Molecular docking and bio-control efficacy of Mesosphaerum suaveolens (L.) Kuntze against mosquito Culex quinquefasciatus Say

South African Journal of Botany, Journal Year: 2025, Volume and Issue: 180, P. 541 - 552

Published: March 31, 2025

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In silico analysis to explore the therapeutic potential of propolis-derived small molecules as matriptase inhibitors to suppress breast cancer growth and metastasis

PLoS ONE, Journal Year: 2025, Volume and Issue: 20(5), P. e0321687 - e0321687

Published: May 14, 2025

Breast cancer is a major cause of death in women, and various drug therapies are used for its treatment. However, current have many side effects limitations. Propolis, resinous product bee hives, possesses variety biological activities, including anticancer chemo-protective properties. The present study aimed to investigate the potential suitability propolis-derived compounds inhibit matriptase (MT-SP1), protein target breast treatment, through comprehensive computational analysis. MT-SP1 structure (PDB ID: 1EAX) was retrieved, energy-minimized, validated. Five with highest binding energies were selected after virtual screening. Molecular docking these ligands revealed ranging from -8.4 -9.1 kcal/mol. Stable complex formation validated by an additional 250 ns molecular dynamics simulations. HOMO-LUMO DFT characteristics provided further evidence chemical reactivity stability five at active site. Screening drug-likeness, pharmacokinetics (ADMET profiles), toxicity identified two promising small molecules (PubChem IDs 72307 129827386) as candidates inhibiting MT-SP1. experimental validation vitro or vivo studies necessary confirm findings explore their therapeutic

Language: Английский

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Phytocompound inhibitors of caspase 3 as beta-cell apoptosis treatment development option: An In-silico approach

Sciences of Phytochemistry, Journal Year: 2023, Volume and Issue: 2(1), P. 17 - 37

Published: March 9, 2023

The prevalence of Diabetes mellitus (DM) is continuously rising worldwide. Among its types, type I characterized by the destruction beta cells triggered various mechanisms, including activation Caspase 3. Studies have demonstrated crucial role 3 in initiating apoptosis DM. Our research aims to identify possible phytocompounds inhibitors using computational approach. We obtained 3D structures and 6511 from Protein Data Bank African Natural Products Database, respectively. were assessed for druglikeness properties, topological polar surface area, preliminary toxicity DataWarrior. subjected molecular docking simulation (MDS) at active site AutoDock-Vina. frontrunner MDS protease inhibition prediction on Molinspiration. pharmacokinetics SwissADME. in-depth profile was evaluated pkCSM web. binding interactions with Discovery Studio Visualizer Maestro. Seventeen found no violation Lipinski's rule had based assessment, better affinity inhibitory scores than references, optimistic bioactivity radar similar amino acids interaction, comparison references. Further studies, which include in-vitro in-vivo will be carried out validate results this study.

Language: Английский

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UNREVEALING THE COMPLEX INTERPLAY: MOLECULAR DOCKING: A COMPREHENSIVE REVIEW ON CURRENT SCENARIO, UPCOMING DIFFICULTIES, FORTHCOMING INITIATIVES, AND VIEWPOINTS

International Journal of Chemistry Research, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 9

Published: Jan. 1, 2024

The computer modelling of structural complexes generated from two or more interacting molecules are referred to as molecular docking. It is an indispensable tool in computer-aided drug design and biology. Using this technology, large libraries compounds may be digitally screened, the results can graded along with assumptions about how ligands impact target's reduction. Recent advances synthesis anti-infectious medicines prompted by insights have enabled application computer-assisted quest for innovative mechanism-or structure-based drugs. Molecular docking important phase development process because it determines best positions occupy when they coupled together predicts effectively will bind once been docked. input structure's also critical, assessed using sampling methods scoring systems. recently developed software Local Move Monte Carlo provides a strong choice customizable receptor strategies. Docking technique determining proteins interact. structurally sound compatible medication design. Successful discovers high-dimensional spaces ranks function utilisation, resulting candidate rating that acceptable. used screen vast offer hypotheses process.

Language: Английский

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Chemical composition, antioxidant, antimicrobial and anticancer activities of endemic Cephalaria tuteliana

South African Journal of Botany, Journal Year: 2024, Volume and Issue: 169, P. 231 - 241

Published: April 27, 2024

Language: Английский

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In-silico screening of Acacia pennata and Bridelia retusa reveals pinocembrin-7-O-β-D-glucopyranoside as a promising β-lactamase inhibitor to combat antibiotic resistance

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: unknown, P. 1 - 13

Published: Aug. 17, 2023

The β-lactamase of Pseudomonas aeruginosa is known to degrade β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems. With the discovery an extended-spectrum in a clinical isolate P. aeruginosa, bacterium has become multi-drug resistant. In this study, we aim identify new inhibitors by virtually screening total 43 phytocompounds from two Indian medicinal plants. molecular docking studies, pinocembrin-7-O-β-D-glucopyranoside (P7G) (-9.6 kcal/mol) Acacia pennata ellagic acid (EA) (-9.2 Bridelia retusa had lower binding energy than moxalactam (-8.4 kcal/mol). P7G EA formed 5 (Ser62, Asn125, Asn163, Thr209, Ser230) 4 (Lys65, Ser123, Glu159) conventional hydrogens bonds with active site residues. 100 ns MD simulations revealed that (but not EA) were able form stable complex. free calculations further (-59.6526 most complex when compared (-46.5669 (-28.4505 HOMO-LUMO other DFT parameters support stability chemical reactivity at β-lactamase. passed all toxicity tests bioavailability indicating it possesses drug-likeness. Among studied compounds, identified A. promising phytocompound combat antibiotic resistance potentially inhibiting aeruginosa.Communicated Ramaswamy H. Sarma.

Language: Английский

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Discovery of dual-target natural antimalarial agents against DHODH and PMT of Plasmodium falciparum : pharmacophore modelling, molecular docking, quantum mechanics, and molecular dynamics simulations

SAR and QSAR in environmental research, Journal Year: 2023, Volume and Issue: 34(9), P. 709 - 728

Published: Sept. 2, 2023

Malaria is a lethal disease that claims thousands of lives worldwide annually. The objective this study was to identify new natural compounds can target two P. falciparum enzymes; Dihydroorotate dehydrogenase (PfDHODH) and phosphoethanolamine methyltransferase (PfPMT). To accomplish this, e-pharmacophore modelling molecular docking were employed against PfDHODH. Following 1201 with scores ≤ -7 kcal/mol docked into the active site second enzyme PMT. top nine subjected further investigation using MM-GBSA free binding energy calculations ADME analysis. results revealed favourable values better than references, as well acceptable pharmacokinetic properties. Compounds ZINC000013377887, ZINC000015113777, ZINC000085595753 scrutinized assess their interaction stability PfDHODH enzyme, chemical reactivity dynamics (MD) simulation density functional theory (DFT) calculations. These findings indicate three are potential candidates for dual PfPMT inhibitors malaria treatment.

Language: Английский

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An In-Silico Investigation on the Molecular Interactions between Ellagic Acid and Pf DHFR-TS

Polycyclic aromatic compounds, Journal Year: 2023, Volume and Issue: 44(6), P. 4081 - 4102

Published: Aug. 14, 2023

AbstractEllagic acid (EA) is an antiplasmodial polyphenol with reported in-vitro activity against Plasmodium falciparum. Studies have that EA acts in the late erythrocytic stages of P. falciparum (Pf) when DNA synthesis taking place. Pf dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) important enzyme for as its inhibition can kill parasite. As there no study on molecular interactions between and PfDHFR-TS, we aim to PfDHFR-TS (PDB ID: 3DGA) through docking, dynamics (MD) simulations, binding free energy (MM-GBSA) calculations, density functional theory (DFT) studies. Site-specific blind docking revealed has a high affinity active site PfDHFR-TS. formed hydrogen bonds multiple residues. MD simulations 100 ns PfDHFR-TS-EA complex was stable. The average throughout −39.84 kcal/mol. difference (ΔE = 0.04089 eV) obtained from DFT studies indicates electrical stability reactivity at We conclude might be attributed ability potentially bind PfDHFR-TS.Keywords: Molecular dockingMD simulationMM-GBSAellagic acidPfDHFR-TS AcknowledgmentsJames H. Zothantluanga thankful University Grants Commission Ministry Tribal Affairs, Government India providing UGC-SRF fellowship (Award No: 202122-NFST-MIZ-03095) support his Ph.D. research project.Author contributionsStudy design: JHZ; Software, analysis, result interpretation: JHZ, AKU, MR; Drafting, figures, editing: WAE, LP, MSB, DT; Supervision, critical review: MRDisclosure statementNo potential conflict interest by authors.Data availability statementAll data will made available upon proper request corresponding author.

Language: Английский

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Revelation of potential drug targets of luteolin in Plasmodium falciparum through multi-target molecular dynamics simulation studies

Journal of Biomolecular Structure and Dynamics, Journal Year: 2023, Volume and Issue: 42(21), P. 11612 - 11628

Published: Sept. 29, 2023

AbstractIn-silico techniques offer a fast, accurate, reliable, and economical approach to studying the molecular interactions between compounds proteins. In this study, our main aim is use in-silico as rational for prediction of drug targets luteolin against Plasmodium falciparum. Multi-target docking, 100 nanoseconds (ns) dynamics (MD) simulations, Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) binding free energy calculations were carried out dihydrofolate reductase thymidylate synthase (PfDHFR-TS), dihydroorotate dehydrogenase (PfDHODH), falcipain-2. The native ligands each protein used reference evaluate performance luteolin. Luteolin outperformed all proteins at docking MD simulations studies. However, in MM-GBSA calculations, ligand only PfDHFR-TS but not PfDHODH Among studied proteins, predicted most favorable target luteolin.Communicated by Ramaswamy H. SarmaKeywords: Drug targetsluteolinMD simulationsmolecular dockingPlasmodium falciparum AcknowledgmentsJames Zothantluanga grateful University Grants Commission Ministry Tribal Affairs, Government India awarding UGC-SRF (Award No: 202122-NFST-MIZ-03095) support his Ph.D. research project. authors are thankful Universitas Tadulako, Indonesia providing computational facilities carry simulations.Authors' contributionsStudy design: JHZ; Software: JHZ, AKU, KA; Result analysis interpretation: KA, DC, SR; Drafting: AKUDisclosure statementNo potential conflict interest was reported author(s).Data availability statementAny data will be made available upon reasonable request corresponding author.Additional informationFundingThe author(s) there no funding associated with work featured article.

Language: Английский

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