Abstract
A large proportion of biomedical research and the development of therapeutics is focused on a small fraction of the human genome. In a strategic effort to map the knowledge gaps around proteins encoded by the human genome and to promote the exploration of currently understudied, but potentially druggable, proteins, the US National Institutes of Health launched the Illuminating the Druggable Genome (IDG) initiative in 2014. In this article, we discuss how the systematic collection and processing of a wide array of genomic, proteomic, chemical and disease-related resource data by the IDG Knowledge Management Center have enabled the development of evidence-based criteria for tracking the target development level (TDL) of human proteins, which indicates a substantial knowledge deficit for approximately one out of three proteins in the human proteome. We then present spotlights on the TDL categories as well as key drug target classes, including G protein-coupled receptors, protein kinases and ion channels, which illustrate the nature of the unexplored opportunities for biomedical research and therapeutic development.
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Change history
23 March 2018
In the version of this article that was originally published online, an older version of the data set categorizing proteins into target development levels was used to create Figure 1 than the version used to create Table 1, and data from Figure 1 were referred to at several points in the text of the article. Figure 1 and the associated text have been updated to match Table 1 in the online and print versions of the article. The authors apologize for any inconvenience that this error may have caused.
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Acknowledgements
This work was supported by US National Institutes of Health (NIH) grants U54 CA189205 and U24 224370 (Illuminating the Druggable Genome Knowledge Management Center (IDG KMC)) at the University of New Mexico, Novo Nordisk Foundation Center for Protein Research, European Bioinformatics Institute (EBI) and University of Miami, U54 CA189201 and U24 CA224260 (A.M., Mount Sinai), P30 CA118100 (T.I.O., G.N.G. and L.A.S., UNM) and UL1 TR001449 (T.I.O. and L.A.S.), UM1 HG006370 (International Mouse Phenotyping Consortium, T.F.M. and I.T.), U01 MH104974 (B.L.R.), U01 MH104984 (S.T.), U01 MH105028 (M.T.M.), U01 MH105026 (J.Q. and A.M., Baylor) and U01 MH104999, R01 CA177993 and U24 DK116204 (S.G. and G.L.J.) and by the European Molecular Biology Laboratory (EMBL) and Wellcome Trust Strategic Awards WT086151/Z/08/Z and WT104104/Z/14/Z (A.G., A.H., A.R.L., A.K., J.P.O., and G.P.); and by Novo Nordisk Foundation Denmark grant NNF14CC0001 (S.B., L.J.L. and D.W). R.G., A.J., D.T.N., A.S., N.S., and G.Z.K. were supported by the Intramural Research Program, National Center for Advancing Translational Sciences (NCATS) and by U54 CA189205. Dedicated to Francisc Schneider (1933–2017).
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S.B. and L.J.J. are co-founders, shareholders and scientific advisory board members of Intomics A/S, an omics data integration company. A.C. and C.R. are employees of IQVIA, a company serving the combined industries of health information technologies and clinical research. I.T. is a current employee of Google Germany. G.P. is a current employee of GlaxoSmithKline, a global health-care company. D.M. is a current employee of AstraZeneca, a global, research-based biopharmaceutical company. J.P.O. is currently an employee of Medicines Discovery Catapult, a UK government-funded facility for collaborative research and development.
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Supplementary information
Supplementary Box S1
Context, time and knowledge management (PDF 190 kb)
Supplementary File S2
Plot of bioactivity values for major target classes. (PDF 675 kb)
Supplementary Information
Supplementary S3 table (XLSX 12754 kb)
Supplementary S4 table
Statistical significance results for the four validating metrics shown in Figure 2a (PDF 117 kb)
Supplementary S5 Box
Spotlight on the ionizing radiation proteome (PDF 301 kb)
Supplementary S7 table
Spotlight on selectivity (PDF 132 kb)
Supplementary information
Supplementary S8 table (XLSX 321 kb)
Supplementary information
Supplementary S9 table (XLSX 1011 kb)
Supplementary information
Supplementary S10 table (XLSX 15 kb)
Supplementary information
Supplementary S11 table (XLSX 111 kb)
Supplementary File S11
IMS Health (MIDAS) global drug sales data (2011-2015), organized by ATC level 2 codes and by protein class, normalized to percentage values. (PDF 1026 kb)
Glossary
- Drug
-
Externally administered, possibly endogenous but mostly xenobiotic, substances that are administered to patients in order to influence the outcome of a disease, syndrome or condition.
- Drug targets
-
Molecular entities present in living systems that, upon interaction with therapeutic agents or their by-products, result in modified biological responses that lead to therapeutic outcomes. The interaction between a drug and its target leads, directly or indirectly, to observable clinical outcomes.
- Druggable genome
-
Originally defined by Hopkins and Groom as the set of genes that encode proteins that could be modulated by an orally administered small molecule, as estimated by Lipinski's 'rule of five' guidelines.
- Mode of action
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Referred to as 'mechanism of action' when the molecular interactions are well understood; describes the way in which drugs exert their intended therapeutic action, resulting in the intended therapeutic outcome.
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Oprea, T., Bologa, C., Brunak, S. et al. Unexplored therapeutic opportunities in the human genome. Nat Rev Drug Discov 17, 317–332 (2018). https://doi.org/10.1038/nrd.2018.14
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DOI: https://doi.org/10.1038/nrd.2018.14
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