Structure, Regulation, and Inhibition of the Quorum-Sensing Signal Integrator LuxO.

In a process called quorum sensing, bacteria communicate with chemical signal molecules called autoinducers to control collective behaviors. In pathogenic vibrios, including Vibrio cholerae, the accumulation of autoinducers triggers repression of genes responsible for virulence factor production and biofilm formation. The vibrio autoinducer molecules bind to transmembrane receptors of the two-component histidine sensor kinase family. Autoinducer binding inactivates the receptors' kinase activities, leading to dephosphorylation and inhibition of the downstream response regulator LuxO. Here, we report the X-ray structure of LuxO in its unphosphorylated, autoinhibited state. Our structure reveals that LuxO, a bacterial enhancer-binding protein of the AAA+ ATPase superfamily, is inhibited by an unprecedented mechanism in which a linker that connects the catalytic and regulatory receiver domains occupies the ATPase active site. The conformational change that accompanies receiver domain phosphorylation likely disrupts this interaction, providing a mechanistic rationale for LuxO activation. We also determined the crystal structure of the LuxO catalytic domain bound to a broad-spectrum inhibitor. The inhibitor binds in the ATPase active site and recapitulates elements of the natural regulatory mechanism. Remarkably, a single inhibitor molecule may be capable of inhibiting an entire LuxO oligomer.

Synthesis of silyloxy dienes by silylene transfer to divinyl ketones: application to the asymmetric synthesis of substituted cyclohexanes.

Silver-catalyzed silylene transfer to divinyl ketones provided 2-silyloxy-1,3-dienes with control of stereochemistry and regioselectivity. The products participated in Diels-Alder reactions with electron-deficient alkenes and imines to form six-membered-ring products diastereoselectively. Cycloaddition reactions with alkenes bearing chiral auxiliaries provided access to chiral, nonracemic cyclohexenes. The methodology, therefore, represents a synthesis of diastereomerically and enantiomerically pure products in a single flask. The highly substituted cyclohexene products could be functionalized stereoselectively to provide cyclohexanols after oxidation of the carbon-silicon bond.

Silylene-mediated polarity reversal of dienoates: additions of dienoates to aldehydes at the δ-position to form trans-dioxasilacyclononenes.

Silylene transfer to α,ß,γ,δ-unsaturated carbonyl compounds produced oxasilacyclopentenes that underwent thermal additions to aldehydes to produce trans-dioxasilacyclononenes as single stereoisomers. This reaction, which converts the δ-position of the unsaturated carbonyl compound into a nucleophilic center, represents an inversion of polarity from the normal pattern of reactivity. The stereospecificity of the reaction suggests that the addition to aldehydes occurred through a closed, chairlike six-membered transition state. This reaction can be used to prepare enantiomerically pure materials by the use of chiral auxiliaries to control the formation of the oxasilacyclopentenes. Functionalization of the resulting trans-cycloalkene occurred with complete stereoselectively.

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 (BRAFV600E) accounts for about 90% of these activating mutations. While BRAFV600E-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 BRAFV600E 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 BRAFV600E 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 BRAFV600E both in vitro and in cells but promotes an inactive dimeric BRAFV600E conformation unable to undergo transactivation. The crystal structure of a BRAFV600E/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 BRAFV600E conformation. These studies have implications for targeting BRAFV600E/RAF heterodimers and other kinase dimers for therapy.

Identification of a novel family of BRAF(V600E) inhibitors.

The BRAF oncoprotein is mutated in about half of malignant melanomas and other cancers, and a kinase activating single valine to glutamate substitution at residue 600 (BRAF(V600E)) accounts for over 90% of BRAF-mediated cancers. Several BRAF(V600E) inhibitors have been developed, although they harbor some liabilities, thus motivating the development of other BRAF(V600E) inhibitor options. We report here the use of an ELISA based high-throughput screen to identify a family of related quinolol/naphthol compounds that preferentially inhibit BRAF(V600E) over BRAF(WT) and other kinases. We also report the X-ray crystal structure of a BRAF/quinolol complex revealing the mode of inhibition, employ structure-based medicinal chemistry efforts to prepare naphthol analogues that inhibit BRAF(V600E) in vitro with IC(50) values in the 80-200 nM range under saturating ATP concentrations, and demonstrate that these compounds inhibit MAPK signaling in melanoma cells. Prospects for improving the potency and selectivity of these inhibitors are discussed.

Stereoselective synthesis of F-ring saturated estrone-derived inhibitors of Hedgehog signaling based on cyclopamine.

Previous work in this laboratory established that the readily available F-ring aromatic analog of cyclopamine is a highly potent inhibitor of Hedgehog signaling. The synthesis and biological evaluation of two F-ring saturated analogs that are more potent than the F-ring aromatic structure are reported.