Exploring α, β-unsaturated carbonyl compounds against bacterial efflux pumps
            <i>via</i>
            computational approach

Dey, Sreenath; Rathod, Sanket; Gumphalwad, Kondba; Yadav, Nikhil; Choudhari, Prafulla; Rajakumara, Eerappa; Dhavale, Rakesh; Mahuli, Deepak

doi:10.1080/07391102.2023.2246568

Cited by 9 publications

(4 citation statements)

References 63 publications

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“…A production run was completed for a period of 100 ns. The resulting MD trajectories were statistically analyzed. , …”

Section: Methodsmentioning

confidence: 99%

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Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy

Lohitha,

Kumar,

Sarveswari

et al. 2024

ACS Omega

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A series of novel 24 phenylhydrazono phenoxyquinoline derivatives were synthesized with moderate to excellent yield and screened for their efficacy against the α-amylase enzyme through in silico studies. The structures were characterized using spectroscopic techniques such as 1 HNMR, 13 CNMR, and HREI-MS. Comprehensive computational studies including, drug-likeness and ADMET profiling, quantum chemical calculations, molecular docking, and molecular dynamics (MD) simulation studies, were performed. A density functional theory study of the synthesized compounds indicated a favorable reactivity profile. The synthesized novel analogues were docked against α-amylase (PDB 6OCN) enzymes to investigate the binding interactions. Based on the docking studies, one of the compounds was found to be the hit with the highest negative binding affinity for α-amylase. A MD simulation study indicated stable binding throughout the simulation.

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“…A production run was completed for a period of 100 ns. The resulting MD trajectories were statistically analyzed. , …”

Section: Methodsmentioning

confidence: 99%

“…The resulting MD trajectories were statistically analyzed. 72,73 ■ ASSOCIATED CONTENT * sı Supporting Information…”

mentioning

confidence: 99%

Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy

Lohitha,

Kumar,

Sarveswari

et al. 2024

ACS Omega

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“…The MD simulation was conducted using Schrödinger, LLC's Desmond 2020.1 software. Employing the OPLS-2005 force field and the TIP3P water model, the system was enclosed within a periodic boundary solvent box to cover the entire complex structure [22,40]. A 0.15 M Na+ion concentration was introduced through NaCl solutions to mimic physiological conditions and neutralize charges.…”

Section: Molecular Dynamics Simulationsmentioning

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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“…The Desmond 2020.1 software by Schrödinger, LLC was employed to conduct MD simulations on the docked protein-ligand complexes. The OPLS-2005 force field, along with an explicit solvent model utilizing TIP3P water molecules was used and the system was enclosed in a periodic boundary solvent box with dimensions of 10 Å x 10 Å x 10 Å (Jorgensen et al 1983;Bowers et al 2006;Chow et al 2008;Dey et al 2023). To counterbalance the charge, Na+ ions were introduced at a concentration of 0.15 M, while NaCl solutions were incorporated to mimic the physiological environment.…”

Section: Simulationsmentioning

confidence: 99%

Exploring binding potential of two new indole alkaloids from Nauclea officinalis against third and fourth generation EGFR: druglikeness, in silico ADMET, docking, DFT, molecular dynamics simulation, and MMGBSA study

Rathod,

Shinde,

Choudhari

et al. 2024

Natural Product Research

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This study investigates the anti-cancer potential of recently discovered indole alkaloids from Nauclea Officinalis against third and fourth generation EGFR mutations using computational tools. Through ADMET profiling, druglikeness prediction, docking, and simulations, we assessed their pharmacokinetics, binding interactions, and stability. Promising druglikeness and binding affinity were observed, particularly for (±)-19-O-butylangustoline, which demonstrated stronger binding against both EGFR mutants. MD simulations confirmed stable interactions, with (±)-19-O-butylangustoline exhibiting the highest stability. These findings highlight these indole alkaloids as potential anti-cancer agents, with (±)-19-O-butylangustoline warranting further optimization for therapeutic development. This study informs their potential through insights into molecular properties and binding energetics.

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Exploring α, β-unsaturated carbonyl compounds against bacterial efflux pumps via computational approach

Cited by 9 publications

References 63 publications

Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy

Synthesis, Characterization, In Silico DFT, Molecular Docking, and Dynamics Simulation Studies of Phenylhydrazono Phenoxyquinolones for Their Hypoglycemic Efficacy

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

Exploring binding potential of two new indole alkaloids from Nauclea officinalis against third and fourth generation EGFR: druglikeness, in silico ADMET, docking, DFT, molecular dynamics simulation, and MMGBSA study

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