SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily A member 2 (SMARCA2), also known as Brahma homologue (BRM), is a Snf2-family DNA-dependent ATPase. BRM and its close homologue Brahma-related gene 1 (BRG1), also known as SMARCA4, are mutually exclusive ATPases of the large ATPdependent SWI/SNF chromatin-remodeling complexes involved in transcriptional regulation of gene expression. No small molecules have been reported that modulate SWI/SNF chromatin-remodeling activity via inhibition of its ATPase activity, an important goal given the well-established dependence of BRG1-deficient cancers on BRM. Here, we describe allosteric dual BRM and BRG1 inhibitors that downregulate BRM-dependent gene expression and show antiproliferative activity in a BRG1mutant-lung-tumor xenograft model upon oral administration. These compounds represent useful tools for understanding the functions of BRM in BRG1-loss-of-function settings and should enable probing the role of SWI/SNF functions more broadly in different cancer contexts and those of other diseases.

Tankyrase 1 and 2 have been shown to be redundant, druggable nodes in the Wnt pathway. As such, there has been intense interest in developing agents suitable for modulating the Wnt pathway in vivo by targeting this enzyme pair. By utilizing a combination of structure-based design and LipE-based structure efficiency relationships, the core of XAV939 was optimized into a more stable, more efficient, but less potent dihydropyran motif 7. This core was combined with elements of screening hits 2, 19, and 33 and resulted in highly potent, selective tankyrase inhibitors that are novel three pocket binders. NVP-TNKS656 (43) was identified as an orally active antagonist of Wnt pathway activity in the MMTV-Wnt1 mouse xenograft model. With an enthalpy-driven thermodynamic signature of binding, highly favorable physicochemical properties, and high lipophilic efficiency, NVP-TNKS656 is a novel tankyrase inhibitor that is well suited for further in vivo validation studies.

SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein–ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3S,4S)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)­thio)­pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro­[4.5]­decan-4-amine (1), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.

SHP2 is a nonreceptor protein tyrosine phosphatase within the mitogen-activated protein kinase (MAPK) pathway controlling cell growth, differentiation, and oncogenic transformation. SHP2 also participates in the programed cell death pathway (PD-1/PD-L1) governing immune surveillance. Small-molecule inhibition of SHP2 has been widely investigated, including in our previous reports describing SHP099 (2), which binds to a tunnel-like allosteric binding site. To broaden our approach to allosteric inhibition of SHP2, we conducted additional hit finding, evaluation, and structure-based scaffold morphing. These studies, reported here in the first of two papers, led to the identification of multiple 5,6-fused bicyclic scaffolds that bind to the same allosteric tunnel as 2. We demonstrate the structural diversity permitted by the tunnel pharmacophore and culminated in the identification of pyrazolopyrimidinones (e.g., SHP389, 1) that modulate MAPK signaling in vivo. These studies also served as the basis for further scaffold morphing and optimization, detailed in the following manuscript.

High throughput screening and subsequent hit validation identified 4-isopropyl-3-(2-((1-phenylethyl)amino)-pyrimidin-4-yl)oxazolidin-2-one as a potent inhibitor of IDH1 R132H . Synthesis of the four separate stereoisomers identified the (S,S)-diastereomer (IDH125, 1f) as the most potent isomer. This also showed reasonable cellular activity and excellent selectivity vs IDH1 wt . Initial structure−activity relationship exploration identified the key tolerances and potential for optimization. X-ray crystallography identified a functionally relevant allosteric binding site amenable to inhibitors, which can penetrate the blood−brain barrier, and aided rational optimization. Potency improvement and modulation of the physicochemical properties identified (S,S)-oxazolidinone IDH889 (5x) with good exposure and 2-HG inhibitory activity in a mutant IDH1 xenograft mouse model. KEYWORDS: Mutant IDH1 inhibitor, allosteric inhibition, 2-HG, preclinical in vivo activity, 3-pyrimidin-4-yloxazolidin-2-one, chirality-defined potency H otspot heterozygous mutations in human cytoplasmic isocitrate dehydrogenase 1 (IDH1) at Arg 132 (R132*) have been identified in multiple cancer types, including acute myeloid leukemia (AML), glioma, chondrosarcoma, and cholangiocarcinoma. 1 These mutations have been shown to confer a neomorphic catalytic activity to produce high levels of intracellular R-2-hydroxyglutarate (2-HG) and effect downstream epigenetic markers on DNA and proteins. Recent clinical trials in AML patients with a specific inhibitor of IDH1 has shown clinical benefit, confirming the causal link between this genetic mutation, the production of 2-HG, and cancer.11 Efforts herein focused on the identification of compounds that could potentially target all classes of mutant-IDH1 tumors, including those in the brain.The substrate-binding site of mutant IDH1 is highly polar as defined by the amino acids lining the pocket (Figure 1), in addition to the active-site magnesium ion and NADPH cofactor. This suggests a low probability of being able to optimize a compound for potent binding to this site while also fulfilling the criteria most conducive to crossing the blood− brain barrier (BBB).12 It was decided to explore the identification of catalytic inhibitors with different mechanisms of action, which may bind distal to this polar substrate-binding site.High throughput screening was carried out with a NADPH fluorescence-based biochemical assay using IDH1 R132H homodimer protein, and orthogonal biochemical inhibition confirmation using an LCMS readout of 2-HG levels. Compounds 1a and 1b were identified as selective and functional inhibitors of IDH1R132H from this screen. Both 1a and 1b were screened as diastereomeric mixtures at the amine (Table 1, Am), which necessitated the independent synthesis of the four separate stereoisomers in order to determine the chiral preference for ligand binding. Potency was found to be most strongly dependent upon the chirality at the amine center (Am), . Amino acids lining the pocket are highl...