p-ERK MSD results in RAS mutant cells ectopically expressed ARAF variants

Proliferation IC50 values for various cell lines and cell line derivatives

In vivo anti-tumor effects of LXH254 and Trametinib

The allosteric inhibitor of the mechanistic target of rapamycin (mTOR) everolimus reduces seizures in tuberous sclerosis complex (TSC) patients through partial inhibition of mTOR functions. Due to its limited brain permeability, we sought to develop a catalytic mTOR inhibitor optimized for central nervous system (CNS) indications. We recently reported an mTOR inhibitor (1) that is able to block mTOR functions in the mouse brain and extend the survival of mice with neuronal-specific ablation of the Tsc1 gene. However, 1 showed the risk of genotoxicity in vitro. Through structure-activity relationship (SAR) optimization, we identified compounds 9 and 11 without genotoxicity risk. In neuronal cell-based models of mTOR hyperactivity, both corrected aberrant mTOR activity and significantly improved the survival rate of mice in the Tsc1 gene knockout model. Unfortunately, 9 and 11 showed limited oral exposures in higher species and dose-limiting toxicities in cynomolgus macaque, respectively. However, they remain optimal tools to explore mTOR hyperactivity in CNS disease models.

Supplementary Figure 2. Western blot analysis of CRISPR-CAS9 cell lines and exogenously expressed ARAF variants used in experiments shown in Figures 3-7.

Growth inhibition IC50 data of LXH254 in CCLE panel

Proliferation and p-ERK IC50 results in RAS-mutant cells expressing only one RAF paralog

Results of Kinativ studies using LXH254 in HCT 116 cells

Table S9. Differential gene analysis of LXH254 sensitive and insensitive cells lines

Supplementary Figure 5. Model for LXH254 interactions with RAF monomers and dimers (A). (B) Upper panel, simulated structure of ARAF (green) overlaid on the structure of BRAF (blue). LXH254 interacting with ARAF is shown in yellow and with BRAF in purple. (B) Lower panel, enhanced view of hydrogen bond interactions between LXH254 (purple) and the backbone carbonyl of F595 of BRAF (Blue) and LXH254 (yellow) and backbone carbonyl of ARAF (green).

Supplementary Figure 3. (A) Shown are western blots using antibodies directed against T202/Y204 phosphorylated ERK1/2 following incubation with a range of concentrations of LXH254 over a 4 - 72 hour period. Which individual RAF protein is not expressed in each HCT 116 variant is indicated above the relevant panels. (B) Shown are western blots using Abs directed against the indicated proteins in either whole cell lysates (WCL) or material immuno-precipitated from cell lysates using Abs directed against ARAF (ARAF IP) or BRAF (BRAF IP). Lysates were generated from either parental MIA PaCa-2 cells or a MIA PaCa-2 variant lacking expression of CRAF. (C) Recombinant MEK1 can be phosphorylated by immuno-precipitates from both LXH254 treated and untreated MIA PaCa-2 and MEL-JUSO cells using an anti-body directed against ARAF contains MEK1 kinase activity. Proteins detected in either whole cell lysates (WCL) or ARAF-Ab immuno-precipitates (IP:ARAF) are indicated on the right. (D) IP-kinase activity on recombinant MEK1 in immuno-precipitates from HEK293 cells expressing FLAG-tagged ARAF using Abs directed against FLAG requires ATP and occurs on both wild type (WT) and kinase-dead (K97M) MEK1. (E) Shown are western blots using antibodies directed against T202/Y204 phosphorylated ERK1/2 following incubation with a range of concentrations of LXH254 over a 4-72 hour period. The individual RAF protein expressed in each HCT 116 variant is indicated above the relevant panels. (F) Shown are western blots of phosphorylated MEK1/2 (S218/S221) and ERK1/2 (T202/Y204) following a 4 hr. incubation with a range of LXH254 concentrations in the RAS/RAF wild type cell line PC-9.

Supplementary Figure 1. Shown in (A) are the IC50 values for the inhibition of proliferation for BRAF ( ), KRAS ( ), and NRAS ( ) mutant as well as "WT" ( ) cell lines. Below the graph Fischer's exact test using 1, 2, and 2.5ï­M sensitivity cutoffs are provided. (B) Comparison of cell line sensitivities for LXH254 and RAF709. LXH254 values are provided in this manuscript (Sup. Table 3) and RAF709 values obtained from (25). (C) mRNA expression (RNASeq, https://portals.broadinstitute.org/ccle/data) for cell lines presented in (A) with the 2.0ï­M LXH254 sensitivity threshold delineated. (D) ARAF mRNA expression in KRAS mutant and wild type cells from TCGA Pan-cancer Atlas Project (47), using the cBIO cancer genomics portal (https://www.cbioportal.org/, (1,2))

Supplementary Figure 4. Growth of individual tumors shown in Fig. 7A-C are given for HCT 116 (A), MIA PaCa-2 (B) and MEL-JUSO (C) cells.

Growth inhibition IC50 values (nM) of several RAF inhibitors in a panel of cell lines

Abstract Purpose: Targeting RAF for antitumor therapy in RAS-mutant tumors holds promise. Herein, we describe in detail novel properties of the type II RAF inhibitor, LXH254. Experimental Design: LXH254 was profiled in biochemical, in vitro, and in vivo assays, including examining the activities of the drug in a large panel of cancer-derived cell lines and a comprehensive set of in vivo models. In addition, activity of LXH254 was assessed in cells where different sets of RAF paralogs were ablated, or that expressed kinase-impaired and dimer-deficient variants of ARAF. Results: We describe an unexpected paralog selectivity of LXH254, which is able to potently inhibit BRAF and CRAF, but has less activity against ARAF. LXH254 was active in models harboring BRAF alterations, including atypical BRAF alterations coexpressed with mutant K/NRAS, and NRAS mutants, but had only modest activity in KRAS mutants. In RAS-mutant lines, loss of ARAF, but not BRAF or CRAF, sensitized cells to LXH254. ARAF-mediated resistance to LXH254 required both kinase function and dimerization. Higher concentrations of LXH254 were required to inhibit signaling in RAS-mutant cells expressing only ARAF relative to BRAF or CRAF. Moreover, specifically in cells expressing only ARAF, LXH254 caused paradoxical activation of MAPK signaling in a manner similar to dabrafenib. Finally, in vivo, LXH254 drove complete regressions of isogenic variants of RAS-mutant cells lacking ARAF expression, while parental lines were only modestly sensitive. Conclusions: LXH254 is a novel RAF inhibitor, which is able to inhibit dimerized BRAF and CRAF, as well as monomeric BRAF, while largely sparing ARAF.

Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.

The monobactam scaffold is attractive for the development of new agents to treat infections caused by drug-resistant Gram-negative bacteria because it is stable to metallo-β-lactamases (MBLs). However, the clinically used monobactam aztreonam lacks stability to serine β-lactamases (SBLs) that are often coexpressed with MBLs.

RAS mutations lead to a constitutively active oncogenic protein that signals through multiple effector pathways. In this chemical biology study, we describe a novel coupled biochemical assay that measures activation of the effector BRAF by prenylated KRASG12V in a lipid-dependent manner. Using this assay, we discovered compounds that block biochemical and cellular functions of KRASG12V with low single-digit micromolar potency. We characterized the structural basis for inhibition using NMR methods and showed that the compounds stabilized the inactive conformation of KRASG12V. Determination of the biophysical affinity of binding using biolayer interferometry demonstrated that the potency of inhibition matches the affinity of binding only when KRAS is in its native state, namely post-translationally modified and in a lipid environment. The assays we describe here provide a first-time alignment across biochemical, biophysical, and cellular KRAS assays through incorporation of key physiological factors regulating RAS biology, namely a negatively charged lipid environment and prenylation, into the in vitro assays. These assays and the ligands we discovered are valuable tools for further study of KRAS inhibition and drug discovery.

PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in anti-tumor efficacy. Here, we describe the identification and optimization of a new class of small molecule PRC2 inhibitors that acts allosterically via the trimethyllysine pocket of the non-catalytic EED subunit. Deconstruction of a larger screening hit to a fragment-sized molecule followed by structure-guided regrowth and careful property modulation were employed to achieve sub-micromolar inhibition in functional assays and cellular activity.