Mutant BRAF V600E is one of the most common oncogenic drivers in metastatic melanoma. While first generation BRAF V600E inhibitors are capable of controlling tumors systemically, they are unable to adequately treat tumors that have metastasized to the brain due to insufficient penetration across the blood-brain barrier (BBB). Through a combination of structure-based drug design (SBDD) and the optimization of physiochemical properties to enhance BBB penetration, we herein report the discovery of the brain-penetrant BRAF V600E inhibitor PF-07284890 (ARRY-461). In mice studies, ARRY-461 proved to be highly brain-penetrant and was able to drive regressions of A375 BRAF V600E tumors implanted both subcutaneously and intracranially. Based on compelling preclinical safety and efficacy studies, ARRY-461 was progressed into a Phase 1 A/B clinical trial (NCT04543188).

The extracellular signal-regulated kinases ERK1/2 represent an essential node within the RAS/RAF/MEK/ERK signaling cascade that is commonly activated by oncogenic mutations in BRAF or RAS or by upstream oncogenic signaling. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. Simultaneous targeting of multiple nodes in the pathway, such as MEK and ERK, offers the prospect of enhanced efficacy as well as reduced potential for acquired resistance. Described herein is the discovery and characterization of GDC-0994 (22), an orally bioavailable small molecule inhibitor selective for ERK kinase activity.

Using structure-based design, a novel series of pyridone ERK1/2 inhibitors was developed. Optimization led to the identification of (S)-14k, a potent, selective, and orally bioavailable agent that inhibited tumor growth in mouse xenograft models. On the basis of its in vivo efficacy and preliminary safety profiles, (S)-14k was selected for further preclinical evaluation.

Abstract Background: The fibroblast growth factor receptor (FGFR1-4) family of tyrosine kinases plays an important role in normal physiologic processes, including angiogenesis, wound healing and regulation of calcium and phosphate metabolism. In addition, dysregulation of FGFR signaling through genetic alterations or altered expression of individual receptors and their ligands has been frequently observed in human tumors. While tyrosine kinase inhibitors (TKIs) with anti-FGFR activity have produced clinical responses in patients whose tumors harbor FGFR alterations, currently available FGFR TKIs inhibit multiple other kinases, including multiple FGFRs. As a result, dose-limiting toxicities have been frequently observed in patients, including hyperphosphatemia which may arise from the inhibition of FGFR1 in the kidney. These toxicities may ultimately limit the efficacy of pan-FGFR inhibitors. However, the ability to develop inhibitors that spare individual FGFRs has been hampered by the high degree of structural similarity between FGFR1, FGFR2, and FGFR3. The development of these tools to distinguish the functional contributions of the individual FGF receptors not only advances the biological understanding of the individual receptors in the context of their expression but may also provide therapeutic agents that have an improved therapeutic index. Methods: In vitro and in vivo evaluations including both enzyme and cell-based assays, pharmacokinetic (PK) studies, measurement of drug metabolism and non-clinical safety evaluation were conducted using standard methods. Tumor growth inhibition and pharmacodynamics (PD) measurements were carried out using subcutaneous xenografts of RT112/84 (which harbor an FGFR3-TACC fusion) bladder cancer cells in nude mice. Results: We have developed compounds with nanomolar FGFR3 enzyme and cell potency, but relatively spare FGFR1 and have minimal activity against an enzyme panel of >200 diverse kinases. This series was further optimized to provide high oral exposure in rodent species. One representative compound was evaluated in a single dose mouse PK at doses of 10, 30 and 100 mg/kg and provided predicted pharmacokinetic coverage of the FGFR3 cell IC50 for >8, >12 and >24 hrs respectively, which correlated with phospho-FGFR3 reduction. The compound demonstrated greater than 40% and greater than 65% tumor regressions of RT112/84 subcutaneous xenografts at doses of 30 and 45 mg/kg/day x 14 day, respectively. These doses were well tolerated and minimal hyperphosphatemia was observed. Conclusions: We have identified potent and selective FGFR inhibitors that spare FGFR1 and other related kinases, and possess high oral bioavailability and favorable PK properties in animals. This next-generation class of compounds will be able to examine selectively the biology of selective FGFR inhibition. The identification of potent and selective FGFR inhibitors with minimal activity against FGFR1 may improve the efficacy and tolerability compared to the currently available pan-FGFR inhibitors. Citation Format: Shannon Winski, Nisha Nanda, Eric Brown, Tony Tang, Barbara Brandhuber, Robyn Hamor, Brian Tuch, Kevin Ebata, Jennifer Low, Francis Sullivan, Darin Smith, Guy Vigers, Megan Strough, Rob Rieger, James Blake, David Moreno, David Chantry, S. Michael Rothenberg, Steven Andrews. Identification of first-in-class, highly potent FGFR kinase inhibitors that spare FGFR1. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C196.

Abstract The extracellular-signal-regulated kinases (ERK1 and ERK2) represent an essential node within the RAS/RAF/MEK/ERK signaling cascade that commonly is activated by oncogenic mutations in BRAF or RAS or by upstream oncogenic signaling, such as receptor tyrosine kinase (RTK) activation. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. Simultaneous targeting of multiple nodes in the pathway, such as MEK and ERK, offers the prospect of enhanced efficacy as well as reduced potential for acquired resistance. Here, we present the discovery and characterization of GDC-0994, an orally bioavailable, small molecule inhibitor of ERK kinase activity. GDC-0994 is highly selective for ERK1 and ERK2, with biochemical potency of 1.1 nM and 0.3 nM, respectively. Daily, oral dosing of GDC-0994 results in significant single-agent activity in multiple in vivo cancer models, including KRAS-mutant and BRAF-mutant human xenograft tumors in mice. PD biomarker inhibition of phospho-p90RSK in these tumors correlates with potency in vitro and in vivo. In contrast to other published ERK inhibitors, GDC-0994 neither increases nor decreases phospho-ERK, suggesting that different ERK inhibitors have alternative mechanisms of action with respect to feedback signaling. Furthermore, we demonstrate a novel approach for targeting the oncogenic signaling through the RAS pathway by combining ERK and MEK inhibitors. GDC-0994 is currently in Phase I clinical development. Citation Format: Kirk Robarge, Jacob Schwarz, Jim Blake, Michael Burkard, Jocelyn Chan, Huifen Chen, Kang-Jye Chou, Dolores Diaz, John Gaudino, Stephen Gould, Jonas Grina, Xin Linghu, Lichuan Liu, Matthew Martinson, David A. Moreno, Christine Orr, Patricia Pacheco, Ann Qin, Kevin Rasor, Li Ren, Sheerin Shahidi-Latham, Jeffrey Stults, Francis Sullivan, Weiru Wang, Peter Yin, Aihe Zhou, Marcia Belvin, Mark Merchant, John G. Moffat. Discovery of GDC-0994, a potent and selective ERK1/2 inhibitor in early clinical development. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr DDT02-03. doi:10.1158/1538-7445.AM2014-DDT02-03

Herein we describe the design of a novel series of ATP competitive B-Raf inhibitors via structure-based methods. These 3-N-methylquinazoline-4(3H)-one based inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. Optimization led to the identification of compound 16, a potent, selective and orally available agent with excellent pharmacokinetic properties and robust tumor growth inhibition in xenograft studies. Our work also demonstrates that by replacing an aryl amide with an aryl sulfonamide, a multikinase inhibitor such as AZ-628, can be converted to a selective B-Raf inhibitor, a finding that should have broad application in kinase drug discovery.

Herein we describe the discovery of a novel series of ATP competitive B-Raf inhibitors via structure based drug design (SBDD). These pyridopyrimidin-7-one based inhibitors exhibit both excellent cellular potency and striking B-Raf selectivity. Optimization led to the identification of compound 17, a potent, selective and orally available agent with excellent pharmacokinetic properties and robust tumor growth inhibition in xenograft studies.

Cell potent inhibitors of B-Raf(V600E) that bind to the kinase in the DFG-out conformation are reported. These compounds utilize the hinge-binding group and lipophilic linker from a previously disclosed series of B-Raf(V600E) inhibitors that bind to the kinase in an atypical DFG-in, αC-helix-out conformation. This new series demonstrates that DFG-out kinase inhibitors can be rationally designed from related inhibitors which utilize an unconventional binding mode. Kinase selectivity profiles are compared. The pattern of kinase selectivity was found to be determined by the feature of the inhibitor which extends into the back pocket of the kinase and leads to the kinase conformation, rather than by the hinge-binding group or other minor modifications.

A single crystal was obtained of a lead B-RafV600E inhibitor with low aqueous solubility. The X-ray crystal structure revealed hydrogen-bonded head-to-tail dimers formed by the pyrazolopyridine and sulfonamide groups of a pair of molecules. This observation suggested a medicinal chemistry strategy to disrupt crystal packing and reduce the high crystal lattice energy of alternative inhibitors. Both a bulkier group at the interface of the dimer and an out-of-plane substituent were required to decrease the compound’s melting point and increase aqueous solubility. These substituents were selected based on previously developed structure–activity relationships so as to concurrently maintain good enzymatic and cellular activity against B-RafV600E.

Structure–activity relationships around a novel series of B-RafV600E inhibitors are reported. The enzymatic and cellular potencies of inhibitors derived from two related hinge-binding groups were compared and3-methoxypyrazolopyridine proved to be superior. The 3-alkoxy group of lead B-RafV600E inhibitor 1 was extended and minimally affected potency. The propyl sulfonamide tail of compound 1, which occupies the small lipophilic pocket formed by an outward shift of the αC-helix, was expanded to a series of arylsulfonamides. X-ray crystallography revealed that this lipophilic pocket unexpectedly enlarges to accommodate the bulkier aryl group.

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An efficient method for the selective "N1" alkylation of indazoles is described. Use of alpha-halo esters, lactones, ketones, amides, and bromoacetonitrile provides good to excellent yield of the desired N1 products.