Convenient preparations of racemic and enantiopure methyl 6-oxopipecolate

Short, convenient syntheses of racemic and enantiopure methyl 6-oxopipecolate are described, starting from either pipecolic acid or (S)-lysine respectively. The sequence for the latter compound relies upon improved methodology for the oxidation of C-6 of lysine.     

Evaluation of a pseudoephedrine linker for asymmetric alkylations on solid phase

[reaction: see text] Immobilized pseudoephedrine amides have been conveniently prepared by attachment of pseudoephedrine to Merrifield resin and acylation on nitrogen. Deprotonation and alkylation of the resin bound amides proceeds smoothly. Products were cleaved from the resin to give ketones and alcohols in high enantiomeric excess and moderate to good overall yield.     

Enantiopure bicyclic piperidinones: stereoselectivity in lactam enolate alkylations

The synthesis and alkylation of [4.3.0]-bicyclic lactams, derived from 6-oxopipecolic acid, have been investigated. Alkylation can proceed with predominantly exo-diastereoselectivity, but the efficiency of this process depends on the substitution at the hemiaminal ether system. These products can be readily deprotected to give substituted hydroxymethyl lactams in good yield.     

Synthesis of Galactose- and N-Acetylglucosamine-Derived Tetrazoles and their evaluation as β-glycosidase inhibitors

The title compounds 6 and 7 have been prepared from the known 2,3-di-O-benzyl-4,6-O-benzylidene-D -galactose ( 18 ) and N²-acetyl-tri-O-benzyl-D -glucosamine oxime ( 29 ) in eight and six steps, respectively. The azidonitrile leading to the benzylated galacto-tetrazole 16 was prepared from 14 and cyclized under the conditions of its formation (Scheme 1). The alcohol 13 was obtained by oxidation of 10 followed by reduction. Better yields and diastereoselectivities were realized, when the benzylidene-protected D -galacto-alcohol 20 was subjected to oxido-reduction, yielding the L -altro-alcohol 22 via the ketone 21 (Scheme 2). Treatment of the corresponding tosylate 24 with NaN₃ yielded the tetrazole 25 , which was deprotected to 6 . The tetrabenzyl ether 16 (from 14 , or from 25 via 27 ) was reduced to 28 and deprotected to give the known deoxygalactostain 8 (Scheme 2). Oxidation of the hydroxynitrile 30 , derived from 29 , followed by reduction of 32 yielded mostly the L -ido-hydroxynitrile (Scheme 3), which was tosylated and treated with NaN₃ to give the tetrazole 35a and its manno-isomer 36a , while Al(N₃)₃ yielded (E)- and (Z)- 38 (Scheme 4). The intermediate azide 39 was isolated besides 40 when NH₄N₃/DMF was used; thermolysis of 39 gave mostly 35a , which was deprotected to 7 , besides some elimination product 41 . Both 6 and 7 are stable in the pH range 1–10; at pH 12, 6 is unaffected but, 7 shows some epimerization to the manno-configurated isomer 43 . The tetrazole 6 is a competitive inhibitor of the β-galactosidases from E. coli (K₁ = 1 μM , pH 6.8) and bovine liver (K₁ = 0.8 μM , pH 7.0); the N-acetyl-β-D -glucosaminidase from bovine kidney is competitively inhibited by 7 (K₁ ? 0.2 μM , pH 4.1).     

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced‐Fit Pocket Stabilized by a Cation–π Interaction

The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein‐bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced‐fit pocket forming a cation–π interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.     

Isoxazole‐Derived Amino Acids are Bromodomain‐Binding Acetyl‐Lysine Mimics: Incorporation into Histone H4 Peptides and Histone H3

A range of isoxazole‐containing amino acids was synthesized that displaced acetyl‐lysine‐containing peptides from the BAZ2A, BRD4(1), and BRD9 bromodomains. Three of these amino acids were incorporated into a histone H4‐mimicking peptide and their affinity for BRD4(1) was assessed. Affinities of the isoxazole‐containing peptides are comparable to those of a hyperacetylated histone H4‐mimicking cognate peptide, and demonstrated a dependence on the position at which the unnatural residue was incorporated. An isoxazole‐based alkylating agent was developed to selectively alkylate cysteine residues in situ. Selective monoalkylation of a histone H4‐mimicking peptide, containing a lysine to cysteine residue substitution (K12C), resulted in acetyl‐lysine mimic incorporation, with high affinity for the BRD4 bromodomain. The same technology was used to alkylate a K18C mutant of histone H3.     

Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates

Based on structural analysis of the human 2-oxoglutarate (2OG) dependent JMJD2 histone N(ε)-methyl lysyl demethylase family, 3-substituted pyridine 2,4-dicarboxylic acids were identified as potential inhibitors with possible selectivity over other human 2OG oxygenases. Microwave-assisted palladium-catalysed cross coupling methodology was developed to install a diverse set of substituents on the sterically demanding C-3 position of a pyridine 2,4-dicarboxylate scaffold. The subsequently prepared di-acids were tested for in vitro inhibition of the histone demethylase JMJD2E and another human 2OG oxygenase, prolyl-hydroxylase domain isoform 2 (PHD2, EGLN1). A subset of substitution patterns yielded inhibitors with selectivity for JMJD2E over PHD2, demonstrating that structure-based inhibitor design can enable selective inhibition of histone demethylases over related human 2OG oxygenases.     

Synthesis of Fused Triazoles as Probes for the Active Site of Retaining β-Glycosidases: From Which Direction Is the Glycoside Protonated?

The structure of the β-glycosidase inhibitors 1–7 and 10–13 suggests that protonation of O–C(1) (the glycosidic O-center) of the substrate by a carboxy group of the retaining β-glycosidases does not occur in the plane perpendicular to the ring of the glycon (β-side; ‘from the top’), but in the plane of the ring (‘from the side’). The triazoles 17 and 18 have been prepared in six steps from the L -xylofuranose 21 . They possess a CH group instead of the N-center of the related tetrazoles 4 and 5 , corresponding to the glycosidic O-atom, and a very similar structure, both in solution and in the solid state. Unlike the tetrazoles, however, which are good-to-medium inhibitors of retaining β-glycosidases, the triazoles do not inhibit the β-glycosidases from sweet almonds, snail, and bovine liver, and only slightly inhibit the β-glucosidase from Caldocellum saccharolyticum. This is in keeping with the proposed direction of protonation in the plane of the saccharide ring and with modelling studies, docking 4 into the active site of the white clover cyanogenic β-glucosidase and 6 into the E. coli β-galactosidase and the Lactococcus lactis 6-phospho-β-galactosidase.     

A selective inhibitor and probe of the cellular functions of Jumonji C domain-containing histone demethylases

Histone methylations are important chromatin marks that regulate gene expression, genomic stability, DNA repair, and genomic imprinting. Histone demethylases are the most recent family of histone-modifying enzymes discovered. Here, we report the characterization of a small-molecule inhibitor of Jumonji C domain-containing histone demethylases. The inhibitor derives from a structure-based design and preferentially inhibits the subfamily of trimethyl lysine demethylases. Its methyl ester prodrug, methylstat, selectively inhibits Jumonji C domain-containing his-tone demethylases in cells and may be a useful small-molecule probe of chromatin and its role in epigenetics.