Identification and characterization of coumestans as novel HCV NS5B polymerase inhibitors

The hepatitis C virus (HCV) NS5B is essential for viral RNA replication and is therefore a prime target for development of HCV replication inhibitors. Here, we report the identification of a new class of HCV NS5B inhibitors belonging to the coumestan family of phytoestrogens. Based on the in vitro NS5B RNA-dependent RNA polymerase (RdRp) inhibition in the low micromolar range by wedelolactone, a naturally occurring coumestan, we evaluated the anti-NS5B activity of four synthetic coumestan analogues bearing different patterns of substitutions in their A and D rings, and observed a good structure-activity correlation. Kinetic characterization of coumestans revealed a noncompetitive mode of inhibition with respect to nucleoside triphosphate (rNTP) substrate and a mixed mode of inhibition towards the nucleic acid template, with a major competitive component. The modified order of addition experiments with coumestans and nucleic acid substrates affected the potencies of the coumestan inhibitors. Coumestan interference at the step of NS5B–RNA binary complex formation was confirmed by cross-linking experiments. Molecular docking of coumestans within the allosteric site of NS5B yielded significant correlation between their calculated binding energies and IC50 values. Coumestans thus add to the diversifying pool of anti-NS5B agents and provide a novel scaffold for structural refinement and development of potent NS5B inhibitors

Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

The eIF2 initiation complex is central to maintaining a functional translation machinery. Extreme stress such as life-threatening sepsis exposes vulnerabilities in this tightly regulated system, resulting in an imbalance between the opposing actions of kinases and phosphatases on the main regulatory subunit eIF2α. Here, we report that translation shutdown is a hallmark of established sepsis-induced kidney injury brought about by excessive eIF2α phosphorylation and sustained by blunted expression of the counterregulatory phosphatase subunit Ppp1r15a. We determined that the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic approaches enabled the derepression of Ppp1r15a, salvaged translation and improved kidney function in an endotoxemia model. We also found that the loss of this uORF has broad effects on the composition and phosphorylation status of the immunopeptidome that extended beyond the eIF2α axis. Collectively, our findings define the breath and potency of the highly conserved Ppp1r15a uORF and provide a paradigm for the design of uORF-based translation rheostat strategies. The ability to accurately control the dynamics of translation during sepsis will open new paths for the development of therapies at codon level precision

Correction: In Vitro Evolution and Affinity-Maturation with Coliphage Qβ Display.

[This corrects the article DOI: 10.1371/journal.pone.0113069.]

Evolutionary Qβ Phage Displayed Nanotag Library and Peptides for Biosensing

We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target selection was achieved through panning with elution by infection. The selected peptide was tested as a transducer for an immunogenic epitope of the foot-and-mouth disease virus (FMDV) on Qβ phage platform separated by a linker. The biotin-tag showed no significant influence on the affinity of the epitope to its cognate antibody (SD6). The nanotag-bound biotin selectively fused either to the C- or N-terminus of the epitope. The epitope would not bind or recognize SD6 while positioned at the N-terminus of the nanotag. Additionally, the biotin competed linearly with the SD6 antibody in a competitive ELISA. Competition assays using the selected recombinant phage itself as a probe or transducer enable the operationalization of this technology as a biosensor toolkit to sense and quantify SD6 analyte. Herein, the published Strep II nanotag (DVEWLDERVPLVET) was used as a control and has similar functionalities to our proposed novel biotin-tag thereby providing a new platform for developing devices for diagnostic purposes

In vitro evolution and affinity-maturation with Coliphage qβ display.

The Escherichia coli bacteriophage, Qβ (Coliphage Qβ), offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV). DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb) SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets

Morphology of wild type vs. hybrid Qβ phage plaques.

<p>Panel A) wild type Qβ phages; Panel B) Qβ-FMDV VP1 G-H loop phages; Panel C) Qβ-GFP rescued phages from <i>E. coli</i> SURE (expression host with F⁺) over-expressing A1-GFP protein infected with wild type Qβ. Panel D) QβΔA1 phages. All at very low multiplicity of infection (MOI), and all plates are exactly 1 day (24 hours) old when photographed.</p

RT-PCR of RNA purified from Qβ-phage plaques.

<p>Panel A) Lane 2: Qβ-HisJ; lane 3: Qβ-tHisF; lane 4: soft agar stab from HisJ plate; lane 4: soft agar stab from tHisF. Panel B) Lanes 2 and 4: wild type Qβ; Lanes 3 and 5: Qβ-GFP. Panel C) Lanes 2 and 4: Qβ-FMDV; Lanes 1 and 5: wild type Qβ (positive control). The 100 bp and 1 kb DNA ladder were used.</p

Agarose gel electrophoresis of the RNA display system vector construction.

<p>Panel A) Lanes 1–3: positive recombinant pUCHisJ plasmid clone (cl) restricted with <i>Afl</i>II and <i>Nsi</i>I; Lanes 5–7: positive pUCtHisF and Lane 8: negative clone. Panel B) Lanes 2–6: positive recombinants pBRT7QβHisJ restricted with <i>Afl</i>II and <i>Nsi</i>I; Lane 7: negative clone. Panel C) Lanes 2–7: positive recombinants pBRT7QβtHisF restricted with <i>Afl</i>II and <i>Nsi</i>I. Panel D): Lane 1: pQβ8 negative control; Lanes 2 and 3: positive recombinants pQβ8ΔA1; Lanes 4 and 5: positive recombinants pBRT7Qβ-FMDV; Lanes 6 and 7: positive recombinants pBRT7QβΔA1 all restricted with <i>Nhe</i>I. Lanes “ladder” were loaded with the 100 bp or 1 kb DNA ladder.</p

Ouchterlony double diffusion assay.

<p>A) Wells 1 and 2 represent Qβ-FMDV phages; wells 3 and 4 represent QβΔA1 phages; wells 5 and 6 represent wild-type Qβ; center well contains polyclonal serum from immunized guinea pig (labeled “Ab”). B) Same as panel A but with 1/3 of the serum concentration. C) Wells 1 and 2 Qβ-FMDV are the same as panel A; wells 5 and 6 contain half the phage titer of wells 1 and 2; well 3 represents phages from pBRT7QβΔA1 and well 4 represents phages from pQβ8ΔA1; center well contains IgGs purified from serum panel A and B (labeled “Ab”). The line of precipitation is visible as a white haze forming a half-circle around some of the wells in the experiments.</p

Schematic representation of the RNA phage display vector construction.

<p>General cloning procedure from PCR fragments to pBRT7Qβ with transient cloning in the pUC18-cassette working plasmid. Step 1: cloning of PCR fragment into pCR2.1 vector; Step 2: cloning of the foreign gene from PCR into the pUC-cassette (with <i>Nsi</i>I) using <i>Af</i>lII and <i>Esp</i>I sites; Step 3: Cloning of the foreign gene into pBRT7Qβ using <i>Afl</i>II and <i>Nsi</i>I. P: promoter; <i>Amp</i>: ampicillinase gene; <i>Kan</i>: kanamycin resistance gene; ori: origin of replication.</p