New antivirals for herpesviruses

The long-term treatment of herpesvirus infections with current antivirals leads to the development of drug-resistant viruses. Because currently available antivirals finally target the viral DNA polymerase, mutant resistant to one drug often shows cross-resistance to other drugs. This evidence highlights the need for the development of new antivirals that have the different viral targets. Recently, high-through-put screening of large compound collections for inhibiting specific viral enzymes, or in vitro cell culture assay, has identified several new antivirals. These include the inhibitors of helicase/primase complex, terminase complex, portal protein and UL97 protein kinase. This review will focus on these new compounds that directly inhibit viral replication.     

Extending human IgG half-life using structure-guided design

Engineering of antibodies for improved pharmacokinetics through enhanced binding to the neonatal Fc receptor (FcRn) has been demonstrated in transgenic mice, non-human primates and humans. Traditionally, such approaches have largely relied on random mutagenesis and display formats, which fail to address related critical attributes of the antibody, such as effector functions or biophysical stability. We have developed a structure- and network-based framework to interrogate the engagement of IgG with multiple Fc receptors (FcRn, C1q, TRIM21, FcγRI, FcγRIIa/b, FcγRIIIa) simultaneously. Using this framework, we identified features that govern Fc-FcRn interactions and identified multiple distinct pathways for enhancing FcRn binding in a pH-specific manner. Network analysis provided a novel lens to study the allosteric impact of half-life-enhancing Fc mutations on FcγR engagement, which occurs distal to the FcRn binding site. Applying these principles, we engineered a panel of unique Fc variants that enhance FcRn binding while maintaining robust biophysical properties and wild type-like binding to activating receptors. An antibody harboring representative Fc designs demonstrates a half-life improvement of > 9 fold in transgenic mice and > 3.5 fold in cynomolgus monkeys, and maintains robust effector functions such as antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity.     

Recent applications of protein crystallography and structure-guided drug design

Technological advances to increase the throughput of purified protein production and co-crystallization of target proteins with small molecules have helped to solidify the role that structure via crystallography has on drug discovery. Visualization of how drug-like molecules bind to the target protein is a key step in driving follow-up or preclinical chemistry to improve characteristics of the molecule. Using structural information to guide small-molecule design and generate new chemical ideas is now a mainstay in the drug discovery process.     

New strategies for the design of catalytic antibodies.

A new approach is advanced which is aimed at expanding the scope of antibody catalysis. It entails the design and synthesis of haptens that will elicit antibodies to catalyze acyl transfer reactions by a methodology which we term "bait and switch" catalysis. What we have done involves the placement of a point charge on the hapten in close proximity to, or in direct substitution for, a chemical functional group we wish to transform in the respective substrate. The haptenic charge should induce a complementary charge (on an amino acid residue) at the binding site. The substrate will lack this charge but will retain a similar overall structure. The monoclonal antibodies that bind these substrates now have the potential to act as general acids/bases for substrates having hydrolyzable functional groups.     

New antivirals - mechanism of action and resistance development

In recent years, several novel treatment modalities emerged for a number of virus infections, including lamivudine for hepatitis B virus, abacavir, adefovir dipivoxyl and apropovir disprometil for human immunodeficiency virus, cidofovir for cytomegalovirus, and famciclovir (the oral prodrug of penciclovir) and cidofovir for other herpesviruses (i.e. herpes simplex virus and varicella-zoster virus). For all drugs, resistance eventually develops upon prolonged administration to the infected individuals, albeit at a varying extent. In addition, new mutations related to multidrug resistance have recently been identified.     

Development of novel strategies to control foot-and-mouth disease: Marker vaccines and antivirals

Foot-and-mouth disease (FMD) is economically the most important viral-induced livestock disease worldwide. The disease is highly contagious and FMD virus (FMDV) replicates and spreads extremely rapidly. Outbreaks in previously FMD-free countries, including Taiwan, the United Kingdom, and Uruguay, and the potential use of FMDV by terrorist groups have demonstrated the vulnerability of countries and the need to develop control strategies that can rapidly inhibit or limit disease spread. The current vaccine, an inactivated whole virus preparation, has a number of limitations for use in outbreaks in disease-free countries. We have developed an alternative approach using a genetically engineered FMD subunit vaccine that only contains the portions of the viral genome required for virus capsid assembly and lacks the coding region for most of the viral nonstructural (NS) proteins including the highly immunogenic 3D protein. Thus, animals inoculated with this marker vaccine can readily be differentiated from infected animals using diagnostic assays employing the NS proteins not present in the vaccine and production of this vaccine, which does not contain infectious FMDV, does not require expensive high-containment manufacturing facilities. One inoculation of this subunit vaccine delivered in a replication-defective human adenovirus vector can induce rapid, within 7 days, and relatively long-lasting protection in swine. Similarly cattle inoculated with one dose of this recombinant vector are rapidly protected from direct and contact exposure to virulent virus. Furthermore, cattle given two doses of this vaccine developed high levels of FMDV-specific neutralizing antibodies, but did not develop antibodies against viral NS proteins demonstrating the ability of FMD subunit vaccinated animals to be differentiated from infected animals. To stimulate early protection prior to the vaccine-induced adaptive immune response we inoculated swine with the antiviral agent, type I interferon, and induced complete protection within 1 day. Protection can last for 3-5 days. The combination of the FMD marker vaccine and type I interferon can induce immediate, within 1 day, and long-lasting protection against FMD. Thus, this combination approach successfully addresses a number of concerns of FMD-free countries with the current disease control plan. By rapidly limiting virus replication and spread this strategy may reduce the number of animals that need to be slaughtered during an outbreak.     

Computer-aided model-building strategies for protein design

Model-building strategies for protein modification and design are developed. These strategies emphasize simple geometric aspects of protein structure, use local coordinate systems defined at particular residues, and systematically consider a large number of alternative sequences and conformations. We have written a computer program, PROTEUS, to implement these search methods. PROTEUS has been used to find positions where disulfide bonds could be added to the N-terminal domain of the lambda repressor and to predict how a loop on the surface of repressor could be shortened.     

Computational design strategies for combinatorial libraries

Medicinal chemistry principles are being increasingly applied to the design of smaller, high purity, information-rich libraries. Recent computational advances in statistical methodology, the design of libraries to reduce ADMET problems, targeting protein families and revisiting natural products as sources of inspiration for scaffolds and reagents are all areas of progressive research.     

New hope for an AIDS vaccine

The twenty-first century has begun with considerable success for new AIDS vaccines in macaque models. A common feature of these vaccines is their ability to induce high-frequency CD8+ T-cell responses that control, rather than prevent, infection with HIV. The new vaccines, which include DNA vaccines and live viral vectors, are based on technologies that have been developed since the start of the AIDS epidemic. The ultimate promise of these vaccines will be realized only when efficacy trials in humans are conducted.     

Synthetic biology: new strategies for directing design

The advancement of synthetic biology is thanks, in large part, to continuing improvements in DNA synthesis. The expansion of synthetic biology into the realm of metabolic engineering has shifted the focus from simply making novel synthetic biological parts to answering the question of how we employ these biological parts to construct genomes that ultimately give rise to useful phenotypes. Much like protein engineering, the answer to this will be arrived at following the combination of rational design and evolutionary approaches. This review will highlight some of the new DNA synthesis-enabled search methods and discuss the application of such methods to the creation of synthetic gene networks and genomes.     

New strategies for combating multidrug-resistant bacteria

Antibiotic resistance is a problem that continues to challenge the healthcare sector. In particular, multidrug resistance is now common in familiar pathogens such as Staphylococcus aureus and Mycobacterium tuberculosis, as well as emerging pathogens such as Acinetobacter baumannii. New antibiotics and new therapeutic strategies are needed to address this challenge. Advances in identifying new sources of antibiotic natural products and expanding antibiotic chemical diversity are providing chemical leads for new drugs. Inhibitors of resistance mechanisms and microbial virulence are orthogonal strategies that are also generating new chemicals that can extend the life of existing antibiotics. This new chemistry, coupled with a growing understanding of the mechanisms, origins and distribution of antibiotic resistance, position us to tackle the challenges of antibiotic resistance in the 21st century.     

New strategies for cardiovascular gene therapy

Cardiovascular diseases are among the major targets for gene therapy. Initially, clinical experiments of gene transfer of vascular endothelial growth factor (VEGF) improved vascularization and prevented the amputation in patients with critical leg ischemia. However, the majority of trials did not provide conclusive results and therefore further preclinical studies are required. Importantly, data indicate the necessity of regulated expression of angiogenic factors, particularly VEGF, to obtain the therapeutic effect. It is also suggested that the combined delivery of two or more genes may improve the formation of mature vasculature and therefore may be more effective in the amelioration of ischemia. Moreover, experimental approaches in animal models displayed the promise of gene transfer modulating the inflammatory processes and oxidant status of the cells. Particularly, the concept of preemptive gene therapy has been tested, and recent studies have demonstrated that overexpression of heme oxygenase-1 or extracellular superoxide dismutase can prevent heart injury by myocardial infarction induced several weeks after gene instillation. The combination of a preemptive strategy with regulated gene expression, using the vectors in which the therapeutic transgene is driven by exogenously or endogenously controllable promoter, offers another modality. However, we hypothesize that regulatable gene therapy, dependent on the activity of endogenous factors, might be prone to limitations owing to the potential disturbance in the expression of endogenous genes. Here, we demonstrated some indications of these drawbacks. Therefore, the final acceptance of these promising strategies for clinical trials requires careful validation in animal experiments.     

New strategies for targeting matrix metalloproteinases

The development of matrix metalloproteinase (MMP) inhibitors has often been frustrated by a lack of specificity and subsequent off-target effects. More recently, inhibitor design has considered secondary binding sites (exosites) to improve specificity. Small molecules and peptides have been developed that bind exosites in the catalytic (CAT) domain of MMP-13, the CAT or hemopexin-like (HPX) domain of MT1-MMP, and the collagen binding domain (CBD) of MMP-2 and MMP-9. Antibody-based approaches have resulted in selective inhibitors for MMP-9 and MT1-MMP that target CAT domain exosites. Triple-helical “mini-proteins” have taken advantage of collagen binding exosites, producing a family of novel probes. A variety of non-traditional approaches that incorporate exosite binding into the design process has yielded inhibitors with desirable selectivities within the MMP family.     

New strategies for improving speech enhancement

We describe two design strategies that could substantially improve the performance of speech enhancement systems. Results from a preliminary study of pulse recovery are presented to illustrate the potential benefits of such strategies. The first strategy is a direct application of a non-linear, adaptive signal processing approach for recovery of speech in noise. The second strategy optimizes performance by maximizing the enhancement system's ability to evoke target speech percepts. This approach may lead to better performance because the design is optimized on a measure directly related to the ultimate goal of speech enhancement: accurate communication of the speech percept. In both systems, recently developed ‘neural network’ learning algorithms can be used to determine appropriate parameters for enhancement processing.     

New strategies for conserving tropical forests

In an interval of just 1-2 decades, the nature of tropical forest destruction has changed. Rather than being dominated by rural farmers, tropical deforestation now is substantially driven by major industries and economic globalization, with timber operations, oil and gas development, large-scale farming and exotic-tree plantations being the most frequent causes of forest loss. Although instigating serious challenges, such changes are also creating important new opportunities for forest conservation. Here we argue that, by increasingly targeting strategic corporations and trade groups with public-pressure campaigns, conservation interests could have a much stronger influence on the fate of tropical forests.