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Noor F, Tahir ul Qamar M, Ashfaq UA, Albutti A, Alwashmi ASS, Aljasir MA. Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals (Basel) 2022; 15:572. [PMID: 35631398 PMCID: PMC9143318 DOI: 10.3390/ph15050572] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
| | - Mohammad Abdullah Aljasir
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
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Venkateswaran MR, Vadivel TE, Jayabal S, Murugesan S, Rajasekaran S, Periyasamy S. A review on network pharmacology based phytotherapy in treating diabetes- An environmental perspective. ENVIRONMENTAL RESEARCH 2021; 202:111656. [PMID: 34265348 DOI: 10.1016/j.envres.2021.111656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/19/2021] [Accepted: 07/04/2021] [Indexed: 06/13/2023]
Abstract
Diabetes has become common lifestyle disorder associated with obesity and cardiovascular diseases. Environmental factors like physical inactivity, polluted surroundings and unhealthy dieting also plays a vital role in diabetes pathogenesis. As the current anti-diabetic drugs possess unprecedented side effects, traditional herbal medicine can be used an alternative therapy. The paramount challenge with the herbal formulation usage is the lack of standardized procedure, entangled with little knowledge on drug safety and mechanism of drug action. Heavy metal contamination is a major environmental hazard where plants tend to accumulate toxic metals like nickel, chromium and lead through industrial and agricultural activities. It becomes inappropriate to use these plants for phytotherapy as it may affect the human health on long term consumption. This review discuss about the environmental risk factors related to diabetes and better implication of medicinal plants in anti-diabetic therapy using network pharmacology. It is an in silico analytical tool that helps to unravel the multi-targeted action of herbal formulations rich in secondary metabolites. Also, a special focus is attempted to pool the databases regarding the medicinal plants for diabetes and associated diseases, their bioactive compounds, possible diabetic targets, drug-target interaction and toxicology reports that may open an aisle in safer, effective and toxicity-free drug discovery.
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Affiliation(s)
- Meenakshi R Venkateswaran
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Tamil Elakkiya Vadivel
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Sasidharan Jayabal
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Selvakumar Murugesan
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India
| | - Subbiah Rajasekaran
- Department of Biochemistry, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Sureshkumar Periyasamy
- Department of Biotechnology, Anna University, BIT-Campus, Tiruchirappalli, 620024, Tamil Nadu, India.
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Al-Nour MY, Arbab AH, Parvez MK, Mohamed AY, Al-Dosari MS. In-vitro Cytotoxicity and In-silico Insights of the Multi-target Anticancer Candidates from Haplophyllum tuberculatum. BORNEO JOURNAL OF PHARMACY 2021. [DOI: 10.33084/bjop.v4i3.1955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
This study aimed to investigate the anticancer activity of Haplophyllum tuberculatum(Forsk.) aerial parts ethanol extract and fractions and reveal the potential anticancer targets, binding modes, pharmacokinetics, and toxicity properties of its phytoconstituents. MTT assay was used to investigate the anticancer activity. TargetNet, ChemProt version 2.0, and CLC-Pred web servers were used for virtual screening, and Cresset Flare software was used for molecular docking with the 26 predicted targets. Moreover, pkCSM, swiss ADME, and eMolTox web servers were used to predict pharmacokinetics and safety. Ethanolic extracts of H. tuberculatum on HepG2 and HeLa cell lines showed promising activities with IC50 values 54.12 and 48.1 µg/mL, respectively. Further, ethyl acetate fraction showed the highest cytotoxicity on HepG2 and HeLa cell lines with IC50 values 41.7 and 52.31 µg/mL. Of 70 compounds screened virtually, polygamain, justicidin A, justicidin B, haplotubine, kusunokinin, and flindersine were predicted as safe anticancer drugs candidates. They showed the highest binding scores with targets involved in cell growth, proliferation, survival, migration, tumor suppression, induction of apoptosis, metastasis, and drug resistance. Our findings revealed the potency of H. tuberculatum as a source of anticancer candidates that further studies should support.
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Achary PGR. Applications of Quantitative Structure-Activity Relationships (QSAR) based Virtual Screening in Drug Design: A Review. Mini Rev Med Chem 2020; 20:1375-1388. [DOI: 10.2174/1389557520666200429102334] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022]
Abstract
The scientists, and the researchers around the globe generate tremendous amount of information
everyday; for instance, so far more than 74 million molecules are registered in Chemical
Abstract Services. According to a recent study, at present we have around 1060 molecules, which are
classified as new drug-like molecules. The library of such molecules is now considered as ‘dark chemical
space’ or ‘dark chemistry.’ Now, in order to explore such hidden molecules scientifically, a good
number of live and updated databases (protein, cell, tissues, structure, drugs, etc.) are available today.
The synchronization of the three different sciences: ‘genomics’, proteomics and ‘in-silico simulation’
will revolutionize the process of drug discovery. The screening of a sizable number of drugs like molecules
is a challenge and it must be treated in an efficient manner. Virtual screening (VS) is an important
computational tool in the drug discovery process; however, experimental verification of the
drugs also equally important for the drug development process. The quantitative structure-activity relationship
(QSAR) analysis is one of the machine learning technique, which is extensively used in VS
techniques. QSAR is well-known for its high and fast throughput screening with a satisfactory hit rate.
The QSAR model building involves (i) chemo-genomics data collection from a database or literature
(ii) Calculation of right descriptors from molecular representation (iii) establishing a relationship
(model) between biological activity and the selected descriptors (iv) application of QSAR model to
predict the biological property for the molecules. All the hits obtained by the VS technique needs to be
experimentally verified. The present mini-review highlights: the web-based machine learning tools, the
role of QSAR in VS techniques, successful applications of QSAR based VS leading to the drug discovery
and advantages and challenges of QSAR.
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Affiliation(s)
- Patnala Ganga Raju Achary
- Department of Chemistry, Faculty of Engineering & Technology (ITER), Siksha ‘O’ Anusandhan, Deemed to be University, Khandagiri Square, Bhubaneswar- 751030, India
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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: 161] [Impact Index Per Article: 40.3] [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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Boberg J, Dybdahl M, Petersen A, Hass U, Svingen T, Vinggaard AM. A pragmatic approach for human risk assessment of chemical mixtures. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2018.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Carvaillo JC, Barouki R, Coumoul X, Audouze K. Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:47005. [PMID: 30994381 PMCID: PMC6785233 DOI: 10.1289/ehp4200] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Available toxicity data can be optimally interpreted if they are integrated using computational approaches such as systems biology modeling. Such approaches are particularly warranted in cases where regulatory decisions have to be made rapidly. OBJECTIVES The study aims at developing and applying a new integrative computational strategy to identify associations between bisphenol S (BPS), a substitute for bisphenol A (BPA), and components of adverse outcome pathways (AOPs). METHODS The proposed approach combines a text mining (TM) procedure and integrative systems biology to comprehensively analyze the scientific literature to enrich AOPs related to environmental stressors. First, to identify relevant associations between BPS and different AOP components, a list of abstracts was screened using the developed text-mining tool AOP-helpFinder, which calculates scores based on the graph theory to prioritize the findings. Then, to fill gaps between BPS, biological events, and adverse outcomes (AOs), a systems biology approach was used to integrate information from the AOP-Wiki and ToxCast databases, followed by manual curation of the relevant publications. RESULTS Links between BPS and 48 AOP key events (KEs) were identified and scored via 31 references. The main outcomes were related to reproductive health, endocrine disruption, impairments of metabolism, and obesity. We then explicitly analyzed co-mention of the terms BPS and obesity by data integration and manual curation of the full text of the publications. Several molecular and cellular pathways were identified, which allowed the proposal of a biological explanation for the association between BPS and obesity. CONCLUSIONS By analyzing dispersed information from the literature and databases, our novel approach can identify links between stressors and AOP KEs. The findings associating BPS and obesity illustrate the use of computational tools in predictive toxicology and highlight the relevance of the approach to decision makers assessing substituents to toxic chemicals. https://doi.org/10.1289/EHP4200.
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Affiliation(s)
- Jean-Charles Carvaillo
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Robert Barouki
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Xavier Coumoul
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Karine Audouze
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
- University Paris Diderot, ComUE Sorbonne Paris Cité, Paris, France
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Abstract
Network-aided in silico approaches have been widely used for prediction of drug-target interactions and evaluation of drug safety to increase the clinical efficiency and productivity during drug discovery and development. Here we review the advances and new progress in this field and summarize the translational applications of several new network-aided in silico approaches we developed recently. In addition, we describe the detailed protocols for a network-aided drug repositioning infrastructure for identification of new targets for old drugs, failed drugs in clinical trials, and new chemical entities. These state-of-the-art network-aided in silico approaches have been used for the discovery and development of broad-acting and targeted clinical therapies for various complex diseases, in particular for oncology drug repositioning. In this chapter, the described network-aided in silico protocols are appropriate for target-centric drug repositioning to various complex diseases, but expertise is still necessary to perform the specific oncology projects based on the cancer targets of interest.
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La MK, Sedykh A, Fourches D, Muratov E, Tropsha A. Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions. Drug Saf 2018; 41:1059-1072. [PMID: 29876834 PMCID: PMC6212308 DOI: 10.1007/s40264-018-0688-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Given that adverse drug effects (ADEs) have led to post-market patient harm and subsequent drug withdrawal, failure of candidate agents in the drug development process, and other negative outcomes, it is essential to attempt to forecast ADEs and other relevant drug-target-effect relationships as early as possible. Current pharmacologic data sources, providing multiple complementary perspectives on the drug-target-effect paradigm, can be integrated to facilitate the inference of relationships between these entities. OBJECTIVE This study aims to identify both existing and unknown relationships between chemicals (C), protein targets (T), and ADEs (E) based on evidence in the literature. MATERIALS AND METHODS Cheminformatics and data mining approaches were employed to integrate and analyze publicly available clinical pharmacology data and literature assertions interrelating drugs, targets, and ADEs. Based on these assertions, a C-T-E relationship knowledge base was developed. Known pairwise relationships between chemicals, targets, and ADEs were collected from several pharmacological and biomedical data sources. These relationships were curated and integrated according to Swanson's paradigm to form C-T-E triangles. Missing C-E edges were then inferred as C-E relationships. RESULTS Unreported associations between drugs, targets, and ADEs were inferred, and inferences were prioritized as testable hypotheses. Several C-E inferences, including testosterone → myocardial infarction, were identified using inferences based on the literature sources published prior to confirmatory case reports. Timestamping approaches confirmed the predictive ability of this inference strategy on a larger scale. CONCLUSIONS The presented workflow, based on free-access databases and an association-based inference scheme, provided novel C-E relationships that have been validated post hoc in case reports. With refinement of prioritization schemes for the generated C-E inferences, this workflow may provide an effective computational method for the early detection of potential drug candidate ADEs that can be followed by targeted experimental investigations.
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Affiliation(s)
- Mary K La
- Division of Practice Advancement and Clinical Education, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, Chapel Hill, NC, 27599, USA
| | - Alexander Sedykh
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, Chapel Hill, NC, 27599, USA
- Sciome LLC, 2 Davis Drive, Research Triangle Park, NC, 27709, USA
| | - Denis Fourches
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, Chapel Hill, NC, 27599, USA
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, Chapel Hill, NC, 27599, USA.
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Audouze K, Taboureau O, Grandjean P. A systems biology approach to predictive developmental neurotoxicity of a larvicide used in the prevention of Zika virus transmission. Toxicol Appl Pharmacol 2018; 354:56-63. [PMID: 29476864 PMCID: PMC6087490 DOI: 10.1016/j.taap.2018.02.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 01/26/2023]
Abstract
The need to prevent developmental brain disorders has led to an increased interest in efficient neurotoxicity testing. When an epidemic of microcephaly occurred in Brazil, Zika virus infection was soon identified as the likely culprit. However, the pathogenesis appeared to be complex, and a larvicide used to control mosquitoes responsible for transmission of the virus was soon suggested as an important causative factor. Yet, it is challenging to identify relevant and efficient tests that are also in line with ethical research defined by the 3Rs rule (Replacement, Reduction and Refinement). Especially in an acute situation like the microcephaly epidemic, where little toxicity documentation is available, new and innovative alternative methods, whether in vitro or in silico, must be considered. We have developed a network-based model using an integrative systems biology approach to explore the potential developmental neurotoxicity, and we applied this method to examine the larvicide pyriproxyfen widely used in the prevention of Zika virus transmission. Our computational model covered a wide range of possible pathways providing mechanistic hypotheses between pyriproxyfen and neurological disorders via protein complexes, thus adding to the plausibility of pyriproxyfen neurotoxicity. Although providing only tentative evidence and comparisons with retinoic acid, our computational systems biology approach is rapid and inexpensive. The case study of pyriproxyfen illustrates its usefulness as an initial or screening step in the assessment of toxicity potentials of chemicals with incompletely known toxic properties.
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Affiliation(s)
- Karine Audouze
- INSERM UMR-S 973, 75013 Paris, France; University of Paris Diderot, 75013 Paris, France
| | - Olivier Taboureau
- INSERM UMR-S 973, 75013 Paris, France; University of Paris Diderot, 75013 Paris, France
| | - Philippe Grandjean
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; University of Southern Denmark, Odense, Denmark.
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da Rocha JLC, da Silva DF, de Santana AR, da Costa DM, Pastore JFB, Alves CQ, Santos Junior MCS, Brandão HN. Asemeia ovata (Polygalaceae): Quantitative determination and evaluation in silico of identified substances by HPLC-DAD. Comput Biol Chem 2018; 75:65-73. [DOI: 10.1016/j.compbiolchem.2018.04.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 11/25/2022]
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Cheng F, Hong H, Yang S, Wei Y. Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Brief Bioinform 2017; 18:682-697. [PMID: 27296652 DOI: 10.1093/bib/bbw051] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 12/12/2022] Open
Abstract
Advances in next-generation sequencing technologies have generated the data supporting a large volume of somatic alterations in several national and international cancer genome projects, such as The Cancer Genome Atlas and the International Cancer Genome Consortium. These cancer genomics data have facilitated the revolution of a novel oncology drug discovery paradigm from candidate target or gene studies toward targeting clinically relevant driver mutations or molecular features for precision cancer therapy. This focuses on identifying the most appropriately targeted therapy to an individual patient harboring a particularly genetic profile or molecular feature. However, traditional experimental approaches that are used to develop new chemical entities for targeting the clinically relevant driver mutations are costly and high-risk. Drug repositioning, also known as drug repurposing, re-tasking or re-profiling, has been demonstrated as a promising strategy for drug discovery and development. Recently, computational techniques and methods have been proposed for oncology drug repositioning and identifying pharmacogenomics biomarkers, but overall progress remains to be seen. In this review, we focus on introducing new developments and advances of the individualized network-based drug repositioning approaches by targeting the clinically relevant driver events or molecular features derived from cancer panomics data for the development of precision oncology drug therapies (e.g. one-person trials) to fully realize the promise of precision medicine. We discuss several potential challenges (e.g. tumor heterogeneity and cancer subclones) for precision oncology. Finally, we highlight several new directions for the precision oncology drug discovery via biotherapies (e.g. gene therapy and immunotherapy) that target the 'undruggable' cancer genome in the functional genomics era.
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Sam E, Athri P. Web-based drug repurposing tools: a survey. Brief Bioinform 2017; 20:299-316. [DOI: 10.1093/bib/bbx125] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Indexed: 12/15/2022] Open
Affiliation(s)
- Elizabeth Sam
- Department of Computer Science & Engineering Amrita, University Bengaluru, India
| | - Prashanth Athri
- Department of Computer Science & Engineering Amrita, University Bengaluru, India
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Murtazalieva KA, Druzhilovskiy DS, Goel RK, Sastry GN, Poroikov VV. How good are publicly available web services that predict bioactivity profiles for drug repurposing? SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:843-862. [PMID: 29183230 DOI: 10.1080/1062936x.2017.1399448] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 06/07/2023]
Abstract
Drug repurposing provides a non-laborious and less expensive way for finding new human medicines. Computational assessment of bioactivity profiles shed light on the hidden pharmacological potential of the launched drugs. Currently, several freely available computational tools are available via the Internet, which predict multitarget profiles of drug-like compounds. They are based on chemical similarity assessment (ChemProt, SuperPred, SEA, SwissTargetPrediction and TargetHunter) or machine learning methods (ChemProt and PASS). To compare their performance, this study has created two evaluation sets, consisting of (1) 50 well-known repositioned drugs and (2) 12 drugs recently patented for new indications. In the first set, sensitivity values varied from 0.64 (TarPred) to 1.00 (PASS Online) for the initial indications and from 0.64 (TarPred) to 0.98 (PASS Online) for the repurposed indications. In the second set, sensitivity values varied from 0.08 (SuperPred) to 1.00 (PASS Online) for the initial indications and from 0.00 (SuperPred) to 1.00 (PASS Online) for the repurposed indications. Thus, this analysis demonstrated that the performance of machine learning methods surpassed those of chemical similarity assessments, particularly in the case of novel repurposed indications.
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Affiliation(s)
- K A Murtazalieva
- a Institute of Biomedical Chemistry , Moscow , Russia
- b Pirogov Russian National Research Medical University , Moscow , Russia
| | | | - R K Goel
- c Punjabi University , Patiala , Punjab , India
| | - G N Sastry
- d CSIR-Indian Institute of Chemical Technology , Hyderabad , India
| | - V V Poroikov
- a Institute of Biomedical Chemistry , Moscow , Russia
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Martin-Moncunill D, Gaona-Garcia PA, Garcia-Barriocanal E, Sanchez-Alonso S. Selection and Use of Search Mechanisms in Learning Object Repositories: the Case of Organic.Edunet. IEEE REVISTA IBEROAMERICANA DE TECNOLOGIAS DEL APRENDIZAJE 2016. [DOI: 10.1109/rita.2016.2554058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kringelum J, Kjaerulff SK, Brunak S, Lund O, Oprea TI, Taboureau O. ChemProt-3.0: a global chemical biology diseases mapping. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:bav123. [PMID: 26876982 PMCID: PMC4752971 DOI: 10.1093/database/bav123] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/08/2015] [Indexed: 12/16/2022]
Abstract
ChemProt is a publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19 504 proteins. Here, we report the implementation of global pharmacological heatmap, supporting a user-friendly navigation of chemogenomics space. This facilitates the visualization and selection of chemicals that share similar structural properties. In addition, the user has the possibility to search by compound, target, pathway, disease and clinical effect. Genetic variations associated to target proteins were integrated, making it possible to plan pharmacogenetic studies and to suggest human response variability to drug. Finally, Quantitative Structure–Activity Relationship models for 850 proteins having sufficient data were implemented, enabling secondary pharmacological profiling predictions from molecular structure. Database URL: http://potentia.cbs.dtu.dk/ChemProt/
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Affiliation(s)
- Jens Kringelum
- Department of Systems Biology, Center for Biological Sequence Analysis, buildin 208, kemitorvet, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Sonny Kim Kjaerulff
- Department of Systems Biology, Center for Biological Sequence Analysis, buildin 208, kemitorvet, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Søren Brunak
- Department of Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation, Center for Protein Research, University of Copenhagen, Blegdamsvej 3A, DK-2200, Copenhagen, Denmark
| | - Ole Lund
- Department of Systems Biology, Center for Biological Sequence Analysis, buildin 208, kemitorvet, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Tudor I Oprea
- Department of Systems Biology, Center for Biological Sequence Analysis, buildin 208, kemitorvet, Technical University of Denmark, DK-2800 Lyngby, Denmark Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, MSC09 5025, Albuquerque 87181, New Mexico, United States of America
| | - Olivier Taboureau
- Department of Systems Biology, Center for Biological Sequence Analysis, buildin 208, kemitorvet, Technical University of Denmark, DK-2800 Lyngby, Denmark INSERM, UMRS-973, MTi, Universite Paris Diderot, 35 rue Helene Brion, 75205 Paris Cedex 13, Sorbonne Paris Cite, France
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Southan C, Sharman JL, Benson HE, Faccenda E, Pawson AJ, Alexander SPH, Buneman OP, Davenport AP, McGrath JC, Peters JA, Spedding M, Catterall WA, Fabbro D, Davies JA. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. Nucleic Acids Res 2016; 44:D1054-68. [PMID: 26464438 PMCID: PMC4702778 DOI: 10.1093/nar/gkv1037] [Citation(s) in RCA: 987] [Impact Index Per Article: 123.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 01/05/2023] Open
Abstract
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options.
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Affiliation(s)
- Christopher Southan
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Joanna L Sharman
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Helen E Benson
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Elena Faccenda
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Adam J Pawson
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Stephen P H Alexander
- School of Biomedical Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK
| | - O Peter Buneman
- Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, EH8 9LE, UK
| | | | - John C McGrath
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | | | - William A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA 98195-7280, USA
| | | | - Jamie A Davies
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, EH8 9XD, UK
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18
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Lavecchia A, Cerchia C. In silico methods to address polypharmacology: current status, applications and future perspectives. Drug Discov Today 2015; 21:288-98. [PMID: 26743596 DOI: 10.1016/j.drudis.2015.12.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/20/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022]
Abstract
Polypharmacology, a new paradigm in drug discovery that focuses on multi-target drugs (MTDs), has potential application for drug repurposing, the process of finding new uses for existing approved drugs, prediction of off-target toxicities and rational design of MTDs. In this scenario, computational strategies have demonstrated great potential in predicting polypharmacology and in facilitating drug repurposing. Here, we provide a comprehensive overview of various computational approaches that enable the prediction and analysis of in vitro and in vivo drug-response phenotypes and outline their potential for drug discovery. We give an outlook on the latest advances in rational design of MTDs and discuss possible future directions of algorithm development in this field.
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Affiliation(s)
- Antonio Lavecchia
- Department of Pharmacy, Drug Discovery Laboratory, University of Napoli Federico II, via D. Montesano 49, I-80131 Napoli, Italy.
| | - Carmen Cerchia
- Department of Pharmacy, Drug Discovery Laboratory, University of Napoli Federico II, via D. Montesano 49, I-80131 Napoli, Italy
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19
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Cardiotoxicity screening: a review of rapid-throughput in vitro approaches. Arch Toxicol 2015; 90:1803-16. [PMID: 26676948 DOI: 10.1007/s00204-015-1651-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/18/2015] [Indexed: 01/07/2023]
Abstract
Cardiac toxicity represents one of the leading causes of drug failure along different stages of drug development. Multiple very successful pharmaceuticals had to be pulled from the market or labeled with strict usage warnings due to adverse cardiac effects. In order to protect clinical trial participants and patients, the International Conference on Harmonization published guidelines to recommend that all new drugs to be tested preclinically for hERG (Kv11.1) channel sensitivity before submitting for regulatory reviews. However, extensive studies have demonstrated that measurement of hERG activity has limitations due to the multiple molecular targets of drug compound through which it may mitigate or abolish a potential arrhythmia, and therefore, a model measuring multiple ion channel effects is likely to be more predictive. Several phenotypic rapid-throughput methods have been developed to predict the potential cardiac toxic compounds in the early stages of drug development using embryonic stem cells- or human induced pluripotent stem cell-derived cardiomyocytes. These rapid-throughput methods include microelectrode array-based field potential assay, impedance-based or Ca(2+) dynamics-based cardiomyocytes contractility assays. This review aims to discuss advantages and limitations of these phenotypic assays for cardiac toxicity assessment.
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20
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Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res 2015; 44:D380-4. [PMID: 26590256 PMCID: PMC4702904 DOI: 10.1093/nar/gkv1277] [Citation(s) in RCA: 894] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022] Open
Abstract
Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH (‘Search Tool for Interacting Chemicals’) that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.
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Affiliation(s)
- Damian Szklarczyk
- Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alberto Santos
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences, University of Zurich and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Molecular Medicine Partnership Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany
| | - Michael Kuhn
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden
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21
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Zhang C, Hong H, Mendrick DL, Tang Y, Cheng F. Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science. Biomark Med 2015; 9:1241-52. [PMID: 26506997 DOI: 10.2217/bmm.15.81] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Improved biomarker-based assessment of drug safety is needed in drug discovery and development as well as regulatory evaluation. However, identifying drug safety-related biomarkers such as genes, proteins, miRNA and single-nucleotide polymorphisms remains a big challenge. The advances of 'omics' and computational technologies such as genomics, transcriptomics, metabolomics, proteomics, systems biology, network biology and systems pharmacology enable us to explore drug actions at the organ and organismal levels. Computational and experimental systems pharmacology approaches could be utilized to facilitate biomarker-based drug safety assessment for drug discovery and development and to inform better regulatory decisions. In this article, we review the current status and advances of systems pharmacology approaches for the development of predictive models to identify biomarkers for drug safety assessment.
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Affiliation(s)
- Chen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Huixiao Hong
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Feixiong Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China.,State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan, China
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22
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Abstract
The emergence of a number of publicly available bioactivity databases, such as ChEMBL, PubChem BioAssay and BindingDB, has raised awareness about the topics of data curation, quality and integrity. Here we provide an overview and discussion of the current and future approaches to activity, assay and target data curation of the ChEMBL database. This curation process involves several manual and automated steps and aims to: (1) maximise data accessibility and comparability; (2) improve data integrity and flag outliers, ambiguities and potential errors; and (3) add further curated annotations and mappings thus increasing the usefulness and accuracy of the ChEMBL data for all users and modellers in particular. Issues related to activity, assay and target data curation and integrity along with their potential impact for users of the data are discussed, alongside robust selection and filter strategies in order to avoid or minimise these, depending on the desired application.
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23
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Audouze K, Taboureau O. Chemical biology databases: from aggregation, curation to representation. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 14:25-29. [PMID: 26194584 DOI: 10.1016/j.ddtec.2015.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/19/2015] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
Systems chemical biology offers a novel way of approaching drug discovery by developing models that consider the global physiological environment of protein targets and their perturbations by drugs. However, the integration of all these data needs curation and standardization with an appropriate representation in order to get relevant interpretations. In this mini review, we present some databases and services, which integrated together with computational tools and data standardization, could assist scientists in decision making during the different drug development process.
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Affiliation(s)
- Karine Audouze
- Université Paris Diderot - Inserm UMR-S973, MTi, 75013 Paris, France
| | - Olivier Taboureau
- Université Paris Diderot - Inserm UMR-S973, MTi, 75013 Paris, France.
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24
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Computational investigations of hERG channel blockers: New insights and current predictive models. Adv Drug Deliv Rev 2015; 86:72-82. [PMID: 25770776 DOI: 10.1016/j.addr.2015.03.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/13/2015] [Accepted: 03/04/2015] [Indexed: 01/08/2023]
Abstract
Identification of potential human Ether-a-go-go Related-Gene (hERG) potassium channel blockers is an essential part of the drug development and drug safety process in pharmaceutical industries or academic drug discovery centers, as they may lead to drug-induced QT prolongation, arrhythmia and Torsade de Pointes. Recent reports also suggest starting to address such issues at the hit selection stage. In order to prioritize molecules during the early drug discovery phase and to reduce the risk of drug attrition due to cardiotoxicity during pre-clinical and clinical stages, computational approaches have been developed to predict the potential hERG blockage of new drug candidates. In this review, we will describe the current in silico methods developed and applied to predict and to understand the mechanism of actions of hERG blockers, including ligand-based and structure-based approaches. We then discuss ongoing research on other ion channels and hERG polymorphism susceptible to be involved in LQTS and how systemic approaches can help in the drug safety decision.
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25
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Tung CW. ChemDIS: a chemical-disease inference system based on chemical-protein interactions. J Cheminform 2015; 7:25. [PMID: 26078786 PMCID: PMC4466364 DOI: 10.1186/s13321-015-0077-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/21/2015] [Indexed: 01/20/2023] Open
Abstract
Background The characterization of toxicities associated with environmental and industrial chemicals is required for risk assessment. However, we lack the toxicological data for a large portion of chemicals due to the high cost of experiments for a huge number of chemicals. The development of computational methods for identifying potential risks associated with chemicals is desirable for generating testable hypothesis to accelerate the hazard identification process. Results A chemical–disease inference system named ChemDIS was developed to facilitate hazard identification for chemicals. The chemical–protein interactions from a large database STITCH and protein–disease relationship from disease ontology and disease ontology lite were utilized for chemical–protein–disease inferences. Tools with user-friendly interfaces for enrichment analysis of functions, pathways and diseases were implemented and integrated into ChemDIS. An analysis on maleic acid and sibutramine showed that ChemDIS could be a useful tool for the identification of potential functions, pathways and diseases affected by poorly characterized chemicals. Conclusions ChemDIS is an integrated chemical–disease inference system for poorly characterized chemicals with potentially affected functions and pathways for experimental validation. ChemDIS server is freely accessible at http://cwtung.kmu.edu.tw/chemdis. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0077-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chun-Wei Tung
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung, 80708 Taiwan ; Ph.D. Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan ; National Environmental Health Research Center, National Health Research Institutes, Miaoli County, 35053 Taiwan
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26
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Wang Z, Li J, Dang R, Liang L, Lin J. PhIN: A Protein Pharmacology Interaction Network Database. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015. [PMID: 26225242 PMCID: PMC4394615 DOI: 10.1002/psp4.25] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Network pharmacology is a new and hot concept in drug discovery for its ability to investigate the complexity of polypharmacology, and becomes more and more important in drug development. Here we report a protein pharmacology interaction network database (PhIN), aiming to assist multitarget drug discovery by providing comprehensive and flexible network pharmacology analysis. Overall, PhIN contains 1,126,060 target–target interaction pairs in terms of shared compounds and 3,428,020 pairs in terms of shared scaffolds, which involve 12,419,700 activity data, 9,414 targets, 314 viral targets, 652 pathways, 1,359,400 compounds, and 309,556 scaffolds. Using PhIN, users can obtain interacting target networks within or across human pathways, between human and virus, by defining the number of shared compounds or scaffolds under an activity cutoff. We expect PhIN to be a useful tool for multitarget drug development. PhIN is freely available at http://cadd.pharmacy.nankai.edu.cn/phin/.
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Affiliation(s)
- Z Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University Tianjin, China
| | - J Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University Tianjin, China ; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology Tianjin, China
| | - R Dang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University Tianjin, China
| | - L Liang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University Tianjin, China ; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology Tianjin, China
| | - J Lin
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University Tianjin, China ; High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology Tianjin, China
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27
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Abstract
Systems toxicology combines novel and historical experimental data to generate increasingly complex models of the biological response to chemical exposure.
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Affiliation(s)
- Nick J. Plant
- School of Biosciences and Medicine
- University of Surrey
- Guildford
- UK
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28
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Cereto-Massagué A, Ojeda MJ, Valls C, Mulero M, Pujadas G, Garcia-Vallve S. Tools for in silico target fishing. Methods 2015; 71:98-103. [DOI: 10.1016/j.ymeth.2014.09.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 12/17/2022] Open
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Audouze K, Brunak S, Grandjean P. A computational approach to chemical etiologies of diabetes. Sci Rep 2014; 3:2712. [PMID: 24048418 PMCID: PMC3965361 DOI: 10.1038/srep02712] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/30/2013] [Indexed: 01/01/2023] Open
Abstract
Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic linkages in type 2 diabetes (T2D) through genome-wide associations, disease similarities, and published empirical evidence. Ten environmental chemicals were found to be potentially linked to T2D, the highest scores were observed for arsenic, 2,3,7,8-tetrachlorodibenzo-p-dioxin, hexachlorobenzene, and perfluorooctanoic acid. For these substances we integrated disease and pathway annotations on top of protein interactions to reveal possible pathogenetic pathways that deserve empirical testing. The approach is general and can address other public health concerns in addition to identifying diabetogenic chemicals, and offers thus promising guidance for future research in regard to the etiology and pathogenesis of complex diseases.
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Affiliation(s)
- Karine Audouze
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
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30
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Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O. Identification of odorant-receptor interactions by global mapping of the human odorome. PLoS One 2014; 9:e93037. [PMID: 24695519 PMCID: PMC3973694 DOI: 10.1371/journal.pone.0093037] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 02/27/2014] [Indexed: 12/14/2022] Open
Abstract
The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPARγ). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome.
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Affiliation(s)
- Karine Audouze
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | - Anne Marie Le Bon
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | - Christine Belloir
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | | | | | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Olivier Taboureau
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- INSERM UMR-S973, Molecules Thérapeutiques In Silico, Paris Diderot University, Paris, France
- * E-mail:
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31
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Kongsbak K, Hadrup N, Audouze K, Vinggaard AM. Applicability of computational systems biology in toxicology. Basic Clin Pharmacol Toxicol 2014; 115:45-9. [PMID: 24528503 DOI: 10.1111/bcpt.12216] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 02/05/2014] [Indexed: 12/31/2022]
Abstract
Systems biology as a research field has emerged within the last few decades. Systems biology, often defined as the antithesis of the reductionist approach, integrates information about individual components of a biological system. In integrative systems biology, large data sets from various sources and databases are used to model and predict effects of chemicals on, for instance, human health. In toxicology, computational systems biology enables identification of important pathways and molecules from large data sets; tasks that can be extremely laborious when performed by a classical literature search. However, computational systems biology offers more advantages than providing a high-throughput literature search; it may form the basis for establishment of hypotheses on potential links between environmental chemicals and human diseases, which would be very difficult to establish experimentally. This is possible due to the existence of comprehensive databases containing information on networks of human protein-protein interactions and protein-disease associations. Experimentally determined targets of the specific chemical of interest can be fed into these networks to obtain additional information that can be used to establish hypotheses on links between the chemical and human diseases. Such information can also be applied for designing more intelligent animal/cell experiments that can test the established hypotheses. Here, we describe how and why to apply an integrative systems biology method in the hypothesis-generating phase of toxicological research.
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Affiliation(s)
- Kristine Kongsbak
- Division of Toxicology and Risk Assessment, National Food Institute, Technical University of Denmark, Søborg, Denmark; Department for Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
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32
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Abstract
VisANT is a Web-based workbench for the integrative analysis of biological networks with unique features such as exploratory navigation of interaction network and multi-scale visualization and inference with integrated hierarchical knowledge. It provides functionalities for convenient construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation and drug target) relations from either the Predictome database or user-defined data sets. Analysis capabilities include network structure analysis, overrepresentation analysis, expression enrichment analysis etc. Additionally, network can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways or any kind of subnetworks. Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., PSI-MI, KGML, BioPAX, SBML(in progress) Multiple species are supported to the extent that interactions or associations are available (i.e., public datasets or Predictome database).
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Affiliation(s)
- Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts
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33
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Rognan D. Towards the Next Generation of Computational Chemogenomics Tools. Mol Inform 2013; 32:1029-34. [PMID: 27481148 DOI: 10.1002/minf.201300054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/11/2013] [Indexed: 01/07/2023]
Affiliation(s)
- D Rognan
- UMR 7200 CNRS-Université de Strasbourg, MEDALIS Drug Discovery Center, 74 route du Rhin, 67400, Illkirch, France.
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34
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Gautier L, Taboureau O, Audouze K. The effect of network biology on drug toxicology. Expert Opin Drug Metab Toxicol 2013; 9:1409-18. [PMID: 23937336 DOI: 10.1517/17425255.2013.820704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The high failure rate of drug candidates due to toxicity, during clinical trials, is a critical issue in drug discovery. Network biology has become a promising approach, in this regard, using the increasingly large amount of biological and chemical data available and combining it with bioinformatics. With this approach, the assessment of chemical safety can be done across multiple scales of complexity from molecular to cellular and system levels in human health. Network biology can be used at several levels of complexity. AREAS COVERED This review describes the strengths and limitations of network biology. The authors specifically assess this approach across different biological scales when it is applied to toxicity. EXPERT OPINION There has been much progress made with the amount of data that is generated by various omics technologies. With this large amount of useful data, network biology has the opportunity to contribute to a better understanding of a drug's safety profile. The authors believe that considering a drug action and protein's function in a global physiological environment may benefit our understanding of the impact some chemicals have on human health and toxicity. The next step for network biology will be to better integrate differential and quantitative data.
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Affiliation(s)
- Laurent Gautier
- Technical University of Denmark, Center for Biological Sequence Analysis, Department of Systems Biology , Lyngby , Denmark
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35
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Yang M, Chen JL, Xu LW, Ji G. Navigating traditional chinese medicine network pharmacology and computational tools. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2013; 2013:731969. [PMID: 23983798 PMCID: PMC3747450 DOI: 10.1155/2013/731969] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/04/2013] [Indexed: 12/17/2022]
Abstract
The concept of "network target" has ushered in a new era in the field of traditional Chinese medicine (TCM). As a new research approach, network pharmacology is based on the analysis of network models and systems biology. Taking advantage of advancements in systems biology, a high degree of integration data analysis strategy and interpretable visualization provides deeper insights into the underlying mechanisms of TCM theories, including the principles of herb combination, biological foundations of herb or herbal formulae action, and molecular basis of TCM syndromes. In this study, we review several recent developments in TCM network pharmacology research and discuss their potential for bridging the gap between traditional and modern medicine. We briefly summarize the two main functional applications of TCM network models: understanding/uncovering and predicting/discovering. In particular, we focus on how TCM network pharmacology research is conducted and highlight different computational tools, such as network-based and machine learning algorithms, and sources that have been proposed and applied to the different steps involved in the research process. To make network pharmacology research commonplace, some basic network definitions and analysis methods are presented.
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Affiliation(s)
- Ming Yang
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jia-Lei Chen
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
| | - Li-Wen Xu
- Longhua Hospital Affiliated to Shanghai University of TCM, Shanghai 200032, China
| | - Guang Ji
- Institute of Digestive Disease, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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36
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Villoutreix BO, Lagorce D, Labbé CM, Sperandio O, Miteva MA. One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. Drug Discov Today 2013; 18:1081-9. [PMID: 23831439 DOI: 10.1016/j.drudis.2013.06.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/18/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022]
Abstract
Online resources enabling and supporting drug discovery have blossomed during the past ten years. However, drug hunters commonly find themselves overwhelmed by the proliferation of these computer-based resources. Ten years ago, we, the authors of this review, felt that a comprehensive list of in silico resources relating to drug discovery was needed. Especially because the internet provides a wealth of inspiring tools that, if fully exploited, could greatly assist the process. We present here a compilation of online tools and databases collected over the past decade. The tools were essentially found through literature and internet searches and, currently, our list contains over 1500 URLs. We also briefly highlight some recently reported services and comment about ongoing and future efforts in the field.
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Affiliation(s)
- Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In Silico, 39 rue Helene Brion, 75013 Paris, France.
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37
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Mavridis L, Mitchell JB. Predicting the protein targets for athletic performance-enhancing substances. J Cheminform 2013; 5:31. [PMID: 23800040 PMCID: PMC3701582 DOI: 10.1186/1758-2946-5-31] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/17/2013] [Indexed: 12/02/2022] Open
Abstract
Background The World Anti-Doping Agency (WADA) publishes the Prohibited List, a manually compiled international standard of substances and methods prohibited in-competition, out-of-competition and in particular sports. It would be ideal to be able to identify all substances that have one or more performance-enhancing pharmacological actions in an automated, fast and cost effective way. Here, we use experimental data derived from the ChEMBL database (~7,000,000 activity records for 1,300,000 compounds) to build a database model that takes into account both structure and experimental information, and use this database to predict both on-target and off-target interactions between these molecules and targets relevant to doping in sport. Results The ChEMBL database was screened and eight well populated categories of activities (Ki, Kd, EC50, ED50, activity, potency, inhibition and IC50) were used for a rule-based filtering process to define the labels “active” or “inactive”. The “active” compounds for each of the ChEMBL families were thereby defined and these populated our bioactivity-based filtered families. A structure-based clustering step was subsequently performed in order to split families with more than one distinct chemical scaffold. This produced refined families, whose members share both a common chemical scaffold and bioactivity against a common target in ChEMBL. Conclusions We have used the Parzen-Rosenblatt machine learning approach to test whether compounds in ChEMBL can be correctly predicted to belong to their appropriate refined families. Validation tests using the refined families gave a significant increase in predictivity compared with the filtered or with the original families. Out of 61,660 queries in our Monte Carlo cross-validation, belonging to 19,639 refined families, 41,300 (66.98%) had the parent family as the top prediction and 53,797 (87.25%) had the parent family in the top four hits. Having thus validated our approach, we used it to identify the protein targets associated with the WADA prohibited classes. For compounds where we do not have experimental data, we use their computed patterns of interaction with protein targets to make predictions of bioactivity. We hope that other groups will test these predictions experimentally in the future.
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Affiliation(s)
- Lazaros Mavridis
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, Purdie Building, University of St Andrews, North Haugh, St Andrews, Scotland KY16 9ST, UK.
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Mathias SL, Hines-Kay J, Yang JJ, Zahoransky-Kohalmi G, Bologa CG, Ursu O, Oprea TI. The CARLSBAD database: a confederated database of chemical bioactivities. Database (Oxford) 2013; 2013:bat044. [PMID: 23794735 PMCID: PMC3689437 DOI: 10.1093/database/bat044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/12/2013] [Accepted: 05/21/2013] [Indexed: 11/30/2022]
Abstract
Many bioactivity databases offer information regarding the biological activity of small molecules on protein targets. Information in these databases is often hard to resolve with certainty because of subsetting different data in a variety of formats; use of different bioactivity metrics; use of different identifiers for chemicals and proteins; and having to access different query interfaces, respectively. Given the multitude of data sources, interfaces and standards, it is challenging to gather relevant facts and make appropriate connections and decisions regarding chemical-protein associations. The CARLSBAD database has been developed as an integrated resource, focused on high-quality subsets from several bioactivity databases, which are aggregated and presented in a uniform manner, suitable for the study of the relationships between small molecules and targets. In contrast to data collection resources, CARLSBAD provides a single normalized activity value of a given type for each unique chemical-protein target pair. Two types of scaffold perception methods have been implemented and are available for datamining: HierS (hierarchical scaffolds) and MCES (maximum common edge subgraph). The 2012 release of CARLSBAD contains 439 985 unique chemical structures, mapped onto 1,420 889 unique bioactivities, and annotated with 277 140 HierS scaffolds and 54 135 MCES chemical patterns, respectively. Of the 890 323 unique structure-target pairs curated in CARLSBAD, 13.95% are aggregated from multiple structure-target values: 94 975 are aggregated from two bioactivities, 14 544 from three, 7 930 from four and 2214 have five bioactivities, respectively. CARLSBAD captures bioactivities and tags for 1435 unique chemical structures of active pharmaceutical ingredients (i.e. 'drugs'). CARLSBAD processing resulted in a net 17.3% data reduction for chemicals, 34.3% reduction for bioactivities, 23% reduction for HierS and 25% reduction for MCES, respectively. The CARLSBAD database supports a knowledge mining system that provides non-specialists with novel integrative ways of exploring chemical biology space to facilitate knowledge mining in drug discovery and repurposing. Database URL: http://carlsbad.health.unm.edu/carlsbad/.
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Affiliation(s)
| | | | | | | | | | | | - Tudor I. Oprea
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, 1 University of New Mexico, MSC09 5025, Albuquerque, NM 87131, USA
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Hu Z, Chang YC, Wang Y, Huang CL, Liu Y, Tian F, Granger B, Delisi C. VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. Nucleic Acids Res 2013; 41:W225-31. [PMID: 23716640 PMCID: PMC3692070 DOI: 10.1093/nar/gkt401] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network analysis of diseases, therapies, genes and drugs. With improved understanding of the mechanisms of complex diseases and drug actions through network analysis, novel drug methods (e.g., drug repositioning, multi-target drug and combination therapy) can be designed. More specifically, the new update includes (i) integrated search and navigation of disease and drug hierarchies; (ii) integrated disease–gene, therapy–drug and drug–target association to aid the network construction and filtering; (iii) annotation of genes/drugs using disease/therapy information; (iv) prediction of associated diseases/therapies for a given set of genes/drugs using enrichment analysis; (v) network transformation to support construction of versatile network of drugs, genes, diseases and therapies; (vi) enhanced user interface using docking windows to allow easy customization of node and edge properties with build-in legend node to distinguish different node type. VisANT is freely available at: http://visant.bu.edu.
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Affiliation(s)
- Zhenjun Hu
- Center for Advanced Genomic Technology, Bioinformatics Program, Boston University, Boston, MA 02215, USA.
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Gong J, Cai C, Liu X, Ku X, Jiang H, Gao D, Li H. ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method. ACTA ACUST UNITED AC 2013; 29:1827-9. [PMID: 23712658 DOI: 10.1093/bioinformatics/btt270] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY ChemMapper is an online platform to predict polypharmacology effect and mode of action for small molecules based on 3D similarity computation. ChemMapper collects >350 000 chemical structures with bioactivities and associated target annotations (as well as >3 000 000 non-annotated compounds for virtual screening). Taking the user-provided chemical structure as the query, the top most similar compounds in terms of 3D similarity are returned with associated pharmacology annotations. ChemMapper is designed to provide versatile services in a variety of chemogenomics, drug repurposing, polypharmacology, novel bioactive compounds identification and scaffold hopping studies. AVAILABILITY http://lilab.ecust.edu.cn/chemmapper/. CONTACT xfliu@ecust.edu.cn or hlli@ecust.edu.cn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiayu Gong
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
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iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions. Drug Discov Today 2013; 18:958-68. [PMID: 23688585 DOI: 10.1016/j.drudis.2013.05.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/06/2013] [Accepted: 05/10/2013] [Indexed: 01/05/2023]
Abstract
The development of small molecule drugs targeting protein-protein interactions (PPI) represents a major challenge, in part owing to the misunderstanding of the PPI chemical space. To this end, we have manually collected the structures, the physicochemical and pharmacological profiles of 1650 PPI inhibitors across 13 families of PPI targets in a database named iPPI-DB. To access iPPI-DB, we propose a user-friendly web application (www.ippidb.cdithem.fr) with customizable queries and intuitive visualizing functionalities for associated properties of the compounds. This could assist scientists to design the next generation of PPI drugs. In this review, we describe iPPI-DB in the context of other low molecular weight molecule databases.
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