As CSNK1A1 was among the 3,799 genes subjected to shRNA-mediated knock-down, we used the CMap to generate a signature of CSNK1A1 loss of function. We then queried all compounds in the database against this signature to identify perturbations that phenocopied CSNK1A1 loss. One unannotated compound, BRD-1868, showed strong connectivity to CSNK1A1 knockdown in two cell types. This suggested that BRD-1868 might function as a novel CSNK1A1 inhibitor. To test this hypothesis, we subjected the compound to kinase specificity profiling, testing its ability to bind to 456 kinases using the Kinomescan assay. This confirmed BRD-1868's ability to bind CSNK1A1 with high specificity and modest potency (KD 2.2 uM). Follow-up enzymatic assays confirmed that BRD-1868 not only binds CSNK1A1, but also inhibits its enzymatic activity (Figure 6B), making it an strong candidate for further chemical optimization. Most importantly, the result highlights the power of the L1000 Connectivity Map as a starting point for drug discovery – even in the absence of prior examples of the drug class.
