Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

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Author Name

Kanchan Devkota

Published 3 Projects

Biochemistry

Matthieu Schapira

Associate Professor, University of Toronto

Published 8 Projects

Bioinformatics Biochemistry Pharmacology And Toxicology Cell Biology

Sumera Perveen

Published 3 Projects

Biochemistry

Aliakbar Khalili Yazdi

Published 3 Projects

Biochemistry

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Fengling Li

Irene Chau

Published 3 Projects

Biochemistry Cell Biology

Pegah Ghiabi

Published 3 Projects

Biochemistry

Taraneh Hajian

Published 4 Projects

Biochemistry

Peter Loppnau

Published 2 Projects

Biochemistry

Albina Bolotokova

Published 4 Projects

Biochemistry Cell Biology

Karla J.F. Satchell

Published 1 Project

Biochemistry

Ke Wang

Published 2 Projects

Biochemistry

Deyao Li

Published 1 Project

Biochemistry

Jing Liu

Published 2 Projects

Biochemistry

David Smil

Minkui Luo

Published 2 Projects

Biochemistry

Jian Jin

Published 3 Projects

Biochemistry

Paul V. Fish

Published 1 Project

Biochemistry

Peter J Brown

Masoud Vedadi

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The COVID-19 pandemic has clearly brought the healthcare systems world-wide to a breaking point along with devastating socioeconomic consequences. The SARS-CoV-2 virus which causes the disease uses RNA capping to evade the human immune system. Non-structural protein (nsp) 14 is one of the 16 nsps in SARS-CoV-2 and catalyzes the methylation of the viral RNA at N7-guanosine in the cap formation process. To discover small molecule inhibitors of nsp14 methyltransferase (MT) activity, we developed and employed a radiometric MT assay to screen a library of 161 in house synthesized S-adenosylmethionine (SAM) competitive methyltransferase inhibitors and SAM analogs. Among seven identified screening hits, SS148 inhibited nsp14 MT activity with an IC50 value of 70 {+/-} 6 nM and was selective against 20 human protein lysine methyltransferases indicating significant differences in SAM binding sites. Interestingly, DS0464 with IC50 value of 1.1 {+/-} 0.2 M showed a bi-substrate competitive inhibitor mechanism of action. Modeling the binding of this compound to nsp14 suggests that the terminal phenyl group extends into the RNA binding site. DS0464 was also selective against 28 out of 33 RNA, DNA, and protein methyltransferases. The structure-activity relationship provided by these compounds should guide the optimization of selective bi-substrate nsp14 inhibitors and may provide a path towards a novel class of antivirals against COVID-19, and possibly other coronaviruses.

Biochemistry
Biochemistry 9 Projects