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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.

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.

SUBMITTER: Baildya N

PROVIDER: S-EPMC8846558 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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

Baildya Nabajyoti N Ghosh Narendra Nath NN Chattopadhyay Asoke P AP Mandal Vivekananda V Majumdar Sourav S Ansary Delwar D Sarkar Md Muttakin MM

Journal of molecular structure 20220215

Using molecular docking and other studies, 20 compounds extracted from <i>Monochoria hastata</i> (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 3 ...[more]

PMID: 35185220

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Project description:Monochoria hastata (L.) Solms (family Pontederiaceae), an ethnomedicinal aquatic herb, is used to remedy several gastrointestinal diseases by various ethnic groups in India. The present study aimed to purify and characterize the antibacterial active ingredient against gastrointestinal (GI) diseases and its mode of action using in vitro experimental models. The active lead molecule in the ethyl acetate extract (EA-Mh) fraction has been purified and characterized through high-performance liquid chromatography (HPLC), proton nuclear magnetic resonance (1H NMR), and electrospray ionization mass spectrometry (ESI-MS) methods. The anti-enteric efficacy has been evaluated against enteropathogenic Gram-positive and Gram-negative bacteria by minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), lactate dehydrogenase (LDH), and scanning electron microscopy (SEM) studies. The synergistic and antagonistic studies were done on E. coli MTCC 723 using standard antibiotics (ampicillin and kanamycin, final conc. 50 µg/ml) in a sterilized 96-well micro-plate, incubated at 37 ℃ for 24 h. The chromatographic and spectroscopic analyses revealed the presence of tridecanoic acid methyl ester (TAME) in the bioactive fraction. The compound causes significant extracellular leakage activity by disrupting cellular morphology in the Enterococcus faecalis MCC 2041 T and Salmonella enterica serovar Typhimurium MTCC 98, at a dose of 375 μg/ml and 750 μg/ml, respectively. The SEM study shows a significant rupturing of E. coli and E. faecalis cells due to TAME induced autolysis. It has synergistic activity with ampicillin. The in silico molecular docking through the AutoDock Vina 4.2 and GROMACS (ver. 5.1) Charmm27 force field results showed that the TAME had a strong binding affinity Escherichia coli DNA Gyrase B (PDB ID: 5l3j.pdb) protein and caused conformational changes. Thus, the manuscript reports the first time on the characterization of TAME from this plant with a detailed antibacterial mode of action studies.

Dataset Information

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.

Publications

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

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