Virogenomics: a novel approach to antiviral drug discovery

Target discovery in virology has been limited to the few open-reading frames encoded by viral genomes. However, several recent examples show that inhibiting host-cell proteins can prevent viral infection. The human genome sequence should, therefore, contain many more genes that are essential for viral propagation than viral genomes. A systematic approach to find these potential cellular antiviral targets is global host gene expression analysis using DNA microarrays. Several recent studies reveal both unique and common strategies by which viruses change the gene expression profile of the host cell. Moreover, work in progress shows that some of the host pathways discovered by expression profiling are important for viral replication. Thus, human genomics tools have the potential to deliver novel antiviral drugs.     

Developing broadly reactive HIV-1/AIDS vaccines: a review of polyvalent and centralized HIV-1 vaccines

The development of an HIV/AIDS vaccine requires consideration of the large diversity of viral isolates. In 2005, there were 5 million new cases of HIV infection and over 4 million deaths due to AIDS. An HIV vaccine is needed to prevent the spread of this virus. One of the greatest challenges to developing a preventative HIV vaccine is the diversity of HIV-1 isolates. Env sequences can differ by as much as 35% between isolates from different clades and by as much as 10% within a clade. Two main strategies to address viral diversity for HIV vaccine development are the use of polymeric- or centralized-based immunogens. Polymeric-based vaccines, which have been used for polio and pneumococcus vaccines, use components from a range of viral isolates to increase the breadth of immune recognition. Centralized sequences decrease the sequence diversity by encoding the most common amino acid at each position from a diverse pool of viral isolates. These sequences are derived using the consensus, center-of-the-tree, or ancestral methods. The use of polyvalent- and centralized-based vaccines induce broadly reactive immune responses, however it is unclear whether the use of these sequences will increase protection against diverse HIV-1 infection. This review will summarize the current uses of polyvalent and centralized vaccines to increase immune breadth that may determine future directions for HIV-1 vaccine development.     

Inhibitors of 3C cysteine proteinases from Picornaviridae

The Picornaviridae are among the smallest icosahedral positive-sense single stranded RNA containing viruses known, and comprise one of the largest and most important families of human and animal pathogens. The hepatitis A virus (HAV) and human rhinovirus (HRV) are important pathogens that belong to the picornavirus family. All picornaviruses have a 3C proteinase that processes an initially biosynthesized precursor protein and is crucial for viral maturation and replication. Although it is a cysteine proteinase, this 3C enzyme has a topology similar to those of the chymotrypsin-like serine proteinases. A series of inhibitors of HAV and HRV 3C proteinases were synthesized and tested as potential lead compounds for the design of therapeutic agents for human picornaviral pathogens. This research shows that thiol-reactive groups or "warheads" such as iodoacetamides, beta-lactones, Michael acceptors, ketones and pseudoxazolones can be used as effective tools to inhibit the HAV and HRV 3C proteinase enzymes. In addition, studies based on enzyme-inhibitor kinetics, mass spectrometry and NMR spectroscopy were effectively used to gain knowledge concerning enzyme-inhibitor mechanism of action and enzyme-inhibitor regiospecific reactivity.     

Arenaviruses other than Lassa virus

The family Arenaviridae includes 23 viral species, of which 5 can cause viral hemorrhagic fevers with a case fatality rate of about 20%. These five viruses are Junin, Machupo, Guanarito, Sabia and Lassa virus, the manipulation of which requires biosafety level 4 facilities. They are included in the Category A Pathogen List established by the Center for Disease Control and Prevention that groups agents with the greatest potential for adverse public health impact and mass casualties whether a situation characterized by a ill-intentioned abuse of natural or engineered arenavirus would be encountered. The aims of this article are to (i) summarize the current situation; (ii) provide information to help anticipating the effects to be expected in such a situation; and to (iii) emphasize the need for fundamental research to allow the development of diagnostic, prevention and therapeutic tools as countermeasures to weaponized arenaviruses.     

Identification of neuraminidase inhibitors by structure-based screening: promising new leads for influenza

Human influenza commonly known as seasonal flu which is caused by a RNA virus has been emerging as a major viral infection over the years. Virus neuraminidase inhibitors and M2 protein inhibitors are the agents which have been used to treat this viral infection. Among these two, viral neuraminidases named oseltamivir and zanamivir are most widely used as antiviral agents to treat influenza. But the recent emergence of resistance strains in the treatment with both zanamivir and oseltamivir creates a big problem to treat this viral infection effectively. In this study, we have designed 68 new human influenza virus neuraminidase inhibitors and reported them as new potential antiviral agents against the complex structure of influenza virus neuraminidase and sialic acid using various in silico tools and molecular docking analysis taking zanamivir as prototype.     

HIV vaccine candidates

Amino acid sequences of the HIV-1 surface protein gp120 show extensive variations. Some of the peptide or DNA vaccines using the V3-loop of gp120 can trigger antibody production against some isolates of HIV, but these antibodies are not protective against other isolates. Thus, more conserved peptides from other HIV proteins have also been tried as vaccines. However, antibodies specific for these peptides cannot prevent the normal entry of HIV into the host cells, followed by integration of viral genomes into host chromosomes. Therefore, we decided to make a careful analysis of the aligned amino acid sequences of gp120 stored at Los Alamos National Laboratory. Unexpectedly, we found that there are several, not just one or two, segments of seven or more consecutive and nearly invariant amino acid residues present in the C1, C2 and C5 regions of this protein. Furthermore, four of these segments are physically close to each other in the known three-dimensional structure of the core portion of gp120. The remaining segments are not in that crystallized region; however, two of these are covalently linked with a disulfide bond. Therefore, we propose that these segments may be combined to form the basis of possible HIV vaccine candidates. In addition, it is necessary to incorporate the processed peptide from gp120 or other proteins and to understand the time-dependent effects of the highly variable loops of gp120 on triggering antibody production in human patients.     

Viruses of the Bunya- and Togaviridae families: potential as bioterrorism agents and means of control

When considering viruses of potential importance as tools for bioterrorism, several viruses in the Bunya- and Togaviridae families have been cited. Among those in the Bunyaviridae family are Rift Valley fever, Crimean-Congo hemorrhagic fever, hanta, and sandfly fever viruses, listed in order of priority. Those particularly considered in the Togaviridae family are Venezuelan, eastern and western equine encephalitis viruses. Factors affecting the selection of these viruses are the ability for them to induce a fatal or seriously incapacitating illness, their ease of cultivation in order to prepare large volumes, their relative infectivity in human patients, their ability to be transmitted by aerosol, and the lack of measures available for their control. Each factor is fully considered in this review. Vaccines for the control of infections induced by these viruses are in varying stages of development, with none universally accepted to date. Viruses in the Bunyaviridae family are generally sensitive to ribavirin, which has been recommended as an emergency therapy for infections by viruses in this family although has not yet been FDA-approved. Interferon and interferon inducers also significantly inhibit these virus infections in animal models. Against infections induced by viruses in the Togaviridae family, interferon-alpha would appear to currently be the most useful for therapy.     

Targeting herpesvirus reliance of the chemokine system

Viral infections depend on an intimate relationship between the infectious agent and the host cells. Viruses need the host cells for replication, while the innate- and adaptive- immunesystem of the host is fighting to kill the infected cell in order to clear out the pathogen and survive the infection. However, since both virus and host exist, the organisms struggle must reach an ecological equilibrium. Among the best-studied interactions between viruses and the host immune system are those between herpesviruses and their hosts. Herpesviruses are known to devote a significant part of their large genomes on immuno-modulatory genes, some encoding chemokines or chemokine receptors. These genes, which may be dispensable for viral replication in vitro, are highly important for viral growth in vivo, for viral dissemination and disease progression. Indeed, all beta and gamma-herpesviruses have acquired homologs of both chemokines and chemokine receptors belonging to the 7 transmembrane (7TM) spanning, G protein-coupled receptor family. 7TM receptors are very efficient drug targets and are currently the most popular class of investigational drug targets. A notable trait for the virus encoded chemokine receptors seems to be their constitutive activity. The biological function of the constitutive activity is still unclear, but it has become clear that the receptors are involved in important parts of the viral lifecycle in vivo, and that the receptor signaling is involved in gamma-herpesvirus mediated cell transformation. Therefore, blocking the signaling of these receptors will provide an efficient and highly specific way to inhibit viral replication in vivo and disease progression in the hosts.     

Section Review Anti-infectives: Developments in viral hepatitis during 1995

The discovery of hepatitis C virus (HCV) in 1987 and the subsequent development of diagnostic tests has accounted for the majority of cases of viral hepatitis throughout the world. However, a significant number of cases cannot be assigned to any of the viral hepatitis groups (A - E). During 1995 two companies reported the identification of novel hepatitis viruses known as GBV-B and hepatitis G virus (HGV), which were found to be responsible for a large proportion of the remaining undiagnosed cases. Sequence analysis of these two viruses revealed them to be isolates of the same virus and, moreover, to be close homologues of HCV. The clinical significance of these new viruses is currently unclear, but preliminary epidemiologic evidence suggests they are often found as co-infections with HCV. The close similarity of these viruses to HCV and the fact that related viruses have also been identified which infect small primates, suggests that they may be useful as surrogate agents for the identification of novel therapeutic agents against HCV. Current therapeutic agents against HCV are still disappointing although more encouraging data have been reported on long-term combination therapy with interferon-′ and ribavirin. Studies have continued aimed towards developing assays for biochemical functions specified by viral proteins and these are stili mainly focused on the multi-functional NS3 protein.     

Strand-specific silencing of a picornavirus by RNA interference: evidence for the superiority of plus-strand specific siRNAs

RNA interference triggered by small interfering RNAs (siRNAs) can be used to effectively contain viral spread. Here, we report on the mechanism of action of siRNAs targeting the medically important coxsackievirus B3 (CVB-3) as a typical representative of viruses with a non-segmented RNA genome in positive-strand orientation. Antiviral siRNAs can be designed to target the genomic (+)-strand, the (-)-strand that occurs as a replication intermediate, or both. In the present study, two complementary and systematic approaches are presented providing direct evidence that silencing of the viral (+)-strand is the key to inhibit CVB-3: first, we used rational siRNA design to direct silencing activity specifically against either of the two viral strands. As a second approach, we employed siRNA containing modified nucleotides to render them specific for one of the virus RNAs. Experiments with infectious coxsackievirus revealed that the inhibitory efficiency correlates exclusively with the activity of the siRNAs directed against the viral (+)-strand. Our finding that only (+)-strand specific siRNAs exert significant antiviral potency may hold true for other RNA viruses with (+)-stranded genomes as well and may therefore be helpful in the development of efficient strategies to inhibit virus propagation.     

Viral safety of biologicals

The viral safety of biologicals, either human blood derivatives or animal products or recombinant proteins issued from biotechnology, relies on the quality of the starting material, the manufacturing process and, if necessary, the control of the final product. The quality of the starting material is highly guaranteed for blood derivatives due to the individual screening for specific markers (antigens, genome, antibodies) for major blood borne viruses such as hepatitis B and C viruses (HBV, HCV) and human immunodeficiency virus (HIV). It can be reinforced by the detection through amplification procedures (polymerase chain reaction) in the plasma pool of genomes from viruses that have been implicated in contaminations of blood derivatives in the past (parvovirus B19, hepatitis A virus). The association in the manufacturing process of different steps dedicated to purification of plasma proteins (partitioning), virus inactivation (solvent/detergent treatment, heat inactivation) or specific procedures allowing virus removal (nanofiltration) allows to reduce the viral risk very efficiently. The validation studies using scaled down systems and model viruses allow to evaluate the virus safety of any product quantitatively. The aim of these procedures is to guarantee the lack of infectivity due to any virus, either known or unknown.     

Tritiated D-ala1-peptide T binding: A pharmacologic basis for the design of drugs which inhibit HIV receptor binding

The HIV virus initiates its infectious cycle through a high-affinity binding interaction between the envelope protein gp 120 and its receptor, the T4 (or CD4) molecule. An octapeptide sequence, termed peptide T, present in the second variable region of gp 120 from the ARV isolate, has been implicated as the attachement site. The core peptide required for activity has been further refined to a pentapeptide, and homologous pentapeptides are similarly positioned in 21 other sequenced HIV isolates. Utilizing a novel direct binding assay of ³H-D-ala¹-peptide T, we now report that synthetic peptides derived from these other isolates are potent competitors of peptide T binding to T4-positive lymphocytes and brain membranes. Direct peptide T binding is also competable by purified virion gp 120, indicating that these ligands are interactive at the same receptor. Peptide T has sequence relatedness to the peptide vasoactive intestinal peptide (VIP), and VIP and its relevant homologous pentapeptide, VIP[7–11], are also potent inhibitors of peptide T binding. To determine the essential structural features responsible for receptor activity we have studied a series of synthetic peptides substituted with single D-amino acid residues. These data reveal that the tyrosine of position 7 in peptide T, present in all natural viral isolates, is obligate for receptor activity. Structure/function analysis for a large number of analogs is presented. Significantly, this binding assay is highly correlated with peptide bioactivity in several independent systems, indicating that this methodology can be used for rapid screening of novel, potential anti-AIDS therapeutics whose target is inhibition of virus gpl20 binding.     

A survey of metabolic databases emphasizing the MetaCyc family

Thanks to the confluence of genome sequencing and bioinformatics, the number of metabolic databases has expanded from a handful in the mid-1990s to several thousand today. These databases lie within distinct families that have common ancestry and common attributes. The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases. The MetaCyc family is described in particular detail. It contains well over 1,000 databases, including highly curated databases for Escherichia coli, Saccharomyces cerevisiae, Mus musculus, and Arabidopsis thaliana. These databases are available through a number of web sites that offer a range of software tools for querying and visualizing metabolic networks. These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets.     

Fast small molecule similarity searching with multiple alignment profiles of molecules represented in one-dimension

Multiple sequence alignment has proven to be a powerful method for creating protein and DNA sequence alignment profiles. These profiles of protein families are useful tools for identifying conserved motifs, such as the catalytic triad of the serine protease family or the seven transmembrane helices of the G-protein coupled receptor family. Ultimately, the understanding of the critical motifs within a family is useful for identifying new members of the family. Due to the complexity of protein-ligand recognition, no universally accepted method exists for clustering small molecules into families with the same or similar biological activity. A combination of the concept of multiple sequence alignment and the 1-dimensional molecular representation described earlier offers a new method for profiling sets of small molecules with the same biological activity. These small molecule profiles can isolate key commonalities within the set of bioactive compounds much like a multiple sequence alignment can isolate critical motifs within a protein family. The small molecule profiles then make useful tools for searching small molecule databases for new compounds with the same biological activity. The technique is demonstrated here using the human ether-a-go-go potassium channel and the kinase SRC.     

Comparative genomics for the investigation of autoimmune diseases

The complete DNA sequence of the human genome and of several related mammals are now available, due to the investments of enormous resources and advances in sequencing technology. Novel technologies have been developed to compare multiple genomes with each other, thus specifying regions of sequence similarity among mammals and with their pathogens. Larger blocks of sequence similarity (syntenic regions) have been determined and made publicly available. In many ways, novel insights can be gained by such data when combining external genetic or clinical information for these syntenic loci. These novel tools have proven to be successful in inferring functional equivalence between loci of multiple genomes. This review reports on the role of comparative genomics in research on autoimmune diseases, a field with strong dependencies on animal models of human diseases and the problem of an adequate information transfer between multiple organisms and research areas.     

Viral vectors for gene transfer: a review of their use in the treatment of human diseases

The efficient delivery of therapeutic genes and appropriate gene expression are the crucial issues for clinically relevant gene therapy. Viruses are naturally evolved vehicles which efficiently transfer their genes into host cells. This ability made them desirable for engineering virus vector systems for the delivery of therapeutic genes. The viral vectors recently in laboratory and clinical use are based on RNA and DNA viruses processing very different genomic structures and host ranges. Particular viruses have been selected as gene delivery vehicles because of their capacities to carry foreign genes and their ability to efficiently deliver these genes associated with efficient gene expression. These are the major reasons why viral vectors derived from retroviruses, adenovirus, adeno-associated virus, herpesvirus and poxvirus are employed in more than 70% of clinical gene therapy trials worldwide. Among these vector systems, retrovirus vectors represent the most prominent delivery system, since these vectors have high gene transfer efficiency and mediate high expression of therapeutic genes. Members of the DNA virus family such as adenovirus-, adeno-associated virus or herpesvirus have also become attractive for efficient gene delivery as reflected by the fast growing number of clinical trials using these vectors. The first clinical trials were designed to test the feasibility and safety of viral vectors. Numerous viral vector systems have been developed for ex vivo and in vivo applications. More recently, increasing efforts have been made to improve infectivity, viral targeting, cell type specific expression and the duration of expression. These features are essential for higher efficacy and safety of RNA- and DNA-virus vectors. From the beginning of development and utilisation of viral vectors it was apparent that they harbour risks such as toxicities, immunoresponses towards viral antigens or potential viral recombination, which limit their clinical use. However, many achievements have been made in vector safety, the retargeting of virus vectors and improving the expression properties by refining vector design and virus production. This review addresses important issues of the current status of viral vector design and discusses their key features as delivery systems in gene therapy of human inherited and acquired diseases at the level of laboratory developments and of clinical applications.     

Discovery of small molecule inhibitors of West Nile virus using a high-throughput sub-genomic replicon screen

West Nile virus (WNV) is a positive-sense, single-stranded RNA virus of the family Flaviviridae. WNV persistently infects insect cells, but can causes acute cytopathic infection of mammalian cells and is an etiologic agent of viral encephalitis in humans. By using a cell line expressing a WNV subgenomic replicon [Rossi, S.L., Zhao, Q., O'Donnell, V.K., Mason, P.W., 2005. Adaptation of West Nile virus replicons to cells in culture and use of replicon-bearing cells to probe antiviral action. Virology 331 (2), 457-470], we developed a high-throughput assay and used it to screen a library of small molecule compounds for inhibitors of WNV replication in the absence of live virus. Here we report the identification of novel small molecule inhibitors for WNV replicon replication. We demonstrate that the compounds inhibited WNV replication-dependent luciferase expression in the replicon cells and reduced WNV viral protein accumulation and viral RNA copy number in the replicon cells. Two classes of compounds with multiple hits, parazolotrahydrothophenes and pyrozolopyrimidines, showed preliminary structure-activity relationships. In WNV infection assays, one pyrozolopyrimidine compound was confirmed to have antiviral activity. These compounds should be valuable for developing anti-WNV therapeutic drugs as well as research tools to study the mechanism of WNV replication.