Infectious Disorders - Drug Targets (Formerly Current Drug Targets - Infectious Disorders) - Volume 9, Issue 5, 2009

In the wake of the “post-genomic” era, a major shift in research strategies against infectious diseases is emerging— from the traditional approach that has based on “playing defensive” to one that is “taking offensive” against the pathogens. With modern high-throughput technology, complete genomic information contents of major pathogens are being deciphered one by one (refer to the Genomes OnLine Database v2.0 at http://www.genomesonline.org). Detailed description of pathogens is now possible to the fullest extent at both its gene and protein levels. Whole genome sequencing opens up a new horizon for the systematic investigation of the complete set of gene products (the proteome), and offers unprecedented opportunities in identifying drug targets. For pathogens with a small genome, research projects have been established to determine the threedimensional structure of ALL of its proteins. While sequencing of larger genomes can take considerable time to complete, bioinformatics strategies have been implemented to identify and prioritize targets for structural studies and drug development. Large-scale collaborative structural genomics projects are advancing rapidly and are being reviewed and updated regularly. Readers are referred to the following issues of journals that are dedicated to the theme of “structural genomics”: Journal of Structural and Functional Genomics, Volume 8, Numbers 2-3 (September, 2007); Current Opinion in Chemical Biology, Volume 12, Issue 1 (February, 2008); Methods In Molecular Biology: Structural Proteomics— High Throughput Methods, Volume 426, 2008.

While three dimensional structures have long been used to search for new drug targets, only a fraction of new drugs coming to the market has been developed with the use of a structure-based drug discovery approach. However, the recent years have brought not only an avalanche of new macromolecular structures, but also significant advances in the protein structure determination methodology only now making their way into structure-based drug discovery. In this paper, we review recent developments resulting from the Structural Genomics (SG) programs, focusing on the methods and results most likely to improve our understanding of the molecular foundation of human diseases. SG programs have been around for almost a decade, and in that time, have contributed a significant part of the structural coverage of both the genomes of pathogens causing infectious diseases and structurally uncharacterized biological processes in general. Perhaps most importantly, SG programs have developed new methodology at all steps of the structure determination process, not only to determine new structures highly efficiently, but also to screen protein/ligand interactions. We describe the methodologies, experience and technologies developed by SG, which range from improvements to cloning protocols to improved procedures for crystallographic structure solution that may be applied in “traditional” structural biology laboratories particularly those performing drug discovery. We also discuss the conditions that must be met to convert the present high-throughput structure determination pipeline into a high-output structure-based drug discovery system.

The waning effectiveness of established tuberculosis treatments due to the rise of multi and extensively drugresistant strains of Mycobacterium tuberculosis, coupled with the synergism of HIV infection, demands basic research efforts to inform focused drug development programs. Structural genomics projects provide rich sources of information for the rational design of anti-tubercular drugs, aiming to exploit unique and novel protein features and interactions based on atomic resolution structures. This review compiles structures of M. tuberculosis proteins elucidated since January 2007 that are promising avenues for drug design, encompassing proteins involved with known and experimental antituberculosis drugs, metabolism, dealing with the hostile environment of the host organism, and information processing.

The NIAID-funded Seattle Structural Genomics Center for Infectious Disease (SSGCID) is a consortium established to apply structural genomics approaches to potential drug targets from NIAID priority organisms for biodefense and emerging and re-emerging diseases. The mission of the SSGCID is to determine ~400 protein structures over five years ending in 2012. In order to maximize biomedical impact, ligand-based drug-lead discovery campaigns will be pursued for a small number of high-impact targets. Here we review the center's target selection processes, which include pro-active engagement of the infectious disease research and drug therapy communities to identify drug targets, essential enzymes, virulence factors and vaccine candidates of biomedical relevance to combat infectious diseases. This is followed by a brief overview of the SSGCID structure determination pipeline and ligand screening methodology. Finally, specifics of our resources available to the scientific community are presented. Physical materials and data produced by SSGCID will be made available to the scientific community, with the aim that they will provide essential groundwork benefiting future research and drug discovery.

The application of structural genomics methods and approaches to proteins from organisms causing infectious diseases is making available the three dimensional structures of many proteins that are potential drug targets and laying the groundwork for structure aided drug discovery efforts. There are a number of structural genomics projects with a focus on pathogens that have been initiated worldwide. The Center for Structural Genomics of Infectious Diseases (CSGID) was recently established to apply state-of-the-art high throughput structural biology technologies to the characterization of proteins from the National Institute for Allergy and Infectious Diseases (NIAID) category A-C pathogens and organisms causing emerging, or re-emerging infectious diseases. The target selection process emphasizes potential biomedical benefits. Selected proteins include known drug targets and their homologs, essential enzymes, virulence factors and vaccine candidates. The Center also provides a structure determination service for the infectious disease scientific community. The ultimate goal is to generate a library of structures that are available to the scientific community and can serve as a starting point for further research and structure aided drug discovery for infectious diseases. To achieve this goal, the CSGID will determine protein crystal structures of 400 proteins and protein-ligand complexes using proven, rapid, highly integrated, and cost-effective methods for such determination, primarily by X-ray crystallography. High throughput crystallographic structure determination is greatly aided by frequent, convenient access to high-performance beamlines at third-generation synchrotron X-ray sources.

Gram-negative bacteria have evolved diverse secretion systems/machineries to translocate substrates across the cell envelope. These various machineries fulfil a wide variety of functions but are also essential for pathogenic bacteria to infect human or plant cells. Secretion systems, of which there are seven, utilize one of two secretion mechanisms: (i) the one-step mechanism, whereby substrates are translocated directly from the bacterial-cytoplasm to the extracellular medium or into the eukaryotic-target cell; (ii) the two-step mechanism, whereby substrates are first translocated across the bacterial-inner membrane; once in the periplasm, substrates are targeted to one of the secretion systems that mediate the transport across the outer membrane and the release outside the bacterial cell. This review describes in details the main structural features of these secretion systems. Structural biology offers the possibility to understand the molecular mechanisms at play in the various secretion systems. It also helps to design specifically drugs that can block these machineries and thus attenuate the virulence of pathogenic bacteria.

Chemokines are small cytokines that are part of a large family of molecules that bind to G-protein coupled receptors, which, as a family, are the most widely targeted group of molecules in the treatment of disease. Chemokines are critical for recruiting and activating the cells of the immune system during inflammation especially during viral infections. However, a number of viruses including the large herpes virus human cytomegalovirus (HCMV) encode mechanisms to impede the effects of chemokines or has gained the ability to use these molecules to its own advantage. The Human Cytomegalovirus (HCMV)-encoded chemokine receptor US28 is the best characterized of the four unique chemokine receptor-like molecules found in the HCMV genome. US28 has been studied as an important virulence factor for HCMVmediated vascular disease and, more recently, in models of HCMV-associated malignancy. US28 is a rare multichemokine family binding receptor with the ability to bind ligands from two distinct chemokine classes. Ligand binding to US28 activates cell-type and ligand-specific signaling pathways leading to cellular migration, which is an important example of receptor functional selectivity. Additionally, US28 has been demonstrated to constitutively activate phospholipase C (PLC) and NF-κB signaling pathways. Understanding the structure/function relationships between US28, its ligands and intracellular signaling molecules will provide essential clues for effective pharmacological targeting of this multifunctional chemokine receptor.

The design of new medications is an intensive, time-consuming and costly process. Over the years, a rational approach that exploits the structural knowledge of a biological target has led to many successes. This procedure can be expedited using computer-aided modelling techniques. The structure-based approach to drug design relies on knowing the three-dimensional structure of the target macromolecule. If an experimental structure has not been determined yet, a good approximation of the protein target structure can be obtained through computational modelling, provided that some structures of its homologues are available to serve as templates. The vast majority of drugs currently on the market act by disrupting the interaction between a protein and its physiological ligand(s). Hence, once a molecular model is available, the next step is to identify and study its putative ligand-binding sites. Molecular “docking” may then be performed in silico to predict the modes of interaction between the ligand and the target. In this review, a list of computational resources for structure-based drug design has been compiled. It is hoped that readers who do not have much experience will be equipped with the appropriate tools to make a first attempt at protein modelling and in silico ligand docking exercises.