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Molecular Docking and Structure-Based Modeling

A Special Issue of International Journal of Molecular Sciences (ISSN 1422-0067) belonging to the section "Molecular Biology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 973

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Guest Editor
Department of Medical Pharmacology, Faculty of Medicine, Kırşehir Ahi Evran University, Kırşehir 40100, Turkey
Interests: plant; molecular biology

Special Issue Information

Dear Colleagues,

The main theme of this Special Issue is the application of molecular docking and structure-based drug design in the treatment of challenging diseases with poor medical options, such as cancer, neurological disorders, and infectious diseases. These diseases remain significant global health challenges due to their complex pathophysiological basis and limited treatment alternatives, despite significant advances in biomedical research. The aim of this Special Issue is to highlight recent advances in computational techniques that enhance the identification and optimization of novel therapeutic alternatives. Contributions related to molecular dynamics simulations, virtual screening, binding affinity estimation, and integrative modeling techniques will be particularly welcome. The scope also includes research using both experimental and computer-based methods. The goal is to create a comprehensive drug development platform by bringing together the latest research in this field and to foster collaboration across different disciplines to create more effective and personalized treatments.

Prof. Dr. Serap Yalçın Azarkan
Guest Editor

Manuscript Submission Information

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Keywords

  • molecular docking
  • structure-based drug design
  • challenging diseases
  • cancer
  • neurological disorders
  • infectious diseases
  • computational technique
  • binding affinity estimation
  • computer-based methods
  • personalized treatments

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Published Papers (1 paper)

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Research

24 pages, 8310 KB  
Article
Multifaceted Integrated Analysis of CDK1 and TOP2A Signaling Pathways for Multi-Target Therapeutic Intervention in Epithelial Ovarian Cancer
by Saber Samadiafshar, Mahla Masoudi, Hossein Azizi and Thomas Skutella
Int. J. Mol. Sci. 2026, 27(12), 5264; https://doi.org/10.3390/ijms27125264 - 10 Jun 2026
Viewed by 509
Abstract
Epithelial ovarian cancer (EOC) remains one of the most aggressive gynecological malignancies, largely due to late-stage diagnosis, therapeutic resistance, and molecular heterogeneity. This study aimed to identify biologically relevant hub genes and evaluate potential dual-target compounds against Cyclin-Dependent Kinase 1 (CDK1) and DNA [...] Read more.
Epithelial ovarian cancer (EOC) remains one of the most aggressive gynecological malignancies, largely due to late-stage diagnosis, therapeutic resistance, and molecular heterogeneity. This study aimed to identify biologically relevant hub genes and evaluate potential dual-target compounds against Cyclin-Dependent Kinase 1 (CDK1) and DNA Topoisomerase II Alpha (TOP2A) through an integrated computational framework. Transcriptomic datasets from GSE28799, GSE54388, and GSE14407 were analyzed to identify overlapping differentially expressed genes, followed by protein–protein interaction analysis, functional enrichment, survival assessment, molecular docking, ADMET profiling, and molecular dynamics simulations. Mechanistically, CDK1 and TOP2A participate in coordinated cell-cycle regulation associated with G2/M progression and chromosomal dynamics in ovarian cancer. Among the identified hub genes, CDK1 and TOP2A demonstrated marked overexpression and central topological importance within the interaction network. Functional enrichment analyses highlighted significant associations with mitotic cell-cycle regulation, DNA replication, and proliferative signaling pathways. Molecular docking analyses identified Naringin as a potential dual-target candidate with favorable binding affinity toward both CDK1 and TOP2A. ADMET profiling suggested acceptable pharmacokinetic and toxicity characteristics, while molecular dynamics simulations supported stable protein–ligand interactions under dynamic conditions. Although survival analyses did not demonstrate statistically significant independent prognostic associations, the findings support the biological relevance of CDK1 and TOP2A in EOC progression. Collectively, this study provides an integrated computational perspective on CDK1/TOP2A-associated oncogenic signaling and prioritizes Naringin as a preliminary candidate for future experimental investigation in epithelial ovarian cancer. Full article
(This article belongs to the Special Issue Molecular Docking and Structure-Based Modeling)
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