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For: Ai D, Cai H, Wei J, Zhao D, Chen Y, Wang L. DEEPCYPs: A deep learning platform for enhanced cytochrome P450 activity prediction. Front Pharmacol 2023;14:1099093. [PMID: 37101544 PMCID: PMC10123292 DOI: 10.3389/fphar.2023.1099093] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/31/2023] [Indexed: 04/28/2023]  Open
Number Cited by Other Article(s)
1
Chen L, Li B, Chen Y, Lin M, Zhang S, Li C, Pang Y, Wang L. ADCNet: a unified framework for predicting the activity of antibody-drug conjugates. Brief Bioinform 2025;26:bbaf228. [PMID: 40421657 DOI: 10.1093/bib/bbaf228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 02/25/2025] [Accepted: 04/28/2025] [Indexed: 05/28/2025]  Open
2
Bhattacharjee A, Kumar A, Ojha PK, Kar S. Artificial intelligence to predict inhibitors of drug-metabolizing enzymes and transporters for safer drug design. Expert Opin Drug Discov 2025;20:621-641. [PMID: 40241626 DOI: 10.1080/17460441.2025.2491669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 04/07/2025] [Indexed: 04/18/2025]
3
Permadi EE, Watanabe R, Mizuguchi K. Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning. J Cheminform 2025;17:66. [PMID: 40307863 PMCID: PMC12044814 DOI: 10.1186/s13321-025-01015-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 04/13/2025] [Indexed: 05/02/2025]  Open
4
Han H, Shaker B, Lee JH, Choi S, Yoon S, Singh M, Basith S, Cui M, Ahn S, An J, Kang S, Yeom MS, Choi S. Employing Automated Machine Learning (AutoML) Methods to Facilitate the In Silico ADMET Properties Prediction. J Chem Inf Model 2025;65:3215-3225. [PMID: 40085003 PMCID: PMC12004515 DOI: 10.1021/acs.jcim.4c02122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 03/07/2025] [Accepted: 03/07/2025] [Indexed: 03/16/2025]
5
Zhao D, Zhang Y, Chen Y, Li B, Zhou W, Wang L. Highly Accurate and Explainable Predictions of Small-Molecule Antioxidants for Eight In Vitro Assays Simultaneously through an Alternating Multitask Learning Strategy. J Chem Inf Model 2024;64:9098-9110. [PMID: 38888465 DOI: 10.1021/acs.jcim.4c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
6
Wei Y, Palazzolo L, Ben Mariem O, Bianchi D, Laurenzi T, Guerrini U, Eberini I. Investigation of in silico studies for cytochrome P450 isoforms specificity. Comput Struct Biotechnol J 2024;23:3090-3103. [PMID: 39188968 PMCID: PMC11347072 DOI: 10.1016/j.csbj.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/28/2024]  Open
7
Ambe K, Nakamori M, Tohno R, Suzuki K, Sasaki T, Tohkin M, Yoshinari K. Machine Learning-Based In Silico Prediction of the Inhibitory Activity of Chemical Substances Against Rat and Human Cytochrome P450s. Chem Res Toxicol 2024;37:1843-1850. [PMID: 39427263 DOI: 10.1021/acs.chemrestox.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
8
Lin M, Cai J, Wei Y, Peng X, Luo Q, Li B, Chen Y, Wang L. MalariaFlow: A comprehensive deep learning platform for multistage phenotypic antimalarial drug discovery. Eur J Med Chem 2024;277:116776. [PMID: 39173285 DOI: 10.1016/j.ejmech.2024.116776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
9
Zonyfar C, Ngnamsie Njimbouom S, Mosalla S, Kim JD. GTransCYPs: an improved graph transformer neural network with attention pooling for reliably predicting CYP450 inhibitors. J Cheminform 2024;16:119. [PMID: 39472986 PMCID: PMC11524008 DOI: 10.1186/s13321-024-00915-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 10/10/2024] [Indexed: 11/02/2024]  Open
10
Fang J, Tang Y, Gong C, Huang Z, Feng Y, Liu G, Tang Y, Li W. Prediction of Cytochrome P450 Substrates Using the Explainable Multitask Deep Learning Models. Chem Res Toxicol 2024;37:1535-1548. [PMID: 39196814 DOI: 10.1021/acs.chemrestox.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
11
Boonyarit B, Yamprasert N, Kaewnuratchadasorn P, Kinchagawat J, Prommin C, Rungrotmongkol T, Nutanong S. GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. J Comput Chem 2024;45:2001-2023. [PMID: 38713612 DOI: 10.1002/jcc.27388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/09/2024]
12
Zahid H, Tayara H, Chong KT. Harnessing machine learning to predict cytochrome P450 inhibition through molecular properties. Arch Toxicol 2024;98:2647-2658. [PMID: 38619593 DOI: 10.1007/s00204-024-03756-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
13
Arav Y. Advances in Modeling Approaches for Oral Drug Delivery: Artificial Intelligence, Physiologically-Based Pharmacokinetics, and First-Principles Models. Pharmaceutics 2024;16:978. [PMID: 39204323 PMCID: PMC11359797 DOI: 10.3390/pharmaceutics16080978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024]  Open
14
Hossam Abdelmonem B, Abdelaal NM, Anwer EKE, Rashwan AA, Hussein MA, Ahmed YF, Khashana R, Hanna MM, Abdelnaser A. Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review. Biomedicines 2024;12:1467. [PMID: 39062040 PMCID: PMC11275228 DOI: 10.3390/biomedicines12071467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024]  Open
15
Gong C, Feng Y, Zhu J, Liu G, Tang Y, Li W. Evaluation of machine learning models for cytochrome P450 3A4, 2D6, and 2C9 inhibition. J Appl Toxicol 2024;44:1050-1066. [PMID: 38544296 DOI: 10.1002/jat.4601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 07/21/2024]
16
Zhao D, Huang P, Yu L, He Y. Pharmacokinetics-Pharmacodynamics Modeling for Evaluating Drug-Drug Interactions in Polypharmacy: Development and Challenges. Clin Pharmacokinet 2024;63:919-944. [PMID: 38888813 DOI: 10.1007/s40262-024-01391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2024] [Indexed: 06/20/2024]
17
Chen Z, Zhang L, Zhang P, Guo H, Zhang R, Li L, Li X. Prediction of Cytochrome P450 Inhibition Using a Deep Learning Approach and Substructure Pattern Recognition. J Chem Inf Model 2024;64:2528-2538. [PMID: 37864562 DOI: 10.1021/acs.jcim.3c01396] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2023]
18
Almehizia AA, Aboulthana WM, Naglah AM, Hassan AS. In vitro biological studies and computational prediction-based analyses of pyrazolo[1,5-a]pyrimidine derivatives. RSC Adv 2024;14:8397-8408. [PMID: 38476172 PMCID: PMC10928850 DOI: 10.1039/d4ra00423j] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024]  Open
19
Wiraswati HL, Bashari MH, Alfarafisa NM, Ma’ruf IF, Sholikhah EN, Wahyuningsih TD, Satriyo PB, Mustofa M, Satria D, Damayanti E. Pyrazoline B-Paclitaxel or Doxorubicin Combination Drugs Show Synergistic Activity Against Cancer Cells: In silico Study. Adv Appl Bioinform Chem 2024;17:33-46. [PMID: 38435441 PMCID: PMC10908341 DOI: 10.2147/aabc.s452281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/10/2024] [Indexed: 03/05/2024]  Open
20
Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci 2024;45:39-55. [PMID: 38072723 DOI: 10.1016/j.tips.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
21
Lv Q, Zhou F, Liu X, Zhi L. Artificial intelligence in small molecule drug discovery from 2018 to 2023: Does it really work? Bioorg Chem 2023;141:106894. [PMID: 37776682 DOI: 10.1016/j.bioorg.2023.106894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
22
Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023;28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023]  Open
23
Durgam L, Pagag J, Indra Neela Y, Guruprasad L. Mutational analyses, pharmacophore-based inhibitor design and in silico validation for Zika virus NS3-helicase. J Biomol Struct Dyn 2023;42:9873-9891. [PMID: 37712848 DOI: 10.1080/07391102.2023.2252929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
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