In silico evaluation of COVID-19 main protease interactions with honeybee natural products for discovery of high potential antiviral compounds

Zarei, Armin; Ramazani, Ali; Pourmand, Saeed; Sattari, Ahmad; Rezaei, Aram; Moradi, Sajad

doi:10.1080/14786419.2021.1974435

Cited by 14 publications

(11 citation statements)

References 33 publications

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“…Molecular mechanics Poisson‐Boltzmann surface area (MM/PBSA) is a prevalent method for estimating the free energy of the binding of small ligands with biological macromolecules in biomolecular studies. For simulation, we used GROMAX 2019.1 software [39] . At first, the protein was modified using the Swiss_PDB viewer (SPDBV) [40] program since the protein had the missing atom.…”

Section: Resultsmentioning

confidence: 99%

Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor

et al. 2022

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3CL protease as the main protease (M pro ) of coronavirus is investigated as a potential target in medicine. Flavonoid compounds with polyphenolic structures exhibited anti-viral, anti-bacterial, immunomodulatory and anti-inflammatory effects against infectious agents. In this study, the inhibitory effect of flavonoid-based compounds was evaluated against coronavirus M pro using molecular docking and dynamic simulations. Molegro Virtual Docker 6.0 (MVD) software was used to ensure the accuracy of the docking analysis. Eventually, four compounds including two herbal-based (Rutin and Quercetin) and two chemical-based (2-Iodoadenosine-5'-O-[(phosphonomethyl)phosphonic Acid] and Camostat) are selected based on the interaction energies and docking scores of the investigated structures. The values of MolDock Score for Rutin was À 174.355 docked to M pro enzyme. The molecular dynamics was performed by using GROMACS in 100 ns to refine the docking simulation results and evaluated the binding stability of Rutin. Potential energy of Rutin/M pro complex stabilization was measured approximately À 1.11 × 10 6 kcal/mol for 100 ns. As a result, Rutin is suggested as a potent inhibitor for M pro and can be used as an effective drug in the treatment and prevention of covid.

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Section: Resultsmentioning

confidence: 99%

Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor

et al. 2022

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“…Molecular docking is an instructive computer‐based tool that sheds light on interactions and affinity between ligand and target 51 . Autodock Vina was used for docking assessments via ADT (AutoDock Tools v 1.5.6).…”

Section: Methodsmentioning

confidence: 99%

“…Autodock Vina was used for docking assessments via ADT (AutoDock Tools v 1.5.6). The affinity of best‐docked pose of the synthetic ligand and targets was estimated according to binding energies (kcal/mol) 51 . 2D structure of synthetic coumarin derivative ligand was optimised and its optimised‐3D structure was obtained using GaussView v 5.0 and saved in sdf format before conversion to pdb format through Discovery Studio v 4.5.…”

Section: Methodsmentioning

confidence: 99%

“…Molecular docking is an instructive computer-based tool that sheds light on interactions and affinity between ligand and target. 51 Autodock Vina was used for docking assessments via ADT (AutoDock Tools v 1.5.6). The affinity of best-docked pose of the synthetic ligand and targets was estimated according to binding energies (kcal/mol).…”

Section: In Silico Assessmentsmentioning

confidence: 99%

“…The affinity of best-docked pose of the synthetic ligand and targets was estimated according to binding energies (kcal/mol). 51 2D structure of synthetic coumarin derivative ligand was optimised and its optimised-3D structure was obtained using GaussView v 5.0 and saved in sdf format before conversion to pdb format through Discovery Studio v 4.5. As for our targets, their 3D structures were retrieved from Protein Data Bank (PDB).…”

Section: In Silico Assessmentsmentioning

confidence: 99%

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A novel synthetised sulphonylhydrazone coumarin (E)‐4‐methyl‐N′‐(1‐(3‐oxo‐3H‐benzo[f]chromen‐2‐ yl)ethylidene)benzenesulphonohydrazide protect against isoproterenol‐induced myocardial infarction in rats by attenuating oxidative damage, biological changes and electrocardiogram

Ghazouani

Khdhiri

Elmufti

et al. 2022

Clin Exp Pharma Physio

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Coumarins and their derivatives are becoming a potential source for new drug discovery due to their vast array of biological activities. The present study was designed to investigate the cardioprotective effects of a newly synthesised coumarin, symbolised as 5,6-PhSHC, against cardiac remodelling process in isoproterenol (ISO) induced myocardial infarction (MI) in male Wistar rats by evaluating haematological, biochemical and cardiac biomarkers. Rats were pre/co-treated with 5,6-PhSHC or clopidogrel (150 μg/kg body weight) daily for a period of 7 days and then MI was induced by injecting ISO (85 mg/kg body weight), at an interval of 24 hours for 2 consecutive days, on the sixth and seventh days. The in vivo exploration indicated that the injection of 5,6-PhSHC improved the electrocardiographic (ECG) pattern and prevented severe heart damage by reducing leakage of the cardiac injury markers, such as troponin-T (cTn-T), lactate dehydrogenase (LDH), and creatine kinase-MB. The cellular architecture of cardiac sections, altered in the myocardium of infracted rats, was reversed by 5,6-PhSHC treatment. Results showed that injection of 5,6-PhSHC elicited significant cardioprotective effects by prevention of myocardium cell necrosis and inflammatory cells infiltration, along with marked decrease in plasma levels of fibrinogen. In addition, the total cholesterol, triglyceride, LDL-c, and HDL profiles underwent remarkable beneficial changes. It was also interesting to note that 5,6-PhSHC enhanced the antioxidative defence mechanisms by increasing myocardial glutathione (GSH) level, superoxide dismutase (SOD), and catalase (CAT) activities, together with reducing the levels of thiobarbituric-acid-reactive substances (TBARS), when compared with ISO-induced rats. Taken together, these findings suggested a beneficial role for 5,6-PhSHC against ISO-induced MI in rats. Furthermore, in silico analysis showed that 5,6-PhSHC possess high computational affinities

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Computational investigation on the potential inhibitory effect of fungal metabolites against viral RdRp of SARS-CoV-2 and HCV

Ansari,

Zarei,

Hosseyni Moghaddam

et al. 2023

Journal of Molecular Liquids

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In silico evaluation of COVID-19 main protease interactions with honeybee natural products for discovery of high potential antiviral compounds

Cited by 14 publications

References 33 publications

Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor

Docking and Molecular Dynamics Simulations of Flavonoids as Inhibitors of Infectious Agents: Rutin as a Coronavirus Protease Inhibitor

A novel synthetised sulphonylhydrazone coumarin (E)‐4‐methyl‐N′‐(1‐(3‐oxo‐3H‐benzo[f]chromen‐2‐ yl)ethylidene)benzenesulphonohydrazide protect against isoproterenol‐induced myocardial infarction in rats by attenuating oxidative damage, biological changes and electrocardiogram

Computational investigation on the potential inhibitory effect of fungal metabolites against viral RdRp of SARS-CoV-2 and HCV

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