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Artificial Intelligence and Computer-Aided Design: Molecular Simulation Technology in Exploring Bioactive Compounds for Health Promotion

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

Deadline for manuscript submissions: 20 February 2026 | Viewed by 1913

Special Issue Editor


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Guest Editor
Food Science and Technology Program, Department of Life Sciences, Beijing Normal-Hong Kong Baptist University, Zhuhai 519087, China
Interests: food science; phytochemicals; nutraceuticals; pharmaceuticals; functional foods; molecular nutrition; cell biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the promotion of interdisciplinary theory, molecular simulation technology (MST) has evolved beyond its initial application in computer-aided drug design. The use of MST now extends to various areas focused on health benefits, including pharmacology, phytomedicine, ethnopharmacology, molecular nutrition, and ethnopharmacology, where it has attained an indispensable position in research concerning bioactive compounds and health promotion.

As an emerging research technique, MST is utilized to explore the interaction mechanisms and structure–activity relationships between bioactive compounds and human curing protein targets and between bioactive compounds and the environment. MST overcomes the limitations of traditional in vitro experimental methods, such as UV–vis spectroscopy, fluorescence spectroscopy, and electrochemical methods, which cannot directly display atomic-level interactions. MST includes molecular docking, molecular dynamics simulations, and quantum mechanics, enabling the precise and intuitive prediction of atomic-level bonding modes and revealing the details of mechanisms that are challenging to uncover through in vitro models.

Because of its ability to surpass the limitations of aimlessness, time-consuming processes and laborious scientific experiments, researchers are increasingly embracing MST to first conduct their research and later validate the simulated results. This Special Issue aims to compile the latest research and reviews about applying molecular MST in pharmacology, phytomedicine, ethnopharmacology, nutrition, food sciences, etc.

Prof. Dr. Baojun Xu
Guest Editor

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Keywords

  • molecular simulation
  • bioactive compounds
  • molecular docking
  • molecular dynamics
  • quantum mechanics
  • functional mechanisms

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Published Papers (2 papers)

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Research

24 pages, 3559 KB  
Article
Computational Discovery of Selective Carbonic Anhydrase IX (CA IX) Inhibitors via Pharmacophore Modeling and Molecular Simulations for Cancer Therapy
by Nahlah Makki Almansour
Int. J. Mol. Sci. 2025, 26(17), 8465; https://doi.org/10.3390/ijms26178465 - 30 Aug 2025
Viewed by 516
Abstract
Carbonic anhydrase IX (CA IX) is a transmembrane metalloenzyme that is increased in tumor cells under hypoxia and plays an important role in solid tumor acidification. It is a marker of tumor hypoxia and a prognostic factor in human malignancies. Given the critical [...] Read more.
Carbonic anhydrase IX (CA IX) is a transmembrane metalloenzyme that is increased in tumor cells under hypoxia and plays an important role in solid tumor acidification. It is a marker of tumor hypoxia and a prognostic factor in human malignancies. Given the critical role of CA IX and their over expression in many cancer tissues, they have emerged as a promising target for developing novel anticancer therapeutics. In this study we designed a pharmacophore model based on known inhibitors to screen small compound libraries to discover potential inhibitors of CA IX. Molecular docking experiments discovered that four compounds ZINC613262012, ZINC427910039, ZINC616453231, and DB00482 exhibited a strong binding affinity towards CA IX, mimicking the interaction pattern similar to native inhibitors. Molecular dynamics simulations and an MM-PBSA analysis revealed ZINC613262012, ZINC427910039, and DB00482 as the most potential and stable inhibitors with the binding free energies −10.92, −18.77, and −12.29 kcal/mol, respectively. In addition, DFT-based analyses supported their favorable electronic properties, further validating their potential as CA IX inhibitors. These three hits demonstrated a greater stability and compactness relative to the known inhibitors, suggesting these might be used CA IX inhibitors to treat tumors. Full article
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22 pages, 11543 KB  
Article
Molecular Mechanisms of Phytochemicals from Chaga Mushroom (Inonotus obliquus) Against Colorectal Cancer: Insights from Network Pharmacology, Molecular Docking, and Bioinformatics
by Yingzi Wu, Jiayin Liu, Jinhai Luo and Baojun Xu
Int. J. Mol. Sci. 2025, 26(16), 7664; https://doi.org/10.3390/ijms26167664 - 8 Aug 2025
Viewed by 866
Abstract
This study aimed to explore the molecular mechanisms of phytochemicals from Chaga mushroom (Inonotus obliquus) against colorectal cancer (CRC) using a combination of network pharmacology, molecular docking, and bioinformatics. Active components and targets of Chaga mushroom and CRC were collected from [...] Read more.
This study aimed to explore the molecular mechanisms of phytochemicals from Chaga mushroom (Inonotus obliquus) against colorectal cancer (CRC) using a combination of network pharmacology, molecular docking, and bioinformatics. Active components and targets of Chaga mushroom and CRC were collected from databases. A drug-compound-target-disease network was constructed, and protein–protein interaction (PPI) analysis was performed to identify core targets. KEGG and GO enrichment analyses were conducted to elucidate the involved pathways. Molecular docking estimated the binding affinities of key compounds to their targets, and bioinformatics analysis assessed differential gene expression and immune infiltration. The study identified 26 bioactive compounds and 244 potential targets. Core targets included AKT1, IFNG, and MMP9. Molecular docking showed strong binding affinities, and bioinformatics analysis revealed significant differential expression and immune infiltration patterns. These findings suggest that Chaga mushroom phytochemicals may exert anticancer effects through multiple pathways, highlighting their potential as novel CRC treatments. This study provides a comprehensive understanding of the molecular mechanisms underlying the anticancer effects of Chaga mushroom phytochemicals on CRC. Future research should focus on experimental validation and further exploration of their therapeutic potential. Full article
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