Therapeutic Target Database Update 2016: Enriched Resource for Bench to Clinical Drug Target and Targeted Pathway Information

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 Nov 19

PMID 26578601

Citations 110

Authors

Hong Yang

Chu Qin

Ying Hong Li

Lin Tao

Jin Zhou

Chun Yan Yu

Feng Xu

Zhe Chen

Feng Zhu

Yu Zong Chen

Affiliations

Soon will be listed here.

Abstract

Extensive drug discovery efforts have yielded many approved and candidate drugs targeting various targets in different biological pathways. Several freely accessible databases provide the drug, target and drug-targeted pathway information for facilitating drug discovery efforts, but there is an insufficient coverage of the clinical trial drugs and the drug-targeted pathways. Here, we describe an update of the Therapeutic Target Database (TTD) previously featured in NAR. The updated contents include: (i) significantly increased coverage of the clinical trial targets and drugs (1.6 and 2.3 times of the previous release, respectively), (ii) cross-links of most TTD target and drug entries to the corresponding pathway entries of KEGG, MetaCyc/BioCyc, NetPath, PANTHER pathway, Pathway Interaction Database (PID), PathWhiz, Reactome and WikiPathways, (iii) the convenient access of the multiple targets and drugs cross-linked to each of these pathway entries and (iv) the recently emerged approved and investigative drugs. This update makes TTD a more useful resource to complement other databases for facilitating the drug discovery efforts. TTD is accessible at http://bidd.nus.edu.sg/group/ttd/ttd.asp.

Citing Articles

Exploration of compatibility rules and discovery of active ingredients in TCM formulas by network pharmacology.

Liu Y, Li X, Chen C, Ding N, Ma S, Yang M Chin Herb Med. 2024; 16(4):572-588.

PMID: 39606260 PMC: 11589340. DOI: 10.1016/j.chmed.2023.09.008.

MSFC: a new feature construction method for accurate diagnosis of mass spectrometry data.

Feng X, Dong Z, Li Y, Cheng Q, Xin Y, Lu Q Sci Rep. 2023; 13(1):15694.

PMID: 37735183 PMC: 10514077. DOI: 10.1038/s41598-023-42395-5.

TTD: Therapeutic Target Database describing target druggability information.

Zhou Y, Zhang Y, Zhao D, Yu X, Shen X, Zhou Y Nucleic Acids Res. 2023; 52(D1):D1465-D1477.

PMID: 37713619 PMC: 10767903. DOI: 10.1093/nar/gkad751.

Exploring the Mechanisms of Self-made Kuiyu Pingchang Recipe for the Treatment of Ulcerative Colitis and Irritable Bowel Syndrome using a Network Pharmacology-based Approach and Molecular Docking.

Wen Y, Wang X, Si K, Xu L, Huang S, Zhan Y Curr Comput Aided Drug Des. 2023; 20(5):534-550.

PMID: 37190808 DOI: 10.2174/1573409919666230515103224.

A Systematic Review of Deep Learning Methodologies Used in the Drug Discovery Process with Emphasis on In Vivo Validation.

Koutroumpa N, Papavasileiou K, Papadiamantis A, Melagraki G, Afantitis A Int J Mol Sci. 2023; 24(7).

PMID: 37047543 PMC: 10095548. DOI: 10.3390/ijms24076573.

References

Zhu F, Han L, Zheng C, Xie B, Tammi M, Yang S . What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical, and systems profiles of successful targets. J Pharmacol Exp Ther. 2009; 330(1):304-15. DOI: 10.1124/jpet.108.149955. View

Jia J, Zhu F, Ma X, Cao Z, Cao Z, Li Y . Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov. 2009; 8(2):111-28. DOI: 10.1038/nrd2683. View

Paul S, Mytelka D, Dunwiddie C, Persinger C, Munos B, Lindborg S . How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov. 2010; 9(3):203-14. DOI: 10.1038/nrd3078. View

Kandasamy K, Mohan S, Raju R, Keerthikumar S, Sameer Kumar G, Venugopal A . NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010; 11(1):R3. PMC: 2847715. DOI: 10.1186/gb-2010-11-1-r3. View

Berg J, Rogers M, Lyster P . Systems biology and pharmacology. Clin Pharmacol Ther. 2010; 88(1):17-9. DOI: 10.1038/clpt.2010.69. View

Nelson A, Dhimolea E, Reichert J . Development trends for human monoclonal antibody therapeutics. Nat Rev Drug Discov. 2010; 9(10):767-74. DOI: 10.1038/nrd3229. View

Barabasi A, Gulbahce N, Loscalzo J . Network medicine: a network-based approach to human disease. Nat Rev Genet. 2010; 12(1):56-68. PMC: 3140052. DOI: 10.1038/nrg2918. View

Croft D, OKelly G, Wu G, Haw R, Gillespie M, Matthews L . Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 2010; 39(Database issue):D691-7. PMC: 3013646. DOI: 10.1093/nar/gkq1018. View

Zarin D, Tse T, Williams R, Califf R, Ide N . The ClinicalTrials.gov results database--update and key issues. N Engl J Med. 2011; 364(9):852-60. PMC: 3066456. DOI: 10.1056/NEJMsa1012065. View

10.

Bunnage M . Getting pharmaceutical R&D back on target. Nat Chem Biol. 2011; 7(6):335-9. DOI: 10.1038/nchembio.581. View

11.

Pammolli F, Magazzini L, Riccaboni M . The productivity crisis in pharmaceutical R&D. Nat Rev Drug Discov. 2011; 10(6):428-38. DOI: 10.1038/nrd3405. View

12.

Zhu F, Shi Z, Qin C, Tao L, Liu X, Xu F . Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res. 2011; 40(Database issue):D1128-36. PMC: 3245130. DOI: 10.1093/nar/gkr797. View

13.

Kelder T, van Iersel M, Hanspers K, Kutmon M, Conklin B, Evelo C . WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2011; 40(Database issue):D1301-7. PMC: 3245032. DOI: 10.1093/nar/gkr1074. View

14.

Zhao S, Iyengar R . Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol. 2012; 52:505-21. PMC: 3619403. DOI: 10.1146/annurev-pharmtox-010611-134520. View

15.

Chen Z, Cheng K, Walton Z, Wang Y, Ebi H, Shimamura T . A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response. Nature. 2012; 483(7391):613-7. PMC: 3385933. DOI: 10.1038/nature10937. View

16.

Zhang J, Jia J, Zhu F, Ma X, Han B, Wei X . Analysis of bypass signaling in EGFR pathway and profiling of bypass genes for predicting response to anticancer EGFR tyrosine kinase inhibitors. Mol Biosyst. 2012; 8(10):2645-56. DOI: 10.1039/c2mb25165e. View

17.

DiMasi J, Reichert J, Feldman L, Malins A . Clinical approval success rates for investigational cancer drugs. Clin Pharmacol Ther. 2013; 94(3):329-35. DOI: 10.1038/clpt.2013.117. View

18.

Law V, Knox C, Djoumbou Y, Jewison T, Guo A, Liu Y . DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2013; 42(Database issue):D1091-7. PMC: 3965102. DOI: 10.1093/nar/gkt1068. View

19.

Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M . Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2013; 42(Database issue):D199-205. PMC: 3965122. DOI: 10.1093/nar/gkt1076. View

20.

Bento A, Gaulton A, Hersey A, Bellis L, Chambers J, Davies M . The ChEMBL bioactivity database: an update. Nucleic Acids Res. 2013; 42(Database issue):D1083-90. PMC: 3965067. DOI: 10.1093/nar/gkt1031. View