Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors

Abstract

Structure-based methods were used to design a potent and highly selective group II p21-activated kinase (PAK) inhibitor with a novel binding mode, compound 17. Hydrophobic interactions within a lipophilic pocket past the methionine gatekeeper of group II PAKs approached by these type I 1/2 binders were found to be important for improving potency. A structure-based hypothesis and strategy for achieving selectivity over group I PAKs, and the broad kinome, based on unique flexibility of this lipophilic pocket, is presented. A concentration-dependent decrease in tumor cell migration and invasion in two triple-negative breast cancer cell lines was observed with compound 17.

P21 activated kinases

“…LCH-779944 reduces proliferation and invasion of gastric cancer cells in vitro, as well as filopodia formation and cell elongation, but it has not been tested in tumors in animals or clinically in cancer patients. Genentech has recently generated a highly specific group B Pak small molecule inhibitor called compound 17,150 which leads to decreased migration and invasiveness in 2 breast cancer cell lines. These types of inhibitors are promising for the future treatment of disease, but important challenges lie ahead.…”

Targeting cancer with kinase inhibitors

“…Despite the considerable technical challenges in developing highly selective kinase inhibitors, recent efforts have been aided by using specialized chemical libraries and structureinformed design (7,112). Importantly, these efforts are meeting with overall success, such as for ATP-competitive small molecules that specifically target PAK4 (113), as well as cysteine-targeted covalent inhibitors of FGFR4 and CDK7 that selectively perturb proliferation and transcriptional regulation (114,115). Additional highly selective kinase inhibitors are expected to be available in the near future to test new clinical hypotheses in the new era of precision medicine.…”

Inhibitors of p21-Activated Kinases (PAKs)

“…PAK4 is often highly expressed in triple-negative breast cancer (TNBC) cells, 21 and therefore, compound 13 was utilized to assess group II PAK-dependent phenotypes in cell lines derived from this tumor subtype. 87 Group II PAK catalytic activity was required for efficient migration and invasion of MDA-MB-436 and MCF10A-PIK3CA(H1047R) cells. 89 Of particular note, inhibition of cellular proliferation by compound 13 was correlated with PAK4 mRNA expression level in a small panel of TNBC cell lines, which is consistent with recent reports relying on genetic loss-of-function approaches for PAK4, 90 and would not be predicted for less selective PAK family small molecule inhibitors.…”

“…This binding mode is unprecedented in the PAK literature; however, propargyl alcohol-driven type I 1 / 2 binding has been demonstrated for AKT and NIK (both also possessing methionine gatekeepers). 87 Further exploration of preferred hinge binding contacts through modifications of both core and hinge binding heterocycle culminated in the identification of compound 13, 87 a highly potent and kinase selective PAK4 inhibitor. In a 222-kinase panel at 0.1 μM concentration, besides PAK4, PAK5, and PAK6, it inhibited only EphB1 at >60% (Figure 14).…”