Molecular docking and simulation studies of natural compounds of<i>Vitex negundo</i>L. against papain-like protease (PL<sup>pro</sup>) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world

Mitra, Debasis; Verma, Devvret; Mahakur, Bhaswatimayee; Kamboj, Anshul; Srivastava, R. K.; Gupta, Saurabh; Pandey, A. K.; Arora, Bhawna; Pant, Kumud; Panneerselvam, P.; Ghosh, Arabinda; Barik, Durga Prasad; Mohapatra, Pradeep Kumar Das

doi:10.1080/07391102.2021.1873185

Cited by 28 publications

(19 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Residues Asp295 (5.27 Å) and Val104 (4.30 Å) interacted via C-H bond and Pi-sigma, respectively. Five residues including Ile106, Gln110, Thr111, Thr292, and Consistent with previous studies which reported the potential inhibitors of M pro (Park et al, 2015;Aanouz et al, 2020;Bello et al, 2020;Chikhale et al, 2020b;Krupanidhi et al, 2020;Matveeva et al, 2020;Muhammad et al, 2020;Tripathi et al, 2020;Mitra et al, 2021;Prasanth et al, 2021;Varadharajan et al, 2021), in our study, screened four compounds (sesamin, sesaminol, sesamolin, and sesamolinol) were found to be tightly fit into the binding pocket of the M pro of COVID-19.…”

Section: Compoundsupporting

confidence: 91%

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

et al. 2021

View full text Add to dashboard Cite

The ongoing COVID-19 pandemic, caused by SARS-CoV-2, has now spread across the nations with high mortality rates and multifaceted impact on human life. The proper treatment methods to overcome this contagious disease are still limited. The main protease enzyme (Mpro, also called 3CLpro) is essential for viral replication and has been considered as one of the potent drug targets for treating COVID-19. In this study, virtual screening was performed to find out the molecular interactions between 36 natural compounds derived from sesame and the Mpro of COVID-19. Four natural metabolites, namely, sesamin, sesaminol, sesamolin, and sesamolinol have been ranked as the top interacting molecules to Mpro based on the affinity of molecular docking. Moreover, stability of these four sesame-specific natural compounds has also been evaluated using molecular dynamics (MD) simulations for 200 nanoseconds. The molecular dynamics simulations and free energy calculations revealed that these compounds have stable and favorable energies, causing strong binding with Mpro. These screened natural metabolites also meet the essential conditions for drug likeness such as absorption, distribution, metabolism, and excretion (ADME) properties as well as Lipinski’s rule of five. Our finding suggests that these screened natural compounds may be evolved as promising therapeutics against COVID-19.

show abstract

Section: Compoundsupporting

confidence: 91%

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The ursolic acid showed the highest docking score (−8.7 kcal/mol) with the M pro followed by other compounds tested, suggesting the potential binding and inhibitory effects of ursolic acid [163] . Ursolic acid showed a high binding affinity (−9.7 kcal/mol) for papain-like protease PL pro of SARS-CoV-2 and forms hydrogen bonding at amino acid residues Asp108 and attaches at Ala107, Pro248 and Tyr264 with alkyl, π-alkyl interaction [164] .…”

Section: Ursolic Acid a Potent Inhibitor Of Viral M Pro Enzymementioning

confidence: 99%

Natural products can be used in therapeutic management of COVID-19: Probable mechanistic insights

Ali

Alam

Khatoon

et al. 2022

Biomedicine & Pharmacotherapy

View full text Add to dashboard Cite

The unexpected emergence of the new Coronavirus disease (COVID-19) has affected more than three hundred million individuals and resulted in more than five million deaths worldwide. The ongoing pandemic has underscored the urgent need for effective preventive and therapeutic measures to develop anti-viral therapy. The natural compounds possess various pharmaceutical properties and are reported as effective anti-virals. The interest to develop an anti-viral drug against the novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2) from natural compounds has increased globally. Here, we investigated the anti-viral potential of selected promising natural products. Sources of data for this paper are current literature published in the context of therapeutic uses of phytoconstituents and their mechanism of action published in various reputed peer-reviewed journals. An extensive literature survey was done and data were critically analyzed to get deeper insights into the mechanism of action of a few important phytoconstituents. The consumption of natural products such as thymoquinone, quercetin, caffeic acid, ursolic acid, ellagic acid, vanillin, thymol, and rosmarinic acid could improve our immune response and thus possesses excellent therapeutic potential. This review focuses on the anti-viral functions of various phytoconstituent and alkaloids and their potential therapeutic implications against SARS-CoV-2. Our comprehensive analysis provides mechanistic insights into phytoconstituents to restrain viral infection and provide a better solution through natural, therapeutically active agents.

show abstract

“…These drugs were found to bind near the proposed catalytic triad [ 74 ]. Phytochemicals from Vitex negundo L. are also found active against PL Pro [ 75 ]. Along with natural compounds, many approved antibacterial and antiviral drugs also have been repurposed [ 76 , 77 , 78 ].…”

Section: Discussionmentioning

confidence: 99%

Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World

et al. 2021

View full text Add to dashboard Cite

The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (MPro), Papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-β-glycyrrhetinic acid have shown a strong binding affinity for MPro, helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PLpro and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2.

show abstract

Molecular docking and simulation studies of natural compounds ofVitex negundoL. against papain-like protease (PL^pro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world

Abstract: (2021): Molecular docking and simulation studies of natural compounds of Vitexnegundo L. against papain-like protease (PL pro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world,

Cited by 28 publications

References 49 publications

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

Natural products can be used in therapeutic management of COVID-19: Probable mechanistic insights

Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World

Contact Info

Product

Resources

About

Molecular docking and simulation studies of natural compounds ofVitex negundoL. against papain-like protease (PLpro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world

Abstract: (2021): Molecular docking and simulation studies of natural compounds of Vitexnegundo L. against papain-like protease (PL pro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world,

Cited by 28 publications

References 49 publications

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

Inhibition Potencies of Phytochemicals Derived from Sesame Against SARS-CoV-2 Main Protease: A Molecular Docking and Simulation Study

Natural products can be used in therapeutic management of COVID-19: Probable mechanistic insights

Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World

Contact Info

Product

Resources

About

Molecular docking and simulation studies of natural compounds ofVitex negundoL. against papain-like protease (PL^pro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world