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Molecular Modeling: Latest Advances and Applications, 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 643

Special Issue Editors


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Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
Interests: molecular modeling; molecular dynamics simulations; modeling of biomolecules and their interactions
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Department DAFAB, Faculty of Biology, University of Bucharest, Splaiul Independenței 91-95, Bucharest, Romania
Interests: molecular modeling; QSAR; bovine serum albumin; hepatitis virus; computational mutagenesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in computational power, algorithmic efficiency, and interdisciplinary collaborations have led to significant breakthroughs in molecular modeling. The goal of this Special Issue is to highlight state-of-the-art research in molecular modeling and its applications in a variety of fields, including new material development and pharmaceuticals. The contributions in this Special Issue highlight the critical role that molecular modeling plays in deepening our understanding of complex molecular systems by examining fresh approaches, theoretical discoveries, and practical applications of this field. This Special Issue offers an overview of current trends, difficulties, and future directions in molecular modeling, offering insightful viewpoints for researchers, practitioners, and educators alike.

Dr. Maria Alexandra Mernea
Prof. Dr. Dan Florin Mihǎilescu
Guest Editors

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Keywords

  • molecular modeling
  • computational chemistry
  • drug design
  • material science
  • biomolecular interactions
  • algorithmic advances
  • theoretical chemistry
  • simulation techniques
  • predictive modeling
  • interdisciplinary applications

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Published Papers (1 paper)

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Research

12 pages, 2768 KB  
Article
Molecular Mechanisms of Phthalates in Depression: An Analysis Based on Network Toxicology and Molecular Docking
by Ruiqiu Zhang, Hairuo Wen, Zhi Lin, Bo Li, Xiaobing Zhou and Qingli Wang
Int. J. Mol. Sci. 2025, 26(17), 8215; https://doi.org/10.3390/ijms26178215 - 24 Aug 2025
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Abstract
This study investigated the molecular mechanisms by which phthalates induce depression, utilizing network toxicology and molecular docking techniques. By integrating the TargetNet, GeneCards, and PharmMapper databases, 658 potential target genes of phthalates were identified. Additionally, 5433 depression-related targets were retrieved from the GeneCards [...] Read more.
This study investigated the molecular mechanisms by which phthalates induce depression, utilizing network toxicology and molecular docking techniques. By integrating the TargetNet, GeneCards, and PharmMapper databases, 658 potential target genes of phthalates were identified. Additionally, 5433 depression-related targets were retrieved from the GeneCards and OMIM databases. Comparative analysis revealed 360 common targets implicated in both phthalate action and depression. A Protein-Protein Interaction (PPI) network was constructed using the STRING database. Subsequently, the CytoHubba plugin (employing the MCC algorithm) within Cytoscape was used to screen the network, identifying the top 20 hub genes. These core genes include AKT1, CASP3, TNF, TP53, BCL2, and IL6, among others. Validation on the GEO dataset (GSE23848) revealed that the expression of multiple core genes was significantly upregulated in patients with depression (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that phthalates mainly regulate biological processes such as extracellular stimulus response, lipopolysaccharide metabolism, and chemical synaptic transmission. Depression is mediated by the AGE-RAGE signaling pathway (a complication of diabetes), lipids and atherosclerosis, Endocrine resistance, and the PI3K-Akt signaling pathway. Molecular docking confirmed that phthalates have strong binding activity with key targets (CASP3, TNF, TP53, BCL2, IL6). These findings present a novel paradigm for evaluating the health risks posed by environmental pollutants. Full article
(This article belongs to the Special Issue Molecular Modeling: Latest Advances and Applications, 2nd Edition)
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