Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic. 2'-O-RNA methyltransferase (MTase) is one of the enzymes of this virus that is a potential target for antiviral therapy as it is crucial for RNA cap formation; an essential process for viral RNA stability. This MTase function is associated with the nsp16 protein, which requires a cofactor, nsp10, for its proper activity. Here we show the crystal structure of the nsp10-nsp16 complex bound to the pan-MTase inhibitor sinefungin in the active site. Our structural comparisons reveal low conservation of the MTase catalytic site between Zika and SARS-CoV-2 viruses, but high conservation of the MTase active site between SARS-CoV-2 and SARS-CoV viruses; these data suggest that the preparation of MTase inhibitors targeting several coronaviruses - but not flaviviruses - should be feasible. Together, our data add to important information for structure-based drug discovery.

Institute of Organic Chemistry and Biochemistry AS CR v v i Flemingovo nam 2 166 10 Prague 6 Czech Republic

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Coronaviridae Study Group of the International Committee on Taxonomy of V. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 2020;5:536–544. doi: 10.1038/s41564-020-0695-z. PubMed DOI PMC

Zumla A, Chan JF, Azhar EI, Hui DS, Yuen KY. Coronaviruses – drug discovery and therapeutic options. Nat. Rev. Drug Discov. 2016;15:327–347. doi: 10.1038/nrd.2015.37. PubMed DOI PMC

Totura AL, Bavari S. Broad-spectrum coronavirus antiviral drug discovery. Expert Opin. Drug Disco. 2019;14:397–412. doi: 10.1080/17460441.2019.1581171. PubMed DOI PMC

De Clercq E. A cutting-edge view on the current state of antiviral drug development. Med. Res. Rev. 2013;33:1249–1277. doi: 10.1002/med.21281. PubMed DOI

Martinez MG, Villeret F, Testoni B, Zoulim F. Can we cure hepatitis B virus with novel direct-acting antivirals? Liver Int.: Off. J. Int. Assoc. Study Liver. 2020;40( Suppl 1):27–34. doi: 10.1111/liv.14364. PubMed DOI

Wu A, et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell host microbe. 2020;27:325–328. doi: 10.1016/j.chom.2020.02.001. PubMed DOI PMC

Snijder EJ, Decroly E, Ziebuhr J. The nonstructural proteins directing coronavirus rna synthesis and processing. Adv. virus Res. 2016;96:59–126. doi: 10.1016/bs.aivir.2016.08.008. PubMed DOI PMC

Ziebuhr J. The coronavirus replicase: insights into a sophisticated enzyme machinery. Nidoviruses: Control Sars Other Nidovirus Dis. 2006;581:3–11. doi: 10.1007/978-0-387-33012-9_1. PubMed DOI PMC

Bradrick SS. Causes and consequences of flavivirus RNA methylation. Front Microbiol. 2017;8:2374. doi: 10.3389/fmicb.2017.02374. PubMed DOI PMC

Dong H, et al. Flavivirus RNA methylation. J. Gen. Virol. 2014;95:763–778. doi: 10.1099/vir.0.062208-0. PubMed DOI

Ramanathan A, Robb GB, Chan SH. mRNA capping: biological functions and applications. Nucleic Acids Res. 2016;44:7511–7526. doi: 10.1093/nar/gkw551. PubMed DOI PMC

Chen Y, Guo D. Molecular mechanisms of coronavirus RNA capping and methylation. Virol. Sin. 2016;31:3–11. doi: 10.1007/s12250-016-3726-4. PubMed DOI PMC

Ivanov KA, et al. Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J. Virol. 2004;78:5619–5632. doi: 10.1128/JVI.78.11.5619-5632.2004. PubMed DOI PMC

Daffis S, et al. 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature. 2010;468:452–456. doi: 10.1038/nature09489. PubMed DOI PMC

Decroly E, et al. Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2′O)-methyltransferase activity. J. Virol. 2008;82:8071–8084. doi: 10.1128/JVI.00407-08. PubMed DOI PMC

Sawicki SG, et al. Functional and genetic analysis of coronavirus replicase-transcriptase proteins. PLoS Pathog. 2005;1:e39. doi: 10.1371/journal.ppat.0010039. PubMed DOI PMC

Minskaia E, et al. Discovery of an RNA virus 3′->5′ exoribonuclease that is critically involved in coronavirus RNA synthesis. Proc. Natl Acad. Sci. USA. 2006;103:5108–5113. doi: 10.1073/pnas.0508200103. PubMed DOI PMC

Ma Y, et al. Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc. Natl Acad. Sci. USA. 2015;112:9436–9441. doi: 10.1073/pnas.1508686112. PubMed DOI PMC

Decroly E, et al. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-O-methyltransferase nsp10/nsp16 complex. PLoS Pathog. 2011;7:e1002059. doi: 10.1371/journal.ppat.1002059. PubMed DOI PMC

Hamil RL, Hoehn MM. A9145, a new adenine-containing antifungal antibiotic. I. Discovery and isolation. J. antibiotics. 1973;26:463–465. doi: 10.7164/antibiotics.26.463. PubMed DOI

Smietanski M, et al. Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation. Nat. Commun. 2014;5:3004. doi: 10.1038/ncomms4004. PubMed DOI PMC

Zhao Y, et al. Molecular basis for specific viral RNA recognition and 2′-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5) Proc. Natl Acad. Sci. USA. 2015;112:14834–14839. doi: 10.1073/pnas.1514978112. PubMed DOI PMC

Joseph JS, et al. Crystal structure of nonstructural protein 10 from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs. J. Virol. 2006;80:7894–7901. doi: 10.1128/JVI.00467-06. PubMed DOI PMC

Policarpo RL, et al. High-Affinity Alkynyl Bisubstrate Inhibitors of Nicotinamide N-Methyltransferase (NNMT) J. medicinal Chem. 2019;62:9837–9873. doi: 10.1021/acs.jmedchem.9b01238. PubMed DOI PMC

Chen, Y. et al. Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2′-O-Methylation by nsp16/nsp10 Protein Complex. PLoS Pathogens7, e1002294 (2011). PubMed PMC

Hercik K, Brynda J, Nencka R, Boura E. Structural basis of Zika virus methyltransferase inhibition by sinefungin. Arch. Virol. 2017;162:2091–2096. doi: 10.1007/s00705-017-3345-x. PubMed DOI

Baumlova A, et al. The crystal structure of the phosphatidylinositol 4-kinase IIalpha. EMBO Rep. 2014;15:1085–1092. doi: 10.15252/embr.201438841. PubMed DOI PMC

Dubankova A, Boura E. Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses. Antivir. Res. 2019;169:104536. doi: 10.1016/j.antiviral.2019.104536. PubMed DOI

Kabsch W. XDS. Acta Crystallogr. Sect. D., Biol. Crystallogr. 2010;66:125–132. doi: 10.1107/S0907444909047337. PubMed DOI PMC

Afonine PV, et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. Sect. D., Biol. Crystallogr. 2012;68:352–367. doi: 10.1107/S0907444912001308. PubMed DOI PMC

Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr. Sect. D., Biol. Crystallogr. 2010;66:486–501. doi: 10.1107/S0907444910007493. PubMed DOI PMC

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