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Collins SP, Mailloux B, Kulkarni S, Gagné M, Long AS, Barton-Maclaren TS. Development and application of consensus in silico models for advancing high-throughput toxicological predictions. Front Pharmacol 2024; 15:1307905. [PMID: 38333007 PMCID: PMC10850302 DOI: 10.3389/fphar.2024.1307905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Abstract
Computational toxicology models have been successfully implemented to prioritize and screen chemicals. There are numerous in silico (quantitative) structure-activity relationship ([Q]SAR) models for the prediction of a range of human-relevant toxicological endpoints, but for a given endpoint and chemical, not all predictions are identical due to differences in their training sets, algorithms, and methodology. This poses an issue for high-throughput screening of a large chemical inventory as it necessitates several models to cover diverse chemistries but will then generate data conflicts. To address this challenge, we developed a consensus modeling strategy to combine predictions obtained from different existing in silico (Q)SAR models into a single predictive value while also expanding chemical space coverage. This study developed consensus models for nine toxicological endpoints relating to estrogen receptor (ER) and androgen receptor (AR) interactions (i.e., binding, agonism, and antagonism) and genotoxicity (i.e., bacterial mutation, in vitro chromosomal aberration, and in vivo micronucleus). Consensus models were created by combining different (Q)SAR models using various weighting schemes. As a multi-objective optimization problem, there is no single best consensus model, and therefore, Pareto fronts were determined for each endpoint to identify the consensus models that optimize the multiple-criterion decisions simultaneously. Accordingly, this work presents sets of solutions for each endpoint that contain the optimal combination, regardless of the trade-off, with the results demonstrating that the consensus models improved both the predictive power and chemical space coverage. These solutions were further analyzed to find trends between the best consensus models and their components. Here, we demonstrate the development of a flexible and adaptable approach for in silico consensus modeling and its application across nine toxicological endpoints related to ER activity, AR activity, and genotoxicity. These consensus models are developed to be integrated into a larger multi-tier NAM-based framework to prioritize chemicals for further investigation and support the transition to a non-animal approach to risk assessment in Canada.
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Affiliation(s)
- Sean P. Collins
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
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2
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Geng C, Wang Z, Tang Y. Machine learning in Alzheimer's disease drug discovery and target identification. Ageing Res Rev 2024; 93:102172. [PMID: 38104638 DOI: 10.1016/j.arr.2023.102172] [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: 10/13/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) stands as a formidable neurodegenerative ailment that poses a substantial threat to the elderly population, with no known curative or disease-slowing drugs in existence. Among the vital and time-consuming stages in the drug discovery process, disease modeling and target identification hold particular significance. Disease modeling allows for a deeper comprehension of disease progression mechanisms and potential therapeutic avenues. On the other hand, target identification serves as the foundational step in drug development, exerting a profound influence on all subsequent phases and ultimately determining the success rate of drug development endeavors. Machine learning (ML) techniques have ushered in transformative breakthroughs in the realm of target discovery. Leveraging the strengths of large dataset analysis, multifaceted data processing, and the exploration of intricate biological mechanisms, ML has become instrumental in the quest for effective AD treatments. In this comprehensive review, we offer an account of how ML methodologies are being deployed in the pursuit of drug discovery for AD. Furthermore, we provide an overview of the utilization of ML in uncovering potential intervention strategies and prospective therapeutic targets for AD. Finally, we discuss the principal challenges and limitations currently faced by these approaches. We also explore the avenues for future research that hold promise in addressing these challenges.
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Affiliation(s)
- Chaofan Geng
- Department of Neurology & Innovation Center for Neurological Disorders, Xuanwu Hospital, Capital Medical University, National Center for Neurological Disorders, Beijing, China
| | - ZhiBin Wang
- Department of Neurology & Innovation Center for Neurological Disorders, Xuanwu Hospital, Capital Medical University, National Center for Neurological Disorders, Beijing, China
| | - Yi Tang
- Department of Neurology & Innovation Center for Neurological Disorders, Xuanwu Hospital, Capital Medical University, National Center for Neurological Disorders, Beijing, China; Neurodegenerative Laboratory of Ministry of Education of the People's Republic of China, Beijing, China.
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3
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Artificial intelligence in virtual screening: models versus experiments. Drug Discov Today 2022; 27:1913-1923. [PMID: 35597513 DOI: 10.1016/j.drudis.2022.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 12/22/2022]
Abstract
A typical drug discovery project involves identifying active compounds with significant binding potential for selected disease-specific targets. Experimental high-throughput screening (HTS) is a traditional approach to drug discovery, but is expensive and time-consuming when dealing with huge chemical libraries with billions of compounds. The search space can be narrowed down with the use of reliable computational screening approaches. In this review, we focus on various machine-learning (ML) and deep-learning (DL)-based scoring functions developed for solving classification and ranking problems in drug discovery. We highlight studies in which ML and DL models were successfully deployed to identify lead compounds for which the experimental validations are available from bioassay studies.
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Kashyap K, Siddiqi MI. Recent trends in artificial intelligence-driven identification and development of anti-neurodegenerative therapeutic agents. Mol Divers 2021; 25:1517-1539. [PMID: 34282519 DOI: 10.1007/s11030-021-10274-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022]
Abstract
Neurological disorders affect various aspects of life. Finding drugs for the central nervous system is a very challenging and complex task due to the involvement of the blood-brain barrier, P-glycoprotein, and the drug's high attrition rates. The availability of big data present in online databases and resources has enabled the emergence of artificial intelligence techniques including machine learning to analyze, process the data, and predict the unknown data with high efficiency. The use of these modern techniques has revolutionized the whole drug development paradigm, with an unprecedented acceleration in the central nervous system drug discovery programs. Also, the new deep learning architectures proposed in many recent works have given a better understanding of how artificial intelligence can tackle big complex problems that arose due to central nervous system disorders. Therefore, the present review provides comprehensive and up-to-date information on machine learning/artificial intelligence-triggered effort in the brain care domain. In addition, a brief overview is presented on machine learning algorithms and their uses in structure-based drug design, ligand-based drug design, ADMET prediction, de novo drug design, and drug repurposing. Lastly, we conclude by discussing the major challenges and limitations posed and how they can be tackled in the future by using these modern machine learning/artificial intelligence approaches.
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Affiliation(s)
- Kushagra Kashyap
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Mohammad Imran Siddiqi
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India. .,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.
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5
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Recent advances in drug repurposing using machine learning. Curr Opin Chem Biol 2021; 65:74-84. [PMID: 34274565 DOI: 10.1016/j.cbpa.2021.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022]
Abstract
Drug repurposing aims to find new uses for already existing and approved drugs. We now provide a brief overview of recent developments in drug repurposing using machine learning alongside other computational approaches for comparison. We also highlight several applications for cancer using kinase inhibitors, Alzheimer's disease as well as COVID-19.
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6
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Neural-based approaches to overcome feature selection and applicability domain in drug-related property prediction. Appl Soft Comput 2019. [DOI: 10.1016/j.asoc.2019.105777] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Wu Q, Cai C, Guo P, Chen M, Wu X, Zhou J, Luo Y, Zou Y, Liu AL, Wang Q, Kuang Z, Fang J. In silico Identification and Mechanism Exploration of Hepatotoxic Ingredients in Traditional Chinese Medicine. Front Pharmacol 2019; 10:458. [PMID: 31130860 PMCID: PMC6509242 DOI: 10.3389/fphar.2019.00458] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDS AND AIMS Recently, a growing number of hepatotoxicity cases aroused by Traditional Chinese Medicine (TCM) have been reported, causing increasing concern. To date, the reported predictive models for drug induced liver injury show low prediction accuracy and there are still no related reports for hepatotoxicity evaluation of TCM systematically. Additionally, the mechanism of herb induced liver injury (HILI) still remains unknown. The aim of the study was to identify potential hepatotoxic ingredients in TCM and explore the molecular mechanism of TCM against HILI. MATERIALS AND METHODS In this study, we developed consensus models for HILI prediction by integrating the best single classifiers. The consensus model with best performance was applied to identify the potential hepatotoxic ingredients from the Traditional Chinese Medicine Systems Pharmacology database (TCMSP). Systems pharmacology analyses, including multiple network construction and KEGG pathway enrichment, were performed to further explore the hepatotoxicity mechanism of TCM. RESULTS 16 single classifiers were built by combining four machine learning methods with four different sets of fingerprints. After systematic evaluation, the best four single classifiers were selected, which achieved a Matthews correlation coefficient (MCC) value of 0.702, 0.691, 0.659, and 0.717, respectively. To improve the predictive capacity of single models, consensus prediction method was used to integrate the best four single classifiers. Results showed that the consensus model C-3 (MCC = 0.78) outperformed the four single classifiers and other consensus models. Subsequently, 5,666 potential hepatotoxic compounds were identified by C-3 model. We integrated the top 10 hepatotoxic herbs and discussed the hepatotoxicity mechanism of TCM via systems pharmacology approach. Finally, Chaihu was selected as the case study for exploring the molecular mechanism of hepatotoxicity. CONCLUSION Overall, this study provides a high accurate approach to predict HILI and an in silico perspective into understanding the hepatotoxicity mechanism of TCM, which might facilitate the discovery and development of new drugs.
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Affiliation(s)
- Qihui Wu
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
- Clinical Research Laboratory, Hainan Province Hospital of Traditional Chinese Medicine, Haikou, China
| | - Chuipu Cai
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Pengfei Guo
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meiling Chen
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoqin Wu
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Jingwei Zhou
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yunxia Luo
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yidan Zou
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ai-lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zaoyuan Kuang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiansong Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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Wu Q, Ke H, Li D, Wang Q, Fang J, Zhou J. Recent Progress in Machine Learning-based Prediction of Peptide Activity for Drug Discovery. Curr Top Med Chem 2019; 19:4-16. [DOI: 10.2174/1568026619666190122151634] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022]
Abstract
Over the past decades, peptide as a therapeutic candidate has received increasing attention in
drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory
peptides (AIPs). It is considered that the peptides can regulate various complex diseases
which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives
the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide-
based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in
the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with
traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly
machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the
peptide activity. In this review, we document the recent progress in machine learning-based prediction
of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.
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Affiliation(s)
- Qihui Wu
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Hanzhong Ke
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, United States
| | - Dongli Li
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiansong Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jingwei Zhou
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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9
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Li Y, Tian Y, Qin Z, Yan A. Classification of HIV-1 Protease Inhibitors by Machine Learning Methods. ACS OMEGA 2018; 3:15837-15849. [PMID: 30556015 PMCID: PMC6288788 DOI: 10.1021/acsomega.8b01843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/24/2018] [Indexed: 05/16/2023]
Abstract
HIV-1 protease plays an important role in the processing of virus infection. Protease is an effective therapeutic target for the treatment of HIV-1. Our data set is based on a selection of 4855 HIV-1 protease inhibitors (PIs) from ChEMBL. A series of 15 classification models for predicting the active inhibitors were built by machine learning methods, including k-nearest neighors (K-NN), decision tree (DT), random forest (RF), support vector machine (SVM), and deep neural network (DNN). The molecular structures were characterized by (1) fingerprint descriptors including MACCS fingerprints and PubChem fingerprints and (2) physicochemical descriptors calculated by CORINA Symphony. The prediction accuracies of all of the models are more than 70% on the test set; the best accuracy of 83.07% was obtained by model 4A, which was built by the SVM method based on MACCS fingerprint descriptors. Nine consensus models were built with three kinds of different descriptors, which combined all of the machine learning methods using the "consensus prediction". Model C3a developed with MACCS fingerprint descriptors showed the highest accuracy on both training set (91.96%) and test set (83.15%). An external validation set including 35 989 compounds from DUD database and 239 active inhibitors from the recent literature was used to verify the performance of our model. The best prediction accuracy of 98.37% was obtained by model 3C, which was built by RF based on CORINA Symphony descriptors. In addition, from the analysis of molecular descriptors, it shows that the aromatic system and atoms related to hydrogen bonding provide important contributions to the bioactivity of PIs.
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Affiliation(s)
- Yang Li
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- Institute
of Science and Technology, Shandong University
of Traditional Chinese Medicine, Ji’nan, Shandong 250355, China
| | - Yujia Tian
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Zijian Qin
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Aixia Yan
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- E-mail: . Phone: +86-10-64421335 (A.Y.)
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10
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Cai C, Fang J, Guo P, Wang Q, Hong H, Moslehi J, Cheng F. In Silico Pharmacoepidemiologic Evaluation of Drug-Induced Cardiovascular Complications Using Combined Classifiers. J Chem Inf Model 2018; 58:943-956. [PMID: 29712429 PMCID: PMC5975252 DOI: 10.1021/acs.jcim.7b00641] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug-induced cardiovascular complications are the most common adverse drug events and account for the withdrawal or severe restrictions on the use of multitudinous postmarketed drugs. In this study, we developed new in silico models for systematic identification of drug-induced cardiovascular complications in drug discovery and postmarketing surveillance. Specifically, we collected drug-induced cardiovascular complications covering the five most common types of cardiovascular outcomes (hypertension, heart block, arrhythmia, cardiac failure, and myocardial infarction) from four publicly available data resources: Comparative Toxicogenomics Database, SIDER, Offsides, and MetaADEDB. Using these databases, we developed a combined classifier framework through integration of five machine-learning algorithms: logistic regression, random forest, k-nearest neighbors, support vector machine, and neural network. The totality of models included 180 single classifiers with area under receiver operating characteristic curves (AUC) ranging from 0.647 to 0.809 on 5-fold cross-validations. To develop the combined classifiers, we then utilized a neural network algorithm to integrate the best four single classifiers for each cardiovascular outcome. The combined classifiers had higher performance with an AUC range from 0.784 to 0.842 compared to single classifiers. Furthermore, we validated our predicted cardiovascular complications for 63 anticancer agents using experimental data from clinical studies, human pluripotent stem cell-derived cardiomyocyte assays, and literature. The success rate of our combined classifiers reached 87%. In conclusion, this study presents powerful in silico tools for systematic risk assessment of drug-induced cardiovascular complications. This tool is relevant not only in early stages of drug discovery but also throughout the life of a drug including clinical trials and postmarketing surveillance.
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Affiliation(s)
- Chuipu Cai
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiansong Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Pengfei Guo
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - Javid Moslehi
- Division of Cardiology, Vanderbilt University, Nashville, TN 37232, USA
- Cardio-Oncology Program, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Feixiong Cheng
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Complex Networks Research, Northeastern University, Boston, MA 02115, USA
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11
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The Mechanisms of Bushen-Yizhi Formula as a Therapeutic Agent against Alzheimer's Disease. Sci Rep 2018; 8:3104. [PMID: 29449587 PMCID: PMC5814461 DOI: 10.1038/s41598-018-21468-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/05/2018] [Indexed: 12/12/2022] Open
Abstract
Bushen-Yizhi prescription (BSYZ) has been an effective traditional Chinese medicine (TCM) prescription in treating Alzheimer’s disease (AD) for hundreds of years. However, the underlying mechanisms have not been fully elucidated yet. In this work, a systems pharmacology approach was developed to reveal the underlying molecular mechanisms of BSYZ in treating AD. First, we obtained 329 candidate compounds of BSYZ by in silico ADME/T filter analysis and 138 AD-related targets were predicted by our in-house WEGA algorithm via mapping predicted targets into AD-related proteins. In addition, we elucidated the mechanisms of BSYZ action on AD through multiple network analysis, including compound-target network analysis and target-function network analysis. Furthermore, several modules regulated by BSYZ were incorporated into AD-related pathways to uncover the therapeutic mechanisms of this prescription in AD treatment. Finally, further verification experiments also demonstrated the therapeutic effects of BSYZ on cognitive dysfunction in APP/PS1 mice, which was possibly via regulating amyloid-β metabolism and suppressing neuronal apoptosis. In conclusion, we provide an integrative systems pharmacology approach to illustrate the underlying therapeutic mechanisms of BSYZ formula action on AD.
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12
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Kang D, Pang X, Lian W, Xu L, Wang J, Jia H, Zhang B, Liu AL, Du GH. Discovery of VEGFR2 inhibitors by integrating naïve Bayesian classification, molecular docking and drug screening approaches. RSC Adv 2018; 8:5286-5297. [PMID: 35542432 PMCID: PMC9078101 DOI: 10.1039/c7ra12259d] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023] Open
Abstract
The high morbidity and mortality of cancer make it one of the leading causes of global death, thus it is an urgent need to develop effective drugs for cancer therapy.
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Affiliation(s)
- De Kang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Xiaocong Pang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Wenwen Lian
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Lvjie Xu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Jinhua Wang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Hao Jia
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Baoyue Zhang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Ai-Lin Liu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
| | - Guan-Hua Du
- Institute of Materia Medica
- Chinese Academy of Medical Sciences
- Peking Union Medical College
- Beijing 100050
- China
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13
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Cai C, Wu Q, Luo Y, Ma H, Shen J, Zhang Y, Yang L, Chen Y, Wen Z, Wang Q. In silico prediction of ROCK II inhibitors by different classification approaches. Mol Divers 2017; 21:791-807. [DOI: 10.1007/s11030-017-9772-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 07/19/2017] [Indexed: 11/25/2022]
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14
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Fang J, Wang L, Li Y, Lian W, Pang X, Wang H, Yuan D, Wang Q, Liu AL, Du GH. AlzhCPI: A knowledge base for predicting chemical-protein interactions towards Alzheimer's disease. PLoS One 2017; 12:e0178347. [PMID: 28542505 PMCID: PMC5460905 DOI: 10.1371/journal.pone.0178347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/11/2017] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) is a complicated progressive neurodegeneration disorder. To confront AD, scientists are searching for multi-target-directed ligands (MTDLs) to delay disease progression. The in silico prediction of chemical-protein interactions (CPI) can accelerate target identification and drug discovery. Previously, we developed 100 binary classifiers to predict the CPI for 25 key targets against AD using the multi-target quantitative structure-activity relationship (mt-QSAR) method. In this investigation, we aimed to apply the mt-QSAR method to enlarge the model library to predict CPI towards AD. Another 104 binary classifiers were further constructed to predict the CPI for 26 preclinical AD targets based on the naive Bayesian (NB) and recursive partitioning (RP) algorithms. The internal 5-fold cross-validation and external test set validation were applied to evaluate the performance of the training sets and test set, respectively. The area under the receiver operating characteristic curve (ROC) for the test sets ranged from 0.629 to 1.0, with an average of 0.903. In addition, we developed a web server named AlzhCPI to integrate the comprehensive information of approximately 204 binary classifiers, which has potential applications in network pharmacology and drug repositioning. AlzhCPI is available online at http://rcidm.org/AlzhCPI/index.html. To illustrate the applicability of AlzhCPI, the developed system was employed for the systems pharmacology-based investigation of shichangpu against AD to enhance the understanding of the mechanisms of action of shichangpu from a holistic perspective.
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Affiliation(s)
- Jiansong Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Yecheng Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Wenwen Lian
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Xiaocong Pang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Hong Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongsheng Yuan
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ai-Lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Guan-Hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
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15
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Fang J, Liu C, Wang Q, Lin P, Cheng F. In silico polypharmacology of natural products. Brief Bioinform 2017; 19:1153-1171. [DOI: 10.1093/bib/bbx045] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Indexed: 12/16/2022] Open
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Fang J, Wang L, Wu T, Yang C, Gao L, Cai H, Liu J, Fang S, Chen Y, Tan W, Wang Q. Network pharmacology-based study on the mechanism of action for herbal medicines in Alzheimer treatment. JOURNAL OF ETHNOPHARMACOLOGY 2017; 196:281-292. [PMID: 27888133 DOI: 10.1016/j.jep.2016.11.034] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Alzheimer's disease (AD), as the most common type of dementia, has brought a heavy economic burden to healthcare system around the world. However, currently there is still lack of effective treatment for AD patients. Herbal medicines, featured as multiple herbs, ingredients and targets, have accumulated a great deal of valuable experience in treating AD although the exact molecular mechanisms are still unclear. MATERIALS AND METHODS In this investigation, we proposed a network pharmacology-based method, which combined large-scale text-mining, drug-likeness filtering, target prediction and network analysis to decipher the mechanisms of action for the most widely studied medicinal herbs in AD treatment. RESULTS The text mining of PubMed resulted in 10 herbs exhibiting significant correlations with AD. Subsequently, after drug-likeness filtering, 1016 compounds were remaining for 10 herbs, followed by structure clustering to sum up chemical scaffolds of herb ingredients. Based on target prediction results performed by our in-house protocol named AlzhCPI, compound-target (C-T) and target-pathway (T-P) networks were constructed to decipher the mechanism of action for anti-AD herbs. CONCLUSIONS Overall, this approach provided a novel strategy to explore the mechanisms of herbal medicine from a holistic perspective.
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Affiliation(s)
- Jiansong Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Pre-Incubator for Innovative Drugs & Medicine, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Tian Wu
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Cong Yang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China
| | - Haobin Cai
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Junhui Liu
- Guangxi University of Chinese Medicine, Nanning 530001, China
| | - Shuhuan Fang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Yunbo Chen
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Wen Tan
- Institute of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Department of Encephalopathy, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China.
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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Fang J, Pang X, Wu P, Yan R, Gao L, Li C, Lian W, Wang Q, Liu AL, Du GH. Molecular Modeling on Berberine Derivatives toward BuChE: An Integrated Study with Quantitative Structure-Activity Relationships Models, Molecular Docking, and Molecular Dynamics Simulations. Chem Biol Drug Des 2016; 87:649-63. [PMID: 26648584 DOI: 10.1111/cbdd.12700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/21/2015] [Accepted: 11/20/2015] [Indexed: 12/31/2022]
Abstract
A dataset of 67 berberine derivatives for the inhibition of butyrylcholinesterase (BuChE) was studied based on the combination of quantitative structure-activity relationships models, molecular docking, and molecular dynamics methods. First, a series of berberine derivatives were reported, and their inhibitory activities toward butyrylcholinesterase (BuChE) were evaluated. By 2D- quantitative structure-activity relationships studies, the best model built by partial least-square had a conventional correlation coefficient of the training set (R(2)) of 0.883, a cross-validation correlation coefficient (Qcv2) of 0.777, and a conventional correlation coefficient of the test set (Rpred2) of 0.775. The model was also confirmed by Y-randomization examination. In addition, the molecular docking and molecular dynamics simulation were performed to better elucidate the inhibitory mechanism of three typical berberine derivatives (berberine, C2, and C55) toward BuChE. The predicted binding free energy results were consistent with the experimental data and showed that the van der Waals energy term (ΔEvdw) difference played the most important role in differentiating the activity among the three inhibitors (berberine, C2, and C55). The developed quantitative structure-activity relationships models provide details on the fine relationship linking structure and activity and offer clues for structural modifications, and the molecular simulation helps to understand the inhibitory mechanism of the three typical inhibitors. In conclusion, the results of this study provide useful clues for new drug design and discovery of BuChE inhibitors from berberine derivatives.
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Affiliation(s)
- Jiansong Fang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Institute of Clinical Pharmacology, Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510006, China
| | - Xiaocong Pang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ping Wu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rong Yan
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Li Gao
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chao Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenwen Lian
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qi Wang
- Institute of Clinical Pharmacology, Guangzhou University of Traditional Chinese Medicine, Guangzhou, 510006, China
| | - Ai-lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Beijing Key Laboratory of Drug Target and Screening Research, Beijing, 100050, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, 100050, China
| | - Guan-hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.,Beijing Key Laboratory of Drug Target and Screening Research, Beijing, 100050, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, 100050, China
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Fang J, Pang X, Yan R, Lian W, Li C, Wang Q, Liu AL, Du GH. Discovery of neuroprotective compounds by machine learning approaches. RSC Adv 2016. [DOI: 10.1039/c5ra23035g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The classification models were constructed to discover neuroprotective compounds against glutamate or H2O2-induced neurotoxicity through machine learning approaches.
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Affiliation(s)
- Jiansong Fang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Institute of Clinical Pharmacology
| | - Xiaocong Pang
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Rong Yan
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Wenwen Lian
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Chao Li
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
| | - Qi Wang
- Institute of Clinical Pharmacology
- Guangzhou University of Traditional Chinese Medicine
- Guangzhou 510006
- China
| | - Ai-Lin Liu
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Beijing Key Laboratory of Drug Target and Screening Research
| | - Guan-Hua Du
- Institute of Materia Medica
- Chinese Academy of Medical Sciences and Peking Union Medical College
- Beijing 100050
- PR China
- Beijing Key Laboratory of Drug Target and Screening Research
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Discovery of Influenza A virus neuraminidase inhibitors using support vector machine and Naïve Bayesian models. Mol Divers 2015; 20:439-51. [PMID: 26689205 DOI: 10.1007/s11030-015-9641-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Neuraminidase (NA) is a critical enzyme in the life cycle of influenza virus, which is known as a successful paradigm in the design of anti-influenza agents. However, to date there are no classification models for the virtual screening of NA inhibitors. In this work, we built support vector machine and Naïve Bayesian models of NA inhibitors and non-inhibitors, with different ratios of active-to-inactive compounds in the training set and different molecular descriptors. Four models with sensitivity or Matthews correlation coefficients greater than 0.9 were chosen to predict the NA inhibitory activities of 15,600 compounds in our in-house database. We combined the results of four optimal models and selected 60 representative compounds to assess their NA inhibitory profiles in vitro. Nine NA inhibitors were identified, five of which were oseltamivir derivatives with large C-5 substituents exhibiting potent inhibition against H1N1 NA with IC50 values in the range of 12.9-185.0 nM, and against H3N2 NA with IC50 values between 18.9 and 366.1 nM. The other four active compounds belonged to novel scaffolds, with IC50 values ranging 39.5-63.8 μM against H1N1 NA and 44.5-114.1 μM against H3N2 NA. This is the first time that classification models of NA inhibitors and non-inhibitors are built and their prediction results validated experimentally using in vitro assays.
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Fang J, Li Y, Liu R, Pang X, Li C, Yang R, He Y, Lian W, Liu AL, Du GH. Discovery of multitarget-directed ligands against Alzheimer's disease through systematic prediction of chemical-protein interactions. J Chem Inf Model 2015; 55:149-64. [PMID: 25531792 DOI: 10.1021/ci500574n] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To determine chemical-protein interactions (CPI) is costly, time-consuming, and labor-intensive. In silico prediction of CPI can facilitate the target identification and drug discovery. Although many in silico target prediction tools have been developed, few of them could predict active molecules against multitarget for a single disease. In this investigation, naive Bayesian (NB) and recursive partitioning (RP) algorithms were applied to construct classifiers for predicting the active molecules against 25 key targets toward Alzheimer's disease (AD) using the multitarget-quantitative structure-activity relationships (mt-QSAR) method. Each molecule was initially represented with two kinds of fingerprint descriptors (ECFP6 and MACCS). One hundred classifiers were constructed, and their performance was evaluated and verified with internally 5-fold cross-validation and external test set validation. The range of the area under the receiver operating characteristic curve (ROC) for the test sets was from 0.741 to 1.0, with an average of 0.965. In addition, the important fragments for multitarget against AD given by NB classifiers were also analyzed. Finally, the validated models were employed to systematically predict the potential targets for six approved anti-AD drugs and 19 known active compounds related to AD. The prediction results were confirmed by reported bioactivity data and our in vitro experimental validation, resulting in several multitarget-directed ligands (MTDLs) against AD, including seven acetylcholinesterase (AChE) inhibitors ranging from 0.442 to 72.26 μM and four histamine receptor 3 (H3R) antagonists ranging from 0.308 to 58.6 μM. To be exciting, the best MTDL DL0410 was identified as an dual cholinesterase inhibitor with IC50 values of 0.442 μM (AChE) and 3.57 μM (BuChE) as well as a H3R antagonist with an IC50 of 0.308 μM. This investigation is the first report using mt-QASR approach to predict chemical-protein interaction for a single disease and discovering highly potent MTDLs. This protocol may be useful for in silico multitarget prediction of other diseases.
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Affiliation(s)
- Jiansong Fang
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050, PR China
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