Inhibitory effect of compounds extracted from Monochoria hastata (L.) Solms on SARS-CoV-2 main protease: An insight from molecular docking and MD-simulation studies

Nabajyoti Baildya; Narendra Nath Ghosh; Asoke P Chattopadhyay; Vivekananda Mandal; Sourav Majumdar; Delwar Ansary; Md Muttakin Sarkar

doi:10.1016/j.molstruc.2022.132644

Inhibitory effect of compounds extracted from Monochoria hastata (L.) Solms on SARS-CoV-2 main protease: An insight from molecular docking and MD-simulation studies

J Mol Struct. 2022 Jun 5:1257:132644. doi: 10.1016/j.molstruc.2022.132644. Epub 2022 Feb 15.

Authors

Nabajyoti Baildya¹, Narendra Nath Ghosh², Asoke P Chattopadhyay¹, Vivekananda Mandal³, Sourav Majumdar⁴, Delwar Ansary⁵, Md Muttakin Sarkar⁵

Affiliations

¹ Department of Chemistry, University of Kalyani, Kalyani 741235, India.
² Department of Chemistry, University of Gour Banga, Mokdumpur, Malda 732103, India.
³ Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, Mokdumpur, Malda 732103, India.
⁴ Department of Chemistry, Kandi Raj College, Kandi, Murshidabad, 742137, India.
⁵ Department of Chemistry, Dumkal College, Murshidabad, Domkal 742406, India.

Abstract

Using molecular docking and other studies, 20 compounds extracted from Monochoria hastata (L.) Solms were screened, and their inhibitory efficiency examined against main protease (3CLpro) of SARS CoV-2. All the compounds were found to binding with 3CLpro through van der Waals and electrostatic forces of attractions. Among them, Azelaic dihydrazide (ADZ) was found to have the highest docking score. 3CLpro-ADZ complex was studied by MD simulation. ADZ was found to disrupt the structure of 3CLpro after 2 ns. RMSD and RMSF analysis along with sequence and binding energy analysis suggest that ADZ can be a potential drug against SARS CoV-2.

Keywords: COVID-19; MD-simulation; Main protease of SARS-CoV-2; Molecular docking; Monochoria hastata (L.) Solms.