Towards designing of some potential new autoimmune disorder inhibitors using crystal structures and Hirshfeld surface analyses in combination with molecular docking and molecular dynamics simulations

Edache, Emmanuel Israel; Uzairu, Adamu; Mamza, Paul Andrew; Shallangwa, Gideon Adamu; Ibrahim, Muhammad Tukur

doi:10.1016/j.ipha.2023.11.008

Intelligent Pharmacy

2024

DOI: 10.1016/j.ipha.2023.11.008

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Towards designing of some potential new autoimmune disorder inhibitors using crystal structures and Hirshfeld surface analyses in combination with molecular docking and molecular dynamics simulations

Emmanuel Israel Edache,

Adamu Uzairu,

Paul Andrew Mamza

et al.

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2024

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Cited by 3 publications

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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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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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show abstract

First report on exploration of structural features of natural compounds (NPACT database) for anti-breast cancer activity (MCF-7): QSAR-based virtual screening, molecular docking, ADMET, MD simulation, and DFT studies

Banjare,

Murmu,

Pandey

et al. 2024

In Silico Pharmacol.

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DFT studies on structure, electronics, bonding nature, NBO analysis, thermodynamic properties, molecular docking, and MM-GBSA evaluation of 4-methyl-3-[2-(4-nitrophenyl)-1,3-dioxo-2,3-dihydro-1H-isoindole-5-amido]benzoic acid: a potent inhibitor of Graves’ disease

Edache,

Uzairu,

Mamza

et al. 2024

J.Umm Al-Qura Univ. Appll. Sci.

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A calculation analysis on the molecular structure and energy of 4-methyl-3-[2-(4-nitrophenyl)-1,3-dioxo-2,3-dihydro-1H-isoindole-5-amido]benzoic acid (COD30) is carried out with the 6-311G (d,p) basis set by the DFT/RB3LYP method as an anti-graves' disease treatment. The calculated FT-IR spectrum is strongly correlated with the vibrational spectra reported in the literature. To evaluate the entire electron density and organic reactive sites of COD30, molecular electrostatic potential (MEP) and frontier molecular orbitals (FMO) were analyzed. The density of states analysis is used to determine the orbital molecular contributions (DOS and PDOS). In comparison to methimazole (MMI) and propylthiouracil, COD30 showed more encouraging docking results, and it also offered golden binding contacts in addition to an improvement in docking energy (PTU). The outcomes of bioactivity prediction and MD simulation indicate that COD30 could be further developed into an inhibitor of Graves' disease.

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Towards designing of some potential new autoimmune disorder inhibitors using crystal structures and Hirshfeld surface analyses in combination with molecular docking and molecular dynamics simulations

Cited by 3 publications

References 64 publications

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

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

First report on exploration of structural features of natural compounds (NPACT database) for anti-breast cancer activity (MCF-7): QSAR-based virtual screening, molecular docking, ADMET, MD simulation, and DFT studies

DFT studies on structure, electronics, bonding nature, NBO analysis, thermodynamic properties, molecular docking, and MM-GBSA evaluation of 4-methyl-3-[2-(4-nitrophenyl)-1,3-dioxo-2,3-dihydro-1H-isoindole-5-amido]benzoic acid: a potent inhibitor of Graves’ disease

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