RETRACTED ARTICLE: Molecular docking simulation, drug-likeness assessment, and pharmacokinetic study of some cephalosporin analogues against a penicillin-binding protein of Salmonella typhimurium

Ameji, Philip John; Uzairu, Adamu; Shallangwa, Gideon Adamu

doi:10.1038/s41429-023-00598-y

Cited by 3 publications

(4 citation statements)

References 27 publications

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“…The target protein was further processed via the addition of Polar hydrogens and Kollman charges with the aid of Auto Dock Vina tool v1.5.7. Finally, the docking calculation between the ligands and the target DNA gyrase was performed using PyRx software of Auto Dock Vina tool by centring the Vina search space at X: -26.4401 Å, Y: 23.0598 Åand Z: 22.0813 Åwith dimensions of X: 51.6292 Å, Y: 53.0044 Åand Z: 51.8136 Å [26][27][33][34].…”

Section: Molecular Optimization and Docking Proceduresmentioning

confidence: 99%

“…Veber's rule, on the other hand stipulates that, for a drug to be orally bioavailable, the number of rotatable bonds (NRB) must be < 10 and topological polar surface area (TPSA) must be < 140 Å 2 . The NRB, TPSA, MW, HBD, HBA, and Log P value of the bioactive ligands were computed using the Swiss ADME (http: //www.swissadme.ch/www.swissadme.ch/) online tool [26][27][33][34].…”

Section: Drug-likeness Estimationmentioning

confidence: 99%

“…The phytochemicals were profiled for their gastrointestinal (GI) absorption, blood brain barrier (BBB) permeation, P-glycoprotein (P-gp) substrate potentials, and cytochrome-P450 enzymes inhibition using the Swiss ADME online server at http://www.swissadme.ch/ index.php. Furthermore, Osiris Data Warrior V5.5.0 chemoinformatics program was used to perform in silico toxicity assay on the ligands using the following toxicity endpoints; mutagenicity, reproductive effect, and irritating effect [26][27][33][34].…”

Section: Admet Profilingmentioning

confidence: 99%

“…This deals with the absorption, distribution, metabolism, excretion, and toxicity (i.e., ADMET) potentials of bioactive ligands. In silico ADMET profiling of drug candidates helps to minimize attrition rates during the preclinical and clinical stages of drug development [26][27][28].This study is aimed at isolation, characterization and application of in vitro & in silico techniques to explore the bioactive molecules present in Bulbs of Calotropisprocera.…”

Section: Introductionmentioning

confidence: 99%

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Isolation, Characterization, Antimicrobial and Theoretical Investigation of Some Bioactive Compounds Obtained from the Bulbs of Calotropisprocera

Khan,

Elum,

Ijeomah

et al. 2023

J. Nig. Soc. Phys. Sci.

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This study characterizes the bioactive molecules from the bulb of Calotropisprocera and investigates the antimicrobial activities of the crude extracts. Theoretical studies on the two isolated compounds in the crude extract were also accomplished.The bulbs were air dried, pulverized, and subjected to extraction procedures by maceration using 500 mL each of normal-hexane, ethyl acetate and methanol. The crude extracts were further tested onmicroorganisms and phytochemical screening using standard procedures. In addition, the bioactive compounds in the extract were screened against DNA gyrase of two Gram negative bacterial species; Escherichia coli and Salmonella typhiusing Molecular Docking simulation techniques and further subjected to ADMET profiling,using the Swiss ADME online server. The Crude ethyl acetate extract has the highest effective activity against Escherichia coli (MIC 2.5mg / mL and MBC/MFC 5mg / mL), Staphylococcus aureus (MIC 2.5mg/mL), Candida albicans, Salmonella typhiand Candida stellafoidea (MIC 5mg/mL). beta-Amyrin acetate and Taraxasterol are the two phytochemicals in the purified white crystalline fractions and were found to fasten to the active sites of DNA gyrase of the Gram negative bacterial species via hydrophobic and hydrogen bond interactions, with binding activity value of -9.6 kcal/mol and -9.5 kcal/mol, respectively. Also, ADMET investigations of the compounds revealed their sound oral bioavailability and excellent pharmacokinetic and toxicity profiles. The findings of this study could provide a platform for discovering safe and potent antibiotics against pathogenic microbes ravaging our society.

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Section: Molecular Optimization and Docking Proceduresmentioning

confidence: 99%

Section: Drug-likeness Estimationmentioning

confidence: 99%

Section: Admet Profilingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Isolation, Characterization, Antimicrobial and Theoretical Investigation of Some Bioactive Compounds Obtained from the Bulbs of Calotropisprocera

Khan,

Elum,

Ijeomah

et al. 2023

J. Nig. Soc. Phys. Sci.

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Investigation into the Quantitative Structure‐Biotoxicity Relationship of Antibiotics and their Estrogenic Receptor Disruption Effects

Zhu,

Chen,

Wang

et al. 2024

Chemistry & Biodiversity

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In light of antibiotics being classified as environmental hormone‐like compounds, their interference with the endocrine system has significantly impacted human health and ecological environments. This study employed Gaussian09 software's Density Functional Theory (DFT) to structurally optimize and perform frequency calculations on 23 representative antibiotic molecules, aiming to obtain microscopic quantum mechanical structural parameters.Physicochemical property parameters were acquired through the RDKit database in the ChemDes platform. Through multiple linear regression analysis, the primary factors affecting antibiotic biotoxicity (pLD50) were identified, leading to the establishment of a QSAR model. The predictive capability of the model was analyzed using leave‐one‐out cross‐validation, and molecular docking was used to investigate the binding mode and mechanism of action between estrogen receptors (ER) and antibiotics. Research outcomes indicate that the established QSAR model C has regression coefficients R2 and leave‐one‐out cross‐validation coefficients Q2 of 0.92474 and 0.74913, respectively, demonstrating good stability and predictive power. Analysis through molecular surface electrostatic potential, frontier molecular orbitals, molecular docking, and molecular dynamics revealed that the potential estrogenic disrupting effects are primarily due to hydrogen bonds and hydrophobic interactions between antibiotics and estrogen receptors. This provides a valuable exploration for identifying and screening PPCPs with potential estrogenic disrupting effects.

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The antibacterial, antioxidant and sun protection potential of a benzophenone from Dolichopentas decora (S. Moore)

Sekandi,

Namukobe,

Byamukama

et al. 2025

Pharmacological Research - Natural Products

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RETRACTED ARTICLE: Molecular docking simulation, drug-likeness assessment, and pharmacokinetic study of some cephalosporin analogues against a penicillin-binding protein of Salmonella typhimurium

Cited by 3 publications

References 27 publications

Isolation, Characterization, Antimicrobial and Theoretical Investigation of Some Bioactive Compounds Obtained from the Bulbs of Calotropisprocera

Isolation, Characterization, Antimicrobial and Theoretical Investigation of Some Bioactive Compounds Obtained from the Bulbs of Calotropisprocera

Investigation into the Quantitative Structure‐Biotoxicity Relationship of Antibiotics and their Estrogenic Receptor Disruption Effects

The antibacterial, antioxidant and sun protection potential of a benzophenone from Dolichopentas decora (S. Moore)

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