Therapeutic Target Database 2020: Enriched Resource for Facilitating Research and Early Development of Targeted Therapeutics

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Nov 7

PMID 31691823

Citations 421

Authors

Yunxia Wang

Song Zhang

Fengcheng Li

Ying Zhou

Ying Zhang

Zhengwen Wang

Runyuan Zhang

Jiang Zhu

Yuxiang Ren

Ying Tan

Chu Qin

Yinghong Li

Xiaoxu Li

YuZong Chen

Feng Zhu

Affiliations

Soon will be listed here.

Abstract

Knowledge of therapeutic targets and early drug candidates is useful for improved drug discovery. In particular, information about target regulators and the patented therapeutic agents facilitates research regarding druggability, systems pharmacology, new trends, molecular landscapes, and the development of drug discovery tools. To complement other databases, we constructed the Therapeutic Target Database (TTD) with expanded information about (i) target-regulating microRNAs and transcription factors, (ii) target-interacting proteins, and (iii) patented agents and their targets (structures and experimental activity values if available), which can be conveniently retrieved and is further enriched with regulatory mechanisms or biochemical classes. We also updated the TTD with the recently released International Classification of Diseases ICD-11 codes and additional sets of successful, clinical trial, and literature-reported targets that emerged since the last update. TTD is accessible at http://bidd.nus.edu.sg/group/ttd/ttd.asp. In case of possible web connectivity issues, two mirror sites of TTD are also constructed (http://db.idrblab.org/ttd/ and http://db.idrblab.net/ttd/).

Citing Articles

Discovery of Herbal Remedies and Key Components for Major Depressive Disorder Through Biased Random Walk Analysis on a Multiscale Network.

Lee J, Choi S, Lee D, Kang H, Lee J, Kim J Int J Mol Sci. 2025; 26(5).

PMID: 40076790 PMC: 11900307. DOI: 10.3390/ijms26052162.

Exploring the active ingredients and potential mechanisms of Pingchan granules in Parkinson's disease treatment through network pharmacology and transcriptomics.

Xu Q, Wang Y, Wang C, Jiang S, Zhang B, Tian J Sci Rep. 2025; 15(1):7847.

PMID: 40050654 PMC: 11885611. DOI: 10.1038/s41598-025-91344-x.

Exploring the molecular mechanism of icariin improving spinal cord injury through network pharmacology combined with experimental verification.

Zhou M, Jiang Z, Zhang M, Feng S, Ma B, Kan S Naunyn Schmiedebergs Arch Pharmacol. 2025; .

PMID: 40014127 DOI: 10.1007/s00210-025-03904-7.

Network Pharmacology Analysis and Biological Validation Systemically Identified the Active Ingredients and Molecular Targets of Kudzu Root on Osteoporosis.

Liu Z, Zhang B, Kwok K, Dong X, Wong K Int J Mol Sci. 2025; 26(3).

PMID: 39940967 PMC: 11818621. DOI: 10.3390/ijms26031202.

Network Pharmacology and Bioinformatics Study of Six Medicinal Food Homologous Plants Against Colorectal Cancer.

Zhao X, Xiu J, Yang H, Han W, Jin Y Int J Mol Sci. 2025; 26(3).

PMID: 39940699 PMC: 11817456. DOI: 10.3390/ijms26030930.

References

Davila M, Riviere I, Wang X, Bartido S, Park J, Curran K . Efficacy and toxicity management of 19-28z CAR T cell therapy in B cell acute lymphoblastic leukemia. Sci Transl Med. 2014; 6(224):224ra25. PMC: 4684949. DOI: 10.1126/scitranslmed.3008226. View

Gohlke B, Nickel J, Otto R, Dunkel M, Preissner R . CancerResource--updated database of cancer-relevant proteins, mutations and interacting drugs. Nucleic Acids Res. 2015; 44(D1):D932-7. PMC: 4702908. DOI: 10.1093/nar/gkv1283. View

Rukov J, Shomron N . MicroRNA pharmacogenomics: post-transcriptional regulation of drug response. Trends Mol Med. 2011; 17(8):412-23. DOI: 10.1016/j.molmed.2011.04.003. View

Pardoll D . The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer. 2012; 12(4):252-64. PMC: 4856023. DOI: 10.1038/nrc3239. View

Yang H, Qin C, Li Y, Tao L, Zhou J, Yu C . Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. Nucleic Acids Res. 2015; 44(D1):D1069-74. PMC: 4702870. DOI: 10.1093/nar/gkv1230. View

Tomaselli D, Lucidi A, Rotili D, Mai A . Epigenetic polypharmacology: A new frontier for epi-drug discovery. Med Res Rev. 2019; 40(1):190-244. PMC: 6917854. DOI: 10.1002/med.21600. View

Neish A, Read M, Thanos D, Pine R, Maniatis T, Collins T . Endothelial interferon regulatory factor 1 cooperates with NF-kappa B as a transcriptional activator of vascular cell adhesion molecule 1. Mol Cell Biol. 1995; 15(5):2558-69. PMC: 230486. DOI: 10.1128/MCB.15.5.2558. View

Kim S, Chen J, Cheng T, Gindulyte A, He J, He S . PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2018; 47(D1):D1102-D1109. PMC: 6324075. DOI: 10.1093/nar/gky1033. View

Keseru G, Makara G . The influence of lead discovery strategies on the properties of drug candidates. Nat Rev Drug Discov. 2009; 8(3):203-12. DOI: 10.1038/nrd2796. View

10.

Salwinski L, Miller C, Smith A, Pettit F, Bowie J, Eisenberg D . The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2003; 32(Database issue):D449-51. PMC: 308820. DOI: 10.1093/nar/gkh086. View

11.

Shaabani S, Huizinga H, Butera R, Kouchi A, Guzik K, Magiera-Mularz K . A patent review on PD-1/PD-L1 antagonists: small molecules, peptides, and macrocycles (2015-2018). Expert Opin Ther Pat. 2018; 28(9):665-678. PMC: 6323140. DOI: 10.1080/13543776.2018.1512706. View

12.

Wang T, Wu X, Guo C, Zhang K, Xu J, Li Z . Development of Inhibitors of the Programmed Cell Death-1/Programmed Cell Death-Ligand 1 Signaling Pathway. J Med Chem. 2018; 62(4):1715-1730. DOI: 10.1021/acs.jmedchem.8b00990. View

13.

Karagkouni D, Paraskevopoulou M, Chatzopoulos S, Vlachos I, Tastsoglou S, Kanellos I . DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res. 2017; 46(D1):D239-D245. PMC: 5753203. DOI: 10.1093/nar/gkx1141. View

14.

The Lancet . ICD-11. Lancet. 2019; 393(10188):2275. DOI: 10.1016/S0140-6736(19)31205-X. View

15.

Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L . PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics. 2015; 32(4):579-86. PMC: 5963357. DOI: 10.1093/bioinformatics/btv597. View

16.

Matys V, Kel-Margoulis O, Fricke E, Liebich I, Land S, Barre-Dirrie A . TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2005; 34(Database issue):D108-10. PMC: 1347505. DOI: 10.1093/nar/gkj143. View

17.

Franchini P, Xiong P, Fruciano C, Schneider R, Woltering J, Hulsey C . MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish. Mol Biol Evol. 2019; 36(11):2498-2511. DOI: 10.1093/molbev/msz168. View

18.

Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M . New approach for understanding genome variations in KEGG. Nucleic Acids Res. 2018; 47(D1):D590-D595. PMC: 6324070. DOI: 10.1093/nar/gky962. View

19.

Cousins K . Computer review of ChemDraw Ultra 12.0. J Am Chem Soc. 2011; 133(21):8388. DOI: 10.1021/ja204075s. View

20.

Yang Q, Zhang Y, Cui H, Chen L, Zhao Y, Lin Y . dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication. Database (Oxford). 2018; 2018. PMC: 5824774. DOI: 10.1093/database/bay015. View