host dsRNA sensors [42], thereby eluding host immunity.…”

Chemical profiling of polyphenols in Thunbergia alata and in silico virtual screening of their antiviral activities against COVID-19

“…A potential target for antiviral therapy is (MTase)which is needed for formation of RNA cap , that required for stability of viral RNA (31)It belongs to a large class of SAM-dependent methyl transferases, this MTase feature is binding to the nsp-16 protein, that needs a co-factor nsp-10, to function properly. ASP6928, LYS6839, LYS6968, and GLU7001 are highly conserved residues in protein nsp-16 that form the catalytic canonical motif (K-D-K-E) conserved among class I MTases (32). Residues LEU6898, ASP6912, CYS6913, MET6928, and PHE6947 stabilize the adenosine moiety of SAM in the nsp-10-nsp-16 complex crystal structure bound to the pan-MTase inhibitor sinefungin (PDB: 6WKQ) at 2.0-A in the active site.…”