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The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory ß-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by > 100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory ß-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus. [ABSTRACT FROM AUTHOR]

Abstract: The HCV non-structural protein NS5A has been established as a viable target for the development of direct acting antiviral therapy. From computational modeling studies strong intra-molecular hydrogen bonds were found to be a common structural moiety within known NS5A inhibitors that have low pico-molar replicon potency. Efforts to reproduce these γ-turn-like substructures provided a novel NS5A inhibitor based on a fluoro-olefin isostere. This fluoro-olefin containing inhibitor exhibited picomolar activity (EC50 =79pM) against HCV genotype 1b replicon without measurable cytotoxicity. This level of activity is comparable to the natural peptide-based inhibitors currently under clinic evaluation, and demonstrates that a peptidomimetic approach can serve as a useful strategy to produce potent and structurally unique inhibitors of HCV NS5A. [Copyright &y& Elsevier]

The sordarins are fungal specific inhibitors of the translation factor eEF2, which catalyzes the translocation of tRNA and mRNA after peptide bond formation. We have determined the crystal structures of eEF2 in complex with two novel sordarin derivatives. In both structures, the three domains of eEF2 that form the ligand-binding pocket are oriented in a different manner relative to the rest of eEF2 compared with our previous structure of eEF2 in complex with the parent natural product sordarin. Yeast eEF2 is also shown to bind adenylic nucleotides, which can be displaced by sordarin, suggesting that ADP or ATP also bind to the three C-terminal domains of eEF2. Fusidic acid is a universal inhibitor of translation that targets EF-G or eEF2 and is widely used as an antibiotic against Gram-positive bacteria. Based on mutations conferring resistance to fusidic acid, cryo-EM reconstructions, and x-ray structures of eEF2, EF-G, and an EF-G homolog, we suggest that the conformation of EF-G stalled on the 70 S ribosome by fusidic acid is similar to that of eEF2 trapped on the 80 S ribosome by sordarin. [ABSTRACT FROM AUTHOR]

A series of 2-phenylspiroindenediones was prepared. The spiroindenediones were found to be less active than the corresponding spiroindenes as estrogen receptor ligands and failed to demonstrate the receptor subtype selectivity that had been anticipated from molecular modeling. [Copyright &y& Elsevier]

Conformationally restricted 2′-spironucleosidesand theirprodrugs were synthesized as potential anti-HCV agents. Although thereplicon activity of the new agents containing pyrimidine bases wasmodest, the triphosphate of a 2′-oxetane cytidine analoguedemonstrated potent intrinsic biochemical activity against the NS5Bpolymerase, with IC50= 8.48 μM. Activity againstNS5B bearing the S282T mutation was reduced. Phosphoramidate prodrugsof a 2′-oxetane 2-amino-6-O-methyl-purinenucleoside demonstrated potent anti-HCV activity in vitro, and thecorresponding triphosphate retained similar potent activity againstboth wild-type and S282T HCV NS5B polymerase. [ABSTRACT FROM AUTHOR]

Abstract: Phenylpropenamides have been reported to be a class of non-nucleoside inhibitors of the hepatitis B virus (HBV). This class of compounds was explored with the objective of developing potent anti-HBV agents, with a novel mechanism of action, that could be combined with nucleos(t)ide analogs currently used to treat HBV infection. To accomplish this objective a series of substituted arylpropenamide derivatives were prepared and the E and Z geometrical isomers were separated. The structural identity of each of the E and Z isomers was determined by single crystal X-ray crystallography. Contrary to previous reports, the activity of this class of molecules resides in the Z isomer. Further structure–activity relationship studies around the active Z isomer identified compounds that displayed potent antiviral activity against HBV with EC90 value of approximately 0.5μM in vitro. Attempts to develop ring constrained analogs did not lead to active HBV inhibitors. [Copyright &y& Elsevier]

Leukotrienes have physiological roles in innate immune responses and pathological roles in inflammatory diseases, such as asthma, allergic rhinitis and atherosclerosis. Anti-leukotriene therapy has proven benefits in the treatment of respiratory disease, either through the inhibition of leukotriene synthesis or the selective antagonism of leukotriene receptors. The first committed step in the synthesis of leukotrienes is the oxidation of arachidonic acid (AA) by 5-lipoxygenase (5-LO), and the integral membrane protein 5-lipoxygenase-activating protein (FLAP) is an essential partner of 5-LO for this process. FLAP was molecularly identified via a photoaffinity probe and an affinity gel based on MK-886, a selective leukotriene inhibitor that has no activity against broken-cell preparations of 5-LO. Several FLAP inhibitors showed efficacy in early clinical trials in asthma but were not developed commercially for unpublished reasons. Recently, the FLAP (ALOX5AP) gene has been linked to risk for myocardial infarction, stroke and restenosis, reigniting pharmaceutical interest in this target. In addition, the recent determination of the crystal structure of inhibitor-bound FLAP offers exciting potential for novel FLAP inhibitor design. [Copyright &y& Elsevier]

Abstract: A series of 2–9a bridged tetrahydrofluorenone derivatives were prepared which exhibited significant binding affinity for ERβ and were highly selective. [Copyright &y& Elsevier]

A series of 2-phenylspiroindenes was prepared. The most active analogue (2) was found to be comparable in potency to raloxifene (1) as an estrogen receptor ligand. [Copyright &y& Elsevier]

A 1X22X41 combinatorial library or 902 compounds of indinavir analogues was synthesized on the solid support to identify a replacement for the aminoindanol moiety at P2′. 2,6-Dimethyl-4-hydroxy phenol was discovered to be a good replacement for aminoindanol. [Copyright &y& Elsevier]

HTS screening identified compound 2a(piperazinonederivative) as a low micromolar HCV genotype 1 (GT-1) inhibitor. Resistancemapping studies suggested that this piperazinone chemotype targetsthe HCV nonstructural protein NS4B. Extensive SAR studies were performedaround 2aand the amide function and the C-3/C-6 cis stereochemistry of the piperazinone corewere essential for HCV activity. A 10-fold increase in GT-1 potencywas observed when the chiral phenylcyclopropyl amide side chain of 2awas replaced with p-fluorophenylisoxazole-carbonylmoiety (67). Replacing the C-6 nonpolarhydrophobic moiety of 67with a phenyl moiety (95) did not diminish the GT-1 potency. A heterocyclic thiophenemoiety (103) and an isoxazole moiety (108) were incorporated as isosteric replacements for the C-6 phenyl moiety (95), resulting in significant improvementin GT-1b and 1a potency. However, the piperazonone class of compoundslacks GT-2 activity and, consequently, were not pursued further intodevelopment. [ABSTRACT FROM AUTHOR]

Abstract: The optimization of a palladium-catalyzed amidation reaction providing a new class of amino acid–tetrahydroanthranilic acid derivatives has been achieved. The scope of the reaction and preliminary conformational analysis of the resulting series of molecules is discussed. [Copyright &y& Elsevier]

Abstract: A series of androstene-3,5-diene derivatives were prepared. Despite lacking the C-3 hydroxyl previously believed necessary for ER activity, some of the analogs retained surprising affinity for ER-β. For example, diene 4 retained excellent selectivity and potency as an ER-β agonist and was more selective for ER-β over the androgen receptor (AR). [Copyright &y& Elsevier]

Abstract: This communication highlights the development of a nicotinamide series of histone deacetylase inhibitors within the benzamide structural class. Extensive exploration around the nicotinamide core led to the discovery of a class I selective HDAC inhibitor that possesses excellent intrinsic and cell-based potency, acceptable ancillary pharmacology, favorable pharmacokinetics, sustained pharmacodynamics in vitro, and achieves in vivo efficacy in an HCT116 xenograft model. [Copyright &y& Elsevier]

Abstract: Benzo[b]thienyl hydroxamic acids, a novel class of histone deacetylase (HDAC) inhibitors, were identified via a targeted screen of small molecule hydroxamic acids. Various substitutions were explored in the C5- and C6-positions of the benzo[b]thiophene core to characterize SAR and develop optimal inhibitors. It was determined that substitution at the C6-position of the benzo[b]thiophene core with a three-atom spacer yielded optimal HDAC1 inhibition and anti-proliferative activity in murine erythroleukemia (SC-9) cells. [Copyright &y& Elsevier]

Abstract: Chemistry was developed to synthesize the title series of compounds. The ability of these novel ligands to bind to the glucocorticoid receptor was investigated. These compounds were also tested in a series of functional assays and some were found to display the profile of a dissociated glucocorticoid. The SAR of the 6,5-bicyclic series differed markedly from the previously reported 6,6-series. Molecular modeling studies were employed to understand the conformational differences between the two series of compounds, which may explain their divergent activity. Two compounds were profiled in vivo and shown to reduce inflammation in a mouse model. An active metabolite is suspected in one case. [Copyright &y& Elsevier]

Abstract: A novel class of indole ligands for estrogen receptor α have been discovered which exhibit potent affinity and high selectivity. Substitution of the bazedoxifene skeleton to the linker present in the HTS lead 1a provided 22b which was found to be 130-fold α-selective and acted as an antagonist of estradiol activity in uterine tissue and MCF-7 cancer cells. [Copyright &y& Elsevier]

Abstract: A series of 19-substituted androstenediol derivatives was prepared. Some of the novel analogs were surprisingly potent and selective ligands for ER-β. [Copyright &y& Elsevier]

Abstract: Two novel side chains which had previously been found to enhance antagonist activity in the dihydrobenzoxathiin SERM series were applied to three existing platforms. The novel side chains did not improve the antagonist activity of the existing platforms. [Copyright &y& Elsevier]

Abstract: The melanocortin subtype-4 receptor (MC4R) has been implicated in the control of feeding behavior and body weight regulation. A series of tetrapeptides, based on Tic-DPhe-Arg-Trp-NH2—a mimic of the putative message sequence “His-Phe-Arg-Trp” and modified at the DPhe position, were prepared and pharmacologically characterized for potency and selectivity. Substitution of His with Tic gave peptides with significant increases in selectivity. The effects of the substitution pattern of DPhe were investigated and it has significant influences on potency and the level of the maximum cAMP accumulation. Intracerebroventricular administration of peptide 10 induced significant inhibition of cumulative overnight food intake and feeding duration in rats. [Copyright &y& Elsevier]

Abstract: Glucocorticoids (GCs) are vital multi-faceted hormones with recognized effects on carbohydrate, protein and lipid metabolism. Previous studies with the steroid antagonist, RU486 have underscored the essential role of GCs in the regulation of these metabolic pathways. This article describes the discovery and characterization of novel GRα selective nonsteroidal antagonists (NSGCAs). NSGCAs 2 and 3 are spirocyclic dihydropyridine derivatives that selectively bind the GRα with IC50s of 2 and 1.5nM, respectively. Importantly, these compounds are full antagonists of the induction by dexamethasone (Dex) of marker genes for glucose and glutamine metabolism; the tyrosine amino transferase (TAT) and glutamine synthetase (GS) enzymes, respectively. In contrast, GC-dependent transcriptional repression of the collagenase 1 (MMP-1) enzyme, an established GRα responsive proinflammatory gene; is poorly antagonized by these compounds. These NSGCAs might have useful applications as tools in metabolic research and drug discovery. [Copyright &y& Elsevier]

A class of flavanoids exhibiting a high degree of selectivity for ERα over ERβ has been discovered. The most active analogue 6 was found to be 66-fold ERα-selective and demonstrated uterine estradiol antagonism. [Copyright &y& Elsevier]

17β-Hydroxysteroid dehydrogenase type 3 (17β-HSD-3) is a member of the short-chain dehydrogenase/reductase (SDR) family and is essential for the reductive conversion of inactive C19-steroid, androstenedione, to the biologically active androgen, testosterone, which plays a central role in the development of the male phenotype. Mutations that inactivate this enzyme give rise to a rare form of male pseudohermaphroditism, referred to as 17β-HSD-3 deficiency. One such mutation is the replacement of arginine at position 80 with glutamine, compromising enzyme activity by increasing the cofactor binding constant 60-fold. In the absence of a 17β-HSD-3 crystal structure, we have grafted its amino acid sequence for the NADPH binding site on the X-ray crystal structures of glutathione reductase (Protein Data Bank code 1gra) and 17β-HSD type 1 (Protein Data Bank codes 1fdv and 1fdu) where we find the trunk of the arginine 80 side chain forms part of the hydrophobic pocket for the purine ring of adenosine while its guanidinium moiety interacts with the 2′-phosphate to both stabilize cofactor binding and neutralize its intrinsic negative charge through two hydrogen bonds. To qualitatively assess the role arginine 80 plays in both selecting and stabilizing NADPH binding, it was replaced with each amino acid and the mutant enzymes subjected to enzymatic analysis. There are only seven enzymes exhibiting any measurable enzymatic activity with arginine∼lysine>leucine>glutamine>methionine>tyrosine>isoleucine. With an aspartic acid at position 58 in 17β-HSD-3 occupying the equivalent space in the cofactor binding pocket as arginine 224 in glutathione reductase or serine 12 in 17β-HSD-1, there was an expectation that some of the mutants might use NADH as a cofactor. In no case was NADH found to substitute for NADPH. [Copyright &y& Elsevier]

Pastor and Cruciani [J. Med. Chem. 38 (1995) 4637] and Kastenholz et al. [J. Med. Chem. 43 (2000) 3033] pioneered methods for comparing related receptors, with the ultimate goal of designing selective ligands. Such methods start with a reasonable superposition of high-resolution three-dimensional (3D) structures of the receptors. Next, molecular field maps are calculated for each receptor. Then the maps are analyzed to determine which map features are correlated with a particular subset of receptors. We present a method FLOGTV, based on the trend vector paradigm [J. Chem. Inf. Comput. Sci. 25 (1985) 64] to perform the analysis. This is mathematically simpler than the GRID/CPCA method of Kastenholz et al. and allows for the simultaneous comparison of many receptor structures. Also, the trend vector paradigm provides a method of selecting isopotential contours that are well above “noise”. We demonstrate the method on four examples: HIV proteases versus two-domain acid proteases, thrombin versus trypsin and factor Xa, bacterial dihydrofolate reductases (DHFRs) versus vertebrate DHFRs, and P38 versus ERK protein kinases. [Copyright &y& Elsevier]

Examines the structure and chemistry of apicidins on cyclic tetrapeptides. Inhibition of histone deacetylase and antiprotozoal agents; Cause of malaria and cryptosporidiosis; Regulation on gene transcription by controlling dynamic process of acetylation and deacetylation of lysine residue.

Investigates the synthesis and characterization of diastereomers of liposidomycin diazepanone. Restriction of bacterial peptidoglycan synthesis by liposidomycins; Conformation of 1,4-diazepan-2-ones by vicinal interactions; Use of x-ray crystallography in analyzing diastereomers.

Focuses on a study which synthesized several nonpeptide somatostatin agonists which binded selectively with the somatostatin receptor subtype 2. Distribution of somatostatin throughout the central nervous system; Identification of two biologically active forms of somatostatin; Methodology used to conduct the study; Results of the study.