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New Insights in Artificial Intelligence for Drug Design and Target Discovery

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

Deadline for manuscript submissions: 20 November 2025 | Viewed by 312

Special Issue Editor


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Guest Editor
School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: artificial intelligence in drug design; computational biology; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Artificial intelligence (AI)-based technologies are having a transformative impact on drug design research. With the advancement of biomedical research, the integration of AI with traditional methodologies is unlocking innovative approaches to address complex challenges in drug development.

In recent years, emerging multimodal large language models, including text-based and biological data-driven foundational models, have become powerful tools for analyzing biomedical text and extracting valuable information on proteins, nucleic acids, and chemical compounds. These models facilitate the identification of novel drug candidates and accelerate biomolecule target discovery. Deep generative models represent another frontier in drug design, enabling the creation of novel chemical entities with desired properties. Furthermore, integrating multi-omics data with AI methods is crucial for understanding drug responses, identifying biomarkers, and discovering potential drug combinations. AI-based network analysis methods are also bridging traditional Chinese medicine (TCM) with modern approaches, unveiling complex disease treatment mechanisms.

We invite researchers to contribute original research articles and review papers that explore the promising applications of AI in the fields of biology and medicine. This Special Issue aims at providing novel insights into the evolving research paradigms of drug design and target discovery by integrating diverse AI methodologies, computational biology techniques, and bioinformatics.

Topics of interest include, but are not limited to, the following:

  1. Applications of large pre-trained language models in drug design;
  2. Drug design using deep generative models;
  3. New drug prediction frameworks based on deep learning;
  4. Prediction of biomolecule binding sites;
  5. Application of multi-omics analysis and AI methods in drug design;
  6. Integration of QSAR modeling, virtual screening, molecular dynamics (MD) simulations, and AI models (e.g., AlphaFold or ESMFold) in drug discovery;
  7. Design and prediction of bioactive peptides;
  8. Applications of AI-based network analysis in traditional Chinese medicine (TCM) research.

Dr. Yanjing Wang
Guest Editor

Manuscript Submission Information

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Keywords

  • pre-trained language models
  • generative models
  • drug prediction
  • binding site prediction
  • peptides
  • multi-omics
  • deep learning
  • QSAR modeling
  • molecular dynamics (MD) simulations

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Published Papers (1 paper)

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Research

44 pages, 18191 KiB  
Article
A Multi-Modal Graph Neural Network Framework for Parkinson’s Disease Therapeutic Discovery
by Ömer Akgüller, Mehmet Ali Balcı and Gabriela Cioca
Int. J. Mol. Sci. 2025, 26(9), 4453; https://doi.org/10.3390/ijms26094453 - 7 May 2025
Viewed by 20
Abstract
Parkinson’s disease (PD) is a complex neurodegenerative disorder lacking effective disease-modifying treatments. In this study, we integrated large-scale protein–protein interaction networks with a multi-modal graph neural network (GNN) to identify and prioritize multi-target drug repurposing candidates for PD. Network analysis and advanced clustering [...] Read more.
Parkinson’s disease (PD) is a complex neurodegenerative disorder lacking effective disease-modifying treatments. In this study, we integrated large-scale protein–protein interaction networks with a multi-modal graph neural network (GNN) to identify and prioritize multi-target drug repurposing candidates for PD. Network analysis and advanced clustering methods delineated functional modules, and a novel Functional Centrality Index was employed to pinpoint key nodes within the PD interactome. The GNN model, incorporating molecular descriptors, network topology, and uncertainty quantification, predicted candidate drugs that simultaneously target critical proteins implicated in lysosomal dysfunction, mitochondrial impairment, synaptic disruption, and neuroinflammation. Among the top hits were compounds such as dithiazanine, ceftolozane, DL-α-tocopherol, bromisoval, imidurea, medronic acid, and modufolin. These findings provide mechanistic insights into PD pathology and demonstrate that a polypharmacology approach can reveal repurposing opportunities for existing drugs. Our results highlight the potential of network-based deep learning frameworks to accelerate the discovery of multi-target therapies for PD and other multifactorial neurodegenerative diseases. Full article
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