101
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Pandit S, Singh P, Sinha M, Parthasarathi R. Integrated QSAR and Adverse Outcome Pathway Analysis of Chemicals Released on 3D Printing Using Acrylonitrile Butadiene Styrene. Chem Res Toxicol 2021; 34:355-364. [PMID: 33416328 DOI: 10.1021/acs.chemrestox.0c00274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Additive manufacturing commonly known as 3D printing has numerous applications in several domains including material and biomedical technologies and has emerged as a tool of capabilities by providing fast, highly customized, and cost-effective solutions. However, the impact of the printing materials and chemicals present in the printing fumes has raised concerns about their adverse potential affecting humans and the environment. Thus, it is necessary to understand the properties of the chemicals emitted during additive manufacturing for developing safe and biocompatible fibers having controlled emission of fumes including its sustainable usage. Therefore, in this study, we have developed a computational predictive risk-assessment framework on the comprehensive list of chemicals released during 3D printing using the acrylonitrile butadiene styrene (ABS) filament. Our results showed that the chemicals present in the fumes of the ABS-based fiber used in additive manufacturing have the potential to lead to various toxicity end points such as inhalation toxicity, oral toxicity, carcinogenicity, hepatotoxicity, and teratogenicity. Moreover, because of their absorption, distribution in the body, metabolism, and excretion properties, most of the chemicals exhibited a high absorption level in the intestine and the potential to cross the blood-brain barrier. Furthermore, pathway analysis revealed that signaling like alpha-adrenergic receptor signaling, heterotrimeric G-protein signaling, and Alzheimer's disease-amyloid secretase pathway are significantly overrepresented given the identified target proteins of these chemicals. These findings signify the adversities associated with 3D printing fumes and the necessity for the development of biodegradable and considerably safer fibers for 3D printing technology.
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Affiliation(s)
- Shraddha Pandit
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prakrity Singh
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Meetali Sinha
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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102
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Paul D, Sanap G, Shenoy S, Kalyane D, Kalia K, Tekade RK. Artificial intelligence in drug discovery and development. Drug Discov Today 2021; 26:80-93. [PMID: 33099022 PMCID: PMC7577280 DOI: 10.1016/j.drudis.2020.10.010] [Citation(s) in RCA: 314] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
Artificial intelligence-integrated drug discovery and development has accelerated the growth of the pharmaceutical sector, leading to a revolutionary change in the pharma industry. Here, we discuss areas of integration, tools, and techniques utilized in enforcing AI, ongoing challenges, and ways to overcome them.
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Affiliation(s)
- Debleena Paul
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India
| | - Gaurav Sanap
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India
| | - Snehal Shenoy
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India
| | - Dnyaneshwar Kalyane
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India
| | - Kiran Kalia
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India
| | - Rakesh K Tekade
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Palaj, Opp. Air Force Station, Gandhinagar, 382355, Gujarat, India.
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103
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Liu X, IJzerman AP, van Westen GJP. Computational Approaches for De Novo Drug Design: Past, Present, and Future. Methods Mol Biol 2021; 2190:139-165. [PMID: 32804364 DOI: 10.1007/978-1-0716-0826-5_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug discovery is time- and resource-consuming. To this end, computational approaches that are applied in de novo drug design play an important role to improve the efficiency and decrease costs to develop novel drugs. Over several decades, a variety of methods have been proposed and applied in practice. Traditionally, drug design problems are always taken as combinational optimization in discrete chemical space. Hence optimization methods were exploited to search for new drug molecules to meet multiple objectives. With the accumulation of data and the development of machine learning methods, computational drug design methods have gradually shifted to a new paradigm. There has been particular interest in the potential application of deep learning methods to drug design. In this chapter, we will give a brief description of these two different de novo methods, compare their application scopes and discuss their possible development in the future.
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Affiliation(s)
- Xuhan Liu
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
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104
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Park J, Kim J, Pané S, Nelson BJ, Choi H. Acoustically Mediated Controlled Drug Release and Targeted Therapy with Degradable 3D Porous Magnetic Microrobots. Adv Healthc Mater 2021; 10:e2001096. [PMID: 33111498 DOI: 10.1002/adhm.202001096] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/09/2020] [Indexed: 12/13/2022]
Abstract
Microrobots for targeted drug delivery are of great interest due to their minimal invasiveness and wireless controllability. Here, a magnetically driven porous degradable microrobot (PDM) is reported that consists of a 3D printed helical soft polymeric chassis made of a poly(ethylene glycol) diacrylate and pentaerythritol triacrylate matrix containing magnetite nanoparticles and the anticancer drug 5-fluorouracil (5-FU). The encapsulated Fe3 O4 nanoparticles render the PDM a precise wireless magnetic actuation by means of rotating magnetic fields (RMFs). The increased surface area of the porous PDM facilitates the acoustically induced drug release due to a higher response to the acoustic energy. The drug release profile from the PDM can be selected on command from three different modes, referred to herein as natural, burst, and constant, by differentiating the ultrasound exposure condition. Finally, in vitro test results reveal different therapeutic results for each release mode. The observed great reduction of cancer cell viability in the burst- and constant-release modes confirms that ultrasound with the proposed PDM can enhance the therapeutic effect by increasing drug concentration and sonoporation.
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Affiliation(s)
- Jongeon Park
- DGIST‐ETH Microrobot Research Center (DEMRC) Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
- Department of Robotics Engineering Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
| | - Jin‐young Kim
- DGIST‐ETH Microrobot Research Center (DEMRC) Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
- Department of Robotics Engineering Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
| | - Salvador Pané
- Institute of Robotics and Intelligent Systems ETH Zurich Zurich CH‐8092 Switzerland
| | - Bradley J. Nelson
- Institute of Robotics and Intelligent Systems ETH Zurich Zurich CH‐8092 Switzerland
| | - Hongsoo Choi
- DGIST‐ETH Microrobot Research Center (DEMRC) Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
- Department of Robotics Engineering Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
- DGIST Robotics Research Center Daegu Gyeongbuk Institute of Science and Technology (DGIST) Daegu 42988 South Korea
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105
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Marmon P, Owen SF, Margiotta-Casaluci L. Pharmacology-informed prediction of the risk posed to fish by mixtures of non-steroidal anti-inflammatory drugs (NSAIDs) in the environment. ENVIRONMENT INTERNATIONAL 2021; 146:106222. [PMID: 33157376 PMCID: PMC7786791 DOI: 10.1016/j.envint.2020.106222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 05/23/2023]
Abstract
The presence of non-steroidal anti-inflammatory drugs (NSAIDs) in the aquatic environment has raised concern that chronic exposure to these compounds may cause adverse effects in wild fish populations. This potential scenario has led some stakeholders to advocate a stricter regulation of NSAIDs, especially diclofenac. Considering their global clinical importance for the management of pain and inflammation, any regulation that may affect patient access to NSAIDs will have considerable implications for public health. The current environmental risk assessment of NSAIDs is driven by the results of a limited number of standard toxicity tests and does not take into account mechanistic and pharmacological considerations. Here we present a pharmacology-informed framework that enables the prediction of the risk posed to fish by 25 different NSAIDs and their dynamic mixtures. Using network pharmacology approaches, we demonstrated that these 25 NSAIDs display a significant mechanistic promiscuity that could enhance the risk of target-mediated mixture effects near environmentally relevant concentrations. Integrating NSAIDs pharmacokinetic and pharmacodynamic features, we provide highly specific predictions of the adverse phenotypes associated with exposure to NSAIDs, and we developed a visual multi-scale model to guide the interpretation of the toxicological relevance of any given set of NSAIDs exposure data. Our analysis demonstrated a non-negligible risk posed to fish by NSAID mixtures in situations of high drug use and low dilution of waste-water treatment plant effluents. We anticipate that this predictive framework will support the future regulatory environmental risk assessment of NSAIDs and increase the effectiveness of ecopharmacovigilance strategies. Moreover, it can facilitate the prediction of the toxicological risk posed by mixtures via the implementation of mechanistic considerations and could be readily extended to other classes of chemicals.
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Affiliation(s)
- Philip Marmon
- Department of Life Sciences, College of Health, Medicine, and Life Sciences, Brunel University London, London, UB8 3PH, UK
| | - Stewart F Owen
- AstraZeneca, Global Environment, Alderley Park, Macclesfield, Cheshire SK10 4TF, UK
| | - Luigi Margiotta-Casaluci
- Department of Life Sciences, College of Health, Medicine, and Life Sciences, Brunel University London, London, UB8 3PH, UK.
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106
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Giblin KA, Basili D, Afzal AM, Rosenbrier-Ribeiro L, Greene N, Barrett I, Hughes SJ, Bender A. New Associations between Drug-Induced Adverse Events in Animal Models and Humans Reveal Novel Candidate Safety Targets. Chem Res Toxicol 2020; 34:438-451. [PMID: 33338378 DOI: 10.1021/acs.chemrestox.0c00311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To improve our ability to extrapolate preclinical toxicity to humans, there is a need to understand and quantify the concordance of adverse events (AEs) between animal models and clinical studies. In the present work, we discovered 3011 statistically significant associations between preclinical and clinical AEs caused by drugs reported in the PharmaPendium database of which 2952 were new associations between toxicities encoded by different Medical Dictionary for Regulatory Activities terms across species. To find plausible and testable candidate off-target drug activities for the derived associations, we investigated the genetic overlap between the genes linked to both a preclinical and a clinical AE and the protein targets found to interact with one or more drugs causing both AEs. We discuss three associations from the analysis in more detail for which novel candidate off-target drug activities could be identified, namely, the association of preclinical mutagenicity readouts with clinical teratospermia and ovarian failure, the association of preclinical reflexes abnormal with clinical poor-quality sleep, and the association of preclinical psychomotor hyperactivity with clinical drug withdrawal syndrome. Our analysis successfully identified a total of 77% of known safety targets currently tested in in vitro screening panels plus an additional 431 genes which were proposed for investigation as future safety targets for different clinical toxicities. This work provides new translational toxicity relationships beyond AE term-matching, the results of which can be used for risk profiling of future new chemical entities for clinical studies and for the development of future in vitro safety panels.
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Affiliation(s)
- Kathryn A Giblin
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Danilo Basili
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Avid M Afzal
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Lyn Rosenbrier-Ribeiro
- Safety Platforms, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Nigel Greene
- Data Science and Artificial Intelligence, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Ian Barrett
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Samantha J Hughes
- Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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107
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Gong L, Xu Y, Liu G, Zheng M, Zhang X, Hang Y, Kang J. Profiling
Drug‐Protein
Interactions by Micro Column Affinity Purification Combined with Label Free Quantification Proteomics
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Li Gong
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Yao Xu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Guizhen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology, ShanghaiTech University Haike Road 100 Shanghai 200120 China
| | - Mengmeng Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Xuepei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Ying Hang
- School of Life Science and Technology, ShanghaiTech University Haike Road 100 Shanghai 200120 China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Physical Science and Technology, ShanghaiTech University Haike Road 100 Shanghai 200120 China
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108
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Dafniet B, Cerisier N, Audouze K, Taboureau O. Drug-target-ADR Network and Possible Implications of Structural Variants in Adverse Events. Mol Inform 2020; 39:e2000116. [PMID: 32725965 PMCID: PMC8047896 DOI: 10.1002/minf.202000116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
Adverse drug reactions (ADRs) are of major concern in drug safety. However, due to the biological complexity of human systems, understanding the underlying mechanisms involved in development of ADRs remains a challenging task. Here, we applied network sciences to analyze a tripartite network between 1000 drugs, 1407 targets, and 6164 ADRs. It allowed us to suggest drug targets susceptible to be associated to ADRs and organs, based on the system organ class (SOC). Furthermore, a score was developed to determine the contribution of a set of proteins to ADRs. Finally, we identified proteins that might increase the susceptibility of genes to ADRs, on the basis of knowledge about genomic structural variation in genes encoding proteins targeted by drugs. Such analysis should pave the way to individualize drug therapy and precision medicine.
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Affiliation(s)
- Bryan Dafniet
- Université de ParisINSERM U1133, CNRS UMR 825175006ParisFrance
| | | | - Karine Audouze
- Université de ParisT3S, INSERM UMR S-112475006ParisFrance
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109
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Chen Y, Kirchmair J. Cheminformatics in Natural Product-based Drug Discovery. Mol Inform 2020; 39:e2000171. [PMID: 32725781 PMCID: PMC7757247 DOI: 10.1002/minf.202000171] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
This review seeks to provide a timely survey of the scope and limitations of cheminformatics methods in natural product-based drug discovery. Following an overview of data resources of chemical, biological and structural information on natural products, we discuss, among other aspects, in silico methods for (i) data curation and natural products dereplication, (ii) analysis, visualization, navigation and comparison of the chemical space, (iii) quantification of natural product-likeness, (iv) prediction of the bioactivities (virtual screening, target prediction), ADME and safety profiles (toxicity) of natural products, (v) natural products-inspired de novo design and (vi) prediction of natural products prone to cause interference with biological assays. Among the many methods discussed are rule-based, similarity-based, shape-based, pharmacophore-based and network-based approaches, docking and machine learning methods.
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Affiliation(s)
- Ya Chen
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH)Department of Computer ScienceFaculty of MathematicsInformatics and Natural SciencesUniversität Hamburg20146HamburgGermany
- Department of Pharmaceutical ChemistryFaculty of Life SciencesUniversity of Vienna1090ViennaAustria
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110
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Cáceres EL, Mew NC, Keiser MJ. Adding Stochastic Negative Examples into Machine Learning Improves Molecular Bioactivity Prediction. J Chem Inf Model 2020; 60:5957-5970. [PMID: 33245237 DOI: 10.1021/acs.jcim.0c00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multitask deep neural networks learn to predict ligand-target binding by example, yet public pharmacological data sets are sparse, imbalanced, and approximate. We constructed two hold-out benchmarks to approximate temporal and drug-screening test scenarios, whose characteristics differ from a random split of conventional training data sets. We developed a pharmacological data set augmentation procedure, Stochastic Negative Addition (SNA), which randomly assigns untested molecule-target pairs as transient negative examples during training. Under the SNA procedure, drug-screening benchmark performance increases from R2 = 0.1926 ± 0.0186 to 0.4269 ± 0.0272 (122%). This gain was accompanied by a modest decrease in the temporal benchmark (13%). SNA increases in drug-screening performance were consistent for classification and regression tasks and outperformed y-randomized controls. Our results highlight where data and feature uncertainty may be problematic and how leveraging uncertainty into training improves predictions of drug-target relationships.
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Affiliation(s)
- Elena L Cáceres
- Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Bakar Computational Health Sciences Institute, Kavli Institute for Fundamental Neuroscience, Institute for Neurodegenerative Diseases, University of California, San Francisco, 675 Nelson Rising Ln NS 416A, San Francisco, California 94143, United States
| | - Nicholas C Mew
- Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Bakar Computational Health Sciences Institute, Kavli Institute for Fundamental Neuroscience, Institute for Neurodegenerative Diseases, University of California, San Francisco, 675 Nelson Rising Ln NS 416A, San Francisco, California 94143, United States
| | - Michael J Keiser
- Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Bakar Computational Health Sciences Institute, Kavli Institute for Fundamental Neuroscience, Institute for Neurodegenerative Diseases, University of California, San Francisco, 675 Nelson Rising Ln NS 416A, San Francisco, California 94143, United States
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111
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Feldmann C, Yonchev D, Bajorath J. Analysis of Biological Screening Compounds with Single- or Multi-Target Activity via Diagnostic Machine Learning. Biomolecules 2020; 10:biom10121605. [PMID: 33260876 PMCID: PMC7761051 DOI: 10.3390/biom10121605] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 01/06/2023] Open
Abstract
Predicting compounds with single- and multi-target activity and exploring origins of compound specificity and promiscuity is of high interest for chemical biology and drug discovery. We present a large-scale analysis of compound promiscuity including two major components. First, high-confidence datasets of compounds with multi- and corresponding single-target activity were extracted from biological screening data. Positive and negative assay results were taken into account and data completeness was ensured. Second, these datasets were investigated using diagnostic machine learning to systematically distinguish between compounds with multi- and single-target activity. Models built on the basis of chemical structure consistently produced meaningful predictions. These findings provided evidence for the presence of structural features differentiating promiscuous and non-promiscuous compounds. Machine learning under varying conditions using modified datasets revealed a strong influence of nearest neighbor relationship on the predictions. Many multi-target compounds were found to be more similar to other multi-target compounds than single-target compounds and vice versa, which resulted in consistently accurate predictions. The results of our study confirm the presence of structural relationships that differentiate promiscuous and non-promiscuous compounds.
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112
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Virtual screening and drug repurposing experiments to identify potential novel selective MAO-B inhibitors for Parkinson's disease treatment. Mol Divers 2020; 25:1775-1794. [PMID: 33237524 DOI: 10.1007/s11030-020-10155-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
The main study's purpose is to detect novel natural products (NPs) that are potentially selective MAO-B inhibitors and, additionally, to computationally reposition the marketed drugs with a new therapeutic role for Parkinson's disease. To reach the goals, 3D similarity search, docking, ADMETox, and drug repurposing approaches were employed. Thus, an unbiased benchmarking dataset was built including selective and nonselective inhibitors for MAO-B compliant with both ligand- and structure-based virtual screening approaches. A retrospective and prospective mining scenario was applied to SPECS NP and DrugBank databases to detect novel scaffolds with potential benefits for Parkinson's disease patients. Out of the three best selected natural products, cardamomin showed excellently predicted drug-like properties, superior pharmacological profile, and specific interactions with MAO-B active site, indicating a potential selectivity over MAO-B. Two marketed drugs, fenamisal and monobenzone, were proposed as promising candidates repurposed for Parkinson's disease. The application of shape, physicochemical, and electrostatic similarity searches protocol emerged as a plausible solution to explore MAO-B inhibitors selectivity. This protocol might serve as a rewarding tool in early drug discovery and can be extended to other protein targets.
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113
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González-Durruthy M, Concu R, Vendrame LFO, Zanella I, Ruso JM, Cordeiro MNDS. Targeting Beta-Blocker Drug-Drug Interactions with Fibrinogen Blood Plasma Protein: A Computational and Experimental Study. Molecules 2020; 25:molecules25225425. [PMID: 33228181 PMCID: PMC7699576 DOI: 10.3390/molecules25225425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/05/2022] Open
Abstract
In this work, one of the most prevalent polypharmacology drug–drug interaction events that occurs between two widely used beta-blocker drugs—i.e., acebutolol and propranolol—with the most abundant blood plasma fibrinogen protein was evaluated. Towards that end, molecular docking and Density Functional Theory (DFT) calculations were used as complementary tools. A fibrinogen crystallographic validation for the three best ranked binding-sites shows 100% of conformationally favored residues with total absence of restricted flexibility. From those three sites, results on both the binding-site druggability and ligand transport analysis-based free energy trajectories pointed out the most preferred biophysical environment site for drug–drug interactions. Furthermore, the total affinity for the stabilization of the drug–drug complexes was mostly influenced by steric energy contributions, based mainly on multiple hydrophobic contacts with critical residues (THR22: P and SER50: Q) in such best-ranked site. Additionally, the DFT calculations revealed that the beta-blocker drug–drug complexes have a spontaneous thermodynamic stabilization following the same affinity order obtained in the docking simulations, without covalent-bond formation between both interacting beta-blockers in the best-ranked site. Lastly, experimental ultrasound density and velocity measurements were performed and allowed us to validate and corroborate the computational obtained results.
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Affiliation(s)
- Michael González-Durruthy
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Correspondence: (M.G.-D.); (M.N.D.S.C.); Tel.: +351-220402502 (M.N.D.S.C.)
| | - Riccardo Concu
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
| | - Laura F. Osmari Vendrame
- Post-Graduate Program in Nanoscience, Franciscana University (UFN), Santa Maria 97010-032, RS, Brazil; (L.F.O.V.); (I.Z.)
| | - Ivana Zanella
- Post-Graduate Program in Nanoscience, Franciscana University (UFN), Santa Maria 97010-032, RS, Brazil; (L.F.O.V.); (I.Z.)
| | - Juan M. Ruso
- Soft Matter and Molecular Biophysics Group, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - M. Natália D. S. Cordeiro
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal;
- Correspondence: (M.G.-D.); (M.N.D.S.C.); Tel.: +351-220402502 (M.N.D.S.C.)
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Feldmann C, Yonchev D, Stumpfe D, Bajorath J. Systematic Data Analysis and Diagnostic Machine Learning Reveal Differences between Compounds with Single- and Multitarget Activity. Mol Pharm 2020; 17:4652-4666. [PMID: 33151084 DOI: 10.1021/acs.molpharmaceut.0c00901] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small molecules with multitarget activity are capable of triggering polypharmacological effects and are of high interest in drug discovery. Compared to single-target compounds, promiscuity also affects drug distribution and pharmacodynamics and alters ADMET characteristics. Features distinguishing between compounds with single- and multitarget activity are currently only little understood. On the basis of systematic data analysis, we have assembled large sets of promiscuous compounds with activity against related or functionally distinct targets and the corresponding compounds with single-target activity. Machine learning predicted promiscuous compounds with surprisingly high accuracy. Molecular similarity analysis combined with control calculations under varying conditions revealed that accurate predictions were largely determined by structural nearest-neighbor relationships between compounds from different classes. We also found that large proportions of promiscuous compounds with activity against related or unrelated targets and corresponding single-target compounds formed analog series with distinct chemical space coverage, which further rationalized the predictions. Moreover, compounds with activity against proteins from functionally distinct classes were often active against unique targets that were not covered by other promiscuous compounds. The results of our analysis revealed that nearest-neighbor effects determined the prediction of promiscuous compounds and that preferential partitioning of compounds with single- and multitarget activity into structurally distinct analog series was responsible for such effects, hence providing a rationale for the presence of different structure-promiscuity relationships.
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Affiliation(s)
- Christian Feldmann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Dimitar Yonchev
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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115
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Cho KW, Lee WH, Kim BS, Kim DH. Sensors in heart-on-a-chip: A review on recent progress. Talanta 2020; 219:121269. [DOI: 10.1016/j.talanta.2020.121269] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/14/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023]
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116
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Yang S, Ye Q, Ding J, Yin, Lu A, Chen X, Hou T, Cao D. Current advances in ligand‐based target prediction. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Su‐Qing Yang
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
| | - Qing Ye
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Jun‐Jie Ding
- Beijing Institute of Pharmaceutical Chemistry Beijing China
| | - Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ai‐Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital Central South University Changsha Hunan China
| | - Ting‐Jun Hou
- College of Pharmaceutical Sciences Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University Hangzhou, Zhejiang China
| | - Dong‐Sheng Cao
- Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine Hong Kong Baptist University Hong Kong China
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117
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Xi Y, Liu J, Wang H, Li S, Yi Y, Du Y. New small-molecule compound Hu-17 inhibits estrogen biosynthesis by aromatase in human ovarian granulosa cancer cells. Cancer Med 2020; 9:9081-9095. [PMID: 33002342 PMCID: PMC7724309 DOI: 10.1002/cam4.3492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/17/2020] [Accepted: 09/08/2020] [Indexed: 12/20/2022] Open
Abstract
Estrogen-dependent cancers (breast, endometrial, and ovarian) are among the leading causes of morbidity and mortality in women worldwide. Aromatase is the main enzyme that catalyzes the biosynthesis of estrogen, which drives proliferation, and antiestrogens can inhibit the growth of these estrogen-dependent cancers. Hu-17, an aromatase inhibitor, is a novel small-molecule compound that suppresses viability of and promotes apoptosis in ovarian cancer cells. Therefore, this study aimed to predict targets of Hu-17 and assess its intracellular signaling in ovarian cancer cells. Using the Similarity Ensemble Approach software to predict the potential mechanism of Hu-17 and combining phospho-proteome arrays with western blot analysis, we observed that Hu-17 could inhibit the ERK pathway, resulting in reduced estrogen synthesis in KGN cells, a cell line derived from a patient with invasive ovarian granulosa cell carcinoma. Hu-17 reduced the expression of CYP19A1 mRNA, responsible for producing aromatase, by suppressing the phosphorylation of cAMP response element binding-1. Hu-17 also accelerated aromatase protein degradation but had no effect on aromatase activity. Therefore, Hu-17 could serve as a potential treatment for estrogen-dependent cancers albeit further investigation is warranted.
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Affiliation(s)
- Yang Xi
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.,Central Laboratory, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Jiansheng Liu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Haiwei Wang
- Institute of Health Sciences, School of Medicine (SJTUSM)/Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Shang Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Yanghua Yi
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
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118
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Qiu ZC, Zhang Y, Xiao HH, Chui-Wa Poon C, Li XL, Cui JF, Wong MK, Yao XS, Wong MS. 8-prenylgenistein exerts osteogenic effects via ER α and Wnt-dependent signaling pathway. Exp Cell Res 2020; 395:112186. [DOI: 10.1016/j.yexcr.2020.112186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/08/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
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119
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Mayr F, Möller G, Garscha U, Fischer J, Rodríguez Castaño P, Inderbinen SG, Temml V, Waltenberger B, Schwaiger S, Hartmann RW, Gege C, Martens S, Odermatt A, Pandey AV, Werz O, Adamski J, Stuppner H, Schuster D. Finding New Molecular Targets of Familiar Natural Products Using In Silico Target Prediction. Int J Mol Sci 2020; 21:E7102. [PMID: 32993084 PMCID: PMC7582679 DOI: 10.3390/ijms21197102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/01/2022] Open
Abstract
Natural products comprise a rich reservoir for innovative drug leads and are a constant source of bioactive compounds. To find pharmacological targets for new or already known natural products using modern computer-aided methods is a current endeavor in drug discovery. Nature's treasures, however, could be used more effectively. Yet, reliable pipelines for the large-scale target prediction of natural products are still rare. We developed an in silico workflow consisting of four independent, stand-alone target prediction tools and evaluated its performance on dihydrochalcones (DHCs)-a well-known class of natural products. Thereby, we revealed four previously unreported protein targets for DHCs, namely 5-lipoxygenase, cyclooxygenase-1, 17β-hydroxysteroid dehydrogenase 3, and aldo-keto reductase 1C3. Moreover, we provide a thorough strategy on how to perform computational target predictions and guidance on using the respective tools.
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Affiliation(s)
- Fabian Mayr
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (F.M.); (V.T.); (B.W.); (S.S.); (H.S.)
| | - Gabriele Möller
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; (G.M.); (J.A.)
| | - Ulrike Garscha
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany; (U.G.); (J.F.)
| | - Jana Fischer
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany; (U.G.); (J.F.)
| | - Patricia Rodríguez Castaño
- Pediatric Endocrinology, Diabetology and Metabolism, University Children’s Hospital Bern, Freiburgstrasse 15, 3010 Bern, Switzerland; (P.R.C.); (A.V.P.)
- Department of Biomedical Research, University of Bern, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Silvia G. Inderbinen
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (S.G.I.); (A.O.)
| | - Veronika Temml
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (F.M.); (V.T.); (B.W.); (S.S.); (H.S.)
| | - Birgit Waltenberger
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (F.M.); (V.T.); (B.W.); (S.S.); (H.S.)
| | - Stefan Schwaiger
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (F.M.); (V.T.); (B.W.); (S.S.); (H.S.)
| | - Rolf W. Hartmann
- Helmholtz Institute of Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization, Campus E8.1, 66123 Saarbrücken, Germany;
- Saarland University, Pharmaceutical and Medicinal Chemistry, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christian Gege
- University of Heidelberg, Institute of Pharmacy and Molecular Biotechnology (IPMB), Medicinal Chemistry, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany;
| | - Stefan Martens
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010 San Michele all’Adige, Italy;
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland; (S.G.I.); (A.O.)
| | - Amit V. Pandey
- Pediatric Endocrinology, Diabetology and Metabolism, University Children’s Hospital Bern, Freiburgstrasse 15, 3010 Bern, Switzerland; (P.R.C.); (A.V.P.)
- Department of Biomedical Research, University of Bern, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany;
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and Metabolism, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; (G.M.); (J.A.)
- Lehrstuhl für Experimentelle Genetik, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85356 Freising-Weihenstephan, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; (F.M.); (V.T.); (B.W.); (S.S.); (H.S.)
| | - Daniela Schuster
- Institute of Pharmacy, Department of Pharmaceutical and Medicinal Chemistry, Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg, Austria
- Institute of Pharmacy/Pharmaceutical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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120
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Agamah FE, Mazandu GK, Hassan R, Bope CD, Thomford NE, Ghansah A, Chimusa ER. Computational/in silico methods in drug target and lead prediction. Brief Bioinform 2020; 21:1663-1675. [PMID: 31711157 PMCID: PMC7673338 DOI: 10.1093/bib/bbz103] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023] Open
Abstract
Drug-like compounds are most of the time denied approval and use owing to the unexpected clinical side effects and cross-reactivity observed during clinical trials. These unexpected outcomes resulting in significant increase in attrition rate centralizes on the selected drug targets. These targets may be disease candidate proteins or genes, biological pathways, disease-associated microRNAs, disease-related biomarkers, abnormal molecular phenotypes, crucial nodes of biological network or molecular functions. This is generally linked to several factors, including incomplete knowledge on the drug targets and unpredicted pharmacokinetic expressions upon target interaction or off-target effects. A method used to identify targets, especially for polygenic diseases, is essential and constitutes a major bottleneck in drug development with the fundamental stage being the identification and validation of drug targets of interest for further downstream processes. Thus, various computational methods have been developed to complement experimental approaches in drug discovery. Here, we present an overview of various computational methods and tools applied in predicting or validating drug targets and drug-like molecules. We provide an overview on their advantages and compare these methods to identify effective methods which likely lead to optimal results. We also explore major sources of drug failure considering the challenges and opportunities involved. This review might guide researchers on selecting the most efficient approach or technique during the computational drug discovery process.
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Affiliation(s)
- Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- African Institute for Mathematical Sciences, Muizenberg, Cape Town 7945, South Africa
| | - Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Christian D Bope
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, PO Box LG 581, Legon, Ghana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
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121
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Pottel J, Armstrong D, Zou L, Fekete A, Huang XP, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, Shoichet BK, Urban L. The activities of drug inactive ingredients on biological targets. Science 2020; 369:403-413. [PMID: 32703874 DOI: 10.1126/science.aaz9906] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 05/18/2020] [Indexed: 12/22/2022]
Abstract
Excipients, considered "inactive ingredients," are a major component of formulated drugs and play key roles in their pharmacokinetics. Despite their pervasiveness, whether they are active on any targets has not been systematically explored. We computed the likelihood that approved excipients would bind to molecular targets. Testing in vitro revealed 25 excipient activities, ranging from low-nanomolar to high-micromolar concentration. Another 109 activities were identified by testing against clinical safety targets. In cellular models, five excipients had fingerprints predictive of system-level toxicity. Exposures of seven excipients were investigated, and in certain populations, two of these may reach levels of in vitro target potency, including brain and gut exposure of thimerosal and its major metabolite, which had dopamine D3 receptor dissociation constant K d values of 320 and 210 nM, respectively. Although most excipients deserve their status as inert, many approved excipients may directly modulate physiologically relevant targets.
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Affiliation(s)
- Joshua Pottel
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Duncan Armstrong
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ling Zou
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Alexander Fekete
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Dallas Bednarczyk
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Steven Whitebread
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Barun Bhhatarai
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Guiqing Liang
- PK Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Hong Jin
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - S Nassir Ghaemi
- Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.,Tufts University School of Medicine, Boston, MA 02111, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Samuel Slocum
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Katalin V Lukacs
- National Heart and Lung Institute, Imperial College, London SW7 2AZ, UK
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ellen L Berg
- Eurofins, DiscoverX, South San Francisco, CA 94080, USA
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27759, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Laszlo Urban
- Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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122
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Sachdev K, Gupta MK. A hybrid ensemble-based technique for predicting drug-target interactions. Chem Biol Drug Des 2020; 96:1447-1455. [PMID: 32638508 DOI: 10.1111/cbdd.13753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/14/2020] [Accepted: 06/14/2020] [Indexed: 11/30/2022]
Abstract
Drug-target interaction is the intercommunication between chemical drugs and target proteins to produce any kind of change in the human body. The laboratory experiments conducted to recognize these potential intercommunications are costly and tedious. Various computational methods have been established recently, including the chemogenomic approach for identifying drug-target intercommunication, that integrates the chemical data of the drugs and the genomic properties of the proteins for identifying the interactions between them. This paper proposes a novel technique based on hybrid ensemble to predict drug target interactions. Hybrid ensembles introduce diversity in classification that helps to improve the performance of prediction. The proposed method has been evaluated by comparing the technique with state-of-the-art methods on two different databases under three cross-validation settings. The comparison clearly shows that the technique produced significant improvement in the interaction prediction.
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Affiliation(s)
- Kanica Sachdev
- School of Computer Science and Engineering, Shri Mata Vaishno Devi University, Jammu and Kashmir, India
| | - Manoj Kumar Gupta
- School of Computer Science and Engineering, Shri Mata Vaishno Devi University, Jammu and Kashmir, India
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123
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Cheng B, Ren Y, Niu X, Wang W, Wang S, Tu Y, Liu S, Wang J, Yang D, Liao G, Chen J. Discovery of Novel Resorcinol Dibenzyl Ethers Targeting the Programmed Cell Death-1/Programmed Cell Death–Ligand 1 Interaction as Potential Anticancer Agents. J Med Chem 2020; 63:8338-8358. [DOI: 10.1021/acs.jmedchem.0c00574] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Binbin Cheng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Yichang Ren
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Xiaoge Niu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Wei Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Shuanghu Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Yingfeng Tu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Shuwen Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Jin Wang
- AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Deying Yang
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People’s Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Guochao Liao
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People’s Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
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124
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Ietswaart R, Arat S, Chen AX, Farahmand S, Kim B, DuMouchel W, Armstrong D, Fekete A, Sutherland JJ, Urban L. Machine learning guided association of adverse drug reactions with in vitro target-based pharmacology. EBioMedicine 2020; 57:102837. [PMID: 32565027 PMCID: PMC7379147 DOI: 10.1016/j.ebiom.2020.102837] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/08/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Adverse drug reactions (ADRs) are one of the leading causes of morbidity and mortality in health care. Understanding which drug targets are linked to ADRs can lead to the development of safer medicines. METHODS Here, we analyse in vitro secondary pharmacology of common (off) targets for 2134 marketed drugs. To associate these drugs with human ADRs, we utilized FDA Adverse Event Reports and developed random forest models that predict ADR occurrences from in vitro pharmacological profiles. FINDINGS By evaluating Gini importance scores of model features, we identify 221 target-ADR associations, which co-occur in PubMed abstracts to a greater extent than expected by chance. Amongst these are established relations, such as the association of in vitro hERG binding with cardiac arrhythmias, which further validate our machine learning approach. Evidence on bile acid metabolism supports our identification of associations between the Bile Salt Export Pump and renal, thyroid, lipid metabolism, respiratory tract and central nervous system disorders. Unexpectedly, our model suggests PDE3 is associated with 40 ADRs. INTERPRETATION These associations provide a comprehensive resource to support drug development and human biology studies. FUNDING This study was not supported by any formal funding bodies.
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Affiliation(s)
- Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States.
| | - Seda Arat
- The Jackson Laboratory, Farmington, CT 06032, United States.
| | - Amanda X Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Saman Farahmand
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, United States
| | - Bumjun Kim
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, United States
| | | | - Duncan Armstrong
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States
| | - Alexander Fekete
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States
| | - Jeffrey J Sutherland
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States.
| | - Laszlo Urban
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, United States.
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125
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Hauser AS, Kooistra AJ, Sverrisdóttir E, Sessa M. Utilizing drug-target-event relationships to unveil safety patterns in pharmacovigilance. Expert Opin Drug Saf 2020; 19:961-968. [PMID: 32510245 DOI: 10.1080/14740338.2020.1780208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION Signal detection is the most pivotal activity of signal management to guarantee that drugs maintain a positive risk-benefit ratio during their lifetime on the market. Signal detection is based on the systematic evaluation of available data sources, which have recently been extended in order to improve timely and comprehensive signal detection of drug safety problems. AREAS COVERED In recent years, attempts have been made to incorporate pharmacological data for the prediction of safety signals. Previous studies have shown that data on the pharmacological targets of drugs are predictive of post-marketing adverse events. However, current approaches limit such predictions to adverse events expected from the interaction of a drug with the main pharmacological target and do not take off-target interactions into consideration. EXPERT OPINION The authors propose the application of predictive modeling techniques utilizing pharmacological data from public databases for predicting drug-target-event relationships deriving from main- and off-target binding and from which potential safety signals can be deduced. Additionally, they provide an operative procedure for the identification of clinically relevant subgroups for predicted safety signals.
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Affiliation(s)
| | - Albert Jelke Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen , Copenhagen, Denmark
| | - Eva Sverrisdóttir
- Department of Drug Design and Pharmacology, University of Copenhagen , Copenhagen, Denmark
| | - Maurizio Sessa
- Department of Drug Design and Pharmacology, University of Copenhagen , Copenhagen, Denmark
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126
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Cortés-Ciriano I, Škuta C, Bender A, Svozil D. QSAR-derived affinity fingerprints (part 2): modeling performance for potency prediction. J Cheminform 2020; 12:41. [PMID: 33431016 PMCID: PMC7339533 DOI: 10.1186/s13321-020-00444-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/16/2020] [Indexed: 01/22/2023] Open
Abstract
Affinity fingerprints report the activity of small molecules across a set of assays, and thus permit to gather information about the bioactivities of structurally dissimilar compounds, where models based on chemical structure alone are often limited, and model complex biological endpoints, such as human toxicity and in vitro cancer cell line sensitivity. Here, we propose to model in vitro compound activity using computationally predicted bioactivity profiles as compound descriptors. To this aim, we apply and validate a framework for the calculation of QSAR-derived affinity fingerprints (QAFFP) using a set of 1360 QSAR models generated using Ki, Kd, IC50 and EC50 data from ChEMBL database. QAFFP thus represent a method to encode and relate compounds on the basis of their similarity in bioactivity space. To benchmark the predictive power of QAFFP we assembled IC50 data from ChEMBL database for 18 diverse cancer cell lines widely used in preclinical drug discovery, and 25 diverse protein target data sets. This study complements part 1 where the performance of QAFFP in similarity searching, scaffold hopping, and bioactivity classification is evaluated. Despite being inherently noisy, we show that using QAFFP as descriptors leads to errors in prediction on the test set in the ~ 0.65-0.95 pIC50 units range, which are comparable to the estimated uncertainty of bioactivity data in ChEMBL (0.76-1.00 pIC50 units). We find that the predictive power of QAFFP is slightly worse than that of Morgan2 fingerprints and 1D and 2D physicochemical descriptors, with an effect size in the 0.02-0.08 pIC50 units range. Including QSAR models with low predictive power in the generation of QAFFP does not lead to improved predictive power. Given that the QSAR models we used to compute the QAFFP were selected on the basis of data availability alone, we anticipate better modeling results for QAFFP generated using more diverse and biologically meaningful targets. Data sets and Python code are publicly available at https://github.com/isidroc/QAFFP_regression .
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Affiliation(s)
- Isidro Cortés-Ciriano
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK.
| | - Ctibor Škuta
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daniel Svozil
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20, Prague, Czech Republic.,CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague, Czech Republic
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127
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Ferro CJ, Solkhon F, Jalal Z, Al‐Hamid AM, Jones AM. Relevance of physicochemical properties and functional pharmacology data to predict the clinical safety profile of direct oral anticoagulants. Pharmacol Res Perspect 2020; 8:e00603. [PMID: 32500654 PMCID: PMC7272392 DOI: 10.1002/prp2.603] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/09/2020] [Indexed: 12/16/2022] Open
Abstract
Direct oral anticoagulants (DOACs) have rapidly become the drug class of choice for anticoagulation therapy in secondary care. It is known that gastrointestinal hemorrhage are potential side effects of the DOAC drug class. In this study we have investigated the relevance of molecular structure and on/off-target pharmacology as a predictor of adverse drug reactions (ADRs) for the DOAC drug class. Use of the Reaxys MedChem module allowed for data mining of all possible reported off-target effects of the DOAC class members. For the first time, the MHRA Yellow card database in combination with prescribing rates in the United Kingdom (data for n = 30 566 936 DOAC Rx (up to 2017) and ADR data n = 22 275 (up to 2018)) were used for our data comparison of DOACs. From the underlying reported data, we were able to rank the DOACs in terms of the likely adverse events we would expect to observe. We identified potential risks of ADRs based on the DOACs pharmacology including the expected GI hemorrhage, but also the unexpected risk of stroke, pulmonary embolism and kidney injury. Statistically significant (P < .001) differences were found between all DOACs and their total number of ADRs. Although the risks are small, strong statistical correlation between observed pharmacology and national ADR data is observed in three out of the five areas of concern.
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Affiliation(s)
- Charles J. Ferro
- Queen Elizabeth HospitalUniversity Hospitals Birmingham NHS Foundation TrustBirminghamUK
| | - Fay Solkhon
- School of PharmacyUniversity of BirminghamBirminghamUK
| | - Zahraa Jalal
- School of PharmacyUniversity of BirminghamBirminghamUK
| | | | - Alan M. Jones
- School of PharmacyUniversity of BirminghamBirminghamUK
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128
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Mathai N, Kirchmair J. Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope. Int J Mol Sci 2020; 21:ijms21103585. [PMID: 32438666 PMCID: PMC7279241 DOI: 10.3390/ijms21103585] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 12/20/2022] Open
Abstract
Computational methods for predicting the macromolecular targets of drugs and drug-like compounds have evolved as a key technology in drug discovery. However, the established validation protocols leave several key questions regarding the performance and scope of methods unaddressed. For example, prediction success rates are commonly reported as averages over all compounds of a test set and do not consider the structural relationship between the individual test compounds and the training instances. In order to obtain a better understanding of the value of ligand-based methods for target prediction, we benchmarked a similarity-based method and a random forest based machine learning approach (both employing 2D molecular fingerprints) under three testing scenarios: a standard testing scenario with external data, a standard time-split scenario, and a scenario that is designed to most closely resemble real-world conditions. In addition, we deconvoluted the results based on the distances of the individual test molecules from the training data. We found that, surprisingly, the similarity-based approach generally outperformed the machine learning approach in all testing scenarios, even in cases where queries were structurally clearly distinct from the instances in the training (or reference) data, and despite a much higher coverage of the known target space.
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Affiliation(s)
- Neann Mathai
- Department of Chemistry and Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway;
| | - Johannes Kirchmair
- Department of Chemistry and Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway;
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
- Correspondence:
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129
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Wang Z, Guo K, Gao P, Pu Q, Wu M, Li C, Hur J. Identification of Repurposable Drugs and Adverse Drug Reactions for Various Courses of COVID-19 Based on Single-Cell RNA Sequencing Data. ARXIV 2020:arXiv:2005.07856v2. [PMID: 33299905 PMCID: PMC7724679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 12/04/2020] [Indexed: 10/26/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has impacted almost every part of human life worldwide, posing a massive threat to human health. There is no specific drug for COVID-19, highlighting the urgent need for the development of effective therapeutics. To identify potentially repurposable drugs, we employed a systematic approach to mine candidates from U.S. FDA-approved drugs and preclinical small-molecule compounds by integrating the gene expression perturbation data for chemicals from the Library of Integrated Network-Based Cellular Signatures project with a publicly available single-cell RNA sequencing dataset from mild and severe COVID-19 patients. We identified 281 FDA-approved drugs that have the potential to be effective against SARS-CoV-2 infection, 16 of which are currently undergoing clinical trials to evaluate their efficacy against COVID-19. We experimentally tested the inhibitory effects of tyrphostin-AG-1478 and brefeldin-a on the replication of the single-stranded ribonucleic acid (ssRNA) virus influenza A virus. In conclusion, we have identified a list of repurposable anti-SARS-CoV-2 drugs using a systems biology approach.
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Affiliation(s)
- Zhihan Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Kai Guo
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Pan Gao
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Qinqin Pu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Changlong Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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130
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Prakash AV, Park JW, Seong JW, Kang TJ. Repositioned Drugs for Inflammatory Diseases such as Sepsis, Asthma, and Atopic Dermatitis. Biomol Ther (Seoul) 2020; 28:222-229. [PMID: 32133828 PMCID: PMC7216745 DOI: 10.4062/biomolther.2020.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
The process of drug discovery and drug development consumes billions of dollars to bring a new drug to the market. Drug development is time consuming and sometimes, the failure rates are high. Thus, the pharmaceutical industry is looking for a better option for new drug discovery. Drug repositioning is a good alternative technology that has demonstrated many advantages over de novo drug development, the most important one being shorter drug development timelines. In the last two decades, drug repositioning has made tremendous impact on drug development technologies. In this review, we focus on the recent advances in drug repositioning technologies and discuss the repositioned drugs used for inflammatory diseases such as sepsis, asthma, and atopic dermatitis.
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Affiliation(s)
- Annamneedi Venkata Prakash
- Convergence Research Center, Department of Pharmacy and Institute of Chronic Disease, Sahmyook University, Seoul 01795, Republic of Korea
| | - Jun Woo Park
- Convergence Research Center, Department of Pharmacy and Institute of Chronic Disease, Sahmyook University, Seoul 01795, Republic of Korea
| | - Ju-Won Seong
- Convergence Research Center, Department of Pharmacy and Institute of Chronic Disease, Sahmyook University, Seoul 01795, Republic of Korea
| | - Tae Jin Kang
- Convergence Research Center, Department of Pharmacy and Institute of Chronic Disease, Sahmyook University, Seoul 01795, Republic of Korea
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131
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Zeng X, Zhu S, Hou Y, Zhang P, Li L, Li J, Huang LF, Lewis SJ, Nussinov R, Cheng F. Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest. Bioinformatics 2020; 36:2805-2812. [PMID: 31971579 PMCID: PMC7203727 DOI: 10.1093/bioinformatics/btaa010] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/24/2019] [Accepted: 01/17/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Systematic identification of molecular targets among known drugs plays an essential role in drug repurposing and understanding of their unexpected side effects. Computational approaches for prediction of drug-target interactions (DTIs) are highly desired in comparison to traditional experimental assays. Furthermore, recent advances of multiomics technologies and systems biology approaches have generated large-scale heterogeneous, biological networks, which offer unexpected opportunities for network-based identification of new molecular targets among known drugs. RESULTS In this study, we present a network-based computational framework, termed AOPEDF, an arbitrary-order proximity embedded deep forest approach, for prediction of DTIs. AOPEDF learns a low-dimensional vector representation of features that preserve arbitrary-order proximity from a highly integrated, heterogeneous biological network connecting drugs, targets (proteins) and diseases. In total, we construct a heterogeneous network by uniquely integrating 15 networks covering chemical, genomic, phenotypic and network profiles among drugs, proteins/targets and diseases. Then, we build a cascade deep forest classifier to infer new DTIs. Via systematic performance evaluation, AOPEDF achieves high accuracy in identifying molecular targets among known drugs on two external validation sets collected from DrugCentral [area under the receiver operating characteristic curve (AUROC) = 0.868] and ChEMBL (AUROC = 0.768) databases, outperforming several state-of-the-art methods. In a case study, we showcase that multiple molecular targets predicted by AOPEDF are associated with mechanism-of-action of substance abuse disorder for several marketed drugs (such as aripiprazole, risperidone and haloperidol). AVAILABILITY AND IMPLEMENTATION Source code and data can be downloaded from https://github.com/ChengF-Lab/AOPEDF.
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Affiliation(s)
- Xiangxiang Zeng
- Department of Computer Science, College of Information Science and Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Siyi Zhu
- Department of Computer Science, Xiamen University, Xiamen 361005, China
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Pengyue Zhang
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA
| | - Lang Li
- Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, USA
| | - Jing Li
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology, Brain Tumor Center, Cincinnati Children’s Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Stephen J Lewis
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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132
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Harada S, Akita H, Tsubaki M, Baba Y, Takigawa I, Yamanishi Y, Kashima H. Dual graph convolutional neural network for predicting chemical networks. BMC Bioinformatics 2020; 21:94. [PMID: 32321421 PMCID: PMC7178944 DOI: 10.1186/s12859-020-3378-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Background Predicting of chemical compounds is one of the fundamental tasks in bioinformatics and chemoinformatics, because it contributes to various applications in metabolic engineering and drug discovery. The recent rapid growth of the amount of available data has enabled applications of computational approaches such as statistical modeling and machine learning method. Both a set of chemical interactions and chemical compound structures are represented as graphs, and various graph-based approaches including graph convolutional neural networks have been successfully applied to chemical network prediction. However, there was no efficient method that can consider the two different types of graphs in an end-to-end manner. Results We give a new formulation of the chemical network prediction problem as a link prediction problem in a graph of graphs (GoG) which can represent the hierarchical structure consisting of compound graphs and an inter-compound graph. We propose a new graph convolutional neural network architecture called dual graph convolutional network that learns compound representations from both the compound graphs and the inter-compound network in an end-to-end manner. Conclusions Experiments using four chemical networks with different sparsity levels and degree distributions shows that our dual graph convolution approach achieves high prediction performance in relatively dense networks, while the performance becomes inferior on extremely-sparse networks.
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Affiliation(s)
| | | | - Masashi Tsubaki
- National Institute of Advanced Industrial Science and Technology, Tokyo, 1350064, Japan
| | | | - Ichigaku Takigawa
- Hokkaido University, Hokkaido, 0600808, Japan.,Riken AIP, Tokyo, 1030027, Japan
| | | | - Hisashi Kashima
- Kyoto University, Kyoto, 6068501, Japan.,Riken AIP, Tokyo, 1030027, Japan
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133
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Kumar M, Pandey S, Swami A, Wangoo N, Saima, Jain R, Sharma RK. Peptide- and Drug-Functionalized Fluorescent Quantum Dots for Enhanced Cell Internalization and Bacterial Debilitation. ACS APPLIED BIO MATERIALS 2020; 3:1913-1923. [PMID: 35025314 DOI: 10.1021/acsabm.9b01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This report illustrates a strategy for designing a nanoconjugate derived vector that efficiently delivers antimicrobial drug directly into bacterial cells. The nanoconjugate comprises of negatively charged CDTe@CdS quantum dots (QDs) with its surface functionalized using cationic BP-100 (KKLFKKILKYL-amide), a known cell-penetrating peptide (CPP), via electrostatic approach. The interactions between QD and CPP in QD-functionalized CPPs (QD-CPP) have been well analyzed using fluorescence spectroscopy, gel electrophoresis, and ζ-potential analysis. The QD-CPP conjugate was internalized into Gram negative (Escherichia coli) as well as Gram positive (Staphylococcus aureus) bacterial strains with confocal studies exhibiting a strong signal in tested microorganisms. Further, to check the applicability of QD-CPP conjugate as a delivery vector for generating an effective therapeutics, ampicillin molecules were conjugated on QD-CPP surface to generate QD-CPP-Amp conjugate. The CPP and drug molecules on the surface of QDs were well quantified using high-performance liquid chromatography (HPLC) data. It was observed that the internalization and bacterial debilitation of the QD-CPP-Amp conjugate is 2- to 4-fold effective as compared to that of bare ampicillin. The morphological changes to the bacterial cells upon the treatment with QD-CPP-Amp conjugates were noted with no cytotoxic effect on tested mammalian cell lines. The results inferred that the proposed QD-CPP vector provides a targeted and proficient approach for cellular internalization of cargo (drug) in bacterial cells with effective tracking through florescent QDs.
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Affiliation(s)
- Munish Kumar
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
| | - Satish Pandey
- Central Scientific Instruments Organisation, Chandigarh 160017, India
| | - Anuradha Swami
- Department of Applied Sciences, University Institute of Engineering & Technology (U.I.E.T.), Panjab University, Sector-25, Chandigarh 160014, India.,Centre for Nanoscience & Nanotechnology, Panjab University, Sector-25, Chandigarh 160014, India
| | - Nishima Wangoo
- Department of Applied Sciences, University Institute of Engineering & Technology (U.I.E.T.), Panjab University, Sector-25, Chandigarh 160014, India
| | - Saima
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Rohit K Sharma
- Department of Chemistry & Centre for Advanced Studies in Chemistry, Panjab University, Sector-14, Chandigarh 160014, India
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134
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A compound attributes-based predictive model for drug induced liver injury in humans. PLoS One 2020; 15:e0231252. [PMID: 32294131 PMCID: PMC7159228 DOI: 10.1371/journal.pone.0231252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/29/2020] [Indexed: 11/19/2022] Open
Abstract
Drug induced liver injury (DILI) is one of the key safety concerns in drug development. To assess the likelihood of drug candidates with potential adverse reactions of liver, we propose a compound attributes-based approach to predicting hepatobiliary disorders that are routinely reported to US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS). Specifically, we developed a support vector machine (SVM) model with recursive feature extraction, based on physicochemical and structural properties of compounds as model input. Cross validation demonstrates that the predictive model has a robust performance with averaged 70% of both sensitivity and specificity over 500 trials. An independent validation was performed on public benchmark drugs and the results suggest potential utility of our model for identifying safety alerts. This in silico approach, upon further validation, would ultimately be implemented, together with other in vitro safety assays, for screening compounds early in drug development.
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135
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Van Norman GA. Limitations of Animal Studies for Predicting Toxicity in Clinical Trials: Part 2: Potential Alternatives to the Use of Animals in Preclinical Trials. JACC Basic Transl Sci 2020; 5:387-397. [PMID: 32363250 PMCID: PMC7185927 DOI: 10.1016/j.jacbts.2020.03.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 12/28/2022]
Abstract
Dramatically rising costs in drug development are in large part because of the high failure rates in clinical phase trials. The poor correlation of animal studies to human toxicity and efficacy have led many developers to question the value of requiring animal studies in determining which drugs should enter in-human trials. Part 1 of this 2-part series examined some of the data regarding the lack of concordance between animal toxicity studies and human trials, as well as some of the potential reasons behind it. This second part of the series focuses on some alternatives to animal trials (hereafter referred to as animal research) as well as current regulatory discussions and developments regarding such alternatives.
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Affiliation(s)
- Gail A. Van Norman
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington
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136
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Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account. ACTA ACUST UNITED AC 2020; 11:e73. [PMID: 31483099 DOI: 10.1002/cpch.73] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The modes of action (MoAs) of drugs frequently are unknown, because many are small molecules initially identified from phenotypic screens, giving rise to the need to elucidate their MoAs. In addition, the high attrition rate for candidate drugs in preclinical studies due to intolerable toxicity has motivated the development of computational approaches to predict drug candidate (cyto)toxicity as early as possible in the drug-discovery process. Here, we provide detailed instructions for capitalizing on bioactivity predictions to elucidate the MoAs of small molecules and infer their underlying phenotypic effects. We illustrate how these predictions can be used to infer the underlying antidepressive effects of marketed drugs. We also provide the necessary functionalities to model cytotoxicity data using single and ensemble machine-learning algorithms. Finally, we give detailed instructions on how to calculate confidence intervals for individual predictions using the conformal prediction framework. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Georgios Drakakis
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Isidro Cortés-Ciriano
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ben Alexander-Dann
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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137
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Scalise M, Pochini L, Galluccio M, Console L, Indiveri C. Glutamine transporters as pharmacological targets: From function to drug design. Asian J Pharm Sci 2020; 15:207-219. [PMID: 32373200 PMCID: PMC7193454 DOI: 10.1016/j.ajps.2020.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/18/2020] [Accepted: 02/29/2020] [Indexed: 12/17/2022] Open
Abstract
Among the different targets of administered drugs, there are membrane transporters that play also a role in drug delivery and disposition. Moreover, drug-transporter interactions are responsible for off-target effects of drugs underlying their toxicity. The improvement of the drug design process is subjected to the identification of those membrane transporters mostly relevant for drug absorption, delivery and side effect production. A peculiar group of proteins with great relevance to pharmacology is constituted by the membrane transporters responsible for managing glutamine traffic in different body districts. The interest around glutamine metabolism lies in its physio-pathological role; glutamine is considered a conditionally essential amino acid because highly proliferative cells have an increased request of glutamine that cannot be satisfied only by endogenous synthesis. Then, glutamine transporters provide cells with this special nutrient. Among the glutamine transporters, SLC1A5, SLC6A14, SLC6A19, SLC7A5, SLC7A8 and some members of SLC38 family are the best characterized, so far, in both physiological and pathological conditions. Few 3D structures have been solved by CryoEM; other structural data on these transporters have been obtained by computational analysis. Interactions with drugs have been described for several transporters of this group. For some of them, the studies are at an advanced stage, for others, the studies are still in nuce and novel biochemical findings open intriguing perspectives.
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Affiliation(s)
- Mariafrancesca Scalise
- Department of DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Arcavacata di Rende (CS) 87036, Italy
| | - Lorena Pochini
- Department of DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Arcavacata di Rende (CS) 87036, Italy
| | - Michele Galluccio
- Department of DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Arcavacata di Rende (CS) 87036, Italy
| | - Lara Console
- Department of DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Arcavacata di Rende (CS) 87036, Italy
| | - Cesare Indiveri
- Department of DiBEST (Biologia, Ecologia e Scienze della Terra), University of Calabria, Arcavacata di Rende (CS) 87036, Italy
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138
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Sebastian-Perez V, García-Rubia A, Seif El-Din SH, Sabra ANA, El-Lakkany NM, William S, Blundell TL, Maes L, Martinez A, Campillo NE, Botros SS, Gil C. Deciphering the enzymatic target of a new family of antischistosomal agents bearing a quinazoline scaffold using complementary computational tools. J Enzyme Inhib Med Chem 2020; 35:511-523. [PMID: 31939312 PMCID: PMC7717570 DOI: 10.1080/14756366.2020.1712595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A previous phenotypic screening campaign led to the identification of a quinazoline derivative with promising in vitro activity against Schistosoma mansoni. Follow-up studies of the antischistosomal potential of this candidate are presented here. The in vivo studies in a S. mansoni mouse model show a significant reduction of total worms and a complete disappearance of immature eggs when administered concomitantly with praziquantel in comparison with the administration of praziquantel alone. This fact is of utmost importance because eggs are responsible for the pathology and transmission of the disease. Subsequently, the chemical optimisation of the structure in order to improve the metabolic stability of the parent compound was carried out leading to derivatives with improved drug-like properties. Additionally, the putative target of this new class of antischistosomal compounds was envisaged by using computational tools and the binding mode to the target enzyme, aldose reductase, was proposed.
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Affiliation(s)
| | | | | | | | | | - Samia William
- Parasitology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Ana Martinez
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
| | | | - Sanaa S Botros
- Pharmacology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Carmen Gil
- Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
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139
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Gu S, Lai LH. Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach. Acta Pharmacol Sin 2020; 41:432-438. [PMID: 31530902 PMCID: PMC7470807 DOI: 10.1038/s41401-019-0306-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
Chinese herbal medicine (CHM) addresses complex diseases through polypharmacological interactions. However, systematic studies of herbal medicine pharmacology remain challenging due to the complexity of CHM ingredients and their interactions with various targets. In this study, we aim to address this challenge with computational approaches. We investigated the herb-target-disease associations of 197 commonly prescribed CHMs using the similarity ensemble approach and DisGeNET database. We demonstrated that this method can be applied to associate herbs with their putative targets. In the case study of three well-known herbs, Radix Glycyrrhizae, Flos Lonicerae, and Rhizoma Coptidis, approximately 70% of the predicted targets were supported by scientific literature. By linking 406 targets to 2439 annotated diseases, we further analyzed the pharmacological functions of 197 herbs. Finally, we proposed a strategy of target-oriented herbal formula design and illustrated the target profiles for four common chronic diseases, namely, Alzheimer's disease, depressive disorder, hypertensive disease, and non-insulin-dependent diabetes mellitus. This computational approach holds great potential in the target identification of herbs, understanding the molecular mechanisms of CHM, and designing novel herbal formulas.
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Affiliation(s)
- Shuo Gu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, and the Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Lu-Hua Lai
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering, and the Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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140
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Lyu J, Wang K, Ye M. Modification-free approaches to screen drug targets at proteome level. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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141
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Vibala B, Praseetha P, Vijayakumar S. Evaluating new strategies for anticancer molecules from ethnic medicinal plants through in silico and biological approach - A review. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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142
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Antolin AA, Ameratunga M, Banerji U, Clarke PA, Workman P, Al-Lazikani B. The kinase polypharmacology landscape of clinical PARP inhibitors. Sci Rep 2020; 10:2585. [PMID: 32066817 PMCID: PMC7026418 DOI: 10.1038/s41598-020-59074-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 01/21/2020] [Indexed: 01/06/2023] Open
Abstract
Polypharmacology plays an important role in defining response and adverse effects of drugs. For some mechanisms, experimentally mapping polypharmacology is commonplace, although this is typically done within the same protein class. Four PARP inhibitors have been approved by the FDA as cancer therapeutics, yet a precise mechanistic rationale to guide clinicians on which to choose for a particular patient is lacking. The four drugs have largely similar PARP family inhibition profiles, but several differences at the molecular and clinical level have been reported that remain poorly understood. Here, we report the first comprehensive characterization of the off-target kinase landscape of four FDA-approved PARP drugs. We demonstrate that all four PARP inhibitors have a unique polypharmacological profile across the kinome. Niraparib and rucaparib inhibit DYRK1s, CDK16 and PIM3 at clinically achievable, submicromolar concentrations. These kinases represent the most potently inhibited off-targets of PARP inhibitors identified to date and should be investigated further to clarify their potential implications for efficacy and safety in the clinic. Moreover, broad kinome profiling is recommended for the development of PARP inhibitors as PARP-kinase polypharmacology could potentially be exploited to modulate efficacy and side-effect profiles.
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Affiliation(s)
- Albert A Antolin
- Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK.
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
| | - Malaka Ameratunga
- Drug Development Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Udai Banerji
- Drug Development Unit, The Institute of Cancer Research, London, SM2 5NG, UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
| | - Bissan Al-Lazikani
- Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK.
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK.
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143
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Yukawa T, Naven R. Utility of Physicochemical Properties for the Prediction of Toxicological Outcomes: Takeda Perspective. ACS Med Chem Lett 2020; 11:203-209. [PMID: 32071689 DOI: 10.1021/acsmedchemlett.9b00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
The role that physicochemical properties play toward increasing the likelihood of toxicity findings in in vivo studies has been well reported, albeit sometimes with different conclusions. We decided to understand the role that physicochemical properties play toward the prediction of in vivo toxicological outcomes for Takeda chemistry using 284 internal compounds. In support of the previously reported "3/75 rule", reducing lipophilicity of molecules decreases toxicity odds noticeably; however, we also found that the trend of toxicity odds is different between compounds classified by their ionization state. For basic molecules, the odds of in vivo toxicity outcomes were significantly impacted by both lipophilicity and polar surface area, whereas neutral molecules were impacted less so. Through an analysis of several project-related compounds, we herein demonstrate that the utilization of the 3/75 rule coupled with consideration of ionization state is a rational strategy for medicinal chemistry design of safer drugs.
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Affiliation(s)
- Tomoya Yukawa
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Russell Naven
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
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144
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Pliakos K, Vens C. Drug-target interaction prediction with tree-ensemble learning and output space reconstruction. BMC Bioinformatics 2020; 21:49. [PMID: 32033537 PMCID: PMC7006075 DOI: 10.1186/s12859-020-3379-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/21/2020] [Indexed: 12/21/2022] Open
Abstract
Background Computational prediction of drug-target interactions (DTI) is vital for drug discovery. The experimental identification of interactions between drugs and target proteins is very onerous. Modern technologies have mitigated the problem, leveraging the development of new drugs. However, drug development remains extremely expensive and time consuming. Therefore, in silico DTI predictions based on machine learning can alleviate the burdensome task of drug development. Many machine learning approaches have been proposed over the years for DTI prediction. Nevertheless, prediction accuracy and efficiency are persisting problems that still need to be tackled. Here, we propose a new learning method which addresses DTI prediction as a multi-output prediction task by learning ensembles of multi-output bi-clustering trees (eBICT) on reconstructed networks. In our setting, the nodes of a DTI network (drugs and proteins) are represented by features (background information). The interactions between the nodes of a DTI network are modeled as an interaction matrix and compose the output space in our problem. The proposed approach integrates background information from both drug and target protein spaces into the same global network framework. Results We performed an empirical evaluation, comparing the proposed approach to state of the art DTI prediction methods and demonstrated the effectiveness of the proposed approach in different prediction settings. For evaluation purposes, we used several benchmark datasets that represent drug-protein networks. We show that output space reconstruction can boost the predictive performance of tree-ensemble learning methods, yielding more accurate DTI predictions. Conclusions We proposed a new DTI prediction method where bi-clustering trees are built on reconstructed networks. Building tree-ensemble learning models with output space reconstruction leads to superior prediction results, while preserving the advantages of tree-ensembles, such as scalability, interpretability and inductive setting.
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Affiliation(s)
- Konstantinos Pliakos
- KU Leuven, Campus KULAK, Faculty of Medicine, Kortrijk, Belgium. .,ITEC, imec research group at KU Leuven, Kortrijk, Belgium.
| | - Celine Vens
- KU Leuven, Campus KULAK, Faculty of Medicine, Kortrijk, Belgium.,ITEC, imec research group at KU Leuven, Kortrijk, Belgium
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145
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Wan F, Zhu Y, Hu H, Dai A, Cai X, Chen L, Gong H, Xia T, Yang D, Wang MW, Zeng J. DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:478-495. [PMID: 32035227 PMCID: PMC7056933 DOI: 10.1016/j.gpb.2019.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022]
Abstract
Accurate identification of compound–protein interactions (CPIs) in silico may deepen our understanding of the underlying mechanisms of drug action and thus remarkably facilitate drug discovery and development. Conventional similarity- or docking-based computational methods for predicting CPIs rarely exploit latent features from currently available large-scale unlabeled compound and protein data and often limit their usage to relatively small-scale datasets. In the present study, we propose DeepCPI, a novel general and scalable computational framework that combines effective feature embedding (a technique of representation learning) with powerful deep learning methods to accurately predict CPIs at a large scale. DeepCPI automatically learns the implicit yet expressive low-dimensional features of compounds and proteins from a massive amount of unlabeled data. Evaluations of the measured CPIs in large-scale databases, such as ChEMBL and BindingDB, as well as of the known drug–target interactions from DrugBank, demonstrated the superior predictive performance of DeepCPI. Furthermore, several interactions among small-molecule compounds and three G protein-coupled receptor targets (glucagon-like peptide-1 receptor, glucagon receptor, and vasoactive intestinal peptide receptor) predicted using DeepCPI were experimentally validated. The present study suggests that DeepCPI is a useful and powerful tool for drug discovery and repositioning. The source code of DeepCPI can be downloaded from https://github.com/FangpingWan/DeepCPI.
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Affiliation(s)
- Fangping Wan
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Zhu
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hailin Hu
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ligong Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Haipeng Gong
- School of Life Science, Tsinghua University, Beijing 100084, China
| | - Tian Xia
- Department of Electronics and Information Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.
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146
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Wang H, Wang J, Dong C, Lian Y, Liu D, Yan Z. A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder. Front Pharmacol 2020; 10:1592. [PMID: 32047432 PMCID: PMC6997437 DOI: 10.3389/fphar.2019.01592] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 12/09/2019] [Indexed: 01/09/2023] Open
Abstract
Drug targets are biomacromolecules or biomolecular structures that bind to specific drugs and produce therapeutic effects. Therefore, the prediction of drug-target interactions (DTIs) is important for disease therapy. Incorporating multiple similarity measures for drugs and targets is of essence for improving the accuracy of prediction of DTIs. However, existing studies with multiple similarity measures ignored the global structure information of similarity measures, and required manual extraction features of drug-target pairs, ignoring the non-linear relationship among features. In this paper, we proposed a novel approach MDADTI for DTIs prediction based on MDA. MDADTI applied random walk with restart method and positive pointwise mutual information to calculate the topological similarity matrices of drugs and targets, capturing the global structure information of similarity measures. Then, MDADTI applied multimodal deep autoencoder to fuse multiple topological similarity matrices of drugs and targets, automatically learned the low-dimensional features of drugs and targets, and applied deep neural network to predict DTIs. The results of 5-repeats of 10-fold cross-validation under three different cross-validation settings indicated that MDADTI is superior to the other four baseline methods. In addition, we validated the predictions of the MDADTI in six drug-target interactions reference databases, and the results showed that MDADTI can effectively identify unknown DTIs.
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Affiliation(s)
- Huiqing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Jingjing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Chunlin Dong
- Dryland Agriculture Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yuanyuan Lian
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Dan Liu
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
| | - Zhiliang Yan
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, China
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147
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Bagherian M, Sabeti E, Wang K, Sartor MA, Nikolovska-Coleska Z, Najarian K. Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. Brief Bioinform 2020; 22:247-269. [PMID: 31950972 PMCID: PMC7820849 DOI: 10.1093/bib/bbz157] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022] Open
Abstract
The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. There is a need to develop novel and efficient prediction approaches in order to avoid costly and laborious yet not-always-deterministic experiments to determine drug–target interactions (DTIs) by experiments alone. These approaches should be capable of identifying the potential DTIs in a timely manner. In this article, we describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, which have been proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also briefly discussed. Lastly, the challenges one may face in prediction of DTI using machine learning approaches are highlighted and we conclude by shedding some lights on important future research directions.
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Affiliation(s)
- Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Elyas Sabeti
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kai Wang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Kayvan Najarian
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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148
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Wesalo JS, Luo J, Morihiro K, Liu J, Deiters A. Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation. Chembiochem 2020; 21:141-148. [PMID: 31664790 PMCID: PMC6980333 DOI: 10.1002/cbic.201900464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/03/2019] [Indexed: 11/06/2022]
Abstract
The Staudinger reduction and its variants have exceptional compatibility with live cells but can be limited by slow kinetics. Herein we report new small-molecule triggers that turn on proteins through a Staudinger reduction/self-immolation cascade with substantially improved kinetics and yields. We achieved this through site-specific incorporation of a new set of azidobenzyloxycarbonyl lysine derivatives in mammalian cells. This approach allowed us to activate proteins by adding a nontoxic, bioorthogonal phosphine trigger. We applied this methodology to control a post-translational modification (SUMOylation) in live cells, using native modification machinery. This work significantly improves the rate, yield, and tunability of the Staudinger reduction-based activation, paving the way for its application in other proteins and organisms.
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Affiliation(s)
- Joshua S. Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Ji Luo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Kunihiko Morihiro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Jihe Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 (USA)
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149
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Zeng X, Zhu S, Lu W, Liu Z, Huang J, Zhou Y, Fang J, Huang Y, Guo H, Li L, Trapp BD, Nussinov R, Eng C, Loscalzo J, Cheng F. Target identification among known drugs by deep learning from heterogeneous networks. Chem Sci 2020; 11:1775-1797. [PMID: 34123272 PMCID: PMC8150105 DOI: 10.1039/c9sc04336e] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
Without foreknowledge of the complete drug target information, development of promising and affordable approaches for effective treatment of human diseases is challenging. Here, we develop deepDTnet, a deep learning methodology for new target identification and drug repurposing in a heterogeneous drug-gene-disease network embedding 15 types of chemical, genomic, phenotypic, and cellular network profiles. Trained on 732 U.S. Food and Drug Administration-approved small molecule drugs, deepDTnet shows high accuracy (the area under the receiver operating characteristic curve = 0.963) in identifying novel molecular targets for known drugs, outperforming previously published state-of-the-art methodologies. We then experimentally validate that deepDTnet-predicted topotecan (an approved topoisomerase inhibitor) is a new, direct inhibitor (IC50 = 0.43 μM) of human retinoic-acid-receptor-related orphan receptor-gamma t (ROR-γt). Furthermore, by specifically targeting ROR-γt, topotecan reveals a potential therapeutic effect in a mouse model of multiple sclerosis. In summary, deepDTnet offers a powerful network-based deep learning methodology for target identification to accelerate drug repurposing and minimize the translational gap in drug development.
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Affiliation(s)
- Xiangxiang Zeng
- College of Information Science and Engineering, Hunan University Changsha Hunan 410082 China
| | - Siyi Zhu
- Department of Computer Science, Xiamen University Xiamen Fujian 361005 China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University Shanghai 200241 China
| | - Zehui Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology Shanghai 200237 China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology Shanghai 200237 China
| | - Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic 9500 Euclid Avenue Cleveland OH 44106 USA +1-216-6361609 +1-216-4447654
| | - Jiansong Fang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic 9500 Euclid Avenue Cleveland OH 44106 USA +1-216-6361609 +1-216-4447654
| | - Yin Huang
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic 9500 Euclid Avenue Cleveland OH 44106 USA +1-216-6361609 +1-216-4447654
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University Nanjing 210009 China
| | - Huimin Guo
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University Nanjing 210009 China
| | - Lang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University Columbus OH 43210 USA
| | - Bruce D Trapp
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Cleveland OH 44022 USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick Frederick MD 21702 USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978 Israel
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic 9500 Euclid Avenue Cleveland OH 44106 USA +1-216-6361609 +1-216-4447654
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University Cleveland OH 44195 USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine Cleveland Ohio 44106 USA
- Taussig Cancer Institute, Cleveland Clinic Cleveland Ohio 44195 USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine Cleveland Ohio 44106 USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston MA 02115 USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic 9500 Euclid Avenue Cleveland OH 44106 USA +1-216-6361609 +1-216-4447654
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University Cleveland OH 44195 USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine Cleveland Ohio 44106 USA
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150
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Ayed M, Lim H, Xie L. Biological representation of chemicals using latent target interaction profile. BMC Bioinformatics 2019; 20:674. [PMID: 31861982 PMCID: PMC6924142 DOI: 10.1186/s12859-019-3241-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery, and many other applications. Chemical fingerprints are a widely used feature to build machine learning models. However, the fingerprints that are derived from chemical structures ignore the biological context, thus, they suffer from several problems such as the activity cliff and curse of dimensionality. Fundamentally, the chemical modulation of biological activities is a multi-scale process. It is the genome-wide chemical-target interactions that modulate chemical phenotypic responses. Thus, the genome-scale chemical-target interaction profile will more directly correlate with in vitro and in vivo activities than the chemical structure. Nevertheless, the scope of direct application of the chemical-target interaction profile is limited due to the severe incompleteness, biasness, and noisiness of bioassay data. Results To address the aforementioned problems, we developed a novel chemical representation method: Latent Target Interaction Profile (LTIP). LTIP embeds chemicals into a low dimensional continuous latent space that represents genome-scale chemical-target interactions. Subsequently LTIP can be used as a feature to build machine learning models. Using the drug sensitivity of cancer cell lines as a benchmark, we have shown that the LTIP robustly outperforms chemical fingerprints regardless of machine learning algorithms. Moreover, the LTIP is complementary with the chemical fingerprints. It is possible for us to combine LTIP with other fingerprints to further improve the performance of bioactivity prediction. Conclusions Our results demonstrate the potential of LTIP in particular and multi-scale modeling in general in predictive modeling of chemical modulation of biological activities.
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Affiliation(s)
- Mohamed Ayed
- Ph.D. Program in Computer Science, The Graduate Center, The City University of New York, New York, NY, USA
| | - Hansaim Lim
- Ph.D. Program in Biochemistry, The Graduate Center, The City University of New York, New York, NY, USA
| | - Lei Xie
- Department of Computer Science, Hunter College, & The Graduate Center, The City University of New York, New York, NY, USA.
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