Application of combinatorial chemistry to antimicrobial drug discovery

The emergence of pathogens resistant to currently available treatments is seen as a public health crisis. Since few new classes of antimicrobial drugs have been developed in the last two decades, it is becoming increasingly probable that healthcare providers will be faced with infections for which no chemotherapeutic agent is available. A renewed emphasis is being placed on employing the most advanced drug discovery technologies in the development of new antimicrobials. The recently introduced technologies of combinatorial chemistry offer new sources of chemical diversity, as well as methods with which to produce and rapidly test them. In the last few years, many groups have adopted a number of approaches in order to apply combinatorial chemistry to antimicrobial drug discovery. These combinatorial strategies, and the manner in which they are used to develop new screening formats or to identify new chemical leads are, reviewed.     

Current directions in the evolution of compound libraries

Synthetic compound libraries have been available for over a century, but in the last 15 years they have become increasing important in early-stage drug discovery projects. The qualities that these libraries possess impart a dramatic effect on hit discovery, on the subsequent steps of hit-to-lead progression, and on lead optimization by medicinal chemists. More recently, synthetic libraries have found an important application in chemical genetics. Concurrently, ideas have evolved regarding the application of the different types of synthetic approaches that are variously described as combinatorial chemistry, high-throughput synthesis, or diversity-oriented synthesis. This review will discuss current directions of synthetic chemistry, natural product chemistry and chemoinformatics, which relate to the various types of compound libraries that are in use in drug discovery and chemical genetics.     

Challenges in antimicrobial drug discovery and the potential of nucleoside antibiotics

Antimicrobial resistance in hospital and community settings is growing at an alarming rate and has been attributed to such organisms as methicillin-resistant staphylococcus aureus, staphylococci with decreased susceptibility to vancomycin, vancomycin-resistant enterococci, multi-drug resistant pseudomonas spp., klebsiella spp., enterobacter spp, and acinetobacter spp., as well as Streptococcus pneumoniae with decreased susceptibility to penicillin and other antibacterials. To address the need for new therapies to combat resistant organisms, drug companies are refocusing their discovery efforts on developing novel agents with new mechanisms of action. The hope is that rapidly emerging technologies including combinatorial chemistry, high throughput screening, proteomics and microbial genomics will have a positive impact on antimicrobial drug discovery. These technologies should aid in the identification of novel drug targets and compounds with unique mechanisms of action other than those currently provided by the traditional antibiotics. Nucleosides are one class of compounds worthy of further investigation as antibacterials since some derivatives have shown moderate to good activity against specific bacterial strains. For example, 5'-peptidyl nucleoside derivatives can inhibit peptide deformylase, an enzyme essential for bacterial survival that is not vital to human cells. This review also includes a list of miscellaneous nucleosides that have been synthesized as potential antibacterials. More detailed investigations on structure, as it relates to the antimicrobial activity of the various classes of nucleosides, need to be conducted in order to maximize the potential of developing a potent nucleoside for the treatment of bacterial infections. This review begins with an introduction to terms followed by discussions regarding the general background and relevance for developing novel antimicrobial agents. Challenges facing the antimicrobial drug discovery process are discussed along with relevant drug targets. An overview of nucleoside chemistry as it relates to antimicrobial activity is presented, followed by a discussion of the evidence which supports the potential of this class of compounds to yield the novel antimicrobial therapies needed in the new millennium.     

When poor solubility becomes an issue: From early stage to proof of concept

Drug absorption, sufficient and reproducible bioavailability and/or pharmacokinetic profile in humans are recognized today as one of the major challenges in oral delivery of new drug substances. The issue arose especially when drug discovery and medicinal chemistry moved from wet chemistry to combinatorial chemistry and high throughput screening in the mid-1990s. Taking into account the drug product development times of 8–12 years, the apparent R&D productivity gap as determined by the number of products in late stage clinical development today, is the result of the drug discovery and formulation development in the late 1990s, which were the early and enthusiastic times of the combinatorial chemistry and high throughput screening. In parallel to implementation of these new technologies, tremendous knowledge has been accumulated on biological factors like transporters, metabolizing enzymes and efflux systems as well as on the physicochemical characteristics of the drug substances like crystal structures and salt formation impacting oral bioavailability. Research tools and technologies have been, are and will be developed to assess the impact of these factors on drug absorption for the new chemical entities.

The conference focused specifically on the impact of compounds with poor solubility on analytical evaluation, prediction of oral absorption, substance selection, material and formulation strategies and development. The existing tools and technologies, their potential utilization throughout the drug development process and the directions for further research to overcome existing gaps and influence these drug characteristics were discussed in detail.     

Anticancer drug discovery using chemical genomics

Cancer is the leading cause of death in United States and World wide. Drug discovery and development for cancer therapeutics takes several years before a patient is benefited from a new drug. The average time length from start to finish is approximately 15 years. This time length includes 4-5 years of basic research, discovery, preclinical development and validation studies. Next, it takes approximately 7-10 years for a drug to go through human clinical trials. This time length is too long and need to be shortened to benefit patients quickly from new technologies and product development ideas. Furthermore, with the recent explosion of genomics and proteomics information, it is now becoming difficult to make rapid and logical decisions on hundreds of potential drug targets available. Thus, there is immediate need to develop and integrate tools and technologies that will not only reduce the time length but also the risk of late clinical drug failure. Chemical Genomics is an emerging field in which tools and technologies from biology and chemistry are utilized in a parallel and cyclic fashion very early in the development process. In addition chemical genomics proposes to integrate latest developments in tools and technologies from a variety of modern fields such as combinatorial chemistry, informatics, synthesis chemistries, cell based assays, microarrays, genomics and proteomics tools to accelerate drug discovery and development. Thus, in cancer therapeutics the aim of chemical genomics is not only to reduce the time length of pre-clinical development but also the risk of late clinical failure by making smart decisions early in the process.     

Microbial genomics - new targets,new drugs

Genomics has changed our view of the biological world in the past decade, providing both new information and new tools to characterise biological systems. Over 100 microbial genomes - including many of substantial clinical importance - have been fully or partially sequenced, pushing the search for novel antimicrobial compounds into the post-genomic era. Genomic information and associated new technologies have the potential to revolutionise the drug discovery process. Genomic methods have created a wealth of potential new antimicrobial targets; strategies are evolving to provide validation for these targets before chemical inhibitors are identified. The ability to obtain large amounts of purified target proteins and advances in X-ray crystallography have caused significant increases in available protein structures, which may foreshadow an increased effort in structure-based drug design. The post-genomics strategies used in antimicrobial drug discovery may have application for small molecule drug discovery in numerous therapeutic areas.     

Microbial genomics – new targets,new drugs

Genomics has changed our view of the biological world in the past decade, providing both new information and new tools to characterise biological systems. Over 100 microbial genomes – including many of substantial clinical importance – have been fully or partially sequenced, pushing the search for novel antimicrobial compounds into the post-genomic era. Genomic information and associated new technologies have the potential to revolutionise the drug discovery process. Genomic methods have created a wealth of potential new antimicrobial targets; strategies are evolving to provide validation for these targets before chemical inhibitors are identified. The ability to obtain large amounts of purified target proteins and advances in X-ray crystallography have caused significant increases in available protein structures, which may foreshadow an increased effort in structure-based drug design. The post-genomics strategies used in antimicrobial drug discovery may have application for small molecule drug discovery in numerous therapeutic areas.     

Discovery of inhibitors of protein-protein interactions from combinatorial libraries

Protein-protein interactions play a central role within numerous processes in the cell. The relevance of the processes in which this type of interactions are implicated make them responsible for many pathological situations. In the last decade protein-protein interfaces have shown their potential as new drug targets, and combinatorial chemistry has been defined as a useful tool in this line. This review gives a global vision of the actual situation of combinatorial chemistry, highlighting its applicability to high-throughput drug discovery and giving some crucial examples of its contribution to find modulators of protein-protein interactions.     

Approaches to the synthesis of immunolides: selective immunomodulatory macrolides for cystic fibrosis

The discovery of the clinical effectiveness of erythromycin and azithromycin in inflammatory airway diseases has inspired the discovery and development of macrolides with selective immunomodulatory activity. Erythromycin degradation continues to be a source of novel macrolides with a variety of selective biological activities. New technologies for drug discovery based in the emerging field of combinatorial biosynthesis provide the medicinal chemist with novel approaches toward the discovery of novel macrolides. Recent efforts to integrate synthetic organic medicinal chemistry with combinatorial biosynthesis have expanded the number of techniques available for macrolide synthesis.     

Large-scale integrated databases supporting drug discovery

Over the past 15 years, genomics, combinatorial chemistry and high-throughput automation have transformed the setting for drug discovery, from an information-poor to a data-rich environment. The next challenge for informatics scientists is to convert the large amount of disparate data produced into useful, integrated information. Consolidation of the different types of information related to drug discovery requires a good working knowledge of database technology, the existence of accepted data standards for achieving uniformity and a complete understanding of the different data systems that are already available. Chemogenomic databases represent the first example of truly integrated systems that make 'omic' technologies directly relevant to small-molecule drug discovery. Researchers within drug discovery programs now have an opportunity to take advantage of new information domains, through the advance and adoption of integrated chemogenomic databases.     

Application of combinatorial and parallel synthesis chemistry methodologies to antiparasitic drug discovery

The discovery and development of novel drugs has been influenced over the last several decades by new techniques in medicinal chemistry. Combinatorial and parallel synthesis chemistry techniques have opened up immense opportunities in drug discovery and development efforts. These techniques, which include solid phase organic synthesis and polymer-assisted synthesis in solution, have been routinely applied to a number of therapeutic areas. Despite the flurry of activity that characterized small molecule drug discovery efforts in the early 1990s, it was only during the mid to late 1990s that combinatorial chemistry began to make an impact on antiparasite chemotherapy. This review focuses on the development and application of combinatorial and parallel synthesis methodologies to antiparasitic drug discovery from the mid 1990s to the end of 2002. Much of this work applies to small organic molecules as inhibitors of parasite targets although some of the early applications were to the synthesis of enzyme substrates.     

The contribution of combinatorial chemistry to lead generation: an interim analysis

In the process of finding new drug candidates medicinal chemists nowadays have a variety of options to choose from, one is to apply combinatorial chemistry techniques. Since the early 1990's synthetic and analytical methods as well as new technologies have been growing rapidly in the area of combinatorial chemistry. Applying these techniques have resulted in the production of large numbers of compounds. A trend is observed towards smaller libraries of compounds with more drug-like properties. An analysis is made to establish the contribution of combinatorial chemistry in providing new lead candidates for (pre)clinical development towards new pharmaceutical products. Ten representative examples are given to describe the impact of ombinatorial chemistry on different levels of the lead discovery and optimization process. Furthermore, reports on combinatorial chemistry products that are already in (pre)clinical development were traced back to their source. The interim analysis showed only limited success of combinatorial chemistry approaches in terms of delivering leads. Second generation libraries appear more drug-like and focussed and may result in more compounds entering clinical studies in the future.     

Comprehensive essential gene identification as a platform for novel anti-infective drug discovery

In large part, antimicrobial drug discovery is driven by the breadth and quality of both potential drug targets and available chemical libraries to screen. Traditionally, targets have been few in number and have been limited to those with known function, from which biochemical assays could be implemented into drug screens. Iterations of this same basic approach, applied to a few biochemically-defined targets have identified a limited set of novel antibiotics and even fewer antifungal agents. Indeed, in the last 50 years less than 30 antimicrobial targets have been exploited commercially. Within infectious disease, the industry was driven largely by chemistry-based approaches, simply making new analogs to existing drugs to overcome the growing problem of drug resistance. Elitra Pharmaceutical s approach has been to enable true functional genomics on a genome-wide scale. Elitra s vision has been to identify all of the essential genes directly in the key pathogenic organisms. Having moved rapidly towards the completion of this goal, we are now faced with the enviable challenge of prioritizing enormous target sets and developing novel sensitive screens for those best suited as definitive drug targets. These highly sensitive, cell-based screening paradigms enable re-screening of even well screened chemical libraries to reveal new chemical entities displaying novel modes of action against new targets. In parallel, we have also begun to shift the paradigm from screening targets singly, towards genome-wide approaches to drug screening.     

Drug discovery and vaccine development using mixture-based synthetic combinatorial libraries

The approaches and concepts that encompass combinatorial chemistry represent a paradigm shift in drug discovery and basic research. Viewed initially as a curiosity by the pharmaceutical industry, combinatorial chemistry approaches are now recognized as essential drug discovery tools that decrease the time taken for discovery and increase the throughput of chemical screening by as much as 1000-fold. Although the use of mixture-based synthetic combinatorial libraries was one of the first approaches presented, its inherent strengths are only recently being recognized. Numerous mixture-based libraries of peptides, peptidomimetics and heterocycles have been synthesized and deconvoluted using the positional scanning approach. Mixture-based library approaches for drug discovery and vaccine development will be reviewed herein.     

38th Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) San Diego, USA, 24–27 September 1998

The renaissance in infections diseases, stimulated by well-documented and publicized microbial resistance, continues. The field is benefiting from the infusion of new technologies, aimed at accelerating the discovery process: genomics, combinatorial chemistry and high throughput screening. At this year's ICAAC, there were numerous reports on drug resistance and drug discovery though no surprises on either front. Microbial resistance to established agents is still edging upwards. Most agents (oxazolidinones, everninomycins, glycopeptides, ketolides, quinolones, β-lactams, azoles, echinocandins, sordarins) introduced in previous years are still in development. Combination antiretroviral chemotherapy (protease inhibitors, NRTIs and NNRTIs) is now the mainstream therapy for AIDS, at least in the developed world. A few antimicrobial agents (augmentin, ciprofloxacin, clarithromycin, fluconazole) are near or past the billion dollar mark, underscoring the healthy state of the market. In conclusion, convergence of medical needs and commercial opportunities has brought microbes and antimicrobials into center stage.     

Virtual screening and its integration with modern drug design technologies

Drug discovery is a highly complex and costly process, which demands integrated efforts in several relevant aspects involving innovation, knowledge, information, technologies, expertise, R&D investments and management skills. The shift from traditional to genomics- and proteomics-based drug research has fundamentally transformed key R&D strategies in the pharmaceutical industry addressed to the design of new chemical entities as drug candidates against a variety of biological targets. Therefore, drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein-ligand interactions. The combination of available knowledge of several 3D protein structures with hundreds of thousands of small-molecules have attracted the attention of scientists from all over the world for the application of structure- and ligand-based drug design approaches. In this context, virtual screening technologies have largely enhanced the impact of computational methods applied to chemistry and biology and the goal of applying such methods is to reduce large compound databases and to select a limited number of promising candidates for drug design. This review provides a perspective of the utility of virtual screening in drug design and its integration with other important drug discovery technologies such as high-throughput screening (HTS) and QSAR, highlighting the present challenges, limitations, and future perspectives in medicinal chemistry.     

Combinatorial compound libraries for drug discovery: an ongoing challenge

Almost 20 years of combinatorial chemistry have emphasized the power of numbers, a key issue for drug discovery in the current genomic era, in which it has been estimated that there might be more than 10,000 potential targets for which it would be desirable to have small-molecule modulators. Combinatorial chemistry is best described as the industrialization of chemistry; the chemistry has not changed, just the way in which it is now carried out, which is principally by exploiting instrumentation and robotics coupled to the extensive use of computers to efficiently control the process and analyse the vast amounts of resulting data. Many researchers have contributed to the general concepts as well as to the technologies in present use. However, some interesting challenges still remain to be solved, and these are discussed here in the context of the application of combinatorial chemistry to drug discovery.     

A decade of fragment-based drug design: strategic advances and lessons learned

Since the early 1990s, several technological and scientific advances - such as combinatorial chemistry, high-throughput screening and the sequencing of the human genome - have been heralded as remedies to the problems facing the pharmaceutical industry. The use of these technologies in some form is now well established at most pharmaceutical companies; however, the return on investment in terms of marketed products has not met expectations. Fragment-based drug design is another tool for drug discovery that has emerged in the past decade. Here, we describe the development and evolution of fragment-based drug design, analyse the role that this approach can have in combination with other discovery technologies and highlight the impact that fragment-based methods have made in progressing new medicines into the clinic.     

Novel molecular targets for antimalarial chemotherapy

The emergence and spread of drug-resistant malaria parasites is a serious public health problem in the tropical world. Malaria control has relied upon the traditional quinoline, antifolate and artemisinin compounds. Very few new antimalarials were developed in the last quarter of the 20th century. An alarming increase in drug-resistant strains of the malaria parasite poses a significant problem for effective control. Recent advances in our knowledge of parasite biology as well as the availability of the genome sequence provide a wide range of novel targets for drug design. Gene products involved in controlling vital aspects of parasite metabolism and organelle function could be attractive targets. It is expected that the application of functional genomic tools in combination with modern approaches such as structure-based drug design and combinatorial chemistry will lead to the development of effective new drugs against drug-resistant malaria strains. This review discusses novel molecular targets of the malaria parasite available to the drug discovery scientist.     

Protein models in drug discovery

Over the last few years, the utilization of protein structural information in drug discovery research has matured and is today applied throughout the process, ranging from genomics-derived target identification and selection to the final design of suitable drug candidates. An especially powerful methodology has arisen from the clear synergies of the combination of target structural information with combinatorial chemistry. Several structural genomics initiatives have recently been started and are now generating 3-D structures of target molecules at an unprecedented rate that will provide a wealth of novel information that can be utilized for rational drug design.