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Fernandes PDO, Martins JPA, de Melo EB, de Oliveira RB, Kronenberger T, Maltarollo VG. Quantitative structure-activity relationship and machine learning studies of 2-thiazolylhydrazone derivatives with anti- Cryptococcus neoformans activity. J Biomol Struct Dyn 2022; 40:9789-9800. [PMID: 34121616 DOI: 10.1080/07391102.2021.1935321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryptococcus neoformans is a fungus responsible for infections in humans with a significant number of cases in immunosuppressed patients, mainly in underdeveloped countries. In this context, the thiazolylhydrazones are a promising class of compounds with activity against C. neoformans. The understanding of the structure-activity relationship of these derivatives could lead to the design of robust compounds that could be promising drug candidates for fungal infections. Specifically, modern techniques such as 4D-QSAR and machine learning methods were employed in this work to generate two QSAR models (one 2D and one 4D) with high predictive power (r2 for the test set equals to 0.934 and 0.831, respectively), and one random forest classification model was reported with Matthews correlation coefficient equals to 1 and 0.62 for internal and external validations, respectively. The physicochemical interpretation of selected models, indicated the importance of aliphatic substituents at the hydrazone moiety to antifungal activity, corroborating experimental data.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Philipe de Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - João Paulo A Martins
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo B de Melo
- Laboratório de Química Medicinal e Ambiental Teórica, Universidade Estadual do Oeste do Paraná, Cascavel, Paraná, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thales Kronenberger
- Department of Pneumonology and Oncology, Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Zhang Y, Luo M, Wu P, Wu S, Lee TY, Bai C. Application of Computational Biology and Artificial Intelligence in Drug Design. Int J Mol Sci 2022; 23:13568. [PMID: 36362355 PMCID: PMC9658956 DOI: 10.3390/ijms232113568] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 08/24/2023] Open
Abstract
Traditional drug design requires a great amount of research time and developmental expense. Booming computational approaches, including computational biology, computer-aided drug design, and artificial intelligence, have the potential to expedite the efficiency of drug discovery by minimizing the time and financial cost. In recent years, computational approaches are being widely used to improve the efficacy and effectiveness of drug discovery and pipeline, leading to the approval of plenty of new drugs for marketing. The present review emphasizes on the applications of these indispensable computational approaches in aiding target identification, lead discovery, and lead optimization. Some challenges of using these approaches for drug design are also discussed. Moreover, we propose a methodology for integrating various computational techniques into new drug discovery and design.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Mengqi Luo
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
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Lu Q. Identifying molecular structural features by pattern recognition methods. RSC Adv 2022; 12:17559-17569. [PMID: 35765452 PMCID: PMC9192268 DOI: 10.1039/d2ra00764a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022] Open
Abstract
Identification of molecular structural features is a central part of computational chemistry. It would be beneficial if pattern recognition techniques could be incorporated to facilitate the identification. Currently, the quantification of the structural dissimilarity is mainly carried out by root-mean-square-deviation (RMSD) calculations such as in molecular dynamics simulations. However, the RMSD calculation underperforms for large molecules, showing the so-called "curse of dimensionality" problem. Also, it requires consistent ordering of atoms in two comparing structures, which needs nontrivial effort to fulfill. In this work, we propose to take advantage of the point cloud recognition using convex hulls as the basis to recognize molecular structural features. Two advantages of the method can be highlighted. First, the dimension of the input data structure is largely reduced from the number of atoms of molecules to the number of atoms of convex hulls. Therefore, the dimensionality curse problem is avoided, and the atom ordering process is saved. Second, the construction of convex hulls can be used to define new molecular descriptors, such as the contact area of molecular interactions. These new molecular descriptors have different properties from existing ones, therefore they are expected to exhibit different behaviors for certain machine learning studies. Several illustrative applications have been carried out, which provide promising results for structure-activity studies.
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Affiliation(s)
- Qing Lu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
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Web-Based Quantitative Structure-Activity Relationship Resources Facilitate Effective Drug Discovery. Top Curr Chem (Cham) 2021; 379:37. [PMID: 34554348 DOI: 10.1007/s41061-021-00349-3] [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: 05/12/2021] [Accepted: 08/17/2021] [Indexed: 12/28/2022]
Abstract
Traditional drug discovery effectively contributes to the treatment of many diseases but is limited by high costs and long cycles. Quantitative structure-activity relationship (QSAR) methods were introduced to evaluate the activity of compounds virtually, which saves the significant cost of determining the activities of the compounds experimentally. Over the past two decades, many web tools for QSAR modeling with various features have been developed to facilitate the usage of QSAR methods. These web tools significantly reduce the difficulty of using QSAR and indirectly promote drug discovery. However, there are few comprehensive summaries of these QSAR tools, and researchers may have difficulty determining which tool to use. Hence, we systematically surveyed the mainstream web tools for QSAR modeling. This work may guide researchers in choosing appropriate web tools for developing QSAR models, and may also help develop more bioinformatics tools based on these existing resources. For nonprofessionals, we also hope to make more people aware of QSAR methods and expand their use.
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Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback? Int J Mol Sci 2021; 22:ijms22105212. [PMID: 34069090 PMCID: PMC8156896 DOI: 10.3390/ijms22105212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/01/2023] Open
Abstract
A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.
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Mendenhall J, Brown BP, Kothiwale S, Meiler J. BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. J Chem Inf Model 2020; 61:189-201. [PMID: 33351632 DOI: 10.1021/acs.jcim.0c01140] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We previously described BCL::Conf, a knowledge-based conformation sampling algorithm utilizing a small molecule fragment rotamer library derived from the Cambridge Structural Database (CSD, license required), as a component of the BioChemical Library (BCL) cheminformatics toolkit. This paper describes substantial improvements made to the BCL::Conf algorithm and a transition to a rotamer library derived from molecules in the Crystallography Open Database (COD, no license required). We demonstrate the performance of the new BCL::Conf on native conformer recovery in the Platinum dataset of high-quality protein-ligand complexes. This set of 2859 structures has previously been used to assess the performance of over a dozen conformer generation algorithms, including the Conformator, Balloon, RDKit DG, ETKDG, Confab, Frog2, MultiConf-DOCK, CSD conformer generator, ConfGenX-OPSL3 force field, Omega, excalc, iCon, and MOE. These benchmarks suggest that the CSD conformer generator is at the state of the art of reported conformer generators. Our results indicate that the improved BCL::Conf significantly outperforms the CSD conformer generation algorithm at binding conformer recovery across a range of ensemble sizes and with similarly fast rates of conformer generation. BCL::Conf is now distributed with the COD-derived rotamer library and is free for academic use. The BCL can be downloaded at http://meilerlab.org/bclcommons for Windows, Linux, or Apple operating systems. BCL::Conf can now also be accessed via webserver at http://meilerlab.org/bclconf.
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Affiliation(s)
- Jeffrey Mendenhall
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 United States
| | - Benjamin P Brown
- Chemical and Physical Biology Program, Medical Scientist Training Program, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 United States
| | - Sandeepkumar Kothiwale
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 United States
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232 United States.,Departments of Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37212 United States.,Institute for Drug Discovery, Leipzig University Medical School, Leipzig SAC 04103, Germany
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Wang YL, Wang F, Shi XX, Jia CY, Wu FX, Hao GF, Yang GF. Cloud 3D-QSAR: a web tool for the development of quantitative structure-activity relationship models in drug discovery. Brief Bioinform 2020; 22:5934782. [PMID: 33140820 DOI: 10.1093/bib/bbaa276] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
Effective drug discovery contributes to the treatment of numerous diseases but is limited by high costs and long cycles. The Quantitative Structure-Activity Relationship (QSAR) method was introduced to evaluate the activity of a large number of compounds virtually, reducing the time and labor costs required for chemical synthesis and experimental determination. Hence, this method increases the efficiency of drug discovery. To meet the needs of researchers to utilize this technology, numerous QSAR-related web servers, such as Web-4D-QSAR and DPubChem, have been developed in recent years. However, none of the servers mentioned above can perform a complete QSAR modeling and supply activity prediction functions. We introduce Cloud 3D-QSAR by integrating the functions of molecular structure generation, alignment, molecular interaction field (MIF) computing and results analysis to provide a one-stop solution. We rigidly validated this server, and the activity prediction correlation was R2 = 0.934 in 834 test molecules. The sensitivity, specificity and accuracy were 86.9%, 94.5% and 91.5%, respectively, with AUC = 0.981, AUCPR = 0.971. The Cloud 3D-QSAR server may facilitate the development of good QSAR models in drug discovery. Our server is free and now available at http://chemyang.ccnu.edu.cn/ccb/server/cloud3dQSAR/ and http://agroda.gzu.edu.cn:9999/ccb/server/cloud3dQSAR/.
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Affiliation(s)
- Yu-Liang Wang
- College of Chemistry, Central China Normal University (CCNU)
| | | | | | - Chen-Yang Jia
- College of Chemistry, Central China Normal University (CCNU)
| | | | - Ge-Fei Hao
- Pesticide Design and Bioinformatics in College of Chemistry, CCNU
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Lopes-Ortiz MA, Panice MR, Borges de Melo E, Ataide Martins JP, Baldin VP, Agostinho Pires CT, Caleffi-Ferracioli KR, Dias Siqueira VL, Bertin de Lima Scodro R, Sarragiotto MH, Cardoso RF. Synthesis and anti-Mycobacterium tuberculosis activity of imide-β-carboline and carbomethoxy-β-carboline derivatives. Eur J Med Chem 2020; 187:111935. [DOI: 10.1016/j.ejmech.2019.111935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 12/11/2022]
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Wu Y, Wang G. Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis. Int J Mol Sci 2018; 19:E2358. [PMID: 30103448 PMCID: PMC6121588 DOI: 10.3390/ijms19082358] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023] Open
Abstract
Toxicity prediction is very important to public health. Among its many applications, toxicity prediction is essential to reduce the cost and labor of a drug's preclinical and clinical trials, because a lot of drug evaluations (cellular, animal, and clinical) can be spared due to the predicted toxicity. In the era of Big Data and artificial intelligence, toxicity prediction can benefit from machine learning, which has been widely used in many fields such as natural language processing, speech recognition, image recognition, computational chemistry, and bioinformatics, with excellent performance. In this article, we review machine learning methods that have been applied to toxicity prediction, including deep learning, random forests, k-nearest neighbors, and support vector machines. We also discuss the input parameter to the machine learning algorithm, especially its shift from chemical structural description only to that combined with human transcriptome data analysis, which can greatly enhance prediction accuracy.
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Affiliation(s)
- Yunyi Wu
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenviroment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Guanyu Wang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenviroment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
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