Identification of Hepatitis C Virus NS5A Inhibitors

Using a cell-based replicon screen, we identified a class of compounds with a thiazolidinone core structure as inhibitors of hepatitis C virus (HCV) replication. The concentration of one such compound, BMS-824, that resulted in a 50% inhibition of HCV replicon replication was ∼5 nM, with a therapeutic index of >10,000. The compound showed good specificity for HCV, as it was not active against several other RNA and DNA viruses. Replicon cells resistant to BMS-824 were isolated, and mutations were identified. A combination of amino acid substitutions of leucine to valine at residue 31 (L31V) and glutamine to leucine at residue 54 (Q54L) in NS5A conferred resistance to this chemotype, as did a single substitution of tyrosine to histidine at amino acid 93 (Y93H) in NS5A. To further explore the region(s) of NS5A involved in inhibitor sensitivity, genotype-specific NS5A inhibitors were used to evaluate a series of genotype 1a/1b hybrid replicons. Our results showed that, consistent with resistance mapping, the inhibitor sensitivity domain also mapped to the N terminus of NS5A, but it could be distinguished from the key resistance sites. In addition, we demonstrated that NS5A inhibitors, as well as an active-site inhibitor that specifically binds NS3 protease, could block the hyperphosphorylation of NS5A, which is believed to play an essential role in the viral life cycle. Clinical proof of concept has recently been achieved with derivatives of these NS5A inhibitors, indicating that small molecules targeting a nontraditional viral protein like NS5A, without any known enzymatic activity, can also have profound antiviral effects on HCV-infected subjects.Hepatitis C virus (HCV) is the major causative agent for non-A, non-B hepatitis worldwide, which affects more than 3% of the world population. HCV establishes chronic infections in a large percentage of infected individuals, increasing the risk for developing liver cirrhosis and, in some cases, hepatocellular carcinoma. Although the current standard of care for HCV infection involves the use of PEGylated interferon and ribavirin, a large proportion of patients fail to respond to this therapy, and treatment is associated with frequent and sometimes serious side effects (9). Given the limited efficacy of the current therapy, the development of safer and more effective therapies is of tremendous importance.HCV is a positive-strand RNA virus belonging to the family Flaviviridae. The HCV genome consists of a ∼9.6-kb RNA with a large open reading frame encoding a polyprotein of ∼3,010 amino acids. The polyprotein is cleaved co- and posttranslationally by both cellular and viral proteases into at least 10 different products (10, 11). The viral proteins required for RNA replication include NS3, NS4A, NS4B, NS5A, and NS5B (4, 19). NS3 consists of an amino-terminal protease domain required for the cleavage of the remaining nonstructural proteins and a carboxyl-terminal helicase/NTPase domain (8, 11, 30). NS4A serves as a cofactor for NS3 protease and helicase activities (8). NS4B is an integral membrane protein involved in the formation of the membranous web, where HCV replication complexes are thought to assemble (7). NS5A is a membrane-associated phosphoprotein present in basally phosphorylated (p56) and hyperphosphorylated (p58) forms (15, 31). It was previously reported that only p58-defective mutants could be complemented in trans (1), and NS5A is involved in HCV virion production (22, 34), suggesting that different forms of NS5A exert multiple functions at various stages of the viral life cycle. The N terminus of NS5A (domain I) has been crystallized in alternative dimer forms and contains zinc- and RNA-binding domains (20, 33). The ability of NS5A to bind to zinc (32) and RNA (14) has been demonstrated in vitro. NS5A has been shown to interact with a number of host proteins, is implicated in interferon resistance in vivo, and has been the subject of several reviews (13, 21). NS5B functions as the viral RNA-dependent RNA polymerase (2). Previous studies have shown that the NS3-NS5B proteins are all essential for HCV replication and are believed to form the HCV replicase complex (4, 18, 19).The development of the cell-based HCV replicon system provides a means for the large-scale screening of HCV inhibitors against multiple viral targets. The use of a cell-based replication assay likely includes essential functions that previously could not be evaluated with in vitro enzyme assays. The disadvantages for the advancement of HCV inhibitors targeting nonenzymatic proteins are (i) the potential for structure-activity relationships (SAR) to be difficult to interpret based on the complexity of cell-based systems, (ii) the lack of a system for validation, and (iii) difficulty in predicting if in vitro potency can translate into in vivo effect. Therefore, during the process of developing HCV NS5A inhibitors, we established a series of assays and checkpoints prior to entering the clinic. This is the first report in a series of articles detailing the development of HCV NS5A inhibitors that has culminated in the demonstration of clinical efficacy for this novel mechanistic class of HCV inhibitor (25).In this report, we have used a previously described cell-based approach (26) to identify a novel compound that specifically inhibits HCV RNA replication. Through the use of resistance selection, we have demonstrated that the inhibitor targets the HCV NS5A protein, thereby establishing that the function of NS5A in replication can be inhibited by small molecules. In addition, using genotype-specific inhibitors, we have further shown that the N terminus of NS5A plays an essential role in compound activity by both 50% effective concentration (EC₅₀) determinations as well as a functional assay to evaluate NS5A hyperphosphorylation.     

Nectarless flowers: ecological correlates and evolutionary stability

In animal-pollinated flowers, the pollinators cannot detect the presence of nectar before entering flowers, and therefore flowers may cheat by not producing nectar. An earlier model suggested that a mixed strategy of producing nectarful and nectarless flowers would be evolutionarily stable. Here we compare nectarless flowers as a cheating strategy with three competing hypotheses namely "visit-more-flowers", "cross-pollination enhancement" and "better contact". We collected field data on 28 species of plants to test some of the differential predictions of the hypotheses. Nectarless flowers were detected in 24 out of 28 plant species. Correlations of percent nectarless flowers with floral and ecological variables support the cheater flower hypothesis. We further model the cost-benefits of cheating and show that an evolutionary stable ratio of nectarless to nectarful flowers can be reached. The equilibrium ratio is mainly decided by factors associated with pollinator density and pollinator learning.     

Comparative analysis of macrophage associated vectors for use in genetic vaccine

Background

Antigen presentation by non professional antigen presenting cells (APC) can lead to anergy. In genetic vaccines, targeting the macrophages and APC for efficient antigen presentation might lead to balanced immune response. One such approach is to incorporate APC specific promoter in the vector to be used.

Methods

Three promoters known to be active in macrophage were selected and cloned in mammalian expressing vector (pAcGFP1-N1) to reconstruct (pAcGFP-MS), (pAcGFP-EMR) and (pAcGFP-B5I) with macrosialin, EmrI and Beta-5 Integrin promoters respectively. As a positive control (pAcGFP-CMV) was used with CMV promoter and promoterless vector (pAcGFP-NIX) which served as a negative control. GFP gene was used as readout under the control of each of the promoter. The expression of GFP was analyzed on macrophage and non-macrophage cell lines using Flow cytometry and qRT-PCR with TaqMan probe chemistries.

Results

All the promoters in question were dominant to macrophage lineage cell lines as observed by fluorescence, Western blot and quantitative RT-PCR. The activity of macrosialin was significantly higher than other macrophage promoters. CMV promoter showed 1.83 times higher activity in macrophage cell lines. The expression of GFP driven by macrosialin promoter after 24 hours was 4.40 times higher in macrophage derived cell lines in comparison with non macrophage cell lines.

Conclusions

Based on this study, macrosialin promoter can be utilized for targeting macrophage dominant expression. In vivo study needs to be carried out for its utility as a vaccine candidate.     

Expert Views on Regulatory Preparedness for Managing the Risks of Nanotechnologies

The potential and promise of nanotechnologies depends in large part on the ability for regulatory systems to assess and manage their benefits and risks. However, considerable uncertainty persists regarding the health and environmental implications of nanomaterials, hence the capacity for existing regulations to meet this challenge has been widely questioned. Here we draw from a survey (N=254) of US-based nano-scientists and engineers, environmental health and safety scientists, and regulatory scientists and decision-makers, to ask whether nano experts regard regulatory agencies as prepared for managing nanomaterial risks. We find that all three expert groups view regulatory agencies as unprepared. The effect is strongest for regulators themselves, and less so for scientists conducting basic, applied, or health and safety work on nanomaterials. Those who see nanotechnology risks as novel, uncertain, and difficult to assess are particularly likely to see agencies as unprepared. Trust in regulatory agencies, views of stakeholder responsibility regarding the management of risks, and socio-political values were also found to be small but significant drivers of perceived agency preparedness. These results underscore the need for new tools and methods to enable the assessment of nanomaterial risks, and to renew confidence in regulatory agencies’ ability to oversee their growing use and application in society.     

pH-Dependent Changes in Photoaffinity Labeling Patterns of the H1 Influenza Virus Hemagglutinin by Using an Inhibitor of Viral Fusion

The hemagglutinin (HA) protein undergoes a low-pH-induced conformational change in the acidic milieu of the endosome, resulting in fusion of viral and cellular membranes. A class of compounds that specifically interact with the HA protein of H1 and H2 subtype viruses and inhibit this conformational change was recently described (G. X. Luo et al., Virology 226:66–76, 1996, and J. Virol. 71:4062–4070, 1997). In this study, purified HA trimers (bromelain-cleaved HA [BHA]) are used to examine the properties and binding characteristics of these inhibitors. Compounds were able to inhibit the low-pH-induced change of isolated trimers, as detected by resistance to digestion with trypsin. Protection from digestion was extremely stable, as BHA-inhibitor complexes could be incubated for 24 h in low pH with almost no change in BHA structure. One inhibitor was prepared as a radiolabeled photoaffinity analog and used to probe for specific drug interactions with the HA protein. Analysis of BHA after photoaffinity analog binding and UV cross-linking revealed that the HA2 subunit of the HA was specifically radiolabeled. Cross-linking of the photoaffinity analog to BHA under neutral (native) pH conditions identified a stretch of amino acids within the α-helix of HA2 that interact with the inhibitor. Interestingly, cross-linking of the analog under acidic conditions identified a different region within the HA2 N terminus which interacts with the photoaffinity compound. These attachment sites help to delineate a potential binding pocket and suggest a model whereby the BHA is able to undergo a partial, reversible structural change in the presence of inhibitor compound.Influenza virus contains a lipid envelope that must fuse with host cell membranes in order to initiate virus infection (42, 43, 49). The hemagglutinin (HA) protein, a trimeric glycoprotein embedded in the viral membrane, is responsible for specific binding to cell surface sialic acid-containing receptors (46) and for the fusion of the two membranes (51). Although the mechanism of viral fusion is not fully elucidated, it is known that the fusion event is preceded by a conformational change occurring in the HA trimer that is triggered by the decreasing pH encountered during endosomal passage of the virus (23, 43, 49, 50). The HA trimer is composed of three identical monomers, each containing two protein subunits (designated HA1 and HA2) attached to each other via a disulfide linkage (36, 52). These monomer subunits are formed from a single chain precursor HA (HA0) that undergoes cleavage during transport from the Golgi to the cell surface (27). Entry of the influenza virus into host cells is facilitated through receptor binding by the HA1 subunit to the sialic acid-containing receptor. The conformational change brought on by the low pH of the endosome exposes the hydrophobic amino terminus of the HA2 subunit, which is believed to be a trigger in the fusion process (8, 17, 19, 40). It is postulated that the native state of the HA is a spring-loaded coiled coil and upon acidification, the hydrophobic fusion peptide is translocated toward the target membrane (9–11). This exposed hydrophobic amino terminus is believed to mediate fusion with the cell membrane (8, 19).Influenza virus HA can be cleaved from viral membrane surfaces with bromelain protease to create a soluble form of the protein (bromelain-cleaved HA [BHA]) (5, 52). The soluble HA remains a trimer with properties identical to those of the native membrane bound protein (44). Upon acidification, BHA undergoes a conformational change and forms rosettes caused by the aggregation of the exposed hydrophobic fusogenic domains of the HA2 subunit (14, 40). In this conformation, the BHA is susceptible to trypsin digestion, while it is resistant to this protease in its native conformation (15, 40).We have previously reported on the identification of a class of compounds that can inhibit influenza virus fusion (29, 30). These compounds are able to inhibit the low pH induced conformational change in the HA protein of H1 and H2 subtype viruses but not of the H3 subtype virus. Of these three subtypes, precise structural information is available only for H3 HA (8, 20, 37, 38, 45, 48). Previously a model of H1 HA was constructed using H3 HA crystal structure data (52) and a potential fusion inhibitor-binding pocket was identified within HA2 based on resistant mutation analysis and inhibitor selectivity (30). In order to probe this binding model and better understand the mechanism of action of these compounds, experiments were carried out with isolated H1 BHA. Various analogs were able to protect BHA from protease digestion following acid treatment and subsequent neutralization. A radiolabeled analog which possessed a photoactivatable azide moiety was synthesized (16). Affinity labeling at a neutral or acidic pH produced very different profiles of labeled amino acids, although in each case the amino acids were in or near the proposed binding pocket in the HA2. The consequences of the differences in HA2 photoaffinity labeling patterns with regard to the mechanism of action of these fusion inhibitors are discussed below.     

Inhibitors of HIV-1 attachment. Part 2: An initial survey of indole substitution patterns

The effects of introducing simple halogen, alkyl, and alkoxy substituents to the 4, 5, 6 and 7 positions of 1-(4-benzoylpiperazin-1-yl)-2-(1H-indol-3-yl)ethane-1,2-dione, an inhibitor of the interaction between HIV gp120 and host cell CD4 receptors, on activity in an HIV entry assay was examined. Small substituents at C-4 generally resulted in increased potency whilst substitution at C-7 was readily tolerated and uniformly produced more potent HIV entry inhibitors. Substituents deployed at C-6 and, particularly, C-5 generally produced a modest to marked weakening of potency compared to the prototype. Small alkyl substituents at N-1 exerted minimal effect on activity whilst increasing the size of the alkyl moiety led to progressively reduced inhibitory properties. These studies establish a basic understanding of the indole element of the HIV attachment inhibitor pharmacophore.     

Sequences in attB that affect the ability of phiC31 integrase to synapse and to activate DNA cleavage

Phage integrases are required for recombination of the phage genome with the host chromosome either to establish or exit from the lysogenic state. ϕC31 integrase is a member of the serine recombinase family of site-specific recombinases. In the absence of any accessory factors integrase is unidirectional, catalysing the integration reaction between the phage and host attachment sites, attP × attB to generate the hybrid sites, attL and attR. The basis for this directionality is due to selective synapsis of attP and attB sites. Here we show that mutations in attB can block the integration reaction at different stages. Mutations at positions distal to the crossover site inhibit recombination by destabilizing the synapse with attP without significantly affecting DNA-binding affinity. These data are consistent with the proposal that integrase adopts a specific conformation on binding to attB that permits synapsis with attP. Other attB mutants with changes close to the crossover site are able to form a stable synapse but cleavage of the substrates is prevented. These mutants indicate that there is a post-synaptic DNA recognition event that results in activation of DNA cleavage.