Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 41, Issue 15, Pages 7045-7054Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2022.2114941
Keywords
Virtual screening; SARS-CoV; COVID-19; SARS-CoV-2 (nCoV); umbrella sampling; NSP16-NSP10; COVID-19
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The COVID-19 pandemic has led to the need for new drugs, and the NSP16-NSP10 complex has been identified as a potential target. The compound CID 135566620 from PubChem shows promise as an inhibitor and further research is required to test its efficacy against COVID-19.
The COVID-19 pandemic, which has already claimed millions of lives, continues to pose a serious threat to human health, requiring the development of new effective drugs. Non-structural proteins of SARS-CoV-2 play an important role in viral replication and infection. Among them, NSP16 (non-structured protein 16) and its cofactor NSP10 (non-structured protein 10) perform C2'-O methylation at the 5' end of the viral RNA, which promotes efficient virus replication. Therefore, the NSP16-NSP10 complex becomes an attractive target for drug development. Using a multi-step virtual screening protocol which includes Lipinski's rule, docking, steered molecular dynamics and umbrella sampling, we searched for potential inhibitors from the PubChem and anti-HIV databases. It has been shown that CID 135566620 compound from PubChem is the best candidate with an inhibition constant in the sub-mu M range. The Van der Waals interaction was found to be more important than the electrostatic interaction in the binding affinity of this compound to NSP16-NSP10. Further in vitro and in vivo studies are needed to test the activity of the identified compound against COVID-19. Communicated by Ramaswamy H. Sarma
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