Drug-target interactions underlie the actions of chemical substances in medicine. Moreover, drug repurposing can expand use profiles while reducing costs and development time by exploiting potential multi-functional pharmacological properties based upon additional target interactions. Nonetheless, drug repurposing relies on the accurate identification and validation of drug-target interactions (DTIs). In this study, a novel drug-target interaction prediction model was developed. The model, based on an interactive inference network, contains embedding, encoding, interaction, feature extraction, and output layers. In addition, this study used Morgan and PubChem molecular fingerprints as additional information for drug encoding. The interaction layer in our model simulates the drug-target interaction process, which assists in understanding the interaction by representing the interaction space. Our method achieves high levels of predictive performance, as well as interpretability of drug-target interactions. Additionally, we predicted and validated 22 Alzheimer's disease-related targets, suggesting our model is robust and effective and thus may be beneficial for drug repurposing.
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http://dx.doi.org/10.3390/ijms25147753 | DOI Listing |
Elife
January 2025
State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
Viral adhesion to host cells is a critical step in infection for many viruses, including monkeypox virus (MPXV). In MPXV, the H3 protein mediates viral adhesion through its interaction with heparan sulfate (HS), yet the structural details of this interaction have remained elusive. Using AI-based structural prediction tools and molecular dynamics (MD) simulations, we identified a novel, positively charged α-helical domain in H3 that is essential for HS binding.
View Article and Find Full Text PDFChem Soc Rev
January 2025
School of Chemistry, Pharmacy & Pharmacology, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development of cryo-EM and protein structure prediction with tools such as RosettaFold and AlphaFold.
View Article and Find Full Text PDFGut Microbes
December 2025
APC Microbiome Ireland, University College Cork, Cork, Ireland.
is a major cause of nosocomial diarrhea. As current antibiotic treatment failures and recurrence of infections are highly frequent, alternative strategies are needed for the treatment of this disease. This study explores the use of bacteriocins, specifically lacticin 3147 and pediocin PA-1, which have reported inhibitory activity against .
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China.
Tryptophan participates in important life activities and is involved in various metabolic processes. The indole and aromatic binuclear ring structure in tryptophan can engage in diverse interactions, including π-π, π-alkyl, hydrogen bonding, cation-π, and CH-π interactions with other side chains and protein targets. These interactions offer extensive opportunities for drug development.
View Article and Find Full Text PDFComb Chem High Throughput Screen
January 2025
Shanghai Key Laboratory of Molecular Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai 201318, China.
Objective: Colorectal Cancer (CRC) has attracted much attention due to its high mortality and morbidity. Cordycepin, also known as 3'-deoxyadenosine (3'-dA), exhibits many biological functions, including antibacterial, anti-inflammatory, antiviral, anti-tumor, and immunomodulatory effects. It has been proven to show anticancer activity in both laboratory research studies and living organisms.
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