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A new series of lactam-derived EZH2 inhibitors was designed via ligand-based and physicochemical-property-based strategies to address metabolic stability and thermodynamic solubility issues associated with previous lead compound 1. The new inhibitors incorporated an sp3 hybridized carbon atom at the 7-position of the lactam moiety present in lead compound 1 as a replacement for a dimethylisoxazole group. This transformation enabled optimization of the physicochemical properties and potency compared to compound 1. Analysis of relationships between calculated log D (clogD) values and in vitro metabolic stability and permeability parameters identified a clogD range that afforded an increased probability of achieving favorable ADME data in a single molecule. Compound 23a exhibited the best overlap of potency and pharmaceutical properties as well as robust tumor growth inhibition in vivo and was therefore advanced as a development candidate (PF-06821497). A crystal structure of 23a in complex with the three-pr...

First generation EGFR TKIs (gefitinib, erlotinib) provide significant clinical benefit for NSCLC cancer patients with oncogenic EGFR mutations. Ultimately, these patients’ disease progresses, often driven by a second-site mutation in the EGFR kinase domain (T790M). Another liability of the first generation drugs is severe adverse events driven by inhibition of WT EGFR. As such, our goal was to develop a highly potent irreversible inhibitor with the largest selectivity ratio between the drug-resistant double mutants (L858R/T790M, Del/T790M) and WT EGFR. A unique approach to develop covalent inhibitors, optimization of reversible binding affinity, served as a cornerstone of this effort. PF-06459988 was discovered as a novel, third generation irreversible inhibitor, which demonstrates (i) high potency and specificity to the T790M-containing double mutant EGFRs, (ii) minimal intrinsic chemical reactivity of the electrophilic warhead, (iii) greatly reduced proteome reactivity relative to earlier irreversible E...

Chromatography is routinely used in drug discovery as a means to isolate intermediates and final compounds. From a sustainability perspective, it is one of the largest contributors of solvent waste in the drug discovery process. The medicinal chemistry subgroup within the American Chemical Society's Green Chemistry Institute Pharmaceutical Roundtable (ACS GCI PR) offers a perspective aimed at providing chemists with practical tools and easily implemented techniques to improve the sustainability of drug discovery through reduction of the waste generated during chromatography. This perspective also offers alternatives to traditional, silica gel-based chromatography as well as information on how to avoid chromatography completely through use of crystallization and reaction telescoping.

The medicinal chemistry subgroup of the American Chemical Society's Green Chemistry Institute Pharmaceutical Roundtable (ACS GCI PR) offers a perspective on the current state of environmentally sustainable practices in medicinal chemistry with the aim of sharing best practices more widely and highlighting some potential future developments.

S6K1 (p70 ribosomal S6 kinase 1) is activated by insulin and growth factors via the PI3K (phosphoinositide 3-kinase) and mTOR (mammalian target of rapamycin) signalling pathways. S6K1 regulates numerous processes, such as protein synthesis, growth, proliferation and longevity, and its inhibition has been proposed as a strategy for the treatment of cancer and insulin resistance. In the present paper we describe a novel cell-permeable inhibitor of S6K1, PF-4708671, which specifically inhibits the S6K1 isoform with a Ki of 20 nM and IC50 of 160 nM. PF-4708671 prevents the S6K1-mediated phosphorylation of S6 protein in response to IGF-1 (insulin-like growth factor 1), while having no effect upon the PMA-induced phosphorylation of substrates of the highly related RSK (p90 ribosomal S6 kinase) and MSK (mitogen- and stress-activated kinase) kinases. PF-4708671 was also found to induce phosphorylation of the T-loop and hydrophobic motif of S6K1, an effect that is dependent upon mTORC1 (mTOR complex 1). PF-4708671 is the first S6K1-specific inhibitor to be reported and will be a useful tool for delineating S6K1-specific roles downstream of mTOR.

A variety of 2,4-diamino-pyrimidine systems can be prepared from the corresponding 2,4-dichloro-pyrimidine by sequential addition of two amines, the first adding selectively to the 4-position. In contrast it was found that 2,4-dichloro-5-trifluoromethyl-pyrimidine yields a 1:1 mixture of the two possible isomers. Lewis acids were employed to increase the ratio of isomers to >10:1 in favor of the 2-addition product. Optimization of the effect of Lewis acid additives on this and other dichloropyrimidine systems will be discussed.

Chromatography is routinely used in drug discovery as a means to isolate intermediates and final compounds. From a sustainability perspective, it is one of the largest contributors of solvent waste in the drug discovery process. The medicinal chemistry subgroup within the American Chemical Society's Green Chemistry Institute Pharmaceutical Roundtable (ACS GCI PR) offers a perspective aimed at providing chemists with practical tools and easily implemented techniques to improve the sustainability of drug discovery through reduction of the waste generated during chromatography. This perspective also offers alternatives to traditional, silica gel-based chromatography as well as information on how to avoid chromatography completely through use of crystallization and reaction telescoping.

Although 4,6-dihydroxyisophthalaldehydes failed to condense with tripyrranes to produce porphyrinoid products, the related dimethoxydialdehydes reacted with tripyrrane 9 to give, following oxidation with aqueous ferric chloride solution, nonaromatic dimethoxybenziporphyrins 20 in excellent yields. In the presence of TFA, dications were generated that showed weakly diatropic properties by proton NMR spectroscopy. This observation was attributed to the ability of the methoxy units to facilitate charge delocalization. Treatment of 20 with 50 equiv. of boron tribromide cleaved one of the methyl ethers to produce the related methoxyoxybenziporphyrins 24. These porphyrinoids showed strong diamagnetic ring currents due to the presence of 18 π-electron delocalization pathways within these structures. On treatment with TFA, the resulting dications show significantly reduced ring currents although their diatropic character is retained to a far greater extent than when the methoxy substituents are absent. For both 20 and 24, the methoxy groups are more effective at charge delocalization, which results in increased diatropicity, when there is no adjacent alkyl substituent. Treatment of 20a with HBr in refluxing acetic acid cleaved both methyl ethers to give the highly insoluble hydroxyoxybenziporphyrin 17. Although the spectroscopic properties of the free base could not be assessed, this compound was soluble in TFA–chloroform and the resulting dication proved to be highly aromatic as judged by NMR and UV–vis spectroscopy. Treatment of the 20b with HBr–acetic acid again cleaved both methyl ethers but also gave an unexpected oxidation to give a diketone bearing a 3° alcohol unit. This novel porphyrinoid retains an 18 π-delocalization pathway, shows porphyrin-like UV–vis spectra and is highly diatropic as the free base and in protonated form as judged by proton NMR spectroscopy.

The use of dilute aqueous FeCl 3 as an oxidant, instead of DDQ, greatly improves the yields of sapphyrin products by the ‘4+1’ methodology; yields for carbasapphyrins were somewhat lower but also greatly benefited from this approach.

The “3 + 1” route for porphyrinoid synthesis is an excellent methodology for preparing aromatic porphyrin analogues with six-membered ring subunits. Condensation of 5-formylsalicylaldehyde with tripyrranes 15, 24, and 25 in the presence of 5% TFA-dichloromethane, followed by neutralization and oxidation with DDQ, afforded a series of semiquinone-containing porphyrinoids 12, 26, and 27 in 35−52% yield. In these novel systems, the macrocycle achieves aromatization by undergoing a keto−enol tautomerization whereby the phenolic subunit is transformed so that the inner three carbon atoms become part of the 18 π-electron aromatic core, whereas the outer carbons generate an enone unit. The aromatic nature of these “oxybenziporphyrins” is evident from their porphyrin-like electronic spectra and the presence of powerful diamagnetic ring currents in their proton NMR spectra, where the inner CH is shifted upfield to δ = −7 ppm, whereas the external meso-protons appear downfield between 8.8 and 10.3 ppm. The presence...

The base-mediated treatment of aromatic mesylates with primary and secondary alcohols allows access to a wide range of aryl ethers.

A general synthesis of aryl ethers from primary and secondary alcohols and aryl mesylates is presented. The reaction proceeds via a sulfonyl-transfer mechanism. In this paper, we compare the sulfonyl transfer reaction to Mitsunobu ether formation. The reaction can be employed in a multistep synthesis where the aryl mesylate is used as a phenol protecting group and then as an activating group for ether formation. This protecting/activating group strategy is demonstrated using raloxifene as the target.

Analogues substituted with various amines at the 6-position of the pyrazine ring on (4-amino-7-isopropyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrazin-2-ylmethanone were discovered as potent and selective inhibitors of PDK1 with potential as anticancer agents. An early lead with 2-pyridine-3-ylethylamine as the pyrazine substituent showed moderate potency and selectivity. Structure-based drug design led to improved potency and selectivity against PI3Kα through a combination of cyclizing the ethylene spacer into a saturated, five-membered ring and substituting on the 4-position of the aryl ring with a fluorine. ADME properties were improved by lowering the lipophilicity with heteroatom replacements in the saturated, five-membered ring. The optimized analogues have a PDK1 Ki of 1 nM and >100-fold selectivity against PI3K/AKT-pathway kinases. The cellular potency of these analogues was assessed by the inhibition of AKT phosphorylation (T308) and by their antiproliferation activity against a number of tumor cell lines.

The reaction of (E)-tert-butyl 4-[3-(dimethylamino)acryloyl]piperidine-1-carboxylate with methylhydrazine leads to the formation of the title compound, C14H23N3O2, with a 1-methyl-1H-pyrazol-5-yl substituent. The plane of the pyrazole ring forms a dihedral angle of 33.4 (1)° with the approximate mirror plane of the piperidine ring.

The synthesis and SAR for a series of diaminopyrimidines as PYK2 inhibitors are described. Using a combination of library and traditional medicinal chemistry techniques, a FAK-selective chemical series was transformed into compounds possessing good PYK2 potency and 10- to 20-fold selectivity against FAK. Subsequent studies found that the majority of the compounds were positive in a reactive metabolite assay, an indicator for potential toxicological liabilities. Based on the proposed mechanism for bioactivation, as well as a combination of structure-based drug design and traditional medicinal chemistry techniques, a follow-up series of PYK2 inhibitors was identified that maintained PYK2 potency, FAK selectivity and HLM stability, yet were negative in the RM assay.

Cancer cells are characterized by the ability to grow in an anchorage-independent manner. The activity of the nonreceptor tyrosine kinase, focal adhesion kinase (FAK), is thought to contribute to this phenotype. FAK localizes in focal adhesion plaques and has a role as a scaffolding and signaling protein for other adhesion molecules. Recent studies show a strong correlation between increased FAK expression and phosphorylation status and the invasive phenotype of aggressive human tumors. PF-562,271 is a potent, ATP-competitive, reversible inhibitor of FAK and Pyk2 catalytic activity with a IC50 of 1.5 and 14 nmol/L, respectively. Additionally, PF-562,271 displayed robust inhibition in an inducible cell-based assay measuring phospho-FAK with an IC50 of 5 nmol/L. PF-562,271 was evaluated against multiple kinases and displays >100× selectivity against a long list of nontarget kinases. PF-562,271 inhibits FAK phosphorylation in vivo in a dose-dependent fashion (calculated EC50 of 93 ng/mL, total) after p.o. administration to tumor-bearing mice. In vivo inhibition of FAK phosphorylation (>50%) was sustained for >4 hours with a single p.o. dose of 33 mg/kg. Antitumor efficacy and regressions were observed in multiple human s.c. xenograft models. No weight loss, morbidity, or mortality were observed in any in vivo experiment. Tumor growth inhibition was dose and drug exposure dependent. Taken together, these data show that kinase inhibition with an ATP-competitive small molecule inhibitor of FAK decreases the phospho-status in vivo, resulting in robust antitumor activity. [Cancer Res 2008;68(6):1935–44]

Sapphyrins are an important group of expanded porphyrins that show valuable anion binding characteristics. In this study, a "4 + 1" route to sapphyrin systems has been developed. Reaction of dialdehydes with a known tetrapyrrole intermediate 11b incorporating a bipyrrolic subunit afforded a wide range of sapphyrin-type products. The best conditions for these reactions involved carrying out the condensation of the dialdehydes with the tetrapyrrole in TFA-dichloromethane, followed by oxidation with dilute aqueous solutions of ferric chloride. A pyrrole dialdehyde reacted under these conditions to give sapphyrin in 50% yield, while furan and thiophene dialdehydes afforded the corresponding oxa- and thiasapphyrins in 66-90% yield. Pyrrole dialdehydes with fused phenanthrene or acenaphthylene rings also reacted with 11b to give the related phenanthro- and acenaphthosapphyrins in excellent yields. As was the case for acenaphthoporphyrins, the acenaphthosapphyrin gave longer wavelength absorptions than the corresponding phenanthrene fused structure, although the differences were not as marked as those seen in the porphyrin series. Reaction of 11b with 1,3-diformylindene gave a benzocarbasapphyrin in 38% yield, while a triformyl cyclopentadiene reacted with the tetrapyrrole to give a carbasapphyrin aldehyde in 7-12% yield. The free base carbasapphyrins were unstable but the monoprotonated hydrochloride salts could easily be isolated and characterized. Carbasapphyrins retain a strong diatropic ring current due to the presence of 22pi electron delocalization pathways. In the presence of trifluoroacetic acid, C-protonated dications are generated. Condensation of 1,3-azulenedicarbaldehyde with 11b gave an azulisapphyrin dihydrochloride salt in 35% yield, and this also showed a strong diatropic ring current. Addition of base gave the unstable free base form, while pyrrolidine formed an unstable adduct that showed an intense Soret band at 480 nm. These results demonstrate that many of the themes observed for modified porphyrins and carbaporphyrins also apply to the sapphyrin series, although in some cases reduced stability hampers these investigations.

The discovery of small molecule kinase inhibitors for use as drugs is a promising approach for the treatment of cancer and other diseases, but the discovery of highly specific agents is challenging because over 850 kinases are expressed in mammalian cells. Systematic modification of the 4-anilino functionality of a selective quinazoline inhibitor of the epidermal growth factor receptor (EGFR) tyrosine kinase can invert selectivity to favor inhibition of the highly homologous erbB2 tyrosine kinase. The selectivity pattern was demonstrated in assays of recombinant kinases and recapitulated in measures of kinase activity in intact cells. The most potent and selective erbB2 inhibitor of the analog series has anti-proliferative activity against an erbB2-overexpressing cell line that was lacking in the original EGFR-selective compound. Subtle changes to the molecular structure of ATP-competitive small molecule inhibitors of tyrosine kinases can yield dramatic changes in potency and selectivity. These results suggest that the discovery of highly selective small molecule inhibitors of very homologous kinases is achievable.

The title compound, C12H13ClN6, was prepared by reaction of 4,5-dichloro-7H-pyrrolo[2,3-d]pyrimidine with 2-(1H-imidazol-4-yl)-N-methylethanamine, and the X-ray study confirmed that chloro-substituent in six-membered ring was replaced in the reaction. The exocyclic N atom environment is approximately coplanar with the pyrrolo[2,3-d]pyrimidine [corresponding dihedral angle is 5.5 (1)°], whereas the mean plane of the N—C—C—C link connecting with the imidazolyl ring is almost exactly orthogonal to the plane of the bicyclic system [dihedral angle = 91.6 (2)°]. The imidazolyl plane itself, however, forms a relatively small dihedral angle of 20.8 (1)° with the pyrrolo[2,3-d]pyrimidine plane. There are two independent N—H...N hydrogen bonds in the structure, which link molecules into layers parallel to (overline{1}03).

Focal adhesion kinase (FAK) is a non-tyrosine kinase that localizes to focal adhesion plaques. It is activated in response to intergin binding to cellular ligands and when phosphorylated inhibits anoikis allowing for anchorage independent cell growth. Recent studies have shown increased FAK expression and phosphorylation status in many types of invasive and aggressive human tumors strongly suggesting FAK is a possible target for anticancer chemotherapy. Literature, in house HTS and de novo studies identified 2, 4-diaminopyrimidines as potent FAK inhibitors. Early SAR efforts quickly determined that smaller substituents, particularly CF3, were optimal in the C5 position. Parallel medicinal chemistry strategies were executed for the C2 and C4 positions. These studies suggested that substituted aryl and fused heteroaryl groups at the C2 position in conjunction with substituted phenyl and heterocycles at the C4 position imparted optimum activity and metabolic stability. Inhibitor-FAK co-crystal structures were utilized to guide in the SAR strategy around the 2, 4-diaminopyrimidine template which afforded several lead compounds. The team's effort culminated in the advancement of PF-562,271 as a potent and reversible inhibitor of FAK (kinase IC50 of 2 nM and cell IC50 of 5 nM) that is > 100x selective against a long list of non-target kinases. In summary, detailed SAR studies were executed on the 2, 4-diaminopyrimidine templates that produced potent inhibitors of FAK with improved ADME properties, and identified a novel and potent series of FAK inhibitors that are selective against most other kinases and have shown activity in clinical trials. This poster will present design, synthesis, challenging chemistry, optimization, and complete inhibitor chemical structures of lead analogs. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A86.