Potential Phytochemical Inhibitors of the Coronavirus RNA Dependent RNA Polymerase: A Molecular Docking Study

P, Ardra.; Singh, Prachi; Vr, Hariprasad; Uv, Babu; Rafiq, Mohamed; Rao, Raghavendra Pralhada

doi:10.21203/rs.3.rs-35334/v1

Cited by 7 publications

(1 citation statement)

References 23 publications

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“…The molecular docking calculations for all phytochemicals with each of the selected enzymes were performed using AutoDockVina v. 1.1.2 [23]. AutoDockVina results designate the Gibbs free energy of binding (ΔG (kcal/mol)) as docking scores which represents the efficacy of ligand binding to chosen receptor [24]. The accuracy of our docking results was validated by re-docking all co-crystallised inhibitory ligands (control inhibitors) into their corresponding protein structures.…”

Section: Grid Box Preparation and Molecular Dockingmentioning

confidence: 99%

Investigation of the Anti-TB Potential of Selected Phytochemicals of Nigella Sativa using Molecular Docking Approach

Mir

2021

JPRI

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Background: Tuberculosis (TB) is one of the foremost causes of human mortality across the world. In general, it is a curable disease and several drugs are available in market for its treatment, however, because of the drug resistance to the currently available anti-TB drugs, the development and/or discovery of new drugs with better efficacy against TB cannot be overlooked. In the present study, we performed virtual screening of the major phytochemicals of the plant Nigella sativa for investigating their potential to inhibit some novel drug targets of Mycobacterium tuberculosis, which included- pantothenate kinase, type 1 (MtPanK), β-ketoacyl ACP synthase I (MtKasA), and decaprenylphosphoryl-β-D-ribose 2′-epimerase 1 (MtDprE1). Methods: The screening of the phytochemicals was investigated through a molecular docking approach using Auto dock vina and the molecular interactions in the protein-ligand complexes were visualized and analysed through PyMol and BioVia Discovery Studio Visualizer. Results: Our in silico observations reveal that, out of the nine selected phytochemicals screened, five compounds, namely α-hederin, dithymoquinone, nigellidine, thymoquinone and thymol binded to one or more of the selected target enzymes with significant docking scores. α-hederin binded to MtDprE1 and MtKasA with a docking score of −8.5kcal/mol and −7.9kcal/mol, respectively, dithymoquinone binded to MtKasA, MtDprE1 and MtPanK with a docking score of −6.5kcal/mol, −8.2kcal/mol and −9.2kcal/mol, respectively and nigellidine binded to MtDprE1 and MtPanK with a docking score of −8.1kcal/mol and −8.2kcal/mol, respectively. Further, thymol as well as thymoquinone were observed to bind MtKasA with a docking score of −6.6kcal/mol. Conclusions: The results of our study indicate that the five phytochemicals of N. sativa, including α-hederin, dithymoquinone, nigellidine, thymoquinone and thymol, are worth studying further for their anti-TB activity, however, additional biological studies are warranted to validate these findings.

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Section: Grid Box Preparation and Molecular Dockingmentioning

confidence: 99%

Investigation of the Anti-TB Potential of Selected Phytochemicals of Nigella Sativa using Molecular Docking Approach

Mir

2021

JPRI

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Computational Modeling of RdRp Inhibitors for the Development of Drugs against Novel Coronavirus (nCoV)

Kumar

Roy

2021

Methods in Pharmacology and Toxicology

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Identification of SARS-CoV-2 RNA-dependent RNA polymerase inhibitors from the major phytochemicals of Nigella sativa: An in silico approach

Mir

Firoz

Alaidarous

et al. 2022

Saudi Journal of Biological Sciences

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The coronavirus disease 2019 (COVID-19), which emerged in December 2019, continues to be a serious health concern worldwide. There is an urgent need to develop effective drugs and vaccines to control the spread of this disease. In the current study, the main phytochemical compounds of Nigella sativa were screened for their binding affinity for the active site of the RNA-dependent RNA polymerase (RdRp) enzyme of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The binding affinity was investigated using molecular docking methods, and the interaction of phytochemicals with the RdRp active site was analyzed and visualized using suitable software. Out of the nine phytochemicals of N. sativa screened in this study, a significant docking score was observed for four compounds, namely α-hederin, dithymoquinone, nigellicine, and nigellidine. Based on the findings of our study, we report that α-hederin, which was found to possess the lowest binding energy (–8.6 kcal/mol) and hence the best binding affinity, is the best inhibitor of RdRp of SARS-CoV-2, among all the compounds screened here. Our results prove that the top four potential phytochemical molecules of N. sativa , especially α-hederin, could be considered for ongoing drug development strategies against SARS-CoV-2. However, further in vitro and in vivo testing are required to confirm the findings of this study.

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Potential Phytochemical Inhibitors of the Coronavirus RNA Dependent RNA Polymerase: A Molecular Docking Study

Cited by 7 publications

References 23 publications

Investigation of the Anti-TB Potential of Selected Phytochemicals of Nigella Sativa using Molecular Docking Approach

Investigation of the Anti-TB Potential of Selected Phytochemicals of Nigella Sativa using Molecular Docking Approach

Computational Modeling of RdRp Inhibitors for the Development of Drugs against Novel Coronavirus (nCoV)

Identification of SARS-CoV-2 RNA-dependent RNA polymerase inhibitors from the major phytochemicals of Nigella sativa: An in silico approach

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