Indrawan McAlpine

Discovery of Pyrroloaminopyrazoles as Novel Pak Inhibitors.

The P21-activated kinases (PAK) are emerging antitumor therapeutic targets. In this paper, we describe the discovery of potent PAK inhibitors guided by structure-based drug design. In addition, the efflux of the pyrrolopyrazole series was effectively reduced by applying multiple medicinal chemistry strategies, leading to a series of PAK inhibitors that are orally active in inhibiting tumor growth in vivo.

Synthesis of Small 3-Fluoro- and 3,3-Difluoropyrrolidines Using Azomethine Ylide Chemistry

Here, we report accessing small 3-fluoropyrrolidines and 3,3-difluoropyrrolidines through a 1,3-dipolar cycloaddition with a simple azomethine ylide and a variety of vinyl fluorides and vinyl difluorides. We demonstrate that vinyl fluorides within α,β-unsaturated, styrenyl and even enol ether systems can participate in the cycloaddition reaction. The vinyl fluorides are relatively easy to synthesize through a variety of methods, making the 3-fluoropyrrolidines very accessible.

Design and Synthesis of Pyridone-Containing 3,4-Dihydroisoquinoline-1(2H)-ones as a Novel Class of Enhancer of Zeste Homolog 2 (EZH2) Inhibitors

A new enhancer of zeste homolog 2 (EZH2) inhibitor series comprising a substituted phenyl ring joined to a dimethylpyridone moiety via an amide linkage has been designed. A preferential amide torsion that improved the binding properties of the compounds was identified for this series via computational analysis. Cyclization of the amide linker resulted in a six-membered lactam analogue, compound 18. This transformation significantly improved the ligand efficiency/potency of the cyclized compound relative to its acyclic analogue. Additional optimization of the lactam-containing EZH2 inhibitors focused on lipophilic efficiency (LipE) improvement, which provided compound 31. Compound 31 displayed improved LipE and on-target potency in both biochemical and cellular readouts relative to compound 18. Inhibitor 31 also displayed robust in vivo antitumor growth activity and dose-dependent de-repression of EZH2 target genes.

Studies on the Regioselective Nucleophilic Aromatic Substitution (SNAr) Reaction of 2-Substituted 3,5-Dichloropyrazines

Differences in regioselectivity were observed during the S(N)Ar reaction of amines with unsymmetrical 3,5-dichloropyrazines. This study revealed that when the 2-position of the pyrazine was occupied with an electron-withdrawing group (EWG), nucleophilic attack occurred preferentially at the 5-position. When the 2-position was substituted with an electron-donating group (EDG), nucleophilic attack occurred preferentially at the 3-position. These results are reported along with a computational rationale for the experimental observations based on the Fukui index at the reacting centers.

Copper-Catalyzed Chan–Lam Cyclopropylation of Phenols and Azaheterocycles

Small molecules containing cyclopropane-heteroatom linkages are commonly needed in medicinal chemistry campaigns yet are problematic to prepare using existing methods. To address this issue, a scalable Chan-Lam cyclopropylation reaction using potassium cyclopropyl trifluoroborate has been developed. With phenol nucleophiles, the reaction effects O-cyclopropylation, whereas with 2-pyridones, 2-hydroxybenzimidazoles, and 2-aminopyridines the reaction brings about N-cyclopropylation. The transformation is catalyzed by Cu(OAc)2 and 1,10-phenanthroline and employs 1 atm of O2 as the terminal oxidant. This method is operationally convenient to perform and provides a simple, strategic disconnection toward the synthesis of cyclopropyl aryl ethers and cyclopropyl amine derivatives bearing an array of functional groups.

Structural modifications of a 3-methoxy-2-aminopyridine compound to reduce potential for mutagenicity and time-dependent drug–drug interaction

(S)-1-((4-(3-(6-Amino-5-methoxypyridin-3-yl)-1-isopropyl-1H-pyrazol-4-yl)pyrimidin-2-yl)amino)propan-2-ol, 1, was recently identified as a potent inhibitor of the oncogenic kinase bRAF. Compounds containing 3-methoxy-2-aminopyridine, as in 1, comprised a promising lead series because of their high ligand efficiency and excellent ADME profile. However, following metabolic oxidation, compounds in this series also demonstrated two significant safety risks: mutagenic potential and time-dependent drug-drug interaction (TDI). Metabolite identification studies revealed formation of a reactive metabolite. We hypothesized that minimizing or blocking the formation of such a metabolite would mitigate the safety liabilities. Our investigation demonstrated that structural modifications which either reduced the electron density of the 3-methoxy-2-aminopyridine ring or blocked the reactive site following metabolic oxidation were successful in reducing TDI and AMES mutagenicity.

Discovery of Allosteric, Potent, Subtype Selective, and Peripherally Restricted TrkA Kinase Inhibitors

Tropomyosin receptor kinases (TrkA, TrkB, TrkC) are activated by hormones of the neurotrophin family: nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT3), and neurotrophin 4 (NT4). Moreover, the NGF antibody tanezumab has provided clinical proof of concept for inhibition of the TrkA kinase pathway in pain leading to significant interest in the development of small molecule inhibitors of TrkA. However, achieving TrkA subtype selectivity over TrkB and TrkC via a Type I and Type II inhibitor binding mode has proven challenging and Type III or Type IV allosteric inhibitors may present a more promising selectivity design approach. Furthermore, TrkA inhibitors with minimal brain availability are required to deliver an appropriate safety profile. Herein, we describe the discovery of a highly potent, subtype selective, peripherally restricted, efficacious, and well-tolerated series of allosteric TrkA inhibitors that culminated in the delivery of candidate quality compound 23.

Abstract PR-2: Discovery of p21‐activated kinase inhibitor PF‐03758309

The p21‐activated kinase (PAK) family members are key effectors of Rho family GTPases, which act as regulatory switches that control such cellular processes as motility, proliferation, and cell survival. Some members of this family (such as Cdc42) have been shown to be required for Ras driven tumorigenesis. PAK4 is a key effector for Cdc42 and mediates downstream signals that control cell motility, proliferation and cell survival. The PAK family consists of PAK1,2,3 (‘group 1’) and PAK4,5,6 (‘group 2’). Both PAK4 and PAK1 have been shown to be required for Ras driven transformation. PAK4 has been shown to be oncogenic and able to drive anchorage independent growth when activated. PAK4 expression and activity is broadly up‐regulated in solid tumors such as colon, ovarian and pancreatic cancers. Pfizer9s PAK4 inhibitor program started with HTS of kinase focus library compounds. Multiple series were identified from the screening effort. Initial optimization mainly focused on kinase selectivity, ADME properties and ability to modulate target in vivo, leading to selection of pyrrolopyrazoles as the lead series. By hybridizing the pyrrolopyrazole core with aminopyrimidine series, we discovered potent PAK4 inhibitors with low to sub nM cellular activity. For the new hybrid series, the challenge was to attain good oral bioavailability. The observed poor absorption was likely due to high efflux nature of the template. Medicinal chemistry strategies, such as reducing molecular charge, lowering polar surface area and improving ligand efficiency, were applied to reduce efflux. As a result, two sub‐series achieved excellent in vivo tumor growth inhibition when dosed orally. PF‐03758309 has demonstrated excellent profile, leading to its selection as a clinical development candidate. PF‐3758309 is a potent ATP‐competitive inhibitor of PAK4 kinase domain (Kd = 4.5 nM). In engineered cell assays, PF‐3758309 inhibited PAK4 dependent phosphorylation of its substrate GEF‐H1 (IC50 = 1 nM). It potently inhibits the anchorage independent growth of HCT116 cells (IC50 = 0.24 nM). PF‐3758309 exhibited broad anti‐proliferative activity across a panel of 67 cell lines (CRC/pancreatic/NSCLC): 66% IC50 70%TGI at 15–20 mg/kg PO) by PF‐3758309: HCT116, A549, MDAMB231, M24met, and Colo205. Broad kinase screening has demonstrated that this is a selective pan‐PAK inhibitor with potential additional activities (e.g. AMPK). The pharmacodynamic and antitumor effects of PF‐3758309 support its evaluation as an anticancer agent. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):PR-2.