2-(2-thienyl)-5,6-dihydroxy-4-carboxypyrimidines as inhibitors of the hepatitis C virus NS5B polymerase: Discovery, SAR, modeling, and mutagenesis

Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The polymerase of HCV is responsible for the replication of viral RNA. We recently disclosed dihydroxypyrimidine carboxylates 2 as novel, reversible inhibitors of the HCV NS5B polymerase. This series was further developed into 5,6-dihydroxy-2-(2- thienyl)pyrimidine-4-carboxylic acids such as 34 (EC50 9.3 \u3bcM), which now show activity in the cell-based HCV replication assay. The structure-activity relationship of these inhibitors is discussed in the context of their physicochemical properties and of the polymerase crystal structure. We also report the results of mutagenesis experiments which support the proposed binding model, which involves pyrophosphate-like chelation of the active site Mg ions

Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors

The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for inhibition. Herein, we present 1H-benzo[de]isoquinoline-1,3(2H)-diones as a new series of selective inhibitors of HCV NS5B polymerase. The HTS hit 1 shows submicromolar potency in two differentHCVreplicons (1b and 2b) and displays no activity on other polymerases (HIV-RT, Poliopol, GBV-b-pol). These inhibitors act during the pre-elongation phase by binding to NS5B non-nucleoside binding site Thumb Site II as demonstrated by crystal structure of compound 1 with the \u394C55-1b and \u394C21-2b enzymes and by mutagenesis studies. SAR in this new series reveals inhibitors, such as 20, with low micromolar activity in the HCV replicon and with good activity/toxicity window in cells

Oxime Amides as a Novel Zinc Binding Group in Histone Deacetylase Inhibitors: Synthesis, Biological Activity, and Computational Evaluation

Several oxime containing molecules, characterized by a SAEA-like structure, were explored to select a potentially new biasing binding element for the zinc in HDAC catalytic site. All compounds were evaluated for their in vitro inhibitory activity against the 11 human HDACs isoforms. After identification of a "hit" molecule, a programmed variation at the cap group and at the linker was carried out in order to increase HDAC inhibition and/or paralogue selectivity. Some of the new derivatives showed increased activity against a number of HDAC isoforms, even if their overall activity range is still far from the inhibition values reported for SAHA. Moreover, different from what was reported for their hydroxamic acid analogues the new alpha-oxime amide derivatives do not select between class I and class 11 HDACs; rather they target specific isoforms in each class. These somehow contradictory results were finally rationalized by a computational assisted SAR, which gave us the chance to understand how the oxime derivatives interact with the catalytic site and justify the observed activity profile

Targeting the Zinc-Dependent Histone Deacetylases (HDACs) for Drug Discovery

In humans, the zinc-dependent histone deacetylases (HDACs) are a family of 11 nonredundant isoforms that catalyze the dynamic reversal of posttranslationally modified acyl-lysine residues back to lysine. At the epigenetic level, HDACs have a critical gene silencing effect, promoting the compaction of histone tails with DNA to prevent transcription. In addition, HDACs deacylate many nonhistone substrates in diverse cellular compartments to profoundly influence protein structure and function. While the action of HDACs is indispensable to normal physiology, their abnormal overexpression is linked to the majority of human diseases. Consequently, the inhibition of HDACs has become a valuable target for therapeutic applications. Numerous potent small molecules are known, of both natural product and synthetic origin, that inhibit HDACs, primarily by reversibly interacting with the zinc cation within the enzyme active site. At the present time, five such HDAC inhibitors have received regulatory approval for the treatment of hematological cancers. This review focuses on the typical zinc-binding groups employed in HDAC inhibitors and the major advances within each class in terms of potency, isoform selectivity, and clinical applications