Inhibitors of BRAF dimers using an allosteric site

Abstract

BRAF kinase, a critical effector of the ERK signaling pathway, is hyperactivated in many cancers. Oncogenic BRAF V600E signals as an active monomer in the absence of active RAS, however, in many tumors BRAF dimers mediate ERK signaling. FDA-approved RAF inhibitors poorly inhibit BRAF dimers, which leads to tumor resistance. We found that Ponatinib, an FDA-approved drug, is an effective inhibitor of BRAF monomers and dimers. Ponatinib binds the BRAF dimer and stabilizes a distinct αC-helix conformation through interaction with a previously unrevealed allosteric site. Using these structural insights, we developed PHI1, a BRAF inhibitor that fully uncovers the allosteric site. PHI1 exhibits discrete cellular selectivity for BRAF dimers, with enhanced inhibition of the second protomer when the first protomer is occupied, comprising a novel class of dimer selective inhibitors. This work shows that Ponatinib and BRAF dimer selective inhibitors will be useful in treating BRAF-dependent tumors.

The mechanism of activation of monomeric B-Raf V600E

“…The first-generation Raf inhibitors, including Vemurafenib (VEM) [51] , [52] and Dabrafenib [53] , are ATP competitive inhibitors that show promising early efficacy, but drug resistance quickly develops [46] , [47] , [54] , [55] , [56] . New inhibitors have been developed including pan-Raf inhibitors (such as LY3009120) [57] that bind to both protomers in Raf dimers, paradox breakers that selectively bind to B-Raf dimers, and allosteric inhibitors that target other sites apart from the ATP binding pocket [58] , [59] . Despite this progress, long term survival rates remain low and additional treatment options are necessary [60] .…”

B-Raf autoinhibition in the presence and absence of 14-3-3

“…Full Raf activation requires KD dimerization (Cotto-Rios et al, 2020;Durrant and Morrison, 2018;Hu et al, 2013;Lavoie et al, 2013;Rajakulendran et al, 2009). Like all kinases, wild-type Raf is expected to spend most of its lifetime in the inactive state.…”

Xeroderma Pigmentosum: Gene Variants and Splice Variants

“…To deal with this resistance mechanism, dimer inhibition is under investigation. Ponatinib, a kinase inhibitor, has been shown to be a promising candidate for the development of new treatments of BRAF-dependent tumors [32]. Interestingly, considering XP an alternative splice variant of an altered allele has been shown to be beneficial in a patient with a mutation in XPG, leading to a less severe form of XP/CS [33].…”