Biochemical and Computational Approach of Selected Phytocompounds from Tinospora crispa in the Management of COVID-19

Rakib, Ahmed; Paul, Arkajyoti; Chy, Md. Nazim Uddin; Sami, Saad Ahmed; Baral, Sumit; Majumder, Mohuya; Tareq, Abu Montakim; Amin, Mohammad Nurul; Shahriar, Asif; Uddin, Zia; Dutta, Mycal; Tallei, Trina Ekawati; Emran, Talha Bin; Simal-Gándara, Jesús

doi:10.3390/molecules25173936

Cited by 86 publications

(62 citation statements)

References 61 publications

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“…Docking of each precision was filtrated and expressed as a glide score [ 19 ]. Subsequently, the ligand (Z45617795) bound to SARS-CoV-2 main protease was extracted from protein-ligand complex and subjected to re-docking through standard precision (SP) docking [ 20 ]. From this, the docking score was obtained as a control (control 1) to compare the value with newly screened drugs.…”

Section: Methodsmentioning

confidence: 99%

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Chowdhury

Mahmud

et al. 2020

Biology

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Novel coronavirus disease (COVID-19) was identified from China in December 2019 and spread rapidly through human-to-human transmission, affecting so many people worldwide. Until now, there has been no specific treatment against the disease and repurposing of the drug. Our investigation aimed to screen potential inhibitors against coronavirus for the repurposing of drugs. Our study analyzed sequence comparison among SARS-CoV, SARS-CoV-2, and MERS-CoV to determine the identity matrix using discovery studio. SARS-CoV-2 Mpro was targeted to generate an E-pharmacophore hypothesis to screen drugs from the DrugBank database having similar features. Promising drugs were used for docking-based virtual screening at several precisions. Best hits from virtual screening were subjected to MM/GBSA analysis to evaluate binding free energy, followed by the analysis of binding interactions. Furthermore, the molecular dynamics simulation approaches were carried out to assess the docked complex’s conformational stability. A total of 33 drug classes were found from virtual screening based on their docking scores. Among them, seven potential drugs with several anticancer, antibiotic, and immunometabolic categories were screened and showed promising MM/GBSA scores. During interaction analysis, these drugs exhibited different types of hydrogen and hydrophobic interactions with amino acid residue. Besides, 17 experimental drugs selected from virtual screening might be crucial for drug discovery against COVID-19. The RMSD, RMSF, SASA, Rg, and MM/PBSA descriptors from molecular dynamics simulation confirmed the complex’s firm nature. Seven promising drugs for repurposing against SARS-CoV-2 main protease (Mpro), namely sapanisertib, ornidazole, napabucasin, lenalidomide, daniquidone, indoximod, and salicylamide, could be vital for the treatment of COVID-19. However, extensive in vivo and in vitro studies are required to evaluate the mentioned drug’s activity.

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Section: Methodsmentioning

confidence: 99%

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Chowdhury

Mahmud

et al. 2020

Biology

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“…AutoDock Vina was implemented via the shell script offered by AutoDock Vina developers [99]. Docking results were observed by the negative score in kcal/mol, as the binding affinity of ligands are depicted in negative energies [100,101]. In addition, for validation of the docking approach, we selected 9-mer peptide from the envelope glycoprotein gp160 from human immunodeficiency virus (HIV) type 1 attached with the crystal structure of HLA-A*68:02 as a positive control and performed molecular docking analysis using the aforementioned similar parameters.…”

Section: Molecular Docking Analysismentioning

confidence: 99%

Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Rakib

Sami

et al. 2020

Molecules

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With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.

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“…Medicinal plants are the richest bioresources of conventional drugs, modern medicines, nutraceuticals, curative intermediates, and artificial drug chemicals. Phytochemical screening has revealed the existence of both physiological and therapeutic activities [27]. In our recent research, A. montanum (Pani heloch) leaves exhibited the presence of secondary metabolites-notably, flavanols, flavonoids, phenols, alkaloids, polyphenols, terpenoids, emodines, glycosides, coumarins, cholesterols, resins, tannins, gums and mucilages, phytosterols, fatty acids, and fixed oils [28].…”

Section: Discussionmentioning

confidence: 99%

Insightful Valorization of the Biological Activities of Pani Heloch Leaves through Experimental and Computer-Aided Mechanisms

et al. 2020

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Pani heloch (Antidesma montanum) is traditionally used to treat innumerable diseases and is a source of wild vegetables for the management of different pathological conditions. The present study explored the qualitative phytochemicals; quantitative phenol and flavonoid contents; in vitro antioxidant, anti-inflammatory, and thrombolytic effects; and in vivo antipyretic and analgesic properties of the methanol extract of A. montanum leaves in different experimental models. The extract exhibited secondary metabolites including alkaloids, flavonoids, flavanols, phytosterols, cholesterols, phenols, terpenoids, glycosides, fixed oils, emodines, coumarins, resins, and tannins. Besides, Pani heloch showed strong antioxidant activity (IC50 = 99.00 µg/mL), while a moderate percentage of clot lysis (31.56%) in human blood and significant anti-inflammatory activity (p < 0.001) was achieved with the standard. Moreover, the analgesic and antipyretic properties appeared to trigger a significant response (p < 0.001) relative to in the control group. Besides, an in silico study of carpusin revealed favorable protein-binding affinities. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity analysis and toxicological properties of all isolated compounds adopted Lipinski’s rule of five for drug-like potential and level of toxicity. Our research unveiled that the methanol extract of A. montanum leaves exhibited secondary metabolites that are a good source for managing inflammation, pyrexia, pain, and cellular toxicity. Computational approaches and further studies are required to identify the possible mechanism which responsible for the biological effects.

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Biochemical and Computational Approach of Selected Phytocompounds from Tinospora crispa in the Management of COVID-19

Cited by 86 publications

References 61 publications

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Epitope-Based Immunoinformatics Approach on Nucleocapsid Protein of Severe Acute Respiratory Syndrome-Coronavirus-2

Insightful Valorization of the Biological Activities of Pani Heloch Leaves through Experimental and Computer-Aided Mechanisms

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