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Drugcentral 2021 Supports Drug Discovery and Repositioning DrugCentral 2021 supports drug discovery and repositioning Avram, Sorin; Bologa, Cristian G.; Holmes, Jayme; Bocci, Giovanni; Wilson, Thomas B.; Nguyen, Dac Trung; Curpan, Ramona; Halip, Liliana; Bora, Alina; Yang, Jeremy J.; Knockel, Jeffrey; Sirimulla, Suman; Ursu, Oleg; Oprea, Tudor I. Published in: Nucleic Acids Research DOI: 10.1093/nar/gkaa997 Publication date: 2021 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Avram, S., Bologa, C. G., Holmes, J., Bocci, G., Wilson, T. B., Nguyen, D. T., Curpan, R., Halip, L., Bora, A., Yang, J. J., Knockel, J., Sirimulla, S., Ursu, O., & Oprea, T. I. (2021). DrugCentral 2021 supports drug discovery and repositioning. Nucleic Acids Research, 49(D1), D1160-D1169. https://doi.org/10.1093/nar/gkaa997 Download date: 02. okt.. 2021 D1160–D1169 Nucleic Acids Research, 2021, Vol. 49, Database issue Published online 5 November 2020 doi: 10.1093/nar/gkaa997 DrugCentral 2021 supports drug discovery and repositioning Sorin Avram1,†, Cristian G. Bologa2,3,†,JaymeHolmes2, Giovanni Bocci2, Thomas Downloaded from https://academic.oup.com/nar/article/49/D1/D1160/5957163 by Royal Library Copenhagen University user on 03 February 2021 B. Wilson4, Dac-Trung Nguyen 5, Ramona Curpan1, Liliana Halip1, Alina Bora1, Jeremy J. Yang2, Jeffrey Knockel6, Suman Sirimulla7,OlegUrsu8 and Tudor I. Oprea 2,8,9,10,* 1Department of Computational Chemistry, “Coriolan Dragulescu” Institute of Chemistry, 24 Mihai Viteazu Blvd, Timis¸oara, Timis¸, 300223, Romania,ˆ 2Translational Informatics Division, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA, 3UNM Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA, 4College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA, 5National Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA, 6Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA, 7Department of Pharmaceutical Sciences, School of Pharmacy, The University of Texas at El Paso, TX 79902, USA, 8Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA, 9Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, 40530 Gothenburg, Sweden and 10Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Received September 17, 2020; Revised October 9, 2020; Editorial Decision October 12, 2020; Accepted October 14, 2020 ABSTRACT INTRODUCTION DrugCentral is a public resource (http://drugcentral. DrugCentral integrates a broad spectrum of drug resources org) that serves the scientific community by provid- related to chemical structures, biological activities, regula- ing up-to-date drug information, as described in pre- tory data, pharmacology and drug formulations (1). Since vious papers. The current release includes 109 newly 2018, DrugCentral has continuously strengthened its role as approved (October 2018 through March 2020) active a key resource for the worldwide scientific community be- ing additionally cross-referenced by several resources, such pharmaceutical ingredients in the US, Europe, Japan as UniProt (2), ChEBI (3), Hetionet (4), GUILDify (5), and other countries; and two molecular entities (e.g. UniChem (6) and Guide to Pharmacology (7). DrugCentral mefuparib) of interest for COVID19. New additions in- served as primary resource for RepoDB, a drug repurpos- clude a set of pharmacokinetic properties for ∼1000 ing database (8), a time-resolved computational drug repur- drugs, and a sex-based separation of side effects, posing algorithm (9), and an adverse drug event network for processed from FAERS (FDA Adverse Event Report- computational toxicology predictions (10). First introduced ing System); as well as a drug repositioning prioriti- and published in the 2017 NAR database issue (1), Drug- zation scheme based on the market availability and Central reconciles the basic scientist’s understanding of the intellectual property rights forFDA approved drugs. ‘drug’ concept (active pharmaceutical ingredient) with the In the context of the COVID19 pandemic, we also in- view of the patient and healthcare practitioner (pharmaceu- corporated REDIAL-2020, a machine learning plat- tical formulation). Since its initial launch, the two Drug- Central papers (1,11) were cited more than 160 times cf. form that estimates anti-SARS-CoV-2 activities, as Google Scholar, and the website is accessed on average by well as the ‘drugs in news’ feature offers a brief enu- ∼8000 visitors monthly, with a monthly average of ∼20 000 meration of the most interesting drugs at the present page views and over 20 000 full database downloads per year moment. The full database dump and data files are (as of 15 September 2020). Throughout regulatory and sci- available for download from the DrugCentral web por- entific documents, several terms are often used interchange- tal. ably: drug substance, new chemical (or molecular) entity and active (pharmaceutical) ingredient. While these terms have precise contextual meaning, in this paper preference *To whom correspondence should be addressed. Tel: +1 505 925 7529; Fax: +1 505 925 7625; Email: [email protected] †The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors. C The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Research, 2021, Vol. 49, Database issue D1161 is given to the term ‘drug’ as synonymous with these three of rare diseases (15,16). Out of the newly added drugs, the concepts. The term ‘formulation’ is used when discussing ChEMBL database (17) indexes 104 (91) of the 111 drugs, pharmaceutical products. KEGG (18) indexes 107, DrugBank captures 105 and the The current update adds newly approved drugs by Guide to Pharmacology 77 drugs, respectively (Table 1). the US Food and Drug Administration (FDA, https:// www.fda.gov/home) and the European Medicines Agency (EMA, https://www.ema.europa.eu/en)upto31March Downloaded from https://academic.oup.com/nar/article/49/D1/D1160/5957163 by Royal Library Copenhagen University user on 03 February 2021 Bioactivity data and mechanism of action 2020. Drugs approved by Japan Pharmaceuticals and Medical Devices Agency (PMDA, https://www.pmda.go.jp/ The present release adds 1379 new bioactivity datapoints english/index.html) were also monitored up to the latest in- from ChEMBL (17) and the Guide to Pharmacology (7) formation available, i.e. November 2019. In addition, for using automated pipelines, 79% and 8%, respectively; and numerous drugs present in DrugCentral since 2018, regu- manually curated scientific literature and approved drug latory agency information was added according to their ap- label data (13%). Newly introduced drugs are associated proval status. with 551 bioactivity points from ChEMBL (65.5%), man- An important component of drug discovery and repo- ual curation from literature (24.14%), the Guide to Phar- sitioning is information related to the pharmacokinetic macology (6.17%) and approved drug labels (4.17%), re- (PK) properties of drugs, e.g. maximum recommended dose spectively; as well as 109 mechanism of action (MoA or or half-life, as well as information related to side effects. Tclin proteins––vide infra) targets, with kinases (26%) and In this regard, DrugCentral 2021 introduces critically re- enzymes (21%) representing the major target categories, fol- viewed information on PK, thus increasing the clinical lowed by G-protein-coupled receptors––GPCRs (17%) and pharmacology-related information coverage for drugs. Fur- tumor-associated antigens (9%). Since 2018, 46 novel MoA thermore, adverse drug events separated by sex are tabu- targets, associated with 32 newly approved drugs, have been lated at the drug level, to increase our understanding of drug introduced (Table 2). safety. Our knowledge-based protein classification19 ( ) bins hu- Sudden outbreaks can rapidly impact global health, as man proteins into four categories, according to their ‘tar- evidenced by the COVID-19 pandemic, caused by severe get development level’ (TDL): Tclin are MoA-designated acute respiratory syndrome coronavirus 2 (SARS-CoV-2). drug targets via which approved drugs act (15,20,21), cur- This pandemic has accelerated the need to rely on com- rently 659 human proteins; Tchem are proteins that are putational platforms (12) capable of identifying and ad- not Tclin, but are known to bind small molecules with vancing novel therapeutics for clinical evaluation. In this high potency; Tbio includes proteins that have Gene On- regard, the current DrugCentral update enables computa- tology (22) ‘leaf’ (lowest level) term annotations based on tional and medicinal chemists with (i) drug repositioning experimental evidence; or meet two of the following three categories, i.e. an in-depth classification of drugs based on conditions: A fractional publication count (23)abovefive,
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