Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAFV600E Conformation

The BRAF kinase, within the mitogen activated protein kinase (MAPK) signaling pathway, harbors activating mutations in about half of melanomas and to a significant extent in many other cancers. A single valine to glutamic acid substitution at residue 600 (BRAF(V600E)) accounts for about 90% of these activating mutations. While BRAF(V600E)-selective small molecule inhibitors, such as debrafenib and vemurafenib, have shown therapeutic benefit, almost all patients develop resistance. Resistance often arises through reactivation of the MAPK pathway, typically through mutation of upstream RAS, downstream MEK, or splicing variants. RAF kinases signal as homo- and heterodimers, and another complication associated with small molecule BRAF(V600E) inhibition is drug-induced allosteric activation of a wild-type RAF subunit (BRAF or CRAF) of the kinase dimer, a process called transactivation or paradoxical activation. Here, we used BRAF(V600E) and vemurafenib as a model system to develop chemically linked kinase inhibitors to lock RAF dimers in an inactive conformation that cannot undergo transactivation. This structure-based design effort resulted in the development of Vem-BisAmide-2, a compound containing two vemurafenib molecules connected by a bis amide linker. We show that Vem-BisAmide-2 has comparable inhibitory potency as vemurafenib to BRAF(V600E) both in vitro and in cells but promotes an inactive dimeric BRAF(V600E) conformation unable to undergo transactivation. The crystal structure of a BRAF(V600E)/Vem-BisAmide-2 complex and associated biochemical studies reveal the molecular basis for how Vem-BisAmide-2 mediates selectivity for an inactive over an active dimeric BRAF(V600E) conformation. These studies have implications for targeting BRAF(V600E)/RAF heterodimers and other kinase dimers for therapy.