Supplementary Data, Yeh, et al. from Biological Characterization of ARRY-142886 (AZD6244), a Potent, Highly Selective Mitogen-Activated Protein Kinase Kinase 1/2 Inhibitor

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 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.

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.

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.

Numerous oncogenic mutations occur within the BRAF kinase domain (BRAFKD). Here we show that stable BRAF-MEK1 complexes are enriched in BRAFWT and KRAS mutant (MT) cells but not in BRAFMT cells. The crystal structure of the BRAFKD in a complex with MEK1 reveals a face-to-face dimer sensitive to MEK1 phosphorylation but insensitive to BRAF dimerization. Structure-guided studies reveal that oncogenic BRAF mutations function by bypassing the requirement for BRAF dimerization for activity or weakening the interaction with MEK1. Finally, we show that conformation-specific BRAF inhibitors can sequester a dormant BRAF-MEK1 complex resulting in pathway inhibition. Taken together, these findings reveal a regulatory role for BRAF in the MAPK pathway independent of its kinase activity but dependent on interaction with MEK.

A hallmark of Alzheimer's disease is the brain deposition of amyloid beta (Aβ), a peptide of 36-43 amino acids that is likely a primary driver of neurodegeneration. Aβ is produced by the sequential cleavage of APP by BACE1 and γ-secretase; therefore, inhibition of BACE1 represents an attractive therapeutic target to slow or prevent Alzheimer's disease. Herein we describe BACE1 inhibitors with limited molecular flexibility and molecular weight that decrease CSF Aβ in vivo, despite efflux. Starting with spirocycle 1a, we explore structure-activity relationships of core changes, P3 moieties, and Asp binding functional groups in order to optimize BACE1 affinity, cathepsin D selectivity, and blood-brain barrier (BBB) penetration. Using wild type guinea pig and rat, we demonstrate a PK/PD relationship between free drug concentrations in the brain and CSF Aβ lowering. Optimization of brain exposure led to the discovery of (R)-50 which reduced CSF Aβ in rodents and in monkey.

Tumor cells extensively utilize the pentose phosphate pathway for the synthesis of ribose. Transketolase is a key enzyme in this pathway and has been suggested as a target for inhibition in the treatment of cancer. In a pharmacodynamic study, nude mice with xenografted HCT-116 tumors were dosed with 1 ('N3'-pyridyl thiamine'; 3-(6-methyl-2-amino-pyridin-3-ylmethyl)-5-(2-hydroxyethyl)-4-methyl-thiazol-3-ium chloride hydrochloride), an analog of thiamine, the co-factor of transketolase. Transketolase activity was almost completely suppressed in blood, spleen, and tumor cells, but there was little effect on the activity of the other thiamine-utilizing enzymes alpha-ketoglutarate dehydrogenase or glucose-6-phosphate dehydrogenase. Synthesis and SAR of transketolase inhibitors is described. (C) 2007 Elsevier Ltd. All rights reserved.

Inhibition of the thiamine-utilizing enzyme transketolase (TK) has been linked with diminished tumor cell proliferation. Most thiamine antagonists have a permanent positive charge on the B-ring, and it has been suggested that this charge is required for diphosphorylation by thiamine pyrophosphokinase (TPPK) and binding to TK. We sought to make neutral thiazolium replacements that would be substrates for TPPK, while not necessarily needing thiamine transporters (ThTr1 and ThTr2) for cell penetration. The synthesis, SAR, and structure-based rationale for highly potent non-thiazolium TK antagonists are presented.

Abstract Purpose: The Ras-Raf-mitogen-activated protein kinase kinase (MEK) pathway is overactive in many human cancers and is thus a target for novel therapeutics. We have developed a highly potent and selective inhibitor of MEK1/2. The purpose of these studies has been to show the biological efficacy of ARRY-142886 (AZD6244) in enzymatic, cellular, and animal models. Experimental Design: The ability of ARRY-142886 to inhibit purified MEK1 as well as other kinases was evaluated. Its effects on extracellular signal-regulated kinase (ERK) phosphorylation and proliferation in several cell lines were also determined. Finally, the inhibitor was tested in HT-29 (colorectal) and BxPC3 (pancreatic) xenograft tumor models. Results: The IC50 of ARRY-142886 was determined to be 14 nmol/L against purified MEK1. This activity is not competitive with ATP, which is consistent with the high specificity of compound for MEK1/2. Basal and epidermal growth factor–induced ERK1/2 phosphorylation was inhibited in several cell lines as well as 12-O-tetradecanoylphorbol-13-acetate–induced ERK1/2 phosphorylation in isolated peripheral blood mononuclear cells. Treatment with ARRY-142886 resulted in the growth inhibition of several cell lines containing B-Raf and Ras mutations but had no effect on a normal fibroblast cell line. When dosed orally, ARRY-142886 was capable of inhibiting both ERK1/2 phosphorylation and growth of HT-29 xenograft tumors in nude mice. Tumor regressions were also seen in a BxPC3 xenograft model. In addition, tumors remained responsive to growth inhibition after a 7-day dosing holiday. Conclusions: ARRY-142886 is a potent and selective MEK1/2 inhibitor that is highly active in both in vitro and in vivo tumor models. This compound is currently being investigated in clinical studies.

OBJECT:The purpose of this study was to establish a cadaveric model for evaluating cervical spine motion in both the intact and injured states and to examine the efficacy of commonly used stabilization techniques in limiting that motion.METHODS:Intubation was performed in fresh human cadavers with intact cervical spines, following the creation of a C4-5 posterior ligamentous injury. Movement of the cervical spine during direct laryngoscopy and intubation was recorded using video fluoroscopy and examined under the following conditions: 1) without external stabilization; 2) with manual in-line cervical immobilization; and 3) with Gardner-Wells traction. Subsequently, segmental motion of the occiput through C-5 (Oc-C5) was measured from digitized frames of the recorded video fluoroscopy. The predominant motion, at all levels measured in the intact spine, was extension. The greatest degree of motion occurred at the atlantooccipital (Oc-C1) junction, followed by the C1-2 junction, with progressively less motion at each more caudal level. After posterior destabilization was induced, the predominant direction of motion at C4-5 changed from extension to flexion, but the degree of motion remained among the least of all levels measured. Traction limited but did not prevent motion at the Oc-C1 junction, but neither traction nor immobilization limited motion at the destabilized C4-5 level.CONCLUSIONS:Cadaveric cervical spine motion accurately reflected previously reported motion in living, anesthetized patients. Traction was the most effective method of reducing motion at the occipitocervical junction, but none of the interventions significantly reduced movement at the subaxial site of injury. These findings should be considered when treating injured patients requiring orotracheal intubation.

Breakdown of the blood-retinal barrier occurs in inflammatory conditions and in ischemic retinal diseases such as diabetic retinopathy. Platelet-activating factor (PAF) is a potent inflammatory mediator which increases vascular permeability. The purpose of this study was to determine if intravitreally-injected PAF would cause breakdown of the blood-retinal barrier and, if so, by what mechanism. Fluorescein angiography was performed before and at 0.5, 1, 2, 3 and 4 hr after PAF injection into the vitreous cavity of rabbit eyes and the eyes were enucleated immediately for light and electron microscopy. Slow flowing thrombi were observed in all PAF-injected eyes. Complete vascular occlusion was observed in 10 of 16 eyes after 3 and 4 hr. There was no fluorescein leakage in any of eyes before or at 0.5 or 1 hr after PAF injection. Fourteen of 20 eyes had fluorescein leakage at 2, 3 and 4 hr after PAF injection. The extent of fluorescein leakage correlated with the degree of polymorphonuclear leukocyte (PMN) margination, disruption of the endothelial cell layer, infiltration into vascular walls and migration into the vitreous cavity. PMNs appeared to migrate by both intercellular and transcellular routes across the endothelium. Pretreatment of rabbits with a PAF inhibitor, BN52021, prevented most of the abnormal findings.