Computational methods in drug discovery

Scholarly Works

• Uslu, H.; Das, B.; Dagdogen, H. A.; Santur, Y.; Yılmaz, S.; Turkoglu, I.; Das, R. Discovery of new anti-HIV candidate molecules with an AI-based multi-stage system approach using molecular docking and ADME predictions. Chemometrics and Intelligent Laboratory Systems 2025, 267, 105543. doi:10.1016/j.chemolab.2025.105543
• Huang, X.; Ting, L.; Dao, T.-K.; Nguyen, T.-X.-H.; Nguyen, T.-T. Optimizing the Drug Discovery Pipeline: A Multi-objective Approach with Genetic Algorithms. Smart Innovation, Systems and Technologies; Springer Nature Singapore, 2025; pp 81–92. doi:10.1007/978-981-96-4434-6_8
• Kumar, D.; Jangir, M.; Sharma, G. C.; Yadav, V.; Sharma, V. Evaluation of cytotoxic and antibacterial activities of multiple compound groups against A549 lung cancer cells and clinically relevant Bacteria. Results in Chemistry 2025, 18, 102863. doi:10.1016/j.rechem.2025.102863
• Soh-Kamdjo, C.; González-Montero, M.-C.; García-Estrada, C.; Melcón-Fernández, E.; Fernández-Rubio, C.; Pérez-Pertejo, Y.; Reguera, R. M.; Balaña-Fouce, R. Discovery of Potential Antileishmanial Compounds Through Phenotypic Screening of an Alkaloid Library. Molecules (Basel, Switzerland) 2025, 30, 4210. doi:10.3390/molecules30214210
• Pala, M. A. XP-GCN: Extreme learning machines and parallel graph convolutional networks for high-throughput prediction of blood-brain barrier penetration based on feature fusion. Computational biology and chemistry 2025, 120, 108755. doi:10.1016/j.compbiolchem.2025.108755
• Tulum, Ö.; Lazonick, W. Cambridge University Press, 2025. doi:10.1017/9781009708012
• Ahmmed, M. S.; Hossan, R.; Ripu, T. R.; Rahman, T.; Alshahrani, M. Y.; Mia, E.; Mandal, P.; Al Hasan, M. S.; Rahaman, M. M.; Islam, M. T. Assessment of antiemetic potential of schaftoside through modulation of dopaminergic, serotonergic and muscarinic signaling pathways: in vivo and in silico investigations. Naunyn-Schmiedeberg's archives of pharmacology 2025. doi:10.1007/s00210-025-04714-7
• Oliveira, J. M. V.; da Silva, A. D.; Soares, A. M. D. S.; de Azevedo, W. F. Molegro Virtual Docker for Docking Screens. Methods in molecular biology (Clifton, N.J.) 2025, 2984, 139–152. doi:10.1007/978-1-0716-4949-7_10
• Pirie, R.; Hall, S. J.; Cole, D. J.; Murphy, T. Riemannian geometry and molecular similarity II: Kähler quantization. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2025, 481. doi:10.1098/rspa.2024.0707
• Shu, X.; Zhu, Y.; Liu, X.; Li, Y.; Yi, B.; Wang, Y. Applications of artificial intelligence in anesthesiology. Anesthesiology and Perioperative Science 2025, 3. doi:10.1007/s44254-025-00131-4
• Dilek, Ö.; Dükel, M.; Zarzour, F.; Karabacak Atay, Ç.; Tilki, T. Structure-activity optimization of Deferasirox-derived aroyl hydrazones: Synthesis, DFT characterization, and mechanistic insights into selective anticancer activity against colon and breast cancer. Bioorganic chemistry 2025, 165, 109061. doi:10.1016/j.bioorg.2025.109061
• Asma, N.; Ramadon, D.; Alwi, R. S.; Mun'im, A. Unraveling new strategies of natural products drug development using deep eutectic solvents: A comprehensive review. Journal of Molecular Liquids 2025, 436, 128257. doi:10.1016/j.molliq.2025.128257
• Garrido-Palazuelos, L. I.; Aguirre-Sánchez, J. R.; Guerra-Meza, O.; Medrano-Félix, J. A.; Sandoval-González, M. F. In Silico Evaluations of the Anticancer Potential of Anthocyanins. Molecular Mechanisms of Action of Polyphenols Against Cancer; Springer Nature Switzerland, 2025; pp 205–230. doi:10.1007/978-3-031-99601-6_9
• Khanna, R.; Pandey, G.; Varshney, V. K. Molecular Docking‐Based Investigation of Antioxidant, Antidiabetic, and Anti‐inflammatory Activities of Bioactive Compounds Identified from Cupressus Torulosa Needles. ChemistrySelect 2025, 10. doi:10.1002/slct.202501052
• Kaushik, A.; Kaushik, J. J.; Lal, N. Phytochemicals and Molecular Docking: A Futuristic Approach for Drug Discovery. Trends in Pharmacology and Toxicology 2025, 1, 49–55. doi:10.21124/tpt.2025.49.55
• Hao, Z.; Han, J.; Zhang, Y.; Zhang, X.; Li, K.; Chen, H.; Wang, Z.; Gao, W.; Tang, L.; Fan, Z. Discovery of Aromatic Amide Derivatives Bearing Oxime Ethers Targeting Succinate Dehydrogenase. Journal of agricultural and food chemistry 2025, 73, 25194–25202. doi:10.1021/acs.jafc.5c02252
• Bosîi, D.; Torres, L. H. M.; Arrais, J. P.; Ribeiro, B. Convolutional Spiking Neural Networks with Molecular Fingerprints for Drug Discovery. Lecture Notes in Computer Science; Springer Nature Switzerland, 2025; pp 375–387. doi:10.1007/978-3-032-05176-9_29
• Mishra, J.; Tripathi, A. K.; Sharma, S.; Mayank; Sahu, A.; Khan, A. A.; Fatima, S.; Ahmad, A. Structural and dynamic implications of the R136H mutation in DNA GyrB: insights into antimicrobial resistance and novobiocin efficacy. New Journal of Chemistry 2025, 49, 15911–15922. doi:10.1039/d5nj00427f
• Dayanand, N. D.; Devi, V.; Kabbekodu, S. P.; Amuthan, A.; Pai B, S.; Chinta, R. Phytochemical and pharmacoinformatics analysis of a traditional antipsoriatic oil formulation for its potential against proinflammatory cytokines TNF-α and IL-17A. PloS one 2025, 20, e0330939. doi:10.1371/journal.pone.0330939
• Banerjee, A.; Paul, S.; Seth, A.; Debnath, B.; Kumar, A.; Das, S. Compound isolation followed by anti-inflammatory bioactivity-based ADME study, network pharmacology, molecular docking and MD simulation reveals a novel O-methylated flavonol, Ombuin from Ipomoea batatas whole plant. Pharmacological Research - Natural Products 2025, 8, 100284. doi:10.1016/j.prenap.2025.100284

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