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Odugbemi AI, Nyirenda C, Christoffels A, Egieyeh SA. Artificial intelligence in antidiabetic drug discovery: The advances in QSAR and the prediction of α-glucosidase inhibitors. Comput Struct Biotechnol J 2024; 23:2964-2977. [PMID: 39148608 PMCID: PMC11326494 DOI: 10.1016/j.csbj.2024.07.003] [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: 04/16/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024] Open
Abstract
Artificial Intelligence is transforming drug discovery, particularly in the hit identification phase of therapeutic compounds. One tool that has been instrumental in this transformation is Quantitative Structure-Activity Relationship (QSAR) analysis. This computer-aided drug design tool uses machine learning to predict the biological activity of new compounds based on the numerical representation of chemical structures against various biological targets. With diabetes mellitus becoming a significant health challenge in recent times, there is intense research interest in modulating antidiabetic drug targets. α-Glucosidase is an antidiabetic target that has gained attention due to its ability to suppress postprandial hyperglycaemia, a key contributor to diabetic complications. This review explored a detailed approach to developing QSAR models, focusing on strategies for generating input variables (molecular descriptors) and computational approaches ranging from classical machine learning algorithms to modern deep learning algorithms. We also highlighted studies that have used these approaches to develop predictive models for α-glucosidase inhibitors to modulate this critical antidiabetic drug target.
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Affiliation(s)
- Adeshina I Odugbemi
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town 7535, South Africa
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town 7535, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), South Africa
| | - Clement Nyirenda
- Department of Computer Science, University of the Western Cape, Cape Town 7535, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town 7535, South Africa
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
| | - Samuel A Egieyeh
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town 7535, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), South Africa
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Zhao J, Xu P, Liu X, Ji X, Li M, Dev S, Qu X, Lu W, Niu B. Application of machine learning methods for the development of antidiabetic drugs. Curr Pharm Des 2021; 28:260-271. [PMID: 34161205 DOI: 10.2174/1381612827666210622104428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/10/2021] [Indexed: 11/22/2022]
Abstract
Diabetes is a chronic non-communicable disease caused by several different routes, which has attracted increasing attention. In order to speed up the development of new selective drugs, machine learning (ML) technology has been applied in the process of diabetes drug development, which opens up a new blueprint for drug design. This review provides a comprehensive portrayal of the application of ML in antidiabetic drug use.
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Affiliation(s)
- Juanjuan Zhao
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Pengcheng Xu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Xiujuan Liu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Xiaobo Ji
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Minjie Li
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Sooranna Dev
- Department of Obstetrics and Gynaecology, Imperial College London, Fulham Road, London SW10 9 NH, United Kingdom
| | - Xiaosheng Qu
- National Engineering Laboratory of Southwest Endangered Medicinal Resources Development, Guangxi Botanical Garden of Medicinal Plants, No. 189, Changgang Road, 530023, Nanning, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, 200444, China
| | - Bing Niu
- School of Life Sciences, Shanghai University, 200444, China
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Diéguez-Santana K, Rivera-Borroto OM, Puris A, Pham-The H, Le-Thi-Thu H, Rasulev B, Casañola-Martin GM. Beyond model interpretability using LDA and decision trees for α-amylase and α-glucosidase inhibitor classification studies. Chem Biol Drug Des 2019; 94:1414-1421. [PMID: 30908888 DOI: 10.1111/cbdd.13518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/17/2019] [Accepted: 03/03/2019] [Indexed: 12/17/2022]
Abstract
In this report are used two data sets involving the main antidiabetic enzyme targets α-amylase and α-glucosidase. The prediction of α-amylase and α-glucosidase inhibitory activity as antidiabetic is carried out using LDA and classification trees (CT). A large data set of 640 compounds for α-amylase and 1546 compounds in the case of α-glucosidase are selected to develop the tree model. In the case of CT-J48 have the better classification model performances for both targets with values above 80%-90% for the training and prediction sets, correspondingly. The best model shows an accuracy higher than 95% for training set; the model was also validated using 10-fold cross-validation procedure and through a test set achieving accuracy values of 85.32% and 86.80%, correspondingly. Additionally, the obtained model is compared with other approaches previously published in the international literature showing better results. Finally, we can say that the present results provided a double-target approach for increasing the estimation of antidiabetic chemicals identification aimed by double-way workflow in virtual screening pipelines.
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Affiliation(s)
| | - Oscar M Rivera-Borroto
- Departamento de Química Física Aplicada, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Amilkar Puris
- Facultad de Ciencias de La Ingeniería, Universidad Técnica Estatal de Quevedo, Quevedo, Ecuador
| | | | - Huong Le-Thi-Thu
- School of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota
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Santos CMM, Freitas M, Fernandes E. A comprehensive review on xanthone derivatives as α-glucosidase inhibitors. Eur J Med Chem 2018; 157:1460-1479. [PMID: 30282319 DOI: 10.1016/j.ejmech.2018.07.073] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/20/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022]
Abstract
α-Glucosidase plays an important role in carbohydrate metabolism and is therefore an attractive therapeutic target for the treatment of diabetes, obesity and other related complications. In the last two decades, considerable interest has been given to natural and synthetic xanthone derivatives in this field of research. Herein, a comprehensive review of the literature on xanthones as inhibitors of α-glucosidase activity, their mechanism of action, experimental procedures and structure-activity relationships have been reviewed for more than 280 analogs. With this overview we intend to motivate and challenge researchers (e.g. chemistry, biology, pharmaceutical and medicinal areas) for the design of novel xanthones as multipotent drugs and exploit the properties of this class of compounds in the management of diabetic complications.
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Affiliation(s)
- Clementina M M Santos
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal; Department of Chemistry, QOPNA &University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - Marisa Freitas
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Eduarda Fernandes
- LAQV, REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
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