Fr Francium

RSC, Cambridge 2011. 332 pp., hardcover £ 132.99.—ISBN 978-1-84973-174-4

By the use of knowledge gained through modeling of drug metabolism mediated by the cytochrome P450 2D6 and 3A4 isoforms, we constructed a 2D-based model for site-of-metabolism prediction for the cytochrome P450 2C9 isoform. The similarities and differences between the models for the 2C9 and 2D6 isoforms are discussed through structural knowledge from the X-ray crystal structures and trends in experimental data. The final model was validated on an independent test set, resulting in an area under the curve value of 0.92, and a site of metabolism was found among the top two ranked atoms for 77 % of the compounds.

Foreseeing the breakdown: We developed a ligand-based model for predicting the site of drug metabolism mediated by cytochrome P450 2C9. The model is compared with two commercial models for two data sets. Because this model is constructed from only three descriptors and does not require 3D structures or electronic calculations, it is extremely rapid.

The FK506 binding protein 51 (FKBP51) is best known as an Hsp90-associated co-chaperone that regulates the responsiveness of steroid hormone receptors. In human genetic association studies, FKBP51 has repeatedly been associated with emotion processing and numerous stress-related affective disorders. It has also been implicated in contributing to the glucocorticoid hyposensitivity observed in New World primates. More recently, several research groups have consistently shown a protective effect of FKBP51 knockout or knockdown on stress endocrinology and stress-coping behavior in animal models of depression and anxiety. The principal druggability of FKBP51 is exemplified by the prototypic FKBP ligands FK506 and rapamycin. Moreover, FKBP51 is highly suited for X-ray co-crystallography, which should facilitate the rational drug design of improved FKBP51 ligands. In summary, FKBP51 has emerged as a promising new drug target for stress-related disorders that should be amenable to drug discovery.

Low-stress target: The FK506 binding protein 51 regulates responsiveness to stress hormones in animals and humans. Herein we summarize the status of FKBP51 as a newly emerged drug target for psychiatric disorders and possibly for endocrine cancers.

To identify novel c-Met inhibitors, sequences and crystal structures of the human kinome were analyzed to find interesting hinge binders that have been underexplored within the tyrosine kinase subfamily. Through this study, the imidazolopyridine ring was selected as a novel c-Met hinge-binding inhibitor scaffold. A series of derivatives was prepared, and the structure–activity relationships were studied. Among these, one compound in particular showed excellent activities in enzymatic and cellular assays, good in vitro metabolic stability, and favorable pharmacokinetic parameters. When administered orally, the compound inhibited tumor growth in an NIH-3T3/TPR-Met xenograft model and did not show adverse effects on body weight. The present work not only conceptually demonstrates a new route for designing novel kinase inhibitors by using known structural information of ligand–hinge interactions but also provides a series of imidazolopyridine derivatives as potent c-Met inhibitors.

Amazing imidazolopyridines: By screening crystal structures of members of the human kinome and analyzing hinge binders, we designed a novel scaffold for inhibitors of c-Met. A series of derivatives were prepared and their SARs were studied; among them, compound 41 showed good in vitro and in vivo activities and proved to be a promising lead compound for further investigation.

From engineering to drug design: Use of the Taguchi method to predict the optimal compound from a dataset could potentially allow the identification of the most biologically active compound without the synthesis of a full combinatorial library of derivatives. Our results show that the method achieved favorable outcomes for biological activities that are measured against specific target proteins. However, limitations were observed when the method was applied to data derived from a cell-based system.

The human immunodeficiency virus 1 (HIV-1) virion infectivity factor (Vif) protein, essential for in vivo viral replication, protects the virus from innate antiviral cellular factor apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (APOBEC3G; A3G) and is an attractive target for the development of novel antiviral therapeutics. We have evaluated the structure–activity relationships of N-(2-methoxyphenyl)-2-((4-nitrophenyl)thio)benzamide (RN-18), a small molecule recently identified as an inhibitor of Vif function that blocks viral replication only in nonpermissive cells expressing A3G, by inhibiting Vif–A3G interactions. Microwave-assisted cross-coupling reactions were developed to prepare a series of RN18 analogues with diverse linkages and substitutions on the phenyl rings. A dual cell-based assay system was used to assess antiviral activity against wild-type HIV-1 in both nonpermissive (H9) and permissive (MT4) cells that also allowed evaluation of specificity. In general, variations of phenyl substitutions were detrimental to antiviral potency and specificity, but isosteric replacements of amide and ether linkages were relatively well tolerated. These structure–activity relationship data define structural requirements for Vif-specific activity, identify new compounds with improved antiviral potency and specificity, and provide leads for further exploration to develop new antiviral therapeutics.

Coupling up!N-(2-Methoxyphenyl)-2-((4-nitrophenyl)thio)benzamide (RN-18) is a small molecule that selectively inhibits Vif–APOBEC interactions and HIV-1 replication. Structure–activity relationship studies define key structural requirements for Vif-specific antiviral activity, and new compounds with improved antiviral potency and specificity were identified, providing leads for the further exploration of these compounds as new antiviral therapeutics.

West Nile virus (WNV), a member of the Flaviviridae family, is a mosquito-borne pathogen that causes a great number of human infections each year. Neither vaccines nor antiviral therapies are currently available for human use. In this study, a WNV NS2B–NS3 protease inhibitor with a 9,10-dihydro-3H,4aH-1,3,9,10a-tetraazaphenanthren-4-one scaffold was identified by screening a small library of non-peptidic compounds. This initial hit was optimized by solution-phase synthesis and screening of a focused library of compounds bearing this scaffold. This led to the identification of a novel, uncompetitive inhibitor (1a40, IC₅₀=5.41±0.45 μM) of WNV NS2B–NS3 protease. Molecular docking of this chiral compound onto the WNV protease indicates that the S enantiomer of 1a40 appears to interfere with the productive interactions between the NS2B cofactor and the NS3 protease domain; (S)-1a40 is a preferred isomer for inhibition of WNV NS3 protease.

Running cofactor interference: In vitro assays with West Nile virus (WNV) NS2B–NS3 protease resulted in the discovery of 9,10-dihydro-3H,4aH-1,3,9,10a-tetraazaphenanthren-4-ones as a new class of inhibitors of this enzyme. Optimization of the lead compound led to an uncompetitive WNV NS2B–NS3 inhibitor with an IC₅₀ value of 5.41±0.45 μM.

A series of GABA uptake inhibitors related to (S)-1-{2-[tris(4-methoxyphenyl)methoxy]ethyl}piperidine-3-carboxylic acid [(S)-SNAP-5114], the most potent mGAT4 inhibitor known so far, were synthesized and biologically evaluated for their inhibitory potency at the four GABA uptake transporters mGAT1–4 stably expressed in HEK-293 cell lines. New analogues were developed with potencies that are similar to or slightly higher than those of current mGAT4 inhibitors, but with distinctly improved chemical stability. (S)-Nipecotic acid derivatives possessing a 2-[1-(4-methoxy-2-methylphenyl)-1,1-bis(4-methoxyphenyl)methoxy]ethyl (DDPM-859) or a 4,4,4-tris(4-methoxyphenyl)but-2-en-1-yl moiety (DDPM-1457) were found to exhibit pIC₅₀ values of 5.78 and 5.87, respectively. Thus, as mGAT4 inhibitors, these compounds compare well with (S)-SNAP-5114 (pIC₅₀=5.71), but are far more stable than the latter. Moreover, DDPM-859 displays a more favorable subtype selectivity for mGAT4 versus mGAT3 than does (S)-SNAP-5114.

Stability is a snap! We developed a series of analogues of (S)-SNAP-5114, the most potent inhibitor of murine γ-aminobutyric acid transporter type 4 (mGAT4) known thus far. These analogues have potencies that are similar to or slightly higher than that of (S)-SNAP-5114 toward mGAT4 (DDPM-1457: pIC₅₀=5.87), but with distinctly improved chemical stability.

The main threat to controlling malaria is the emerging multidrug resistance of Plasmodium sp. parasites. Bis-alkylamidines were developed as a potential new chemotherapy that targets plasmodial phospholipid metabolism. Unfortunately, these compounds are not orally available. To solve this absorption issue, we investigated a prodrug strategy based on sulfonate derivatives of alkylamidoximes. A total of 25 sulfonates were synthesized as prodrug candidates of one bis-N-alkylamidine and of six N-substituted bis-C-alkylamidines. Their antimalarial activities were evaluated in vitro against P. falciparum and in vivo against P. vinckei in mice to define structure–activity relationships. Small alkyl substituents on the sulfonate group of both C-alkyl- and N-alkylamidines led to the best oral antimalarial activities; alkylsulfonate derivatives are chemically transformed into the corresponding alkylamidines.

Improved bioavailability: Bis-alkylamidines were originally developed as potential new antimalarial agents that target phospholipid metabolism, but these compounds are not orally bioavailable. To solve this issue, 25 sulfonates were investigated as prodrug candidates. Their antimalarial activities were evaluated in vitro and in vivo to define structure–activity relationships.

Novel compounds incorporating a pentacycloundecane (PCU) diol moiety were designed, synthesized, and evaluated as inhibitors of the wild-type C-South African (C-SA) HIV-1 protease. Seven compounds are reported herein, three of which displayed IC₅₀ values in the 0.5–0.6 μM range. The cytotoxicity of PCU cage peptides toward human MT-4 cells appears to be several orders of magnitude less toxic than the current antiviral medications ritonavir and lopinavir. NMR studies based on the observed through-space ¹H,¹H distances/contacts in the EASY-ROESY spectra of three of the considered PCU peptide inhibitors enabled us to describe their secondary solution structure. Conserved hydrogen bonding interactions were observed between the hydroxy group of the PCU diol inhibitors and the catalytic triad (Asp25, Ile26, Gly27) of HIV protease in docking and molecular dynamics simulations. The biological significance and possible mode of inhibition by PCU-based HIV protease inhibitors discussed herein facilitates a deeper understanding of this family of inhibitors and their potential application to a vast number of alternative diseases related to proteases.

Cage peptides unleashed: The combination of drug design with in vitro assays, NMR techniques, and molecular modeling has enabled us to rationalize the observed inhibitory activities toward HIV protease by the various cage peptides in this series. EASY-ROESY NMR data show that the entire range of inhibitors exhibit a relatively stable interaction between the cage side chain and the cage protons.