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This study evaluated the utility of an integrated drug discovery strategy that combines three emerging data-driven approaches: real-world data analysis, in silico screening, and network pharmacology. First, transcriptomic data from public gene expression databases and adverse event reports were analyzed to address myocarditis induced by immune checkpoint inhibitors. The findings suggested a preventive effect of non-steroidal anti-inflammatory drugs, particularly those targeting the arachidonic acid metabolism pathway. Second, to identify therapeutic options for trastuzumab-resistant HER2-positive breast cancer, a cheminformatics approach was applied. A machine learning classification model and structure-based docking simulations enabled efficient in silico screening of approved drugs, identifying novel YES1 kinase inhibitors. Third, network-based analysis evaluated the topological distance between disease-associated gene modules and statin-induced gene modules in drug-induced peripheral neuropathy. This analysis indicated that certain statins may protect against drug-induced peripheral neuropathy through modulation of shared targets and neurodegenerative pathways. These findings demonstrate that integrating heterogeneous data modalities-from transcriptomics and chemical structure to protein-protein interaction networks and real-world clinical observations-can enable the discovery of repositioning candidates and risk-mitigating therapies. The study highlights the potential of multi-layered, data-driven strategies in constructing translational drug discovery frameworks aimed at both efficacy and safety.
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http://dx.doi.org/10.1254/fpj.25037 | DOI Listing |
Anal Chem
September 2025
Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
DNA-encoded libraries have become widely used in drug discovery, and several different setups to link chemical compounds to DNA have been employed in the field, including single-stranded and double-stranded DNA tags as well as a variety of linker chemistries. In our previous study, we observed distinct differences in binding affinities between ligands coupled either to single-stranded or double-stranded DNA; however, the molecular basis for these differences remained unclear. Here, we present a native ion mobility mass spectrometry approach that incorporates gas- and solution-phase activation techniques to systematically investigate these differences, specifically the impact of DNA tags on binding performance in protein-ligand interactions.
View Article and Find Full Text PDFPLoS One
September 2025
School of Mechanical and Automotive Engineering, Qingdao University of Technology, Qingdao, Shandong, China.
Drug-target interaction (DTI) prediction is essential for the development of novel drugs and the repurposing of existing ones. However, when the features of drug and target are applied to biological networks, there is a lack of capturing the relational features of drug-target interactions. And the corresponding multimodal models mainly depend on shallow fusion strategies, which results in suboptimal performance when trying to capture complex interaction relationships.
View Article and Find Full Text PDFChemMedChem
September 2025
Laboratorio de Síntesis Orgánica, Facultad de Farmacia, Universidad Central de Venezuela, Apartado 47206, Los Chaguaramos, Caracas, 1041-A, Venezuela.
Due to the advantages of drug repurposing, the discovery of new chemotherapeutic agents for the treatment of Chagas disease based on approved drugs has become a strategy for identifying new candidates. In this work, the antidepressant drug sertraline is reported, with an IC of 7.8 ± 1.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
September 2025
State Key Laboratory of Bioactive Molecules and Druggability Assessment, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug De
Proliferative retinopathy is a leading cause of irreversible blindness in humans; however, the molecular mechanisms behind the immune cell-mediated retinal angiogenesis remain poorly elucidated. Here, using single-cell RNA sequencing in an oxygen-induced retinopathy (OIR) model, we identified an enrichment of sorting nexin (SNX)-related pathways, with SNX3, a member of the SNX family that is involved in endosomal sorting and trafficking, being significantly upregulated in the myeloid cell subpopulations of OIR retinas. Immunostaining showed that SNX3 expression is markedly increased in the retinal microglia/macrophages of mice with OIR, which is mainly located within and around the neovascular tufts.
View Article and Find Full Text PDFAppl Biochem Biotechnol
September 2025
School of Biological Sciences, University of the Punjab, Quaid-E-Azam Campus, P.O. 54590, Lahore, Pakistan.
Recombinant DNA technology is widely used to produce industrially and pharmaceutically important proteins. In silico analysis, performed before executing wet lab experiments has been greatly helpful in this connection. A shift in protein analysis has been observed over the past decade, driven by advancements in bioinformatics databases, tools, software, and web servers.
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