In vivo selection of protease cleavage sites by using chimeric Sindbis virus libraries

A comparative analysis of the substrate permissiveness of HCV and GBV-B NS3/4A proteases reveals genetic evidence for an interaction with NS4B protein during genome replication

The hepatitis C virus (HCV) serine protease (NS3/4A) processes the NS3-NS5B segment of the viral polyprotein and also cleaves host proteins involved in interferon signaling, making it an important target for antiviral drug discovery and suggesting a wide breadth of substrate specificity. We compared substrate specificities of the HCV protease with that of the GB virus B (GBV-B), a distantly related nonhuman primate hepacivirus, by exchanging amino acid sequences at the NS4B/5A and/or NS5A/5B cleavage junctions between these viruses within the backbone of subgenomic replicons. This mutagenesis study demonstrated that the GBV-B protease had a broader substrate tolerance, a feature corroborated by structural homology modeling. However, despite efficient polyprotein processing, GBV-B RNAs containing HCV sequences at the C-terminus of NS4B had a pseudo-lethal replication phenotype. Replication-competent revertants contained second-site substitutions within the NS3 protease or NS4B N-terminus, providing genetic evidence for an essential interaction between NS3 and NS4B during genome replication.

In vitro selection and characterization of hepatitis C virus serine protease variants resistant to an active-site peptide inhibitor

The hepatitis C virus (HCV) serine protease is necessary for viral replication and represents a valid target for developing new therapies for HCV infection. Potent and selective inhibitors of this enzyme have been identified and shown to inhibit HCV replication in tissue culture. The optimization of these inhibitors for clinical development would greatly benefit from in vitro systems for the identification and the study of resistant variants. We report the use HCV subgenomic replicons to isolate and characterize mutants resistant to a protease inhibitor. Taking advantage of the replicons' ability to transduce resistance to neomycin, we selected replicons with decreased sensitivity to the inhibitor by culturing the host cells in the presence of the inhibitor and neomycin. The selected replicons replicated to the same extent as those in parental cells. Sequence analysis followed by transfection of replicons containing isolated mutations revealed that resistance was mediated by amino acid substitutions in the protease. These results were confirmed by in vitro experiments with mutant enzymes and by modeling the inhibitor in the three-dimensional structure of the protease.

Approaching a new era for hepatitis C virus therapy: inhibitors of the NS3-4A serine protease and the NS5B RNA-dependent RNA polymerase

The treatment of chronic disease caused by the hepatitis C virus (HCV) is an unmet clinical need, since current therapy is only partially effective and limited by undesirable side effects. The viral serine protease and the RNA-dependent RNA polymerase are the best-studied targets for the development of novel therapeutic agents. These enzymes have been extensively characterized at the biochemical and structural level and thus used to set up screening assays for the identification of selective inhibitors. These efforts lead to the discovery of several classes of compounds with potential antiviral activity. The hepatitis C virus does not replicate in the laboratory. The formidable challenge posed by the difficulty of developing cell-based assays and preclinical animal systems has been partially overcome with several alternative approaches. The development of new assays permitted the optimization of enzyme inhibitors leading eventually to molecules with the desired drug-like properties, the most advanced of which are being considered for clinical trials.

Engineered viruses to select genes encoding secreted and membrane-bound proteins in mammalian cells

We have developed a functional genomics tool to identify the subset of cDNAs encoding secreted and membrane-bound proteins within a library (the 'secretome'). A Sindbis virus replicon was engineered such that the envelope protein precursor no longer enters the secretory pathway. cDNA fragments were fused to the mutant precursor and expression screened for their ability to restore membrane localization of envelope proteins. In this way, recombinant replicons were released within infectious viral particles only if the cDNA fragment they contain encodes a secretory signal. By using engineered viral replicons to selectively export cDNAs of interest in the culture medium, the methodology reported here efficiently filters genetic information in mammalian cells without the need to select individual clones. This adaptation of the 'signal trap' strategy is highly sensitive (1/200 000) and efficient. Indeed, of the 2546 inserts that were retrieved after screening various libraries, more than 97% contained a putative signal peptide. These 2473 clones encoded 419 unique cDNAs, of which 77% were previously annotated. Of the 94 cDNAs encoding proteins of unknown function, 24% either had no match in databases or contained a secretory signal that could not be predicted from electronic data.

Phage display substrate: a blind method for determining protease specificity

Phage display substrate enables rapid determination of protease specificity by exposing vast numbers of recombinant peptides to a given protease. Peptides released through specific cleavage are amplified in an expression system. Phage display substrate has been widely exploited and developed further. The number of proteases (from various sources) characterized by this approach testifies to its power. To conserve their advantage over chemical methods, however, phage libraries must be constructed accordingly. The current phenomenal progress in genomics steadily increases the number of protease to be studied. Phage display substrate should prove a powerful method to exploit this wealth of new knowledge.

Hepatitis C virus cell culture replication systems: their potential use for the development of antiviral therapies

Hepatitis C virus is a significant public health problem. Current drug regimens have low efficacy against some hepatitis C virus genotypes, while no vaccine is available. The absence of an efficient cell culture system and an accessible small animal model to study hepatitis C virus replication and pathogenesis are major obstacles to the development of effective antiviral therapies. Studies of surrogate model systems, either related viruses or chimeric viruses containing part of the hepatitis C virus genome, have given insight into hepatitis C virus replication, in addition to being a powerful tool for drug discovery. The recent development of an efficient system for the initiation of replication in cell culture provides a viable screen for inhibitors of hepatitis C virus replication. It also brings us much closer to the ultimate goal of an infectious cell culture system for hepatitis C virus.