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Nguyen ATN, Nguyen DTN, Koh HY, Toskov J, MacLean W, Xu A, Zhang D, Webb GI, May LT, Halls ML. The application of artificial intelligence to accelerate G protein-coupled receptor drug discovery. Br J Pharmacol 2024; 181:2371-2384. [PMID: 37161878 DOI: 10.1111/bph.16140] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/14/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
The application of artificial intelligence (AI) approaches to drug discovery for G protein-coupled receptors (GPCRs) is a rapidly expanding area. Artificial intelligence can be used at multiple stages during the drug discovery process, from aiding our understanding of the fundamental actions of GPCRs to the discovery of new ligand-GPCR interactions or the prediction of clinical responses. Here, we provide an overview of the concepts behind artificial intelligence, including the subfields of machine learning and deep learning. We summarise the published applications of artificial intelligence to different stages of the GPCR drug discovery process. Finally, we reflect on the benefits and limitations of artificial intelligence and share our vision for the exciting potential for further development of applications to aid GPCR drug discovery. In addition to making the drug discovery process "faster, smarter and cheaper," we anticipate that the application of artificial intelligence will create exciting new opportunities for GPCR drug discovery. LINKED ARTICLES: This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
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Affiliation(s)
- Anh T N Nguyen
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Diep T N Nguyen
- Department of Information Technology, Faculty of Engineering and Technology, Vietnam National University, Cau Giay, Hanoi, Vietnam
| | - Huan Yee Koh
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Monash Data Futures Institute and Department of Data Science and Artificial Intelligence, Monash University, Clayton, Victoria, Australia
| | - Jason Toskov
- Monash DeepNeuron, Monash University, Clayton, Victoria, Australia
| | - William MacLean
- Monash DeepNeuron, Monash University, Clayton, Victoria, Australia
| | - Andrew Xu
- Monash DeepNeuron, Monash University, Clayton, Victoria, Australia
| | - Daokun Zhang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Monash Data Futures Institute and Department of Data Science and Artificial Intelligence, Monash University, Clayton, Victoria, Australia
| | - Geoffrey I Webb
- Monash Data Futures Institute and Department of Data Science and Artificial Intelligence, Monash University, Clayton, Victoria, Australia
| | - Lauren T May
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024; 74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
This article investigates the role of recent advances in Artificial Intelligence (AI) to revolutionise the study of G protein-coupled receptors (GPCRs). AI has been applied to many areas of GPCR research, including the application of machine learning (ML) in GPCR classification, prediction of GPCR activation levels, modelling GPCR 3D structures and interactions, understanding G-protein selectivity, aiding elucidation of GPCRs structures, and drug design. Despite progress, challenges in predicting GPCR structures and addressing the complex nature of GPCRs remain, providing avenues for future research and development.
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Affiliation(s)
- João P L Velloso
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Aaron S Kovacs
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.
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El-Atawneh S, Goldblum A. Activity Models of Key GPCR Families in the Central Nervous System: A Tool for Many Purposes. J Chem Inf Model 2023. [PMID: 37257045 DOI: 10.1021/acs.jcim.2c01531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
G protein-coupled receptors (GPCRs) are targets of many drugs, of which ∼25% are indicated for central nervous system (CNS) disorders. Drug promiscuity affects their efficacy and safety profiles. Predicting the polypharmacology profile of compounds against GPCRs can thus provide a basis for producing more precise therapeutics by considering the targets and the anti-targets in that family of closely related proteins. We provide a tool for predicting the polypharmacology of compounds within prominent GPCR families in the CNS: serotonin, dopamine, histamine, muscarinic, opioid, and cannabinoid receptors. Our in-house algorithm, "iterative stochastic elimination" (ISE), produces high-quality ligand-based models for agonism and antagonism at 31 GPCRs. The ISE models correctly predict 68% of CNS drug-GPCR interactions, while the "similarity ensemble approach" predicts only 33%. The activity models correctly predict 56% of reported activities of DrugBank molecules for these CNS receptors. We conclude that the combination of interactions and activity profiles generated by screening through our models form the basis for subsequent designing and discovering novel therapeutics, either single, multitargeting, or repurposed.
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Affiliation(s)
- Shayma El-Atawneh
- Molecular Modelling and Drug Design Lab, Institute for Drug Research and Fraunhofer Project Center for Drug Discovery and Delivery, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
| | - Amiram Goldblum
- Molecular Modelling and Drug Design Lab, Institute for Drug Research and Fraunhofer Project Center for Drug Discovery and Delivery, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91905, Israel
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Velloso JPL, Ascher DB, Pires DEV. pdCSM-GPCR: predicting potent GPCR ligands with graph-based signatures. BIOINFORMATICS ADVANCES 2021; 1:vbab031. [PMID: 34901870 PMCID: PMC8651072 DOI: 10.1093/bioadv/vbab031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/30/2021] [Accepted: 11/02/2021] [Indexed: 01/26/2023]
Abstract
MOTIVATION G protein-coupled receptors (GPCRs) can selectively bind to many types of ligands, ranging from light-sensitive compounds, ions, hormones, pheromones and neurotransmitters, modulating cell physiology. Considering their role in many essential cellular processes, they are one of the most targeted protein families, with over a third of all approved drugs modulating GPCR signalling. Despite this, the large diversity of receptors and their multipass transmembrane architectures make the identification and development of novel specific, and safe GPCR ligands a challenge. While computational approaches have the potential to assist GPCR drug development, they have presented limited performance and generalization capabilities. Here, we explored the use of graph-based signatures to develop pdCSM-GPCR, a method capable of rapidly and accurately screening potential GPCR ligands. RESULTS Bioactivity data (IC50, EC50, Ki and Kd) for individual GPCRs were curated. After curation, we used the data for developing predictive models for 36 major GPCR targets, across 4 classes (A, B, C and F). Our models compose the most comprehensive computational resource for GPCR bioactivity prediction to date. Across stratified 10-fold cross-validation and blind tests, our approach achieved Pearson's correlations of up to 0.89, significantly outperforming previous methods. Interpreting our results, we identified common important features of potent GPCRs ligands, which tend to have bicyclic rings, leading to higher levels of aromaticity. We believe pdCSM-GPCR will be an invaluable tool to assist screening efforts, enriching compound libraries and ranking candidates for further experimental validation. AVAILABILITY AND IMPLEMENTATION pdCSM-GPCR predictive models and datasets used have been made available via a freely accessible and easy-to-use web server at http://biosig.unimelb.edu.au/pdcsm_gpcr/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- João Paulo L Velloso
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte 30190-009, Brazil,Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,Baker Department of Cardiometabolic Health, Melbourne Medical School, University of Melbourne, Melbourne 3052, Australia,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK,To whom correspondence should be addressed. or
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne 3052, Australia,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne 3052, Australia,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne 3004, Australia,School of Computing and Information Systems, University of Melbourne, Melbourne 3053, Australia,To whom correspondence should be addressed. or
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Jabeen A, de March CA, Matsunami H, Ranganathan S. Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors. Int J Mol Sci 2021; 22:ijms222111546. [PMID: 34768977 PMCID: PMC8583936 DOI: 10.3390/ijms222111546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/29/2022] Open
Abstract
Olfactory receptors (ORs) constitute the largest superfamily of G protein-coupled receptors (GPCRs). ORs are involved in sensing odorants as well as in other ectopic roles in non-nasal tissues. Matching of an enormous number of the olfactory stimulation repertoire to its counterpart OR through machine learning (ML) will enable understanding of olfactory system, receptor characterization, and exploitation of their therapeutic potential. In the current study, we have selected two broadly tuned ectopic human OR proteins, OR1A1 and OR2W1, for expanding their known chemical space by using molecular descriptors. We present a scheme for selecting the optimal features required to train an ML-based model, based on which we selected the random forest (RF) as the best performer. High activity agonist prediction involved screening five databases comprising ~23 M compounds, using the trained RF classifier. To evaluate the effectiveness of the machine learning based virtual screening and check receptor binding site compatibility, we used docking of the top target ligands to carefully develop receptor model structures. Finally, experimental validation of selected compounds with significant docking scores through in vitro assays revealed two high activity novel agonists for OR1A1 and one for OR2W1.
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Affiliation(s)
- Amara Jabeen
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia;
| | - Claire A. de March
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC 27710, USA
- Correspondence: (H.M.); (S.R.)
| | - Shoba Ranganathan
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia;
- Correspondence: (H.M.); (S.R.)
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Li M, Rong L, Zhou S, Xiao X, Wu L, Fan Y, Lu C, Zou X. Dissipation of Sulfonamides in Soil Emphasizing Taxonomy and Function of Microbiomes by Metagenomic Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13594-13607. [PMID: 33172257 DOI: 10.1021/acs.jafc.0c04496] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sulfonamides (SAs) are widespread in soils, and their dissipation behavior is important for their fate, risk assessment, and pollution control. In this work, we investigated the dissipation behavior of different SAs in a soil under aerobic condition, focusing on revealing the relationship between overall dissipation (without sterilization and in dark) and individual abiotic (sorption, hydrolysis)/biotic (with sterilization and in dark) factors and taxonomy/function of microbiomes. The results showed that dissipation of all SAs in the soil followed the pseudo-first-order kinetic model with dissipation time at 50% removal (DT50) of 2.16-15.27 days. Based on, experimentally, abiotic/biotic processes and, theoretically, partial least-squares modeling, a relationship between overall dissipation and individual abiotic/biotic factors was developed with microbial degradation as the dominant contributor. Metagenomic analysis showed that taxonomic genera like Bradyrhizobium/Sphingomonas/Methyloferula and functions like CAZy family GT51/GH23/GT2, eggNOG category S, KEGG pathway ko02024/ko02010, and KEGG ortholog K01999/K03088 are putatively involved in SA microbial degradation in soil. Spearman correlation suggests abundant genera being multifunctional. This study provides some new insights into SA dissipation and can be applied to other antibiotics/soils in the future.
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Affiliation(s)
- Mi Li
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Lingling Rong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Shifan Zhou
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiaoyu Xiao
- School of Life Science, Jinggangshan University, Ji'an 343009, China
- Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an 343016, China
| | - Ligui Wu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Yuxing Fan
- School of Life Science, Jinggangshan University, Ji'an 343009, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Conghui Lu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
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Qiao K, Fu W, Jiang Y, Chen L, Li S, Ye Q, Gui W. QSAR models for the acute toxicity of 1,2,4-triazole fungicides to zebrafish (Danio rerio) embryos. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114837. [PMID: 32460121 DOI: 10.1016/j.envpol.2020.114837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/27/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
In recent decades, the 1,2,4-triazole fungicides are widely used for crop diseases control, and their toxicity to wild lives and pollution to ecosystem have attracted more and more attention. However, how to quickly and efficiently evaluate the toxicity of these compounds to environmental organisms is still a challenge. In silico method, such like Quantitative Structure-Activity Relationship (QSAR), provides a good alternative to evaluate the environmental toxicity of a large number of chemicals. At the present study, the acute toxicity of 23 1,2,4-triazole fungicides to zebrafish (Danio rerio) embryos was firstly tested, and the LC50 (median lethal concentration) values were used as the bio-activity endpoint to conduct QSAR modelling for these triazoles. After the comparative study of several QSAR models, the 2D-QSAR model was finally constructed using the stepwise multiple linear regression algorithm combining with two physicochemical parameters (logD and μ), an electronic parameter (QN1) and a topological parameter (XvPC4). The optimal model could be mathematically described as following: pLC50 = -7.24-0.30XvPC4 + 0.76logD - 26.15QN1 - 0.08μ. The internal validation by leave-one-out (LOO) cross-validation showed that the R2adj (adjusted noncross-validation squared correlation coefficient), Q2 (cross-validation correlation coefficient) and RMSD (root-mean-square error) was 0.88, 0.84 and 0.17, respectively. The external validation indicated the model had a robust predictability with the q2 (predictive squared correlation coefficient) of 0.90 when eliminated tricyclazole. The present study provided a potential tool for predicting the acute toxicity of new 1,2,4-triazole fungicides which contained an independent triazole ring group in their molecules to zebrafish embryos, and also provided a reference for the development of more environmentally-friendly 1,2,4-triazole pesticides in the future.
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Affiliation(s)
- Kun Qiao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China; Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wenjie Fu
- Institute of Insect Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Yao Jiang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Lili Chen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Shuying Li
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China
| | - Qingfu Ye
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wenjun Gui
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, PR China.
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Wang D, Hong RY, Guo M, Liu Y, Chen N, Li X, Kong DX. Novel C7-Substituted Coumarins as Selective Monoamine Oxidase Inhibitors: Discovery, Synthesis and Theoretical Simulation. Molecules 2019; 24:molecules24214003. [PMID: 31694262 PMCID: PMC6864482 DOI: 10.3390/molecules24214003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/02/2022] Open
Abstract
There is a continued need to develop new selective human monoamine oxidase (hMAO) inhibitors that could be beneficial for the treatment of neurological diseases. However, hMAOs are closely related with high sequence identity and structural similarity, which hinders the development of selective MAO inhibitors. “Three-Dimensional Biologically Relevant Spectrum (BRS-3D)” method developed by our group has demonstrated its effectiveness in subtype selectivity studies of receptor and enzyme ligands. Here, we report a series of novel C7-substituted coumarins, either synthesized or commercially purchased, which were identified as selective hMAO inhibitors. Most of the compounds demonstrated strong activities with IC50 values (half-inhibitory concentration) ranging from sub-micromolar to nanomolar. Compounds, FR1 and SP1, were identified as the most selective hMAO-A inhibitors, with IC50 values of 1.5 nM (selectivity index (SI) < −2.82) and 19 nM (SI < −2.42), respectively. FR4 and FR5 showed the most potent hMAO-B inhibitory activity, with IC50 of 18 nM and 15 nM (SI > 2.74 and SI > 2.82). Docking calculations and molecular dynamic simulations were performed to elucidate the selectivity preference and SAR profiles.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Ren-Yuan Hong
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Ji’nan 250012, Shandong, China;
| | - Mengyao Guo
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Yi Liu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Nianhang Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
| | - Xun Li
- Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, No 18877, Jingshi Road, Ji’nan 250002, Shandong, China
- Correspondence: (X.L.); (D.-X.K.); Tel.: +86-531-88382005 (X.L.); +86-27-8728 0877 (D.-X.K.)
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; (M.G.); (Y.L.); (N.C.)
- Correspondence: (X.L.); (D.-X.K.); Tel.: +86-531-88382005 (X.L.); +86-27-8728 0877 (D.-X.K.)
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Al-Attraqchi OH, Attimarad M, Venugopala KN, Nair A, Al-Attraqchi NH. Adenosine A2A Receptor as a Potential Drug Target - Current Status and Future Perspectives. Curr Pharm Des 2019; 25:2716-2740. [DOI: 10.2174/1381612825666190716113444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
Adenosine receptors (ARs) are a class of G-protein coupled receptors (GPCRs) that are activated by
the endogenous substance adenosine. ARs are classified into 4 subtype receptors, namely, the A1, A2A, A2B and A3
receptors. The wide distribution and expression of the ARs in various body tissues as well as the roles they have
in controlling different functions in the body make them potential drug targets for the treatment of various pathological
conditions, such as cardiac diseases, cancer, Parkinson’s disease, inflammation and glaucoma. Therefore,
in the past decades, there have been extensive investigations of ARs with a high number of agonists and antagonists
identified that can interact with these receptors. This review shall discuss the A2A receptor (A2AAR) subtype
of the ARs. The structure, properties and the recent advances in the therapeutic potential of the receptor are discussed
with an overview of the recent advances in the methods of studying the receptor. Also, molecular modeling
approaches utilized in the design of A2AAR ligands are highlighted with various recent examples.
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Affiliation(s)
- Omar H.A. Al-Attraqchi
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O BOX (1), Philadelphia University-19392, Amman, Jordan
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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Jabeen A, Ranganathan S. Applications of machine learning in GPCR bioactive ligand discovery. Curr Opin Struct Biol 2019; 55:66-76. [PMID: 31005679 DOI: 10.1016/j.sbi.2019.03.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022]
Abstract
GPCRs constitute the largest druggable family having targets for 475 Food and Drug Administration (FDA) approved drugs. As GPCRs are of great interest to pharmaceutical industry, enormous efforts are being expended to find relevant and potent GPCR ligands as lead compounds. There are tens of millions of compounds present in different chemical databases. In order to scan this immense chemical space, computational methods, especially machine learning (ML) methods, are essential components of GPCR drug discovery pipelines. ML approaches have applications in both ligand-based and structure-based virtual screening. We present here a cheminformatics overview of ML applications to different stages of GPCR drug discovery. Focusing on olfactory receptors, which are the largest family of GPCRs, a case study for predicting agonists for an ectopic olfactory receptor, OR1G1, compares four classical ML methods.
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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Identification of novel monoamine oxidase selective inhibitors employing a hierarchical ligand-based virtual screening strategy. Future Med Chem 2019; 11:801-816. [PMID: 31140884 DOI: 10.4155/fmc-2018-0596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: Due to the pivotal role in the oxidative deamination of monoamine neurotransmitters, two distinct monoamine oxidase (MAO) subtypes, MAO-A and MAO-B, present a significant pharmacological interest. Here, we reported a hierarchical and time-efficient ligand-based virtual screening strategy to identify potent selective and reversible MAO inhibitors. Result: A total of 130 compounds were assessed in dose–response biochemical assay against MAOs. Among them, 70 compounds were active with inhibition higher than 70%, involving 25 compounds with IC50 values less than 1 μM. Conclusion: Our research demonstrated the validity of Biologically Relevant Spectrum (BRS-3D) in predicting subtype-selective ligands and afforded a novel highly efficient way to develop selective inhibitors in the early stage of drug discovery.
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Marquina S, Maldonado-Santiago M, Sánchez-Carranza JN, Antúnez-Mojica M, González-Maya L, Razo-Hernández RS, Alvarez L. Design, synthesis and QSAR study of 2'-hydroxy-4'-alkoxy chalcone derivatives that exert cytotoxic activity by the mitochondrial apoptotic pathway. Bioorg Med Chem 2018; 27:43-54. [PMID: 30482548 DOI: 10.1016/j.bmc.2018.10.045] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/17/2018] [Accepted: 10/30/2018] [Indexed: 12/11/2022]
Abstract
Eleven 4'-alkoxy chalcones were synthesized and biologically evaluated for their antiproliferative activity against four human tumor cell lines (PC-3, MCF-7, HF-6, and CaSki). Compounds 3a-3d and 3f were selective against PC-3, with IC50 values ranging from 8.08 to 13.75 μM. In addition, chalcones 3a-3c did not affect the normal fibroblasts BJ cells. The most active and selective compounds were further evaluated for their effect on the progression of cell cycle in PC-3 cells, and chalcones 3a and 3c induced a G2/M phase arrest. Furthermore, it was found that these three chalcones induced the mitochondrial apoptotic pathway by regulating Bax and Bcl-2 transcripts and by increasing caspase 3/7 activation. Otherwise, the QSAR model indicates that the double bond of the α,β-unsaturated carbonyl, as well as the planar structure geometry, are important to the biological activity of the synthetized chalcones. Based on these studies, it was concluded that withdrawing substituents in ring A, decrease the antiproliferative activity. This is related to the possible mechanism of action of these compounds, where a Michael addition needs to take place in order to be a potent anticancer agent.
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Affiliation(s)
- Silvia Marquina
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
| | - Maritza Maldonado-Santiago
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
| | - Jessica Nayelli Sánchez-Carranza
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Mayra Antúnez-Mojica
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
| | - Leticia González-Maya
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
| | - Rodrigo Said Razo-Hernández
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
| | - Laura Alvarez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Chamilpa, Cuernavaca, Morelos 62209, Mexico.
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Sagawa T, Mashiko R, Yokota Y, Naruse Y, Okada M, Kojima H. Logistic Regression of Ligands of Chemotaxis Receptors Offers Clues about Their Recognition by Bacteria. Front Bioeng Biotechnol 2018; 5:88. [PMID: 29404321 PMCID: PMC5786873 DOI: 10.3389/fbioe.2017.00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/26/2017] [Indexed: 11/13/2022] Open
Abstract
Because of relative simplicity of signal transduction pathway, bacterial chemotaxis sensory systems have been expected to be applied to biosensor. Tar and Tsr receptors mediate chemotaxis of Escherichia coli and have been studied extensively as models of chemoreception by bacterial two-transmembrane receptors. Such studies are typically conducted using two canonical ligands: l-aspartate for Tar and l-serine for Tsr. However, Tar and Tsr also recognize various analogs of aspartate and serine; it remains unknown whether the mechanism by which the canonical ligands are recognized is also common to the analogs. Moreover, in terms of engineering, it is important to know a single species of receptor can recognize various ligands to utilize bacterial receptor as the sensor for wide range of substances. To answer these questions, we tried to extract the features that are common to the recognition of the different analogs by constructing classification models based on machine-learning. We computed 20 physicochemical parameters for each of 38 well-known attractants that act as chemoreception ligands, and 15 known non-attractants. The classification models were generated by utilizing one or more of the seven physicochemical properties as descriptors. From the classification models, we identified the most effective physicochemical parameter for classification: the minimum electron potential. This descriptor that occurred repeatedly in classification models with the highest accuracies, This descriptor used alone could accurately classify 42/53 of compounds. Among the 11 misclassified compounds, eight contained two carboxyl groups, which is analogous to the structure of characteristic of aspartate analog. When considered separately, 16 of the 17 aspartate analogs could be classified accurately based on the distance between their two carboxyl groups. As shown in these results, we succeed to predict the ligands for bacterial chemoreceptors using only a few descriptors; single descriptor for single receptor. This result might be due to the relatively simple topology of bacterial two-transmembrane receptors compared to the G-protein-coupled receptors of seven-transmembrane receptors. Moreover, this distance between carboxyl groups correlated with the receptor binding affinity of the aspartate analogs. In view of this correlation, we propose a common mechanism underlying ligand recognition by Tar of compounds with two carboxyl groups.
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Affiliation(s)
- Takashi Sagawa
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Ryota Mashiko
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yusuke Yokota
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Yasushi Naruse
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
| | - Masato Okada
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan.,Department of Complexity Science and Engineering, The University of Tokyo, Kashiwa, Japan
| | - Hiroaki Kojima
- National Institute of Information and Communications Technology (NICT), Advanced ICT Research Institute, Kobe, Japan
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14
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Hu B, Kuang ZK, Feng SY, Wang D, He SB, Kong DX. Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. Molecules 2016; 21:E1554. [PMID: 27869685 PMCID: PMC6273508 DOI: 10.3390/molecules21111554] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023] Open
Abstract
The crystallized ligands in the Protein Data Bank (PDB) can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule to bind with the targets. In this paper, we proposed a shape similarity profile that can be used as a molecular descriptor for ligand-based virtual screening. First, through three-dimensional (3D) structural clustering, 300 diverse ligands were extracted from the druggable protein-ligand database, sc-PDB. Then, each of the molecules under scrutiny was flexibly superimposed onto the 300 ligands. Superimpositions were scored by shape overlap and property similarity, producing a 300 dimensional similarity array termed the "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)". Finally, quantitative or discriminant models were developed with the 300 dimensional descriptor using machine learning methods (support vector machine). The effectiveness of this approach was evaluated using 42 benchmark data sets from the G protein-coupled receptor (GPCR) ligand library and the GPCR decoy database (GLL/GDD). We compared the performance of BRS-3D with other 2D and 3D state-of-the-art molecular descriptors. The results showed that models built with BRS-3D performed best for most GLL/GDD data sets. We also applied BRS-3D in histone deacetylase 1 inhibitors screening and GPCR subtype selectivity prediction. The advantages and disadvantages of this approach are discussed.
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Affiliation(s)
- Ben Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zheng-Kun Kuang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shi-Yu Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Song-Bing He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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