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In silico analysis of Phyllanthus amarus phytochemicals as potent drugs against SARS-CoV-2 main protease

ABSTRACT: Phyllanthus amarus, also known as Bhui Korma in India, is well known for its medicinal properties and is used to treat several diseases worldwide. This study aims to identify phytochemicals from P. amarus and assess their anti-viral activity through in silico methods against the main protease (3CLPro/MPro) enzyme of the novel coronavirus. 190 compounds were obtained from literature and docked against 3CLPro and 16 compounds showed higher binding affinity with 3CLPro with their values lying between -8.9 kcal/mol to -9.6 kcal/mol. The top two compounds, Myricitrin (CID: 5352000) and Quercetin-3-O-glucuronide (CID: 12004528) gave high binding affinity values of -9.6 kcal/mol and -9.4 kcal/mol respectively and also display favourable binding interactions with the 3CLPro. Both the compounds were further subjected to molecular dynamics simulation and MM-PBSA based binding free energy calculations. ADMET and drug-likeness properties were studied to assess the pharmacokinetic properties of the compounds. Favourable pharmacokinetic results reinforced the applicability of the compounds assessed. Along with continuous studies being carried out with chemical compounds, research needs to expand into all areas, including the use of natural compounds as drug compounds. The identified hits from this study can be taken further for in vitro and in vivo studies to examine their efficacy against COVID-19. Graphical abstract Image 1

SUBMITTER: Murthy T

PROVIDER: S-EPMC8364217 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has resulted in outbreak of global pandemic, fatal pneumonia in human referred as Coronavirus Disease-2019 (Covid-19). Ayurveda, the age old practice of treating human ailments in India, can be considered against SARS-CoV-2. Attempt was made to provide preliminary evidences for interaction of 35 phytochemicals from two plants (Phyllanthus amarus and Andrographis paniculata used in Ayurveda) with SARS-CoV-2 proteins (open & closed state S protein, 3CLpro, PLpro and RdRp) through in silico docking analysis. The nucleotide analogue remdesivir, being used in treatment of SARS-CoV-2, was used as a positive control. The results revealed that 18 phytochemicals from P. amarus and 14 phytochemicals from A. paniculata shown binding energy affinity/dock score < - 6.0 kcal/mol, which is considered as minimum threshold for any compound to be used for drug development. Phytochemicals used for docking studies in the current study from P. amarus and A. paniculata showed binding affinity up to - 9.10 kcal/mol and - 10.60 kcal/mol, respectively. There was no significant difference in the binding affinities of these compounds with closed and open state S protein. Further, flavonoids (astragalin, kaempferol, quercetin, quercetin-3-O-glucoside and quercetin) and tannins (corilagin, furosin and geraniin) present in P. amarus have shown more binding affinity (up to - 10.60 kcal/mol) than remdesivir (up to - 9.50 kcal/mol). The pharmacokinetic predictions suggest that compounds from the two plants species studied in the current study are found to be non-carcinogenic, water soluble and biologically safe. The phytochemicals present in the extracts of P. amarus and A. paniculata might have synergistic effect with action on multiple target sites of SARS-CoV-2. The information generated here might serve as preliminary evidence for anti SARS-CoV-2 activity of phytochemicals present from P. amarus and A. paniculata and the potential of Ayurveda medicine in combating the virus.Supplementary informationThe online version contains supplementary material available at 10.1007/s13205-020-02578-7.

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In silico analysis of Phyllanthus amarus phytochemicals as potent drugs against SARS-CoV-2 main protease

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