Structure-based design and synthesis of new benzothiophene derivatives as potent PRPF4 kinase inhibitors

Pre-mRNA Processing Factor 4 (PRPF4) is a kinase associated with splicing regulation1 and cancer cell survival,2 although it remains largely understudied. The first PRPF4 inhibitor described in the literature,3 a non-hinge binder (Cmpd-A), has failed to achieve chemical probe criteria. Using this compound as a starting point, we synthesized a series of analogs aiming at improving potency, selectivity, and cell permeability. Compounds were tested in the differential scanning fluorimetry (DSF), MDCK permeability assays, and against a selectivity panel of 320 kinases. The best analog (ACH-000224) exhibited potency equivalent to Cmpd-A with gains in permeability and selectivity. Despite excellent selectivity, further optimization is required to attenuate activity against DYRK1A and PIM1. The co-crystal structure between ACH-000224 and PRPF4 displays hydrogen bonds between the ligand and Lys717 and Glu776, and the potential of a covalent interaction with Cys833. Those interactions will be explored to design more potent and selective PRPF4 inhibitors.