Mining nematode genome data for novel drug targets

Expressed sequence tag projects have currently produced over 400 000 partial gene sequences from more than 30 nematode species and the full genomic sequences of selected nematodes are being determined. In addition, functional analyses in the model nematode Caenorhabditis elegans have addressed the role of almost all genes predicted by the genome sequence. This recent explosion in the amount of available nematode DNA sequences, coupled with new gene function data, provides an unprecedented opportunity to identify pre-validated drug targets through efficient mining of nematode genomic databases. This article describes the various information sources available and strategies that can expedite this process.     

In vivo drug target discovery: identifying the best targets from the genome

A vast number of genes of unknown function threaten to clog drug discovery pipelines. To develop therapeutic products from novel genomic targets, it will be necessary to correlate biology with gene sequence information. Industrialized mouse reverse genetics is being used to determine gene function in the context of mammalian physiology and to identify the best targets for drug development.     

Tick anti-hemostatics: targets for future vaccines and therapeutics

For ticks, a significant obstacle in obtaining a blood meal is counteracting the hemostatic system of the host. To this end, ticks have developed a broad array of anti-hemostatics, which is reflected in the presence of structurally related tick proteins with different functions. Disruption of blood flow which blocks successful tick feeding makes anti-hemostatics attractive targets for anti-tick vaccines. Moreover, the limited number of drugs currently available for a range of important cardio-vascular diseases makes ticks a potential source of novel therapeutics. This review aims to summarize the key features of tick anti-hemostatics, their structures, mode of action and possible future application as vaccines and novel therapeutic agents.     

In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets

Recent advances in DNA sequencing technology have enabled elucidation of whole genome information from a plethora of organisms. In parallel with this technology, various bioinformatics tools have driven the comparative analysis of the genome sequences between species and within isolates. While drawing meaningful conclusions from a large amount of raw material, computer-aided identification of suitable targets for further experimental analysis and characterization, has also led to the prediction of non-human homologous essential genes in bacteria as promising candidates for novel drug discovery. Here, we present a comparative genomic analysis to identify essential genes in Burkholderia pseudomallei. Our in silico prediction has identified 312 essential genes which could also be potential drug candidates. These genes encode essential proteins to support the survival of B. pseudomallei including outer-inner membrane and surface structures, regulators, proteins involved in pathogenenicity, adaptation, chaperones as well as degradation of small and macromolecules, energy metabolism, information transfer, central/intermediate/miscellaneous metabolism pathways and some conserved hypothetical proteins of unknown function. Therefore, our in silico approach has enabled rapid screening and identification of potential drug targets for further characterization in the laboratory.     

Tuberculosis vaccines: beyond bacille Calmette-Guerin

Tuberculosis (TB) disease caused by Mycobacterium tuberculosis (M. tb) remains one of the leading infectious causes of death and disease throughout the world. The only licensed vaccine, Mycobacterium bovis bacille Calmette-Guérin (BCG) confers highly variable protection against pulmonary disease. An effective vaccination regimen would be the most efficient way to control the epidemic. However, BCG does confer consistent and reliable protection against disseminated disease in childhood, and most TB vaccine strategies being developed incorporate BCG to retain this protection. Cellular immunity is necessary for protection against TB and all the new vaccines in development are focused on inducing a strong and durable cellular immune response. There are two main strategies being pursued in TB vaccine development. The first is to replace BCG with an improved whole organism mycobacterial priming vaccine, which is either a recombinant BCG or an attenuated strain of M. tb. The second is to develop a subunit boosting vaccine, which is designed to be administered after BCG vaccination, and to enhance the protective efficacy of BCG. This article reviews the leading candidate vaccines in development and considers the current challenges in the field with regard to efficacy testing.     

Staphylococci in colonization and disease: prospective targets for drugs and vaccines

Pathogenic staphylococci are now regarded in the scientific community as antibiotic resistant 'superbugs' because they have an amazing capacity to acquire resistance traits. Surprisingly, antibiotic development has decelerated. Promising targets for drug development are enzymes involved in the biosynthesis of cell envelope structures such as peptidoglycan, teichoic acids, membrane lipids, or cell wall associated adhesins. Compounds that inactivate or neutralize the most aggressive toxins such as the superantigens and the pore forming toxins have also been considered. In the past decade, global regulatory systems have been studied that contribute to virulence and might be candidates for target development. Targets that are particularly promising include all enzymatic reactions that are unique to bacteria and that are involved in central metabolism, such as methionine-tRNA(fMet) formyltransferase or the peptide deformylase, which have been successfully used for designing new inhibitors. There are also several known antibiotics that have roused new interest especially if they are active against multi-resistant staphylococci. Various cell wall components are promising candidates for active and passive immunization strategies such as capsule, slime, teichoic acids or cell wall bound adhesins. Several new targets for drugs or vaccines will arise from the functional analysis of the staphylococcal genomes that contain many hitherto unknown targets.     

Sirtuins: multifaceted drug targets

Sirtuin (Sir2) proteins being key regulators of numerous cellular processes have been, over the recent past, the subject of intense study. Sirs have been implicated in diverse physiological processes ranging from aging and cancer to neurological dysfunctions. Studies on Sir2s using tools of genetics, molecular biology, biochemistry and structural biology have provided significant insight into the diverse functions of this class of deacetylases. This apart, medicinal chemistry approaches have enabled the discovery of modulators (both activators and inhibitors) of Sir2 activity of diverse chemical structures and properties. The availability of these small molecule modulators of Sir2 activity not only has pharmacological significance but also opens up the possibility of exploiting chemical genetic approaches in understanding the role of this multi-functional enzyme in cellular processes.     

Tuberculosis vaccine design: influence of the completed genome sequence

Tuberculosis continues to be a major health problem, with more adults dying from Mycobacterium tuberculosis than any other pathogen world-wide.With the onset of the HIV epidemic and an increase in drug-resistant M. tuberculosis strains, the need for an improved vaccine has become an international priority.The recent completion of the genome sequences for two M. tuberculosis strains provides a wealth of information that can be used to design new strategies for vaccine development. The challenge comes in making rational choices from among the 4,000 genes of the most probable candidate immunogens or virulence genes.Thus, a well-designed screen is needed to reduce the number of candidates that must be tested. Presently, the most valuable role that bioinformatics can play is to provide such a screen.     

Apicoplast translation, transcription and genome replication: targets for antimalarial antibiotics

Several antibiotics possess antimalarial properties, although the mechanisms by which they kill malaria parasites have been poorly understood. Recent data suggest that the target for multiple antimalarial antibiotics is the apicoplast, a chloroplast-like organelle of uncertain function. Translation inhibitors (such as tetracyclines, clindamycin and macrolides) and gyrase inhibitors (such as ciprofloxacin) cause modest antimalarial effects initially but are much more potent against the progeny of treated parasites. These progeny inherit nonfunctional apicoplasts, suggesting that blocking production of apicoplast proteins causes the 'delayed-death effect'. Interestingly, the antibiotics thiostrepton and rifampin are fast acting and might target additional processes outside the apicoplast.     

疾病干预的新靶点:嘌呤与嘧啶受体

内源性核苷、核苷酸通过嘌呤与嘧啶受体(P受体),参与机体组织器官多种功能的调节。在肿瘤、细胞凋亡、局部缺血、伤口愈合、骨质疏松、药物毒性、炎症及痛觉等病理状态下,P受体的内源性配体核苷与核苷酸发挥保护作用,P1、P2受体及其受体亚型的选择性激动剂和桔抗剂具有宽广的临床应用前景。     

Host-bacterial coevolution and the search for new drug targets

Understanding the coevolution between humans and our microbial symbionts and pathogens requires complementary approaches, ranging from community analysis to in-depth analysis of individual genomes. Here we review the evidence for coevolution between symbionts and their hosts, the role of horizontal gene transfer in coevolution, and genomic and metagenomic approaches to identify drug targets. Recent studies have shown that our symbiotic microbes confer many metabolic capabilities that our mammalian genomes lack, and that targeting mechanisms of horizontal gene transfer is a promising new direction for drug discovery. Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities.     

Functional genomics: identifying drug targets for parasitic diseases

The genomic sequences of parasitic diseases are rapidly becoming available and, recently, the full sequence of Plasmodium falciparum has been published. Much has been promised from this genomic revolution including the identification of new drug targets and novel chemotherapeutic treatments for the control of parasitic diseases. The challenge to use this information efficiently will require functional genomics tools such as bioinformatics, microarrays, proteomics and chemical genomics to identify potential drug targets, and to allow the development of optimized lead compounds. The information generated from these tools will provide a crucial link from genomic analysis to drug discovery.     

Acetyl-coenzyme A carboxylases: versatile targets for drug discovery

Acetyl-coenzyme A carboxylases (ACCs) have crucial roles in fatty acid metabolism in humans and most other living organisms. They are attractive targets for drug discovery against a variety of human diseases, including diabetes, obesity, cancer, and microbial infections. In addition, ACCs from grasses are the targets of herbicides that have been in commercial use for more than 20 years. Significant progresses in both basic research and in drug discovery have been made over the past few years in the studies on these enzymes. At the basic research level, the crystal structures of the biotin carboxylase (BC) and the carboxyltransferase (CT) components of ACC have been determined, and the molecular basis for ACC inhibition by small molecules are beginning to be understood. At the drug discovery level, a large number of nanomolar inhibitors of mammalian ACCs have been reported and the extent of their therapeutic potential is being aggressively explored. This review summarizes these new progresses and also offers some prospects in terms of the future directions for the studies on these important enzymes.     

GPCRs: Emerging anti-cancer drug targets

G protein-coupled receptors (GPCRs) constitute the largest and most diverse protein family in the human genome with over 800 members identified to date. They play critical roles in numerous cellular and physiological processes, including cell proliferation, differentiation, neurotransmission, development and apoptosis. Consequently, aberrant receptor activity has been demonstrated in numerous disorders/diseases, and as a result GPCRs have become the most successful drug target class in pharmaceuticals treating a wide variety of indications such as pain, inflammation, neurobiological and metabolic disorders. Many independent studies have also demonstrated a key role for GPCRs in tumourigenesis, establishing their involvement in cancer initiation, progression, and metastasis. Given the growing appreciation of the role(s) that GPCRs play in cancer pathogenesis, it is surprising to note that very few GPCRs have been effectively exploited in pursuit of anti-cancer therapies. The present review provides a broad overview of the roles that various GPCRs play in cancer growth and development, highlighting the potential of pharmacologically modulating these receptors for the development of novel anti-cancer therapeutics.     

New targets for an old drug

Methotrexate has been a clinical agent used in cancer, immunosuppression, rheumatoid arthritis, and other highly proliferative diseases for many years, yet its underlying molecular mechanism of action in these therapeutic areas is still unclear. We have previously reported using a chemical proteomics technique on several other potential pharmacodynamic targets of methotrexate. Here, using a frontal affinity chromatography with mass spectrometry detection, we confirm one of these targets, hypoxanthine-guanine amidophosphoribosyltransferase, as a true binder of methotrexate with a K_d of 4.2 μM. These results complement and confirm our recent study, but more importantly, shed light into the mechanism of action of methotrexate in oncology and other highly proliferative diseases and may help explain some unaccounted for effects of this drug. For example, despite the fact that DNA salvage pathway enzymes are highly active, methotrexate can be effective if it only targets enzymes of the de novo pathway.     

New targets for an old drug

Methotrexate has been a clinical agent used in cancer, immunosuppression, rheumatoid arthritis and other highly proliferative diseases for many years, yet its underlying molecular mechanism of action in these therapeutic areas is still unclear. We present a chemical proteomics approach that uses ultra-sensitive mass spectrometry coupled to an inverse protein-ligand docking computational technique to unravel the mechanism of action of this drug. Using methotrexate tethered to a solid support we were able to isolate a signficant number of proteins. We effectively captured a large portion of the de novo purine metaolome and propose a pathway architecture similar to that seen in signaling pathways and consistent with substrate channeling. More importantly, we were able to capture protein targets that could potentially provide new insights into the mechanism of action of methotrexate in rheumatoid arthritis and immunosuppression. The application of this approach to other drugs and drug candidates may facilitate the prediction of unknown and secondary therapeutic target proteins and those related to the side effects and toxicity. These results demonstrate that this proteomics technology could play an important role in drug discovery and development since it allows monitoring of the interactions between a drug and the protein content of a cell.     

Mapping the genome of Plasmodium falciparum on the drug-like chemical space reveals novel anti-malarial targets and potential drug leads

The parasite Plasmodium falciparum is the main agent responsible for malaria. In this study, we exploited a recently published chemical library from GlaxoSmithKline (GSK) that had previously been confirmed to inhibit parasite growth of the wild type (3D7) and the multi-drug resistance (D2d) strains, in order to uncover the weak links in the proteome of the parasite. We predicted 293 proteins of P. falciparum, including the six out of the seven verified targets for P. falciparum malaria treatment, as targets of 4645 GSK active compounds. Furthermore, we prioritized druggable targets, based on a number of factors, such as essentiality for growth, lack of homology with human proteins, and availability of experimental data on ligand activity with a non-human homologue of a parasite protein. We have additionally prioritized predicted ligands based on their polypharmacology profile, with focus on validated essential proteins and the effect of their perturbations on the metabolic network of P. falciparum, as well as indication of drug resistance emergence. Finally, we predict potential off-target effects on the human host with associations to cancer, neurological and dermatological disorders, based on integration of available chemical-protein and protein-protein interaction data. Our work suggests that a large number of the P. falciparum proteome is potentially druggable and could therefore serve as novel drug targets in the fight against malaria. At the same time, prioritized compounds from the GSK library could serve as lead compounds to medicinal chemists for further optimization.     

P-type ATPases as drug targets: Tools for medicine and science

P-type ATPases catalyze the selective active transport of ions like H⁺, Na⁺, K⁺, Ca²⁺, Zn²⁺, and Cu²⁺ across diverse biological membrane systems. Many members of the P-type ATPase protein family, such as the Na⁺,K⁺-, H⁺,K⁺-, Ca²⁺-, and H⁺-ATPases, are involved in the development of pathophysiological conditions or provide critical function to pathogens. Therefore, they seem to be promising targets for future drugs and novel antifungal agents and herbicides. Here, we review the current knowledge about P-type ATPase inhibitors and their present use as tools in science, medicine, and biotechnology. Recent structural information on a variety of P-type ATPase family members signifies that all P-type ATPases can be expected to share a similar basic structure and a similar basic machinery of ion transport. The ion transport pathway crossing the membrane lipid bilayer is constructed of two access channels leading from either side of the membrane to the ion binding sites at a central cavity. The selective opening and closure of the access channels allows vectorial access/release of ions from the binding sites. Recent structural information along with new homology modeling of diverse P-type ATPases in complex with known ligands demonstrate that the most proficient way for the development of efficient and selective drugs is to target their ion transport pathway.     

Aotus monkeys: their great value for anti-malaria vaccines and drug testing

Non-human primates represent a valuable resource for testing potential vaccines candidates and drugs for human use. Malaria remains one of the greatest burdens for the humanity represented by approximately 500 million new clinical cases per year worldwide and at least two million deaths caused annually. Additional control measures such as vaccines and new anti-malarial compounds are therefore urgently needed. Safety and protective efficacy studies in animal models are critical steps for vaccines and drugs development and primate models are probably the most appropriate for this purpose. Although Aotus genus provides several species susceptible to both Plasmodium falciparum and Plasmodium vivax, having different susceptibility to malaria, Aotus lemurinus griseimembra represents the best current malaria primate model because of its high susceptibility to infection by blood forms and sporozoites of both species of Plasmodium. Although the ultimate validation of this model depends upon human trials, over the past two decades these monkeys have proved very useful to test multiple malaria vaccine candidates prior to trials in humans. A good correlation between the B- and T-cell epitopes recognised by humans and by immunised monkeys has been documented, and cross reactivity between reagents for human and Aotus cytokines and lymphocyte markers have been identified and are facilitating the selection of vaccine candidates for clinical trials. Aotus also represents a good model for the screening of anti-malarial drugs and the understanding of malaria pathogenesis as well. In view of the decreasing availability of these primates, breeding programs and biomedical research facilities must be improved in countries of primate origin.