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Kumar N, Acharya V. Advances in machine intelligence-driven virtual screening approaches for big-data. Med Res Rev 2024; 44:939-974. [PMID: 38129992 DOI: 10.1002/med.21995] [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: 09/12/2022] [Revised: 07/15/2023] [Accepted: 10/29/2023] [Indexed: 12/23/2023]
Abstract
Virtual screening (VS) is an integral and ever-evolving domain of drug discovery framework. The VS is traditionally classified into ligand-based (LB) and structure-based (SB) approaches. Machine intelligence or artificial intelligence has wide applications in the drug discovery domain to reduce time and resource consumption. In combination with machine intelligence algorithms, VS has emerged into revolutionarily progressive technology that learns within robust decision orders for data curation and hit molecule screening from large VS libraries in minutes or hours. The exponential growth of chemical and biological data has evolved as "big-data" in the public domain demands modern and advanced machine intelligence-driven VS approaches to screen hit molecules from ultra-large VS libraries. VS has evolved from an individual approach (LB and SB) to integrated LB and SB techniques to explore various ligand and target protein aspects for the enhanced rate of appropriate hit molecule prediction. Current trends demand advanced and intelligent solutions to handle enormous data in drug discovery domain for screening and optimizing hits or lead with fewer or no false positive hits. Following the big-data drift and tremendous growth in computational architecture, we presented this review. Here, the article categorized and emphasized individual VS techniques, detailed literature presented for machine learning implementation, modern machine intelligence approaches, and limitations and deliberated the future prospects.
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Affiliation(s)
- Neeraj Kumar
- Artificial Intelligence for Computational Biology Lab (AICoB), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Vishal Acharya
- Artificial Intelligence for Computational Biology Lab (AICoB), Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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Nwadiugwu M, Onwuekwe I, Ezeanolue E, Deng H. Beyond Amyloid: A Machine Learning-Driven Approach Reveals Properties of Potent GSK-3β Inhibitors Targeting Neurofibrillary Tangles. Int J Mol Sci 2024; 25:2646. [PMID: 38473895 PMCID: PMC10931970 DOI: 10.3390/ijms25052646] [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: 01/13/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Current treatments for Alzheimer's disease (AD) focus on slowing memory and cognitive decline, but none offer curative outcomes. This study aims to explore and curate the common properties of active, drug-like molecules that modulate glycogen synthase kinase 3β (GSK-3β), a well-documented kinase with increased activity in tau hyperphosphorylation and neurofibrillary tangles-hallmarks of AD pathology. Leveraging quantitative structure-activity relationship (QSAR) data from the PubChem and ChEMBL databases, we employed seven machine learning models: logistic regression (LogR), k-nearest neighbors (KNN), random forest (RF), support vector machine (SVM), extreme gradient boosting (XGB), neural networks (NNs), and ensemble majority voting. Our goal was to correctly predict active and inactive compounds that inhibit GSK-3β activity and identify their key properties. Among the six individual models, the NN demonstrated the highest performance with a 79% AUC-ROC on unbalanced external validation data, while the SVM model was superior in accurately classifying the compounds. The SVM and RF models surpassed NN in terms of Kappa values, and the ensemble majority voting model demonstrated slightly better accuracy to the NN on the external validation data. Feature importance analysis revealed that hydrogen bonds, phenol groups, and specific electronic characteristics are important features of molecular descriptors that positively correlate with active GSK-3β inhibition. Conversely, structural features like imidazole rings, sulfides, and methoxy groups showed a negative correlation. Our study highlights the significance of structural, electronic, and physicochemical descriptors in screening active candidates against GSK-3β. These predictive features could prove useful in therapeutic strategies to understand the important properties of GSK-3β candidate inhibitors that may potentially benefit non-amyloid-based AD treatments targeting neurofibrillary tangles.
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Affiliation(s)
- Martin Nwadiugwu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Ikenna Onwuekwe
- Neurology Unit, Department of Medicine, University of Nigeria Teaching Hospital, Ituku-Ozalla 400001, Enugu, Nigeria;
- Department of Medicine, College of Medicine, University of Nigeria, Enugu Campus, Nsukka 400001, Enugu, Nigeria
| | - Echezona Ezeanolue
- Center for Translation and Implementation Research (CTAIR), University of Nigeria, Nsukka 410001, Enugu, Nigeria;
- Healthy Sunrise Foundation, Las Vegas, NV 89107, USA
| | - Hongwen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, Tulane University, New Orleans, LA 70112, USA
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Sun G, Bai P, Fan T, Zhao L, Zhong R, McElhinney RS, McMurry TBH, Donnelly DJ, McCormick JE, Kelly J, Margison GP. QSAR and Chemical Read-Across Analysis of 370 Potential MGMT Inactivators to Identify the Structural Features Influencing Inactivation Potency. Pharmaceutics 2023; 15:2170. [PMID: 37631385 PMCID: PMC10458236 DOI: 10.3390/pharmaceutics15082170] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) constitutes an important cellular mechanism for repairing potentially cytotoxic DNA damage induced by guanine O6-alkylating agents and can render cells highly resistant to certain cancer chemotherapeutic drugs. A wide variety of potential MGMT inactivators have been designed and synthesized for the purpose of overcoming MGMT-mediated tumor resistance. We determined the inactivation potency of these compounds against human recombinant MGMT using [3H]-methylated-DNA-based MGMT inactivation assays and calculated the IC50 values. Using the results of 370 compounds, we performed quantitative structure-activity relationship (QSAR) modeling to identify the correlation between the chemical structure and MGMT-inactivating ability. Modeling was based on subdividing the sorted pIC50 values or on chemical structures or was random. A total of nine molecular descriptors were presented in the model equation, in which the mechanistic interpretation indicated that the status of nitrogen atoms, aliphatic primary amino groups, the presence of O-S at topological distance 3, the presence of Al-O-Ar/Ar-O-Ar/R..O..R/R-O-C=X, the ionization potential and hydrogen bond donors are the main factors responsible for inactivation ability. The final model was of high internal robustness, goodness of fit and prediction ability (R2pr = 0.7474, Q2Fn = 0.7375-0.7437, CCCpr = 0.8530). After the best splitting model was decided, we established the full model based on the entire set of compounds using the same descriptor combination. We also used a similarity-based read-across technique to further improve the external predictive ability of the model (R2pr = 0.7528, Q2Fn = 0.7387-0.7449, CCCpr = 0.8560). The prediction quality of 66 true external compounds was checked using the "Prediction Reliability Indicator" tool. In summary, we defined key structural features associated with MGMT inactivation, thus allowing for the design of MGMT inactivators that might improve clinical outcomes in cancer treatment.
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Affiliation(s)
- Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (P.B.); (T.F.); (L.Z.); (R.Z.)
| | - Peiying Bai
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (P.B.); (T.F.); (L.Z.); (R.Z.)
| | - Tengjiao Fan
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (P.B.); (T.F.); (L.Z.); (R.Z.)
- Department of Medical Technology, Beijing Pharmaceutical University of Staff and Workers, Beijing 100079, China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (P.B.); (T.F.); (L.Z.); (R.Z.)
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China; (P.B.); (T.F.); (L.Z.); (R.Z.)
| | - R. Stanley McElhinney
- Chemistry Department, Trinity College, D02 PN40 Dublin, Ireland; (T.B.H.M.); (D.J.D.)
| | - T. Brian H. McMurry
- Chemistry Department, Trinity College, D02 PN40 Dublin, Ireland; (T.B.H.M.); (D.J.D.)
| | - Dorothy J. Donnelly
- Chemistry Department, Trinity College, D02 PN40 Dublin, Ireland; (T.B.H.M.); (D.J.D.)
| | - Joan E. McCormick
- Chemistry Department, Trinity College, D02 PN40 Dublin, Ireland; (T.B.H.M.); (D.J.D.)
| | - Jane Kelly
- Carcinogenesis Department, Paterson Institute for Cancer Research, Manchester M20 9BX, UK;
| | - Geoffrey P. Margison
- Carcinogenesis Department, Paterson Institute for Cancer Research, Manchester M20 9BX, UK;
- Epidemiology and Public Health Group, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PG, UK
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Kumar N, Acharya V. Machine intelligence-driven framework for optimized hit selection in virtual screening. J Cheminform 2022; 14:48. [PMID: 35869511 PMCID: PMC9306080 DOI: 10.1186/s13321-022-00630-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractVirtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit activity when examined in biochemical assays, which accounts for many false positive hits, making it an arduous task. Attempts for conquering false-hit rates were developed through either ligand-based or structure-based VS separately; however, nonetheless performed remarkably well. Here, we present an advanced VS framework—automated hit identification and optimization tool (A-HIOT)—comprises chemical space-driven stacked ensemble for identification and protein space-driven deep learning architectures for optimization of an array of specific hits for fixed protein receptors. A-HIOT implements numerous open-source algorithms intending to integrate chemical and protein space leading to a high-quality prediction. The optimized hits are the selective molecules which we retrieve after extreme refinement implying chemical space and protein space modules of A-HIOT. Using CXC chemokine receptor 4, we demonstrated the superior performance of A-HIOT for hit molecule identification and optimization with tenfold cross-validation accuracies of 94.8% and 81.9%, respectively. In comparison with other machine learning algorithms, A-HIOT achieved higher accuracies of 96.2% for hit identification and 89.9% for hit optimization on independent benchmark datasets for CXCR4 and 86.8% for hit identification and 90.2% for hit optimization on independent test dataset for androgen receptor (AR), thus, shows its generalizability and robustness. In conclusion, advantageous features impeded in A-HIOT is making a reliable approach for bridging the long-standing gap between ligand-based and structure-based VS in finding the optimized hits for the desired receptor. The complete resource (framework) code is available at https://gitlab.com/neeraj-24/A-HIOT.
Graphical Abstract
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Sahu R, Gupta PK, Mishra A, Kumar A. Ayurveda and in silico Approach: A Challenging Proficient Confluence for Better Development of Effective Traditional Medicine Spotlighting Network Pharmacology. Chin J Integr Med 2022; 29:470-480. [PMID: 36094769 PMCID: PMC9465656 DOI: 10.1007/s11655-022-3584-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 11/03/2022]
Abstract
Coalescence of traditional medicine Ayurveda and in silico technology is a rigor for supplementary development of future-ready effective traditional medicine. Ayurveda is a popular traditional medicine in South Asia, emanating worldwide for the treatment of metabolic disorders and chronic illness. Techniques of in silico biology are not much explored for the investigation of a variety of bioactive phytochemicals of Ayurvedic herbs. Drug repurposing, reverse pharmacology, and polypharmacology in Ayurveda are areas in silico explorations that are needed to understand the rich repertoire of herbs, minerals, herbo-minerals, and assorted Ayurvedic formulations. This review emphasizes exploring the concept of Ayurveda with in silico approaches and the need for Ayurinformatics studies. It also provides an overview of in silico studies done on phytoconstituents of some important Ayurvedic plants, the utility of in silico studies in Ayurvedic phytoconstituents/formulations, limitations/challenges, and prospects of in silico studies in Ayurveda. This article discusses the convergence of in silico work, especially in the least explored field of Ayurveda. The focused coalesce of these two domains could present a predictive combinatorial platform to enhance translational research magnitude. In nutshell, it could provide new insight into an Ayurvedic drug discovery involving an in silico approach that could not only alleviate the process of traditional medicine research but also enhance its effectiveness in addressing health care.
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Affiliation(s)
- Rashmi Sahu
- Department of Balroga, Shri NPA Govt. Ayurveda College, Raipur, Chhattisgarh, 492010, India
| | - Prashant Kumar Gupta
- Department of Balroga, Shri NPA Govt. Ayurveda College, Raipur, Chhattisgarh, 492010, India.,Ayurinformatics Lab, Department of Kaumarabhritya, All India Institute of Ayurveda, Sarita Vihar, New Delhi, 110076, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, 492010, India.
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Tan RK, Liu Y, Xie L. Reinforcement learning for systems pharmacology-oriented and personalized drug design. Expert Opin Drug Discov 2022; 17:849-863. [PMID: 35510835 PMCID: PMC9824901 DOI: 10.1080/17460441.2022.2072288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Many multi-genic systemic diseases such as neurological disorders, inflammatory diseases, and the majority of cancers do not have effective treatments yet. Reinforcement learning powered systems pharmacology is a potentially effective approach to designing personalized therapies for untreatable complex diseases. AREAS COVERED In this survey, state-of-the-art reinforcement learning methods and their latest applications to drug design are reviewed. The challenges on harnessing reinforcement learning for systems pharmacology and personalized medicine are discussed. Potential solutions to overcome the challenges are proposed. EXPERT OPINION In spite of successful application of advanced reinforcement learning techniques to target-based drug discovery, new reinforcement learning strategies are needed to address systems pharmacology-oriented personalized de novo drug design.
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Affiliation(s)
- Ryan K. Tan
- Department of Computer Science, Hunter College, The City University of New York
| | - Yang Liu
- Department of Computer Science, Hunter College, The City University of New York
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York,Ph.D. Program in Computer Science, Biology & Biochemistry, The Graduate Center, The City University of New York,Helen and Robert Appel Alzheimer’s Disease Research Institute, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University,Correspondence should be addressed to Lei Xie -
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Bajusz D, Keserű GM. Maximizing the integration of virtual and experimental screening in hit discovery. Expert Opin Drug Discov 2022; 17:629-640. [PMID: 35671403 DOI: 10.1080/17460441.2022.2085685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Experimental and virtual screening contributes to the discovery of more than 50% of clinical candidates. Considering the similar concept and goals, early-phase drug discovery would benefit from the effective integration of these approaches. AREAS COVERED After reviewing the recent trends in both experimental and virtual screening, the authors discuss different integration strategies from parallel, focused, sequential, and iterative screening. Strategic considerations are demonstrated in a number of real-life case studies. EXPERT OPINION Experimental and virtual screening are complementary approaches that should be integrated in lead discovery settings. Virtual screening can access extremely large synthetically feasible chemical space that can be effectively searched on GPU clusters or cloud architectures. Experimental screening provides reliable datasets by quantitative HTS applications, and DNA-encoded libraries (DEL) have enlarged the chemical space covered by these technologies. These developments, together with the use of artificial intelligence methods, represent new options for their efficient integration. The case studies discussed here demonstrate the benefits of complementary strategies, such as focused and iterative screening.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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Halder AK, Ambure P, Perez-Castillo Y, Cordeiro MND. Turning deep-eutectic solvents into value-added products for CO2 capture: A desirability-based virtual screening study. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.101926] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Li WX, Tong X, Yang PP, Zheng Y, Liang JH, Li GH, Liu D, Guan DG, Dai SX. Screening of antibacterial compounds with novel structure from the FDA approved drugs using machine learning methods. Aging (Albany NY) 2022; 14:1448-1472. [PMID: 35150482 PMCID: PMC8876917 DOI: 10.18632/aging.203887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/28/2022] [Indexed: 11/25/2022]
Abstract
Bacterial infection is one of the most important factors affecting the human life span. Elderly people are more harmed by bacterial infections due to their deficits in immunity. Because of the lack of new antibiotics in recent years, bacterial resistance has increasingly become a serious problem globally. In this study, an antibacterial compound predictor was constructed using the support vector machines and random forest methods and the data of the active and inactive antibacterial compounds from the ChEMBL database. The results showed that both models have excellent prediction performance (mean accuracy >0.9 and mean AUC >0.9 for the two models). We used the predictor to screen potential antibacterial compounds from FDA-approved drugs in the DrugBank database. The screening results showed that 1087 small-molecule drugs have potential antibacterial activity and 154 of them are FDA-approved antibacterial drugs, which accounts for 76.2% of the approved antibacterial drugs collected in this study. Through molecular fingerprint similarity analysis and common substructure analysis, we screened 8 predicted antibacterial small-molecule compounds with novel structures compared with known antibacterial drugs, and 5 of them are widely used in the treatment of various tumors. This study provides a new insight for predicting antibacterial compounds by using approved drugs, the predicted compounds might be used to treat bacterial infections and extend lifespan.
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Affiliation(s)
- Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Xin Tong
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Peng-Peng Yang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Yang Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Ji-Hao Liang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
| | - Dahai Liu
- School of Medicine, Foshan University, Foshan 528000, Guangdong, China
| | - Dao-Gang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Shao-Xing Dai
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, Yunnan, China
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Peng X, Gibbs E, Silverman JM, Cashman NR, Plotkin SS. A method for systematically ranking therapeutic drug candidates using multiple uncertain screening criteria. Stat Methods Med Res 2021; 30:1502-1522. [PMID: 33847541 PMCID: PMC8189013 DOI: 10.1177/09622802211002861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multiple different screening tests for candidate leads in drug development may often yield conflicting or ambiguous results, sometimes making the selection of leads a nontrivial maximum-likelihood ranking problem. Here, we employ methods from the field of multiple criteria decision making (MCDM) to the problem of screening candidate antibody therapeutics. We employ the SMAA-TOPSIS method to rank a large cohort of antibodies using up to eight weighted screening criteria, in order to find lead candidate therapeutics for Alzheimer's disease, and determine their robustness to both uncertainty in screening measurements, as well as uncertainty in the user-defined weights of importance attributed to each screening criterion. To choose lead candidates and measure the confidence in their ranking, we propose two new quantities, the Retention Probability and the Topness, as robust measures for ranking. This method may enable more systematic screening of candidate therapeutics when it becomes difficult intuitively to process multi-variate screening data that distinguishes candidates, so that additional candidates may be exposed as potential leads, increasing the likelihood of success in downstream clinical trials. The method properly identifies true positives and true negatives from synthetic data, its predictions correlate well with known clinically approved antibodies vs. those still in trials, and it allows for ranking analyses using antibody developability profiles in the literature. We provide a webserver where users can apply the method to their own data: http://bjork.phas.ubc.ca.
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Affiliation(s)
- Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Ebrima Gibbs
- Brain Research Center, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Judith M Silverman
- Brain Research Center, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Neil R Cashman
- Brain Research Center, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
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Abstract
Introduction: Artificial Intelligence (AI) has become a component of our everyday lives, with applications ranging from recommendations on what to buy to the analysis of radiology images. Many of the techniques originally developed for other fields such as language translation and computer vision are now being applied in drug discovery. AI has enabled multiple aspects of drug discovery including the analysis of high content screening data, and the design and synthesis of new molecules.Areas covered: This perspective provides an overview of the application of AI in several areas relevant to drug discovery including property prediction, molecule generation, image analysis, and organic synthesis planning.Expert opinion: While a variety of machine learning methods are now being routinely used to predict biological activity and ADME properties, methods of representing molecules continue to evolve. Molecule generation methods are relatively new and unproven but hold the potential to access new, unexplored areas of chemical space. The application of AI in drug discovery will continue to benefit from dedicated research, as well as AI developments in other fields. With this pairing algorithmic advancements and high-quality data, the impact of AI in drug discovery will continue to grow in the coming years.
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Affiliation(s)
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
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Jiménez-Luna J, Grisoni F, Weskamp N, Schneider G. Artificial intelligence in drug discovery: recent advances and future perspectives. Expert Opin Drug Discov 2021; 16:949-959. [PMID: 33779453 DOI: 10.1080/17460441.2021.1909567] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Artificial intelligence (AI) has inspired computer-aided drug discovery. The widespread adoption of machine learning, in particular deep learning, in multiple scientific disciplines, and the advances in computing hardware and software, among other factors, continue to fuel this development. Much of the initial skepticism regarding applications of AI in pharmaceutical discovery has started to vanish, consequently benefitting medicinal chemistry.Areas covered: The current status of AI in chemoinformatics is reviewed. The topics discussed herein include quantitative structure-activity/property relationship and structure-based modeling, de novo molecular design, and chemical synthesis prediction. Advantages and limitations of current deep learning applications are highlighted, together with a perspective on next-generation AI for drug discovery.Expert opinion: Deep learning-based approaches have only begun to address some fundamental problems in drug discovery. Certain methodological advances, such as message-passing models, spatial-symmetry-preserving networks, hybrid de novo design, and other innovative machine learning paradigms, will likely become commonplace and help address some of the most challenging questions. Open data sharing and model development will play a central role in the advancement of drug discovery with AI.
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Affiliation(s)
- José Jiménez-Luna
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nils Weskamp
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riss, Germany
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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Bugeac CA, Ancuceanu R, Dinu M. QSAR Models for Active Substances against Pseudomonas aeruginosa Using Disk-Diffusion Test Data. Molecules 2021; 26:molecules26061734. [PMID: 33808845 PMCID: PMC8003670 DOI: 10.3390/molecules26061734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacillus included among the six “ESKAPE” microbial species with an outstanding ability to “escape” currently used antibiotics and developing new antibiotics against it is of the highest priority. Whereas minimum inhibitory concentration (MIC) values against Pseudomonas aeruginosa have been used previously for QSAR model development, disk diffusion results (inhibition zones) have not been apparently used for this purpose in the literature and we decided to explore their use in this sense. We developed multiple QSAR methods using several machine learning algorithms (support vector classifier, K nearest neighbors, random forest classifier, decision tree classifier, AdaBoost classifier, logistic regression and naïve Bayes classifier). We used four sets of molecular descriptors and fingerprints and three different methods of data balancing, together with the “native” data set. In total, 32 models were built for each set of descriptors or fingerprint and balancing method, of which 28 were selected and stacked to create meta-models. In terms of balanced accuracy, the best performance was provided by KNN, logistic regression and decision tree classifier, but the ensemble method had slightly superior results in nested cross-validation.
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Affiliation(s)
- Cosmin Alexandru Bugeac
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, Sector 2, 020956 Bucharest, Romania;
| | - Robert Ancuceanu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, Sector 2, 020956 Bucharest, Romania;
- Correspondence:
| | - Mihaela Dinu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Street, Sector 2, 020956 Bucharest, Romania;
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Mouchlis VD, Afantitis A, Serra A, Fratello M, Papadiamantis AG, Aidinis V, Lynch I, Greco D, Melagraki G. Advances in de Novo Drug Design: From Conventional to Machine Learning Methods. Int J Mol Sci 2021; 22:1676. [PMID: 33562347 PMCID: PMC7915729 DOI: 10.3390/ijms22041676] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/31/2021] [Accepted: 01/31/2021] [Indexed: 12/11/2022] Open
Abstract
. De novo drug design is a computational approach that generates novel molecular structures from atomic building blocks with no a priori relationships. Conventional methods include structure-based and ligand-based design, which depend on the properties of the active site of a biological target or its known active binders, respectively. Artificial intelligence, including machine learning, is an emerging field that has positively impacted the drug discovery process. Deep reinforcement learning is a subdivision of machine learning that combines artificial neural networks with reinforcement-learning architectures. This method has successfully been employed to develop novel de novo drug design approaches using a variety of artificial networks including recurrent neural networks, convolutional neural networks, generative adversarial networks, and autoencoders. This review article summarizes advances in de novo drug design, from conventional growth algorithms to advanced machine-learning methodologies and highlights hot topics for further development.
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Affiliation(s)
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus;
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
| | - Anastasios G. Papadiamantis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia 1046, Cyprus;
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Vassilis Aidinis
- Institute for Bioinnovation, Biomedical Sciences Research Center Alexander Fleming, Fleming 34, 16672 Athens, Greece;
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (A.S.); (M.F.); (D.G.)
- BioMEdiTech Institute, Tampere University, 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Finnish Center for Alternative Methods (FICAM), Tampere University, 33520 Tampere, Finland
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, 16672 Vari, Greece
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15
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Lambrinidis G, Tsantili-Kakoulidou A. Multi-objective optimization methods in novel drug design. Expert Opin Drug Discov 2020; 16:647-658. [PMID: 33353441 DOI: 10.1080/17460441.2021.1867095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: In multi-objective drug design, optimization gains importance, being upgraded to a discipline that attracts its own research. Current strategies are broadly classified into single - objective optimization (SOO) and multi-objective optimization (MOO).Areas covered: Starting with SOO and the ways used to incorporate multiple criteria into it, the present review focuses on MOO techniques, their comparison, advantages, and restrictions. Pareto analysis and the concept of dominance stand in the core of MOO. The Pareto front, Pareto ranking, and limitations of Pareto-based methods, due to high dimensions and data uncertainty, are outlined. Desirability functions and the weighted sum approaches are described as stand-alone techniques to transform the MOO problem to SOO or in combination with pareto analysis and evolutionary algorithms. Representative applications in different drug research areas are also discussed.Expert opinion: Despite their limitations, the use of combined MOO techniques, as well as being complementary to SOO or in conjunction with artificial intelligence, contributes dramatically to efficient drug design, assisting decisions and increasing success probabilities. For multi-target drug design, optimization is supported by network approaches, while applicability of MOO to other fields like drug technology or biological complexity opens new perspectives in the interrelated fields of medicinal chemistry and molecular biology.
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Affiliation(s)
- George Lambrinidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Anna Tsantili-Kakoulidou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
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16
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Mervin LH, Johansson S, Semenova E, Giblin KA, Engkvist O. Uncertainty quantification in drug design. Drug Discov Today 2020; 26:474-489. [PMID: 33253918 DOI: 10.1016/j.drudis.2020.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/13/2020] [Accepted: 11/23/2020] [Indexed: 01/03/2023]
Abstract
Machine learning and artificial intelligence are increasingly being applied to the drug-design process as a result of the development of novel algorithms, growing access, the falling cost of computation and the development of novel technologies for generating chemically and biologically relevant data. There has been recent progress in fields such as molecular de novo generation, synthetic route prediction and, to some extent, property predictions. Despite this, most research in these fields has focused on improving the accuracy of the technologies, rather than on quantifying the uncertainty in the predictions. Uncertainty quantification will become a key component in autonomous decision making and will be crucial for integrating machine learning and chemistry automation to create an autonomous design-make-test-analyse cycle. This review covers the empirical, frequentist and Bayesian approaches to uncertainty quantification, and outlines how they can be used for drug design. We also outline the impact of uncertainty quantification on decision making.
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Affiliation(s)
- Lewis H Mervin
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
| | - Simon Johansson
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden; Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Elizaveta Semenova
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Kathryn A Giblin
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ola Engkvist
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
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17
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TranScreen: Transfer Learning on Graph-Based Anti-Cancer Virtual Screening Model. BIG DATA AND COGNITIVE COMPUTING 2020. [DOI: 10.3390/bdcc4030016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Deep learning’s automatic feature extraction has proven its superior performance over traditional fingerprint-based features in the implementation of virtual screening models. However, these models face multiple challenges in the field of early drug discovery, such as over-training and generalization to unseen data, due to the inherently unbalanced and small datasets. In this work, the TranScreen pipeline is proposed, which utilizes transfer learning and a collection of weight initializations to overcome these challenges. An amount of 182 graph convolutional neural networks are trained on molecular source datasets and the learned knowledge is transferred to the target task for fine-tuning. The target task of p53-based bioactivity prediction, an important factor for anti-cancer discovery, is chosen to showcase the capability of the pipeline. Having trained a collection of source models, three different approaches are implemented to compare and rank them for a given task before fine-tuning. The results show improvement in performance of the model in multiple cases, with the best model increasing the area under receiver operating curve ROC-AUC from 0.75 to 0.91 and the recall from 0.25 to 1. This improvement is vital for practical virtual screening via lowering the false negatives and demonstrates the potential of transfer learning. The code and pre-trained models are made accessible online.
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18
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Ntie-Kang F, Nyongbela KD, Ayimele GA, Shekfeh S. “Drug-likeness” properties of natural compounds. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Our previous work was focused on the fundamental physical and chemical concepts behind “drug-likeness” and “natural product (NP)-likeness”. Herein, we discuss further details on the concepts of “drug-likeness”, “lead-likeness” and “NP-likeness”. The discussion will first focus on NPs as drugs, then a discussion of previous studies in which the complexities of the scaffolds and chemical space of naturally occurring compounds have been compared with synthetic, semisynthetic compounds and the Food and Drug Administration-approved drugs. This is followed by guiding principles for designing “drug-like” natural product libraries for lead compound discovery purposes. In addition, we present a tool for measuring “NP-likeness” of compounds and a brief presentation of machine-learning approaches. A binary quantitative structure–activity relationship for classifying drugs from nondrugs and natural compounds from nonnatural ones is also described. While the studies add to the plethora of recently published works on the “drug-likeness” of NPs, it no doubt increases our understanding of the physicochemical properties that make NPs fall within the ranges associated with “drug-like” molecules.
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19
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Ullrich CI, Aloni R, Saeed MEM, Ullrich W, Efferth T. Comparison between tumors in plants and human beings: Mechanisms of tumor development and therapy with secondary plant metabolites. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 64:153081. [PMID: 31568956 DOI: 10.1016/j.phymed.2019.153081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Human tumors are still a major threat to human health and plant tumors negatively affect agricultural yields. Both areas of research are developing largely independent of each other. Treatment of both plant and human tumors remains unsatisfactory and novel therapy options are urgently needed. HYPOTHESIS The concept of this paper is to compare cellular and molecular mechanisms of tumor development in plants and human beings and to explore possibilities to develop novel treatment strategies based on bioactive secondary plant metabolites. The interdisciplinary discourse may unravel commonalities and differences in the biology of plant and human tumors as basis for rational drug development. RESULTS Plant tumors and galls develop upon infection by bacteria (e.g. Agrobacterium tumefaciens and A. vitis, which harbor oncogenic T-DNA) and by insects (e.g. gall wasps, aphids). Plant tumors are benign, i.e. they usually do not ultimately kill their host, but they can lead to considerable economic damage due to reduced crop yields of cultivated plants. Human tumors develop by biological carcinogenesis (i.e. viruses and other infectious agents), chemical carcinogenesis (anthropogenic and non-anthropogenic environmental toxic xenobiotics) and physical carcinogenesis (radioactivity, UV-radiation). The majority of human tumors are malignant with lethal outcome. Although treatments for both plant and human tumors are available (antibiotics and apathogenic bacterial strains for plant tumors, cytostatic drugs for human tumors), treatment successes are non-satisfactory, because of drug resistance and the severe adverse side effects. In human beings, attacks by microbes are repelled by cellular immunity (i.e. innate and acquired immune systems). Plants instead display chemical defense mechanisms, whereby constitutively expressed phytoanticipin compounds compare to the innate human immune system, the acquired human immune system compares to phytoalexins, which are induced by appropriate biotic or abiotic stressors. Some chemical weapons of this armory of secondary metabolites are also active against plant galls. There is a mutual co-evolution between plant defense and animals/human beings, which was sometimes referred to as animal plant warfare. As a consequence, hepatic phase I-III metabolization and excretion developed in animals and human beings to detoxify harmful phytochemicals. On the other hand, plants invented "pro-drugs" during evolution, which are activated and toxified in animals by this hepatic biotransformation system. Recent efforts focus on phytochemicals that specifically target tumor-related mechanisms and proteins, e.g. angiogenic or metastatic inhibitors, stimulators of the immune system to improve anti-tumor immunity, specific cell death or cancer stem cell inhibitors, inhibitors of DNA damage and epigenomic deregulation, specific inhibitors of driver genes of carcinogenesis (e.g. oncogenes), inhibitors of multidrug resistance (i.e. ABC transporter efflux inhibitors), secondary metabolites against plant tumors. CONCLUSION The exploitation of bioactive secondary metabolites to treat plant or human tumors bears a tremendous therapeutic potential. Although there are fundamental differences between human and plant tumors, either isolated phytochemicals and their (semi)synthetic derivatives or chemically defined and standardized plant extracts may offer new therapy options to decrease human tumor incidence and mortality as well as to increase agricultural yields by fighting crown galls.
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Affiliation(s)
- Cornelia I Ullrich
- Department of Biology, Darmstadt University of Technology, Schnittspahnstr. 3-5, Darmstadt 64287, Germany
| | - Roni Aloni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mohamed E M Saeed
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
| | - Wolfram Ullrich
- Department of Biology, Darmstadt University of Technology, Schnittspahnstr. 3-5, Darmstadt 64287, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany.
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20
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Schneider P, Schneider G. Polypharmacological Drug−target Inference for Chemogenomics. Mol Inform 2018; 37:e1800050. [DOI: 10.1002/minf.201800050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 04/24/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Petra Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Swiss Federal Institute of Technology (ETH); Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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21
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Perez-Castillo Y, Sánchez-Rodríguez A, Tejera E, Cruz-Monteagudo M, Borges F, Cordeiro MNDS, Le-Thi-Thu H, Pham-The H. A desirability-based multi objective approach for the virtual screening discovery of broad-spectrum anti-gastric cancer agents. PLoS One 2018; 13:e0192176. [PMID: 29420638 PMCID: PMC5805264 DOI: 10.1371/journal.pone.0192176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/17/2018] [Indexed: 01/09/2023] Open
Abstract
Gastric cancer is the third leading cause of cancer-related mortality worldwide and despite advances in prevention, diagnosis and therapy, it is still regarded as a global health concern. The efficacy of the therapies for gastric cancer is limited by a poor response to currently available therapeutic regimens. One of the reasons that may explain these poor clinical outcomes is the highly heterogeneous nature of this disease. In this sense, it is essential to discover new molecular agents capable of targeting various gastric cancer subtypes simultaneously. Here, we present a multi-objective approach for the ligand-based virtual screening discovery of chemical compounds simultaneously active against the gastric cancer cell lines AGS, NCI-N87 and SNU-1. The proposed approach relays in a novel methodology based on the development of ensemble models for the bioactivity prediction against each individual gastric cancer cell line. The methodology includes the aggregation of one ensemble per cell line using a desirability-based algorithm into virtual screening protocols. Our research leads to the proposal of a multi-targeted virtual screening protocol able to achieve high enrichment of known chemicals with anti-gastric cancer activity. Specifically, our results indicate that, using the proposed protocol, it is possible to retrieve almost 20 more times multi-targeted compounds in the first 1% of the ranked list than what is expected from a uniform distribution of the active ones in the virtual screening database. More importantly, the proposed protocol attains an outstanding initial enrichment of known multi-targeted anti-gastric cancer agents.
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Affiliation(s)
- Yunierkis Perez-Castillo
- Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito, Ecuador
- * E-mail: (YPC); (HPT)
| | | | - Eduardo Tejera
- Facultad de Ingenieria y Ciencias Agropecuarias, Universidad de Las Américas, Quito, Ecuador
| | - Maykel Cruz-Monteagudo
- CIQUP/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of General Education, West Coast University—Miami Campus, Doral, Florida, United States of America
| | - Fernanda Borges
- CIQUP/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - M. Natália D. S. Cordeiro
- REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Huong Le-Thi-Thu
- VNU School of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Hai Pham-The
- Hanoi University of Pharmacy, Hanoi, Vietnam
- * E-mail: (YPC); (HPT)
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22
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Abstract
Molecular docking is an in silico method widely applied in drug discovery programs to predict the binding mode of a given molecule interacting with a specific biological target. This computational technique is today emerging also in the field of predictive toxicology for regulatory purposes, being for instance successfully applied to develop classification models for the prediction of the endocrine disruptor potential of chemicals. Herein, we describe the protocol for adapting molecular docking to the purposes of predictive toxicology.
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23
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Trisciuzzi D, Alberga D, Mansouri K, Judson R, Novellino E, Mangiatordi GF, Nicolotti O. Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals. J Chem Inf Model 2017; 57:2874-2884. [PMID: 29022712 DOI: 10.1021/acs.jcim.7b00420] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a practical and easy-to-run in silico workflow exploiting a structure-based strategy making use of docking simulations to derive highly predictive classification models of the androgenic potential of chemicals. Models were trained on a high-quality chemical collection comprising 1689 curated compounds made available within the CoMPARA consortium from the US Environmental Protection Agency and were integrated with a two-step applicability domain whose implementation had the effect of improving both the confidence in prediction and statistics by reducing the number of false negatives. Among the nine androgen receptor X-ray solved structures, the crystal 2PNU (entry code from the Protein Data Bank) was associated with the best performing structure-based classification model. Three validation sets comprising each 2590 compounds extracted by the DUD-E collection were used to challenge model performance and the effectiveness of Applicability Domain implementation. Next, the 2PNU model was applied to screen and prioritize two collections of chemicals. The first is a small pool of 12 representative androgenic compounds that were accurately classified based on outstanding rationale at the molecular level. The second is a large external blind set of 55450 chemicals with potential for human exposure. We show how the use of molecular docking provides highly interpretable models and can represent a real-life option as an alternative nontesting method for predictive toxicology.
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Affiliation(s)
- Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro" , Via E. Orabona 4, I-70126 Bari, Italy
| | - Domenico Alberga
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro" , Via E. Orabona 4, I-70126 Bari, Italy.,Centro Ricerche TIRES, Università degli Studi di Bari "Aldo Moro" , Via Amendola 173, I-70126 Bari, Italy
| | - Kamel Mansouri
- Oak Ridge Institute for Science and Education , Oak Ridge, Tennessee 37830, United States.,National Center for Computational Toxicology, U.S. Environmental Protection Agency , 109 T.W. Alexander Drive, Research Triangle Park, North Carolina 27711, United States.,ScitoVation LLC , 6 Davis Drive, Research Triangle Park, North Carolina 27709, United States
| | - Richard Judson
- National Center for Computational Toxicology, U.S. Environmental Protection Agency , 109 T.W. Alexander Drive, Research Triangle Park, North Carolina 27711, United States
| | - Ettore Novellino
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II" , Via D. Montesano 49, 80131 Napoli, Italy
| | - Giuseppe Felice Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro" , Via E. Orabona 4, I-70126 Bari, Italy.,Centro Ricerche TIRES, Università degli Studi di Bari "Aldo Moro" , Via Amendola 173, I-70126 Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro" , Via E. Orabona 4, I-70126 Bari, Italy.,Centro Ricerche TIRES, Università degli Studi di Bari "Aldo Moro" , Via Amendola 173, I-70126 Bari, Italy
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