Molecular docking and dynamic simulations of <i>Ocimum basilicum</i> compounds against HCC and structural, vibrational, quantum, and chemical investigation of campesterol

Sangeetha, R.; Prabha, E. Arockia Jeya Yasmi; Lakshmi, A. Bhagya; Sangavi, P.; Kulanthaivel, Langeswaran

doi:10.1080/07391102.2021.1997816

Cited by 5 publications

(2 citation statements)

References 10 publications

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“…To gain further insights into mutation impact on drug binding, we applied an in-silico pipeline to model lenvatinib-, infigratinib-, and pemigatinib-FGFR2 bound systems, encompassing WT, N549K, N549D, E565A, E565G, V562L, V564F, and V564I mutations, followed by classical all-atom MD simulations. FGFR2 MD studies were previously reported in work by Sangeetha et al 54 ; however, with a total timescale of 48 µs in our work, we go far beyond the reported data. Our results suggest that lenvatinib’s superior inhibitory performance occurs not only due to a more favorable interaction pattern but to a set of additional factors such as hydrophobic stabilization, increased flexibility of the lenvatinib in the gate area and back cleft and superior free energy ligand efficiency (for additional information see Supplementary Methods, Results and Discussion).…”

Section: Discussionsupporting

confidence: 50%

The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma

Spahn,

Kleinhenz,

Shevchenko

et al. 2024

Nat Commun

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Fibroblast growth factor receptor (FGFR)−2 can be inhibited by FGFR-selective or non-selective tyrosine kinase inhibitors (TKIs). Selective TKIs are approved for cholangiocarcinoma (CCA) with FGFR2 fusions; however, their application is limited by a characteristic pattern of adverse events or evocation of kinase domain mutations. A comprehensive characterization of a patient cohort treated with the non-selective TKI lenvatinib reveals promising efficacy in FGFR2-driven CCA. In a bed-to-bench approach, we investigate FGFR2 fusion proteins bearing critical tumor-relevant point mutations. These mutations confer growth advantage of tumor cells and increased resistance to selective TKIs but remain intriguingly sensitive to lenvatinib. In line with clinical observations, in-silico analyses reveal a more favorable interaction pattern of lenvatinib with FGFR2, including an increased flexibility and ligand efficacy, compared to FGFR-selective TKIs. Finally, the treatment of a patient with progressive disease and a newly developed kinase mutation during therapy with a selective inhibitor results in a striking response to lenvatinib. Our in vitro, in silico, and clinical data suggest that lenvatinib is a promising treatment option for FGFR2-driven CCA, especially when insurmountable adverse reactions of selective TKIs or acquired kinase mutations occur.

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Section: Discussionsupporting

confidence: 50%

The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma

Spahn,

Kleinhenz,

Shevchenko

et al. 2024

Nat Commun

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“…It enables the analysis of the system's physical evolution through time and is a valuable tool for interpolating between theory and experimentation. MD performed in GROMACS package with 50 ns by using GRO-MOS96 43a1 force feld [19]. Te compound with the lowest binding energy was selected for molecular dynamics (MD) simulation.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Antioxidant, Anti-Inflammatory, and Anticarcinogenic Efficacy of an Ayurvedic Formulation: Amritotharanam Kashyam

Raman

Shanmuganathan²,

Chandrashekar

et al. 2023

Advances in Pharmacological and Pharmaceutical Sciences

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Amritotharanam Kashyam, a specific Ayurvedic drug, was the focus of the current inquiry to evaluate its efficacy. For liver and digestive-related issues, this medication is suggested. This was obtained from a standard Ayurvedic vendor in Chennai (India), and GC-MS analysis was carried out according to the standard procedure. A few critical biomolecules include benzoic acid, hexadecanoic acid, 6,9-octadecadienoic acid, 9-octadecenoic acid, methyl ester (E)-, heptadecanoic acid, 16-methyl, methyl ester, methyl 18-methylnonadecanoate, tetracosanoic acid, distearin, hexadecanoic acid, and 1-(hydroxymethyl)-1,2-ethanediol ester. The obtained biomolecules exhibited some significant therapeutic functions, including acidification, inhibition of arachidonic acid formation, increase in the aromatic amino acid decarboxylase, suppression of uric acid generation, inhibitors of catechol-O-methyltransferase, urine acidifiers, etc. The anticancer and antiviral potential of these phytocompounds were investigated using molecular docking and dynamics. The phytocompounds pharmacokinetic characteristics were investigated using ADME analysis. Through docking and dynamics simulation, in silico tests demonstrated the phytocompounds' inhibitory efficiency against the target proteins. These functions reasonably relate to the medicinal function of Amritotharanam Kashyam. The MTT assay findings demonstrated this medication’s anticancer effects. The ability to be an effective drug is demonstrated by its antioxidant, anti-inflammatory, and membrane-stabilizing properties.

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Unraveling the Interaction Mechanism of the Compounds From Cladophora sp to Recognize Prospective Larvicidal and Bactericidal Activities: In vitro and In Silico Approaches

Nachammai,

Amaradeepa,

Raageshwari

et al. 2023

Mol Biotechnol

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Molecular docking and dynamic simulations of Ocimum basilicum compounds against HCC and structural, vibrational, quantum, and chemical investigation of campesterol

Cited by 5 publications

References 10 publications

The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma

The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma

Antioxidant, Anti-Inflammatory, and Anticarcinogenic Efficacy of an Ayurvedic Formulation: Amritotharanam Kashyam

Unraveling the Interaction Mechanism of the Compounds From Cladophora sp to Recognize Prospective Larvicidal and Bactericidal Activities: In vitro and In Silico Approaches

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