Anticancer benzoxaboroles block pre-mRNA processing by directly inhibiting CPSF3

A series of benzoxaboroles were reported to have anticancer activity in cultured cancer cells and antitumor activity in pre-clinical models of cancer through an unknown mechanism. We discovered mutations in CPSF3 that reduce benzoxaborole binding and confer resistance. CPSF3 is the catalytic component of two different 3'-end processing complexes including cleavage/polyadenylation machinery and U7 snRNP. Benzoxaboroles inhibit this endonuclease activity in vitro and also curb transcriptional termination in cells. Runaway transcription leads to the expression of downstream genes that are otherwise silent, and concomitantly, downregulates thousands of constitutively expressed genes. Using X-ray crystallography, we show that benzoxaboroles bind to the active site of CPSF3 in a manner that is distinct from the other known inhibitors of CPSF3. The benzoxaborole compound impeded the growth of most cancer cell lines derived from many different lineages. These findings have implications for clinical development of CPSF3 inhibitors.