Kinase Chemogenomics

The human genome contains hundreds of dark kinases that are poorly characterized and for which little is known about their role in human disease. SGC-UNC scientists have championed a method of studying the biology of dark kinases, called chemogenomics. The approach utilizes ATP-competitive kinase inhibitors that show cross-activity on multiple kinases. The most useful ‘narrow-spectrum’ inhibitors have activity on 2 to 10 kinases. SGC-UNC scientists have assembled a large matrix of these narrow-spectrum kinase inhibitors into a chemogenomic set to probe the cell biology of the dark kinases.

Our first chemogenomic set contained 367 small molecule kinase inhibitors that were previously published by chemists at GSK. The set was named the Published Kinase Inhibitor Set (PKIS). It was carefully selected to maximize chemical and biological diversity of the inhibitors. Broad profiling at NanoSyn and the SGC Oxford showed that PKIS had activity across over 150 human kinases. PKIS was made available to the scientific community as a resource to study kinase biology and to uncover potential new targets for drug discovery. To date over 50 peer-reviewed papers have been published that report on the use of PKIS in the biomedical research.

Building on this success, a second chemogenomics set of kinase inhibitors from GSK, Takeda, and Pfizer was assembled as PKIS2. This set contained 645 inhibitors and included many additional chemotypes that were not represented in the original set. PKIS2 was profiled using the DiscoverX KINOMEscan affinity capture technology and shown to index 250 human kinases. PKIS2 was also made widely available to the scientific community.

PKIS and PKIS2 demonstrated the power of reusing published kinase inhibitors to build diverse chemogenomic sets. Detailed analysis of their activity profiles has allowed the design of an improved Kinase ChemoGenomic Set (KCGS) with the following properties:

  • Annotation across 400 human kinases using the KINOMEscan technology

  • Inclusion of only narrow spectrum inhibitors as confirmed by broad profiling

  • Addition of new chemotypes from academic collaborators and multiple pharmaceutical companies

  • Synthesis of new inhibitors designed to fill the remaining gaps in the set

KCGS has been designed to replace PKIS and PKIS2, supplies of which have been depleted. KCGS has improved coverage of the human kinome and contains no promiscuous compounds, thereby facilitating the annotation of phenotypic data and hypothesis generation. KCGS is now available from the SGC.

KCGS Figure.jpg

Figure. Coverage of human kinases by KCGS. Kinases are ranked by the number of publications in PubMed. Each bar represents a kinase that is covered by one or more of the narrow spectrum inhibitors.

Funding to support the assembly and annotation of KCGS was provided by the UNC Eshelman Institute for Innovation and the NIH Illuminating the Druggable Genome. Kinase inhibitors were made available by GSK, AbbVie, Bayer, Boehringer Ingelheim, Merck Sharp & Dohme, Pfizer, Takeda, AstraZeneca, and Vertex. Additional kinase inhibitors were provided by Nathanael Gray (Dana Farber Cancer Institute) and Julian Blagg (Cancer Research UK). Screening assays were supported by Promega and Eurofins (DiscoverX).