High-Throughput Screening and Dynamic Studies of Selected Compounds Against Sars-Cov-2

Bhowmik, Ratul; Nath, Ranajit; Sharma, Sameer; ROY, RATNA; Biswas, Riya

doi:10.22159/ijap.2022v14i1.43105

Cited by 8 publications

(3 citation statements)

References 13 publications

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“…The molecular docking was analyzed based on the binding affinity exhibited by the ligands at zero RMSD (Root Mean Square Deviation) towards the target GFRs [18]. The bestdocked complexes were further visualized in DS Biovia Discovery Studio Visualizer for the molecular interaction at the binding pocket of the target proteins [19].…”

Section: Molecular Dockingmentioning

confidence: 99%

Molecular Docking and Investigation of Boswellia Serrata Phytocompounds as Cancer Therapeutics to Target Growth Factor Receptors: An in Silico Approach

B. R.,

J. S.,

et al. 2023

Int J App Pharm

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Objective: Boswellia serrata is a plant with a long history of use in traditional medicine, particularly for its anti-inflammatory and anti-cancer properties. Growth factors and their receptors are significant components in the initiation and progression of malignancy, and aberrant functioning of these pathways can result in unrestrained cell division and expansion. Methods: In this study, an in silico approach was used to explore the potential of Boswellia serrata phytochemicals as cancer therapeutics to target growth factor receptors. The virtual screening involved molecular docking simulations (PyRx) to predict the binding affinity between the phytochemicals and the receptors. Results: The seventy-four phytocompounds identified from Boswellia serrata were preliminarily screened based on their binding towards growth factor receptors. The ligands demonstrated better binding with the GFR targets, and the binding score less than-7 kcal/mol was considered for further investigation results demonstrated that Alpha-boswellic exhibited strong binding affinity to the receptors, suggesting their potential as targeted cancer therapies. This study provides a foundation for future in vitro and in vivo experiments to validate the efficacy of these phytochemicals as cancer treatments. Conclusion: The results suggest that Boswellic acid derivatives from Boswellia serrata could be a promising source of new cancer therapies.

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Section: Molecular Dockingmentioning

confidence: 99%

Molecular Docking and Investigation of Boswellia Serrata Phytocompounds as Cancer Therapeutics to Target Growth Factor Receptors: An in Silico Approach

B. R.,

J. S.,

et al. 2023

Int J App Pharm

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“…12A-D. The B-factor correlates with the deformation of protein molecule at all amino acid residues and hinges will be predicted along with the normal mode analysis (NMA) (Bhowmik R et al, 2022). The change can be observed between the NMA and B-factor, it may represent the changes in the protein macromolecule upon to the addition of the external ligand.…”

Section: Effect Of Glucose On Micrornas In U87mg Cellsmentioning

confidence: 99%

High Glucose modulates the cancer cell fate by regulation of mTOR-HDAC-microRNA axis

Ramaiah

Kumar

Sriniva

et al. 2022

Preprint

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Glioblastoma multiforme (GBM) is the most dangerous cancers of the brain. Despite availability of various treatment modalities, GBM chemotherapy remains obscure. Cancer metabolism is considered as one of the important factors for the tumor aggressiveness. Glucose is an important energy source for the cellular metabolism and was found to affect the GBM cancer aggressiveness, and chemo-resistance. Studies have found that GBM cancer is driven by epigenetic proteins. HDACs are important epigenetic proteins that regulate the gene expression by chromatin epigenetics changes, and there by involved in gene transcription in cancer cells. In this study, we have evaluated the role of glucose on GBM cancer cells and identified the cell viability effects. Further, the cell-cycle studies have indicated the apoptotic effects of high dose of glucose. Further the histone deacetylase (HDAC) gene expression was examined during increased glucose availability. We have observed a drastic enhancement in HDAC gene expression. Further, the cancer cell metabolism was analysed by studying the gene expression pertaining to mammalian target of rapamycin (mTOR) pathway. Glucose has induced changes in gene expression of class I HDACs and mTOR pathway genes. Furthermore, the study has also identified the microRNA modulatory effect of glucose. The molecular modelling studies have indicated the interaction of glucose with mTOR, Rictor and caspase-3 proteins suggesting the functional regulatory role of glucose on the expression of genes. The caspase-3 (i. e. the effector caspase) studies confirmed the effect of glucose on caspase-3 activity and the effect was enhanced by the treatment with mTOR complex inhibitors. Proteomic study has identifed the involvement of MAPK, Rho kinase, S6 kinase pathways, Bromodomain, histone acetyl transferases during combined treatment of mTOR complex inhibitor and high glucose combination treatment. Thus, the present study has elucidated the role of glucose on GBM cancer proliferation, and molecular modulatory effect mediated by glucose by varying the chromatin epigenetics, and microRNA modulation.

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“…In recent years, berberine has been the subject of much scientific research, and its potential health benefits have been further investigated [3]. Computational studies, also known as in silico investigations, have become a mainstay of contemporary science across a wide range of disciplines [4][5][6]. In order to better understand complicated processes, current studies use computerbased simulations, modeling, and data analysis [7].…”

Section: Introductionmentioning

confidence: 99%

In Silico Exploration of Berberine as a Potential Wound Healing Agent via Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

SACHDEO,

KHANWELKAR,

SHETE

2024

Int J App Pharm

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Objective: Wound healing remains a complex biological process crucial for tissue repair and homeostasis. Our goal in this paper is to focus on the application of advanced computational techniques to explore the potential of naturally occurring compound berberine in addressing molecular targets related to wound healing. Methods: Network pharmacology, molecular docking analysis, in silico ADMET prediction, and extensive 100 ns molecular dynamics simulations was performed to gain a holistic understanding of the therapeutic potential of berberine against molecular targets involved in wound healing. This study predicted drug-likeness scores, potential side effects, ADMET profiles, carcinogenicity, MolLogP, molecular volume analysis, and molecular polar surface area for berberine. Results: Findings of the study revealed that berberine displayed a remarkable binding affinity for the epidermal growth factor receptor (EGFR), with a binding energy of-8.14 kcal/mol, surpassing the crystal ligand's binding energy of-7.15 kcal/mol. This indicates a strong potential for berberine in modulating EGFR-related pathways critical for wound healing. The culmination of the investigation was a 100 ns molecular dynamics simulation, which demonstrated consistent binding and stability over time, reinforcing the potential of berberine as a wound healing agent. Conclusion: The integration of gene expression analysis, enrichment studies, network analysis, molecular docking, and molecular dynamics simulations unveiled crucial mechanisms underlying efficacy of berberine as a potent wound-healing agent.

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High-Throughput Screening and Dynamic Studies of Selected Compounds Against Sars-Cov-2

Cited by 8 publications

References 13 publications

Molecular Docking and Investigation of Boswellia Serrata Phytocompounds as Cancer Therapeutics to Target Growth Factor Receptors: An in Silico Approach

Molecular Docking and Investigation of Boswellia Serrata Phytocompounds as Cancer Therapeutics to Target Growth Factor Receptors: An in Silico Approach

High Glucose modulates the cancer cell fate by regulation of mTOR-HDAC-microRNA axis

In Silico Exploration of Berberine as a Potential Wound Healing Agent via Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

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