https://users.cs.duke.edu/~brd/Teaching/Bio/asmb/current/Papers/Lit4Docking/Gold_dock.pdf

Development and validation of a genetic algorithm for flexible docking.

Antiviral immunity against a pathogen is mounted upon recognition by the host of virally associated structures. One of these viral 'signatures', double-stranded (ds) RNA, is a replication product of most viruses within infected cells and is sensed by Toll-like receptor 3 (TLR3) and the recently identified cytosolic RNA helicases RIG-I (retinoic acid inducible gene I, also known as Ddx58) and Mda5 (melanoma differentiation-associated gene 5, also known as Ifih1 or Helicard). Both helicases detect dsRNA, and through their protein-interacting CARD domains, relay an undefined signal resulting in the activation of the transcription factors interferon regulatory factor 3 (IRF3) and NF-kappaB. Here we describe Cardif, a new CARD-containing adaptor protein that interacts with RIG-I and recruits IKKalpha, IKKbeta and IKKvarepsilon kinases by means of its C-terminal region, leading to the activation of NF-kappaB and IRF3. Overexpression of Cardif results in interferon-beta and NF-kappaB promoter activation, and knockdown of Cardif by short interfering RNA inhibits RIG-I-dependent antiviral responses. Cardif is targeted and inactivated by NS3-4A, a serine protease from hepatitis C virus known to block interferon-beta production. Cardif thus functions as an adaptor, linking the cytoplasmic dsRNA receptor RIG-I to the initiation of antiviral programmes.

Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus

Many aspects of the hepatitis C virus (HCV) life cycle have not been reproduced in cell culture, which has slowed research progress on this important human pathogen. Here, we describe a full-length HCV genome that replicates and produces virus particles that are infectious in cell culture (HCVcc). Replication of HCVcc was robust, producing nearly 10(5) infectious units per milliliter within 48 hours. Virus particles were filterable and neutralized with a monoclonal antibody against the viral glycoprotein E2. Viral entry was dependent on cellular expression of a putative HCV receptor, CD81. HCVcc replication was inhibited by interferon-alpha and by several HCV-specific antiviral compounds, suggesting that this in vitro system will aid in the search for improved antivirals.

/pdf/complete-replication-of-hepatitis-c-virus-in-cell-culture-4qr0ko8zoa.pdf

Complete Replication of Hepatitis C Virus in Cell Culture

Review of recent research on hepatitis C therapy for 54th annual meeting of the American association for the study of liver diseases

Viral hepatitis B

Metal-free coupling of azoles with 2- and 3-haloindoles providing access to novel 2- or 3-(azol-1-yl)indole derivatives.

A series of HIV protease inhibitors containing a novel (hydroxyethyl)amidosuccinoyl core has been synthesized. These peptidomimetic structures inhibit viral protease activity at low nanomolar concentrations (IC50 < 10 nM for HIV-1 protease). The inhibition constant (Ki) for inhibitor 19 was determined to be 7.5 pM against HIV-1 and 1.2 nM against HIV-2 proteases, respectively. Several compounds (19−24) inhibited HIV-1 replication in cell culture assays with 50% effective concentrations (EC50) = 3.7−35 nM. This series of inhibitors was found to exhibit poor bioavailability (<10%) in the rat, following oral administration. The synthesis and biological properties of these compounds are discussed. In addition, an X-ray structure of one of these inhibitors (23) in complex with HIV-2 protease provides insight into the binding mode of this novel class of HIV protease inhibitors.

Potent HIV Protease Inhibitors Containing a Novel (Hydroxyethyl)amide Isostere

Starting from palinavir (1), our lead HIV protease inhibitor, we have discovered a new series of truncated analogues in which the P3-P2 quinaldic-valine portion of 1 was replaced by 2‘,6‘-dimethylp...

2‘,6‘-Dimethylphenoxyacetyl: A New Achiral High Affinity P3-P2 Ligand for Peptidomimetic-Based HIV Protease Inhibitors

The HCV NS5B polymerase, when complexed with certain inhibitors, adopts a confirmation in which the finger loop region defined by amino acid residues 18 to 35 is displaced to expose a binding pocket defined generally by amino acid residues 392, 393, 395, 396, 399, 424, 425, 428, 429, 492, 493, 494, 495, 496, 500 and 503. This newly exposed binding pocket defines a novel target in the search of further chemical entities which are capable of binding to HCV NS5B and modulating, or preferably inhibiting, the polymerase activity of HCV NS5B.

Hepatitis c virus ns5b polymerase inhibitor binding pocket

This invention relates to compounds of formula (I) wherein Ring a, A, B, C, D, E, R and Q are defined herein. These compounds possess the ability to disrupt the interaction between regulatory proteins possessing one or more SH2 domains and their native ligands.

Pierre L. Beaulieu

Papers

Metal-free coupling of azoles with 2- and 3-haloindoles providing access to novel 2- or 3-(azol-1-yl)indole derivatives.

Potent HIV Protease Inhibitors Containing a Novel (Hydroxyethyl)amide Isostere

2‘,6‘-Dimethylphenoxyacetyl: A New Achiral High Affinity P3-P2 Ligand for Peptidomimetic-Based HIV Protease Inhibitors

Hepatitis c virus ns5b polymerase inhibitor binding pocket

Pyridones as src family sh2 domain inhibitors