Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRASG12C, selective inhibition of KRASG12D presents a significant challenge due to the requirement of inhibitors to bind KRASG12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRASG12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRASG12D mutant xenograft mouse tumor model.

Abstract The ability to effectively target mutated KRAS has remained elusive despite decades of research. By solving a highly informative set of ligand-complexed co-crystal structures coupled with iterative structure-based drug design, substituted tetrahydropyridopyrimidines were identified as selective, covalent inhibitors of mutant KRAS G12C. Key molecular interactions with the protein were optimized, with the potency of lead compounds evaluated by (a) mass spectrometric quantification of modified KRAS protein with and without treatment of test compounds, and (b) measurement of phospho-ERK in a whole-cell assay using H358 cells after incubation with test compounds for 3 hours. These efforts identified MRTX1257 as a potent and selective inhibitor of mutant KRAS G12C activity. This lead compound was utilized as a research tool to aid in a deeper understanding of therapeutic susceptibility and KRAS dependence. MRTX1257 makes a covalent bond with the codon 12 cysteine and binds in the “Switch-2” pocket of KRAS, stabilizing the protein in the inactive, GDP-bound state. MRTX1257 contains a cyanomethyl group that displaces a water found near Gly10 in co-crystal structures of less potent analogs and contains an 8-methylnaphthyl group that fills a hydrophobic pocket, resulting in enhanced potency compared with unsubstituted naphthyl analogs. MRTX1257 demonstrated rapid, irreversible modification of GDP-bound recombinant KRAS G12C and suppressed ERK phosphorylation with an IC50 = 1 nM in the H358 cell line. In proteomics studies designed to assess global protein modification, MRTX1257 was shown to be highly selective for the targeted Cys12 of KRAS G12C versus other surface-exposed cysteine residues in NCI-H358 cells. Finally, at a 30mg/kg PO dose, MRTX1257 exhibited 31% bioavailability in mouse, demonstrated near-complete inhibition of KRAS signaling in tumor tissue, and complete durable tumor regression in MIA PaCa-2 xenografts. The discovery of the tetrahydropyridopyrimidine series, the structure-based optimization to MRTX1257 and its preclinical potency, selectivity, ADME and efficacy profile will be presented. Citation Format: Matthew A. Marx, Brian R. Baer, Joshua Ballard, James F. Blake, Karyn Bouhana, David M. Briere, Laurence E. Burgess, Michael R. Burkhard, Harrah Chiang, Mark J. Chicarelli, James G. Christensen, John P. Fischer, Jill Hallin, Macedonia J. Mejia, Peter Olson, Pavel Savechenkov, Niranjan Sudhakar, Tony P. Tang, Guy P. Vigers, Jay B. Fell. Structure-based drug discovery of MRTX1257, a selective, covalent KRAS G12C inhibitor with oral activity in animal models of cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B30.

Capping off an era marred by drug development failures and punctuated by waning interest and presumed intractability toward direct targeting of KRAS, new technologies and strategies are aiding in the target's resurgence. As previously reported, the tetrahydropyridopyrimidines were identified as irreversible covalent inhibitors of KRASG12C that bind in the switch-II pocket of KRAS and make a covalent bond to cysteine 12. Using structure-based drug design in conjunction with a focused in vitro absorption, distribution, metabolism and excretion screening approach, analogues were synthesized to increase the potency and reduce metabolic liabilities of this series. The discovery of the clinical development candidate MRTX849 as a potent, selective covalent inhibitor of KRASG12C is described.

Conformational selection by small molecules expands inhibitory possibilities for protein kinases. Nuclear magnetic resonance (NMR) measurements of the mitogen-activated protein (MAP) kinase ERK2 have shown that activation by dual phosphorylation induces global motions involving exchange between two states, L and R. We show that ERK inhibitors Vertex-11e and SCH772984 exploit the small energetic difference between L and R to shift the equilibrium in opposing directions. An X-ray structure of active 2P-ERK2 complexed with AMP-PNP reveals a shift in the Gly-rich loop along with domain closure to position the nucleotide in a more catalytically productive conformation relative to inactive 0P-ERK2:ATP. X-ray structures of 2P-ERK2 complexed with Vertex-11e or GDC-0994 recapitulate this closure, which is blocked in a complex with a SCH772984 analog. Thus, the L→R shift in 2P-ERK2 is associated with movements needed to form a competent active site. Solution measurements by hydrogen-exchange mass spectrometry (HX-MS) reveal distinct binding interactions for Vertex-11e, GDC-0994, and AMP-PNP with active vs. inactive ERK2, where the extent of HX protection correlates with R state formation. Furthermore, Vertex-11e and SCH772984 show opposite effects on HX near the activation loop. Consequently, these inhibitors differentially affect MAP kinase phosphatase activity toward 2P-ERK2. We conclude that global motions in ERK2 reflect conformational changes at the active site that promote productive nucleotide binding and couple with changes at the activation loop to allow control of dephosphorylation by conformationally selective inhibitors.

Abstract Despite decades of research, efforts to directly target KRAS have been challenging. MRTX849 was identified as a potent, selective, and covalent KRASG12C inhibitor that exhibits favorable drug-like properties, selectively modifies mutant cysteine 12 in GDP-bound KRASG12C, and inhibits KRAS-dependent signaling. MRTX849 demonstrated pronounced tumor regression in 17 of 26 (65%) KRASG12C-positive cell line– and patient-derived xenograft models from multiple tumor types, and objective responses have been observed in patients with KRASG12C-positive lung and colon adenocarcinomas. Comprehensive pharmacodynamic and pharmacogenomic profiling in sensitive and partially resistant nonclinical models identified mechanisms implicated in limiting antitumor activity including KRAS nucleotide cycling and pathways that induce feedback reactivation and/or bypass KRAS dependence. These factors included activation of receptor tyrosine kinases (RTK), bypass of KRAS dependence, and genetic dysregulation of cell cycle. Combinations of MRTX849 with agents that target RTKs, mTOR, or cell cycle demonstrated enhanced response and marked tumor regression in several tumor models, including MRTX849-refractory models. Significance: The discovery of MRTX849 provides a long-awaited opportunity to selectively target KRASG12C in patients. The in-depth characterization of MRTX849 activity, elucidation of response and resistance mechanisms, and identification of effective combinations provide new insight toward KRAS dependence and the rational development of this class of agents. See related commentary by Klempner and Hata, p. 20. This article is highlighted in the In This Issue feature, p. 1

KRAS is the most frequently mutated driver oncogene in human cancer, and KRAS mutations are commonly associated with poor prognosis and resistance to standard treatment. The ability to effectively target and block the function of mutated KRAS has remained elusive despite decades of research. Recent findings have demonstrated that directly targeting KRAS-G12C with electrophilic small molecules that covalently modify the mutated codon 12 cysteine is feasible. We have discovered a series of tetrahydropyridopyrimidines as irreversible covalent inhibitors of KRAS-G12C with in vivo activity. The PK/PD and efficacy of compound 13 will be highlighted.

Abstract High-grade serous ovarian carcinoma (HGSOC) has the poorest prognosis amongst all gynecological cancers with a median survival of approximately 5 years. While most patients (pts) initially respond to therapy, few achieve long-term remission or cure; thus, new treatment strategies are needed. Paclitaxel (Pac), an agent commonly used in the treatment of HGSOC, induces the Ras/Raf/MEK/ERK pathway and resistance may be partially mediated through activation of MEK/ERK, suggesting a rationale for combining a MEK inhibitor with Pac. Binimetinib (MEK162) is an oral, potent, selective, allosteric small-molecule MEK1/2 inhibitor. The combination of binimetinib and Pac was studied in a panel of in vivo ovarian carcinoma xenograft models derived from either cell lines (A2780, SK-OV-3) or primary patient tumor resections pathologically confirmed to be HGSOC (OVC38B1, OVC604, OVC629, OVC104) and propagated solely in mice (pt-derived xenograft [PDX]). Three of these PDX models were from newly diagnosed pts, while 1 (OVC38B1) was from a pt who had relapsed following a prior response to a platinum/taxane regimen. All models were sequenced for cancer-specific genes by next-generation sequencing; no mutations were found in Ras, Raf, MEK or ERK. To evaluate single-agent and combination activity, tumor-bearing mice received 25 mg/kg Pac IP (days 1,5,9) and/or 30 mg/kg binimetinib PO (days 2-15). Single-agent binimetinib was modestly effective in 3/6 models (tumor growth inhibition [TGI] ≥ 50%), which is consistent with the lack of MAPK pathway mutations in these models. Single-agent Pac was highly effective in 3/6 models (TGI ≥ 90%) including OVC38B1 and 2 PDX models from newly diagnosed pts; the remaining models were taxane-resistant. This is consistent with expected high rates of response in the setting of newly diagnosed pts and/or prior responders. Binimetinib plus Pac had superior efficacy to either agent alone in 4/6 models including all taxane-resistant models. In 2 PDX models from newly diagnosed pts, combination activity was not improved, but Pac was highly effective as a single agent (72-82% regression) leaving little room for enhancement. Encouragingly, the combination induced tumor regressions in 2 taxane-resistant models in which no single-agent regressions were observed. In conclusion, in vivo drug sensitivity studies with binimetinib and Pac recapitulate the response expected in HGSOC based on stage, genetic background and clinical history. In models of taxane-resistant disease, combination with binimetinib had improved activity over taxane alone warranting further study of this approach in HGSOC. Citation Format: Shannon L. Winski, Karyn Bouhana, Susan Rhodes, LouAnn Cable, Deborah Anderson, Lance Williams, Brian Tunquest, Tiffany Logan, Guy Vigers, Patrice Lee. Activity of the MEK inhibitor Binimetinib (MEK162) in combination with paclitaxel in patient-derived xenograft models of high-grade serous ovarian carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 666. doi:10.1158/1538-7445.AM2015-666

Background: Activating mutations and oncogenic fusions of the RET receptor tyrosine kinase have been identified in multiple tumor types, including thyroid, lung, breast and colon carcinoma. Furthermore, tyrosine kinase inhibitors (TKIs) with anti-RET activity have produced clinical responses in patients whose tumors harbor RET alterations. However, currently available RET inhibitors were initially developed to target kinases other than RET and are only moderately potent against RET, inhibit multiple kinases other than RET or poorly inhibit secondary resistance mutations (e.g. gatekeeper mutations) common to other TKIs. We have discovered novel, potent and selective RET inhibitors. The resulting compounds exhibit nanomolar potency against wild type RET and select RET mutants, including the KIF5B-RET fusion and V804M gatekeeper mutation, in both enzyme and cellular assays, with minimal activity against highly related kinases. AR025 is representative of this series; the activity of AR025 and related analogs in relevant in vitro and in vivo models will be presented here. Methods: In vitro and in vivo evaluations, including enzyme and cell-based assays, pharmacokinetic (PK)/pharmacodynamics (PD) correlations, drug metabolism characterization, and non-clinical safety evaluation, were conducted using standard methods. Tumor growth inhibition and PD studies were carried out using subcutaneous allografts of NIH-3T3 cells expressing KIF5B-RET in nude mice. Results: AR025 demonstrated nanomolar potency against both wild type and mutant RET proteins in enzyme and cellular assays. AR025 had minimal activity against an enzyme panel of >200 diverse kinases and demonstrated >50x cellular selectivity against VEGFR, with similar selectivity against other related kinases. AR025 possessed low intravenous clearance and high oral exposure in mice, rats and dogs. Finally, a single oral dose of 30mg/kg produced more than 90% inhibition of phospho-RET in NIH-3T3-KIF5B-RET mouse allografts, while twice-per-day continuous dosing resulted in greater than 90% tumor growth inhibition. Notably, AR025 was minimally toxic at doses up to 100mg/kg per day. Conclusions: We have identified a series of potent and selective RET inhibitors with high oral bioavailability and favorable PK properties in animals. One of these, AR025, demonstrated potent inhibition of RET in enzyme and cellular assays, with minimal activity against highly related kinases. In an NIH3T3-KIF5B-RET allograft model, AR025 effectively inhibited phospho-RET and caused dramatic tumor growth inhibition without significant toxicity. The identification of potent and selective RET inhibitors with significant in vivo activity and minimal toxicity may overcome the limitations of currently available inhibitors with anti-RET activity. Citation Format: Barbara J. Brandhuber, Nisha Nanda, Julia Haas, Karyn Bouhana, Lance Williams, Shannon Winski, Michael Burkard, Brian Tuch, Kevin Ebata, Jennifer Low, Francis Sullivan, Lauren Hanson, Tony Morales, Guy Vigers, Jessica Gaffney, Ross D. Wallace, James Blake, Yutong Jiang, S. Michael Rothenberg, Steven Andrews. Identification and characterization of highly potent and selective RET kinase inhibitors for the treatment of RET-driven cancers. [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 B192.

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.

The development of 1,3,4,4a,5,10a-hexahydropyrano[3,4-b]chromene analogs as BACE1 inhibitors is described. Introduction of the spirocyclic pyranochromene scaffold yielded several advantages over previous generation cores, including increased potency, reduced efflux, and reduced CYP2D6 inhibition. Compound 13 (BACE1 IC50=110 nM) demonstrated a reduction in CSF Aβ in wild type rats after a single dose.

HCV serine protease NS3 represents an attractive drug target because it is not only essential for viral replication but also implicated in the viral evasion of the host immune response pathway through direct cleavage of key proteins in the human innate immune system. Through structure-based drug design and optimization, macrocyclic peptidomimetic molecules bearing both a lipophilic P2 isoindoline carbamate and a P1/P1' acylsulfonamide/acylsulfamide carboxylic acid bioisostere were prepared that possessed subnanomolar potency against the NS3 protease in a subgenomic replicon-based cellular assay (Huh-7). Danoprevir (compound 49) was selected as the clinical development candidate for its favorable potency profile across multiple HCV genotypes and key mutant strains and for its good in vitro ADME profiles and in vivo target tissue (liver) exposures across multiple animal species. X-ray crystallographic studies elucidated several key features in the binding of danoprevir to HCV NS3 protease and proved invaluable to our iterative structure-based design strategy.

A series of 2,3,4,4a,10,10a-hexahydropyrano[3,2-b]chromene analogs was developed that demonstrated high selectivity (>2000-fold) for BACE1 vs Cathepsin D (CatD). Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Guided by structure based design, changes to P2' and P3 moieties were explored. A conformationally restricted P2' methyl group provided inhibitors with excellent cell potency (37-137 nM) and selectivity (435 to >2000-fold) for BACE1 vs CatD. These efforts lead to compound 59, which demonstrated a 69% reduction in rat CSF Aβ1-40 at 60 mg/kg (PO).

A series of unique bicyclic aminooxazolines were synthesized and found to exhibit micromolar inhibition of β-secretase-1 (BACE-1). The aminooxazolines were procured by an intramolecular diethylaminosulfur trifluoride (DAST)-mediated ring closure of a benzylic urea onto a secondary alcohol.

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.

In an attempt to increase selectivity vs Cathepsin D (CatD) in our BACE1 program, a series of 1,3,4,4a,10,10a-hexahydropyrano[4,3-b]chromene analogues was developed. Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Using structure-based design, substitutions to improve binding to both the S3 and S2' sites of BACE1 were explored. An acyl guanidine moiety provided the most potent analogues. These compounds demonstrated 10-420 fold selectivity for BACE1 vs CatD, and were highly potent in a cell assay measuring Aβ1-40 production (5-99 nM). They also suffered from high efflux. Despite this undesirable property, two of the acyl guanidines achieved free brain concentrations (Cfree,brain) in a guinea pig PD model sufficient to cover their cell IC50s. Moreover, a significant reduction of Aβ1-40 in guinea pig, rat, and cyno CSF (58%, 53%, and 63%, respectively) was observed for compound 62.