A new antiviral scaffold for human norovirus identified with computer-aided approaches on the viral polymerase

Human norovirus is the leading cause of acute gastroenteritis worldwide, affecting every year 685 million people. In about one third of cases, this virus affects children under five years of age, causing each year up to 200,000 child deaths, mainly in the developing countries. Norovirus outbreaks are associated with very significant economic losses, with an estimated societal cost of 60 billion dollars per year. Despite the marked socio-economic consequences associated, no therapeutic options or vaccines are currently available to treat or prevent this infection. One promising target to identify new antiviral agents for norovirus is the viral polymerase, which has a pivotal role for the viral replication and lacks closely homologous structures in the host. Starting from the scaffold of a novel class of norovirus polymerase inhibitors recently discovered in our research group with a computer-aided method, different new chemical modifications were designed and carried out, with the aim to identify improved agents effective against norovirus replication in cell-based assays. While different new inhibitors of the viral polymerase were found, a further computer-aided ligand optimisation approach led to the identification of a new antiviral scaffold for norovirus, which inhibits human norovirus replication at low-micromolar concentrations.status: Published onlin

Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan

CD8+ T cells provide robust antiviral immunity, but how epitope-specific T cells evolve across the human lifespan is unclear. Here we defined CD8+ T cell immunity directed at the prominent influenza epitope HLA-A*02:01-M158–66 (A2/M158) across four age groups at phenotypic, transcriptomic, clonal and functional levels. We identify a linear differentiation trajectory from newborns to children then adults, followed by divergence and a clonal reset in older adults. Gene profiles in older adults closely resemble those of newborns and children, despite being clonally distinct. Only child-derived and adult-derived A2/M158+CD8+ T cells had the potential to differentiate into highly cytotoxic epitope-specific CD8+ T cells, which was linked to highly functional public T cell receptor (TCR)αβ signatures. Suboptimal TCRαβ signatures in older adults led to less proliferation, polyfunctionality, avidity and recognition of peptide mutants, although displayed no signs of exhaustion. These data suggest that priming T cells at different stages of life might greatly affect CD8+ T cell responses toward viral infections

Human CD8+ T cell cross-reactivity across influenza A, B and C viruses

Influenza A, B and C viruses (IAV, IBV and ICV, respectively) circulate globally and infect humans, with IAV and IBV causing the most severe disease. CD8+ T cells confer cross-protection against IAV strains, however the responses of CD8+ T cells to IBV and ICV are understudied. We investigated the breadth of CD8+ T cell cross-recognition and provide evidence of CD8+ T cell cross-reactivity across IAV, IBV and ICV. We identified immunodominant CD8+ T cell epitopes from IBVs that were protective in mice and found memory CD8+ T cells directed against universal and influenza-virus-type-specific epitopes in the blood and lungs of healthy humans. Lung-derived CD8+ T cells displayed tissue-resident memory phenotypes. Notably, CD38+Ki67+CD8+ effector T cells directed against novel epitopes were readily detected in IAV- or IBV-infected pediatric and adult subjects. Our study introduces a new paradigm whereby CD8+ T cells confer unprecedented cross-reactivity across all influenza viruses, a key finding for the design of universal vaccines

Cross-genotypic examination of hepatitis c virus polymerase inhibitors reveals a novel mechanism of action for thumb binders

Direct-acting antivirals (DAAs) targeting proteins encoded by the hepatitis C virus (HCV) genome have great potential for the treatment of HCV infections. However, the efficacy of DAAs designed to target genotype 1 (G1) HCV against non-G1 viruses has not been characterized fully. In this study, we investigated the inhibitory activities of nonnucleoside inhibitors (NNIs) against the HCV RNA-dependent RNA polymerase (RdRp). We examined the ability of six NNIs to inhibit G1b, G2a, and G3a subgenomic replicons in cell culture, as well as in vitro transcription by G1b and G3a recombinant RdRps. Of the six G1 NNIs, only the palm II binder nesbuvir demonstrated activity against G1, G2, and G3 HCV, in both replicon and recombinant enzyme models. The thumb I binder JTK-109 also inhibited G1b and G3a replicons and recombinant enzymes but was 41-fold less active against the G2a replicon. The four other NNIs, which included a palm I binder (setrobuvir), two thumb II binders (lomibuvir and filibuvir), and a palm β-hairpin binder (tegobuvir), all showed at least 40-fold decreases in potency against G2a and G3a replicons and the G3a enzyme. This antiviral resistance was largely conferred by naturally occurring amino acid residues in the G2a and G3a RdRps that are associated with G1 resistance. Lomibuvir and filibuvir (thumb II binders) inhibited primer-dependent but not de novo activity of the G1b polymerase. Surprisingly, these compounds instead specifically enhanced the de novo activity at concentrations of >100 nM. These findings highlight a potential differential mode of RdRp inhibition for HCV NNIs, depending on their prospective binding pockets, and also demonstrate a surprising enhancement of de novo activity for thumb RdRp binders. These results also provide a better understanding of the antiviral coverage for these polymerase inhibitors, which will likely be used in future combinational interferon-free therapies

Non-nucleoside inhibitors of viral RNA polymerases; scaffolds for rational drug design

The hepatitis C virus (HCV) and norovirus (NoV) are significant human pathogens posing a substantial health and economic burden in both developing and developed countries. Controlling the spread of these viruses through the development of both vaccines and antivirals has proven to be difficult, partly because of the refractoriness in growing these viruses in cell culture. The current standard treatment for HCV is expensive, poorly tolerated, has a long duration, and is only partly effective. Although new direct-acting antivirals (DAA) are entering clinical treatment, these emerging molecules have been mainly targeted against one of six HCV genotypes, namely G1. Conversely, there are no antivirals for the treatment of chronic NoV infections, or for use as a prophylactic measure in an outbreak setting, which typically affects hospitals, nursing homes and other enclosed environments. The viral RNA-dependent RNA polymerases (RdRp) of HCV and NoV are prime targets for antiviral development, given their crucial role for the viral replication, and the absence of a homologous human enzyme. This study describes the discovery and characterisation of the first non-nucleoside inhibitors (NNI) specifically targeted against the RdRp of HCV G3a, a neglected but increasingly important genotype of HCV. Chemical scaffolds and derivatives were identified with low micromolar inhibitory activity against recombinant RdRp, and the HCV replicon cell culture model. Furthermore, the efficacy of previously identified inhibitors against the HCV G3a RdRp was examined, and a novel mechanism of enhancement of de novo transcription was discovered for a subclass of these antivirals; the T2 and P-β binding NNIs. This study also describes the high-throughput identification of the first four NoV-directed NNI scaffolds, which provide a strong platform for future rational drug design for antivirals against another pathogen with thus far limited control measure

Inhibitors of the hepatitis C virus polymerase; mode of action and resistance

The hepatitis C virus (HCV) is a pandemic human pathogen posing a substantial health and economic burden in both developing and developed countries. Controlling the spread of HCV through behavioural prevention strategies has met with limited success and vaccine development remains slow. The development of antiviral therapeutic agents has also been challenging, primarily due to the lack of efficient cell culture and animal models for all HCV genotypes, as well as the large genetic diversity between HCV strains. On the other hand, the use of interferon-α-based treatments in combination with the guanosine analogue, ribavirin, achieved limited success, and widespread use of these therapies has been hampered by prevalent side effects. For more than a decade, the HCV RNA-dependent RNA polymerase (RdRp) has been targeted for antiviral development. Direct acting antivirals (DAA) have been identified which bind to one of at least six RdRp inhibitor-binding sites, and are now becoming a mainstay of highly effective and well tolerated antiviral treatment for HCV infection. Here we review the different classes of RdRp inhibitors and their mode of action against HCV. Furthermore, the mechanism of antiviral resistance to each class is described, including naturally occurring resistance-associated variants (RAVs) in different viral strains and genotypes. Finally, we review the impact of these RAVs on treatment outcomes with the newly developed regimens

Gestational diabetes mellitus: a model for the genetics of type 2 diabetes

The striking similarity between Gestational Diabetes Mellitus (GDM) and Type 2 Diabetes (T2D) in terms of the pathophysiologies and the risk factors has led to the hypothesis that GDM is an early manifestation of T2D, expressed under the stress of pregnancy, and therefore both diseases should share similar susceptibility genes. GDM patients may provide a more homogeneous sample for the genetic causes of the disease than T2D, and therefore make a useful group for the identification of the genes involved. Over 200 GDM affected sib-pairs from 178 families were investigated, with parents available in 40% of cases.Genomic regions from 4 different chromosomes, 6, 8, 14 and 18 were chosen from regions that showed clustering for positive linkage scores in previous linkage studies on T2D and one control region on 13, where no previous positive linkage was reported. A total of 19 microsatellite markers were analysed for linkage to GDM using sib-pair analysis. Subset analyses were performed by ranking sib-pairs on GDM-related variables, e.g. mean BMI of sibs, age at GDM episode, etc. GENEHUNTER was run multiple times, each time including the next highest ranked family in the analysis. This gave a continuous range of scores where increasing or decreasing NPL scores indicated heterogeneity associated with different environmental factors such as age and weight. To evaluate the significance of the subset analyses, the results were compared to 10,000 permutations generated by randomly ranking the sib-pairs.Using the entire dataset, the analysis showed no significant linkage to a disease locus. Positive evidence for linkage was found with the subset analysis on chromosomes 8 and 14, suggesting heterogeneity between sib-pairs in the dataset. Marker D8S1742 on 8p23 showed an NPL score of 3.01 (p=0.001) when age at GDM diagnosis was used as a covariate. Using waist-to-hip ratio (WHR), marker D14S275 on 14q12 showed an NPL score of 2.474 (p=0.006). When adjusted for multiple testing, the results were not statistically significant for linkage to a diabetes disease locus, but gave evidence that GDM and T2D share similar genetic determinants, and defined groups of siblings for follow-up analysis of both types of diabetes

Envelope-specific IgG3 and IgG1 responses are associated with clearance of acute hepatitis C virus infection

Hepatitis C virus (HCV) can be cleared naturally in a subset of individuals. However, the asymptomatic nature of acute HCV infection makes the study of the early immune response and defining the correlates of protection challenging. Despite this, there is now strong evidence implicating the humoral immune response, specifically neutralising antibodies, in determining the clearance or chronicity outcomes of primary HCV infection. In general, immunoglobulin G (IgG) plays the major role in viral neutralisation. However, there are limited investigations of anti-HCV envelope protein 2 (E2) isotypes (IgM, IgG, IgA) and IgG subclasses (IgG1–4) in early HCV infection. In this study, using a rare cohort of 14 very recently HCV-infected individuals (4–45 days) with varying disease outcome (n = 7 clearers), the timing and potency of anti-HCV E2 isotypes and IgG subclasses were examined longitudinally, in relation to neutralising antibody activity. Clearance was associated with anti-E2 IgG, specifically IgG1 and IgG3, and appeared essential to prevent the emergence of new HCV variants and the chronic infection outcome. Interestingly, these IgG responses were accompanied by IgM antibodies and were associated with neutralising antibody activity in the subjects who cleared infection. These findings provide novel insights into the early humoral immune response characteristics associated with HCV disease outcome