Genomic filtering: an approach to discovering novel antiparasitics

Genomic filtering is a rapid approach to identifying and prioritizing molecular targets for drug discovery. For infectious disease applications, comparative genomics filters allow the selection of pathogen-specific gene products, whereas functional genomics filters, such as RNA interference (RNAi), allow the selection of gene products essential for pathogen survival. The approach is especially applicable to antiparasitic drug discovery where the phylogenetic distance between parasite and host make the likelihood of drug cross-toxicity due to conservation of molecular targets greater than for more distantly related pathogens such as prokaryotes. This article discusses some of the inherent challenges of applying genomics to the early steps of drug discovery and describes one successful comparative and functional genomics filtering strategy that has been implemented to prioritize molecular targets and identify chemical leads for nematode control.     

The challenges of developing novel antiparasitic drugs

Only a few novel classes of antiparasitic drugs have emerged over the last few decades, reflecting the difficulties associated with bringing a safe, effective molecule to market. In recent years, the screening paradigm has shifted from empirical whole parasite screening towards mechanism-based high throughput screening. This approach requires investment in molecular parasitology and in understanding the basic biology of parasites, as well as requiring considerable investment in an infrastructure for screening. Add to this the fact that the drug discovery process is iterative with high attrition, the Animal Health industry by necessity must focus on discovering medicines for diseases, which will deliver a return on investment. In recent years the rapid progression of genomics has unlocked a plethora of tools for target identification, validation and screening, revolutionising mechanism-based screening for antiparasitic drug discovery. The challenge still remains; however, to identify novel chemical entities with the properties required to deliver a safe, effective antiparasitic drug.     

Discovery of veterinary antiparasitic agents in the 21st Century: A view from industry

Discovery of antiparasitic agents is a challenging process, requiring discovery of molecules with the ability to kill parasites but not their hosts. Customer preference is for fewer doses and ease of application, but this is not always compatible with reduced withdrawal times, human food safety and/or user safety. This article describes some of the difficulties faced by researchers in the search for new antiparasitic agents, while highlighting advances that may improve the discovery process and the chance of success in discovering novel drugs.     

Drug discovery for parasitic diseases: powered by technology,enabled by pharmacology,informed by clinical science

While prevention is a bedrock of public health, innovative therapeutics are needed to complement the armamentarium of interventions required to achieve disease control and elimination targets for neglected diseases. Extraordinary advances in drug discovery technologies have occurred over the past decades, along with accumulation of scientific knowledge and experience in pharmacological and clinical sciences that are transforming many aspects of drug R&D across disciplines. We reflect on how these advances have propelled drug discovery for parasitic infections, focusing on malaria, kinetoplastid diseases, and cryptosporidiosis. We also discuss challenges and research priorities to accelerate discovery and development of urgently needed novel antiparasitic drugs.     

The changing landscape of antiparasitic drug discovery for veterinary medicine

Changes in economic imperatives in the pharmaceutical industry have led to a wave of consolidation, which has had the unintended side effect of shrinking the resource devoted to antiparasitic drug discovery in animal health companies. Scientific changes have altered the way in which drugs could be discovered in the future. New science and business models will need to be implemented to address the demand for innovative antiparasitic drugs in veterinary medicine. Novel drugs are needed to combat drug resistance and for currently non-addressed problems. At the center of the future for this field, however, lies the need for more support into the basic research on the biology of parasites.     

Serendipity and new drugs for infectious disease

Serendipity, in various shades of semantic legitimacy, is abundantly evident in the history of the chemotherapy of infectious disease. We may be on the threshold of a new era of rational drug design, but most medications for infectious diseases have arisen, and continue to arise, from chance observation, clinical experience, and the empirical search for substances active against pathogens. Chance does not produce drugs; but where chance has played a pivotal role in drug discovery, the event may be considered serendipitous to a greater or lesser degree. In a deliberate search for new drugs, it is often difficult to assess the degree to which any resulting discovery is serendipitous, and the usefulness of the term becomes debatable. Many therapeutic advances emerge from research involving animals, and a triggering "happy accident" may reside in the most basic aspects of animal care or in the most arcane knowledge of animals. The examples discussed in this article deal mostly with parasitic disease and the use of animal models in the discovery of antiparasitic agents. In this area, as in others, chance has laid the groundwork for scientific advancement and practical benefit. Although the applicability of the word serendipity to drug discovery may often be uncertain, the role played by chance should be recognized and welcomed.     

Functional cell-based uHTS in chemical genomic drug discovery

The availability of genomic information significantly increases the number of potential targets available for drug discovery, although the function of many targets and their relationship to disease is unknown. In a chemical genomic research approach, ultra-high throughput screening (uHTS) of genomic targets takes place early in the drug discovery process, before target validation. Target-selective modulators then provide drug leads and pharmacological research tools to validate target function. Effective implementation of a chemical genomic strategy requires assays that can perform uHTS for large numbers of genomic targets. Cell-based functional assays are capable of the uHTS throughput required for chemical genomic research, and their functional nature provides distinct advantages over ligand-binding assays in the identification of target-selective modulators.     

Design and evaluation of Trypanosoma brucei metacaspase inhibitors

Metacaspase (MCA) is an important enzyme in Trypanosoma brucei, absent from humans and differing significantly from the orthologous human caspases. Therefore MCA constitutes a new attractive drug target for antiparasitic chemotherapeutics, which needs further characterization to support the discovery of innovative drug candidates. A first series of inhibitors has been prepared on the basis of known substrate specificity and the predicted catalytic mechanism of the enzyme. In this Letter we present the first inhibitors of TbMCA2 with low micromolar enzymatic and antiparasitic activity in vitro combined with low cytotoxicity.     

Assessing the impact of predictive biosimulation on drug discovery and development

Systems biology is creating a context for interpreting the vast amounts of genomic and proteomic data being produced by pharmaceutical companies in support of drug development. While major data collection efforts capitalize on technical advances in miniaturization and automation and represent an industrialization of existing laboratory research, the transition from mental models to predictive computer simulations is setting the pace for advances in this field. This article addresses current approaches to the mathematical modeling of biological systems and assesses the potential impact of predictive biosimulation on drug discovery and development.     

Deep within the filarial genome: progress of the filarial genome project.

Four years ago, a WHO/United Nations Development Programme/World Bank-sponsored genome project to study the filarial lymphatic nematode parasite Brugia malayi was initiated. The project took as its aims gene discovery for drug target and vaccine candidate identification, genome mapping, dissemination of genomic data to the world community and training of endemic country partners in genomic research. In this article, the principal investigators in the laboratories behind the project describe the background to the project, the data now emerging and goals for the future. Open access to filarial genome data is emphasized.     

Drug discovery for malaria: a very challenging and timely endeavor

The prevalence of resistance to known antimalarial drugs has resulted in the expansion of antimalarial drug discovery efforts. Academic and nonprofit institutions are partnering with the pharmaceutical industry to develop new antimalarial drugs. Several new antimalarial agents are undergoing clinical trials, mainly those resurrected from previous antimalarial drug discovery programs. Novel antimalarials are being advanced through the drug development process, of course, with the anticipated high failure rate typical of drug discovery. Many of these are summarized in this review. Mechanisms for funding antimalarial drug discovery and genomic information to aid drug target selection have never been better. It remains to be seen whether ongoing efforts will be sufficient for reducing malaria burden in the developing world.     

Membrane lipidomics for the discovery of new antiparasitic drug targets

Advances in lipid separation methods and mass spectrometry technologies allow the fine characterization of the lipidome of parasites, ranging from unicellular protists to worms, which cause threatening infections in vertebrates, including humans. Specific lipid structures or lipid metabolic pathways can inspire the development of novel antiparasitic drugs. Changes in the lipid balance in membranes of parasites can also provide clues on the dynamics of drugs and some mechanisms of drug resistance. This review highlights recent trends in parasite lipidomics, combined with functional analyses, for the discovery of novel targets and the development of novel drugs.     

Pharmacogenomics of cystic fibrosis

Pharmacogenomics is becoming a frontline instrument of drug discovery, where the drug-dependent patterns of global gene expression are employed as biologically relevant end points. In the case of cystic fibrosis (CF), cells and tissues from CF patients provide the starting points of genomic analysis. The end points for drug discovery are proposed to reside in gene expression patterns of CF cells that have been corrected by gene therapy. A case is made here that successful drug therapy and gene therapy should, hypothetically, converge at a common end point. In response to a virtual tidal wave of genomic data, bioinformatics algorithms are needed to identify those genes that truly reveal drug efficacy. As examples, we describe the hierarchical clustering, GRASP, and GENESAVER algorithms, particularly within a hypothesis-driven context that focuses on data for a CF candidate drug. Pharmacogenomic approaches to CF, and other similar diseases, may eventually give us the opportunity to create drugs that work in a patient- or mutation-specific manner.     

Targeting malaria parasite at the level of apicoplast: an update

In 1996, the discovery of a relic chloroplast in Plasmodium and Toxoplasma cells has strongly changed our vision of these parasites in the "Tree of Life", and has opened an unexpected new field of investigation in the search for antiparasitic treatments, including antimalarials. This review details our current understanding of the sophisticated evolution of the parasites of the Apicomplexa phylum and briefly covers a decade of research and development in drug discovery, trying to target the malaria parasite at the level of its plant-like organelle. Fifteen years after the discovery of the apicoplast and ten years after the publication of the genome of Plasmodium falciparum, it seems that we have completed a first phase of tests of available antibiotics and herbicides. In the human host, the liver phase is the only parasitic stage, for which biological functions harbored by the apicoplast, such as fatty acid biosynthesis, seem indispensable. During the erythrocytic phase, recent results have focused the attention on the processes controlling the biogenesis of the apicoplast, and one of the functions harbored by the apicoplast, i.e. the biosynthesis of isoprenoids, as major -promising targets for future treatments.     

Natural products discovery from micro-organisms in the post-genome era†

With the decision to award the Nobel Prize in Physiology or Medicine to Drs. S. ōmura, W.C. Campbell, and Y. Tu, the importance and usefulness of natural drug discovery and development have been revalidated. Since the end of the twentieth century, many genome analyses of organisms have been conducted, and accordingly, numerous microbial genomes have been decoded. In particular, genomic studies of actinomycetes, micro-organisms that readily produce natural products, led to the discovery of biosynthetic gene clusters responsible for producing natural products. New explorations for natural products through a comprehensive approach combining genomic information with conventional methods show great promise for the discovery of new natural products and even systematic generation of unnaturally occurring compounds.     

Mining bacterial genomes for antimicrobial targets

The elucidation of whole-genome sequences is expected to have a revolutionary impact on the discovery of novel medicines. With the availability of complete genome sequences of more than 30 different species, the field of antimicrobial drug discovery has the opportunity to access a remarkable diversity of genomic information. In this review, I summarize how microbial genomics has changed strategies of drug discovery by applying bioinformatics, novel genetic approaches and genomics-based technologies, including analysis of gene expression using DNA microarrays.     

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.     

Chemical genomics: a systematic approach in biological research and drug discovery

The knowledge of complete sequences of different organisms is dramatically changing the landscape of biological research and pharmaceutical development. We are experiencing a transition from a trial-and-error approach in traditional biological research and natural product drug discovery to a systematic operation in genomics and target-specific drug design and selection. Small, cell-permeable and target-specific chemical ligands are particularly useful in systematic genomic approaches to study biological questions. On the other hand, genomic sequence information, comparative and structural genomics, when combined with the cutting edge technologies in synthetic chemistry and ligand screening/identification, provide a powerful way to produce target-specific and/or function-specific chemical ligands and drugs. Chemical genomics or chemogenomics is a new term that describes the development of target-specific chemical ligands and the use of such chemical ligands to globally study gene and protein functions. We anticipate that chemical genomics plays a critical role in the genomic age of biological research and drug discovery.     

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.