In silico research in drug discovery

Target and lead discovery constitute the main components of today's early pharmaceutical research. The aim of target discovery is the identification and validation of suitable drug targets for therapeutic intervention, whereas lead discovery identifies novel chemical molecules that act on those targets. With the near completion of the human genome sequencing, bioinformatics has established itself as an essential tool in target discovery and the in silico analysis of gene expression and gene function are now an integral part of it, facilitating the selection of the most relevant targets for a disease under study. In lead discovery, advances in chemoinformatics have led to the design of compound libraries in silico that can be screened virtually. Moreover, computational methods are being developed to predict the drug-likeness of compounds. Thus, drug discovery is already on the road towards electronic R&D.     

Aptamers as tools for target prioritization and lead identification

The increasing number of potential drug target candidates has driven the development of novel technologies designed to identify functionally important targets and enhance the subsequent lead discovery process. Highly specific synthetic nucleic acid ligands – also known as aptamers – offer a new exciting route in the drug discovery process by linking target validation directly with HTS. Recently, aptamers have proven to be valuable tools for modulating the function of endogenous cellular proteins in their natural environment. A set of technologies has been developed to use these sophisticated ligands for the validation of potential drug targets in disease models. Moreover, aptamers that are specific antagonists of protein function can act as substitute interaction partners in HTS assays to facilitate the identification of small-molecule lead compounds.     

Biophysics: for HTS hit validation,chemical lead optimization,and beyond

Introduction: There are many challenges to the drug discovery process, including the complexity of the target, its interactions, and how these factors play a role in causing the disease. Traditionally, biophysics has been used for hit validation and chemical lead optimization. With its increased throughput and sensitivity, biophysics is now being applied earlier in this process to empower target characterization and hit finding.

Areas covered: In this article, the authors provide an overview of how biophysics can be utilized to assess the quality of the reagents used in screening assays, to validate potential tool compounds, to test the integrity of screening assays, and to create follow-up strategies for compound characterization. They also briefly discuss the utilization of different biophysical methods in hit validation to help avoid the resource consuming pitfalls caused by the lack of hit overlap between biophysical methods.

Expert opinion: The use of biophysics early on in the drug discovery process has proven crucial to identifying and characterizing targets of complex nature. It also has enabled the identification and classification of small molecules which interact in an allosteric or covalent manner with the target. By applying biophysics in this manner and at the early stages of this process, the chances of finding chemical leads with novel mechanisms of action are increased. In the future, focused screens with biophysics as a primary readout will become increasingly common.     

Microbial genomics and novel antibiotic discovery: new technology to search for new drugs

The process of prokaryotic drug discovery has been a model of success for over fifty years, yet the number of exploited bacterial targets is a mere fraction, less than 0.1% of the potential targets (based on total number of bacterial genes identified by gene sequence projects). To better understand the potential for drug intervention, multiple paradigms have been established in the pharmaceutical industry, all with some semblance of commonality and uniqueness to provide proprietary positioning, yet no company has been successful to date in taking a genomics approach to the finish line of having a genomics-based drug on the market. Within this overview, we provide a strategic overview of a sample process for the identification, validation and exploitation of novel antibacterial targets ascertained through a bioinformatics-based genomics drug discovery program.     

Antibody-enabled small-molecule drug discovery

Although antibody-based therapeutics have become firmly established as medicines for serious diseases, the value of antibodies as tools in the early stages of small-molecule drug discovery is only beginning to be realized. In particular, antibodies may provide information to reduce risk in small-molecule drug discovery by enabling the validation of targets and by providing insights into the design of small-molecule screening assays. Moreover, antibodies can act as guides in the quest for small molecules that have the ability to modulate protein-protein interactions, which have traditionally only been considered to be tractable targets for biological drugs. The development of small molecules that have similar therapeutic effects to current biologics has the potential to benefit a broader range of patients at earlier stages of disease.     

Fulfilling the promise: drug discovery in the post-genomic era

The genomic era has brought with it a basic change in experimentation, enabling researchers to look more comprehensively at biological systems. The sequencing of the human genome coupled with advances in automation and parallelization technologies have afforded a fundamental transformation in the drug target discovery paradigm, towards systematic whole genome and proteome analyses. In conjunction with novel proteomic techniques, genome-wide annotation of function in cellular models is possible. Overlaying data derived from whole genome sequence, expression and functional analysis will facilitate the identification of causal genes in disease and significantly streamline the target validation process. Moreover, several parallel technological advances in small molecule screening have resulted in the development of expeditious and powerful platforms for elucidating inhibitors of protein or pathway function. Conversely, high-throughput and automated systems are currently being used to identify targets of orphan small molecules. The consolidation of these emerging functional genomics and drug discovery technologies promises to reap the fruits of the genomic revolution.     

Target validation

With the publication of draft maps of the human genome and an interim agreement that the human genome comprises approximately 21000 genes, there has been considerable anticipation that many novel disease-specific molecular targets will be rapidly identified and that these will form the basis of many new drug discovery programs. Genes associated with a given disease can thus be identified using genotyping and microarray approaches. However, transitioning from the identification to the subsequent validation and prioritization of their cognate proteins as bona fide drug targets using proteomic techniques--a process that could appropriately be termed targetomics--is still very much in its infancy, with expectations far exceeding present capabilities. The criteria for target validation have yet to be determined and the timing to success has been underestimated. Integrated pharmacological approaches that involve the use of the traditional null hypothesis approach and statistically validated replication have been largely overlooked in the enthusiasm to be the first to find new targets. Inevitably, the only useful measure of target validation occurs when a drug-like molecule, selective for the identified target, is advanced to the clinic where it can be shown to be efficacious in the appropriate human disease state.     

Rethinking target discovery in polygenic diseases

Despite an extraordinary investment in R&D the yield of successful new drugs has been disproportionately low in recent years, suggesting that the whole process of drug development requires rethinking and reform. Most analyses on this issue focus on molecular target discovery considerations. Target identification is characterized by a surplus of potential targets, but there is a translational bottleneck primarily due to limitations of currently employed target validation platforms. Meanwhile, the clinical entities, to which treatments are directed, are also highly complex in terms of pathophysiologic mechanisms and manifestations. In the present study we discuss the limitations of current molecular target discovery approaches mainly in regard to selectivity and efficacy. We also describe the constraints imposed on drug development by the current diagnostic constructs and the tendency towards dissecting the complex clinical phenotypes to component intermediate phenotypes. Finally, we describe how the reconsideration of molecular and clinical targets in polygenic diseases may lead to new strategies of pharmacological intervention directed against component dysfunctions, rather than the whole complex phenotype. Such strategies involve the combination of single ligands that act selectively on multiple molecules involved in a particular disease, or the employment of "multi-targeted" drugs, i.e. single drug molecules that hit selectively multiple receptors sharing common binding sites.     

药物分子与靶蛋白相互作用的研究进展

药物发挥作用是以药物分子与其靶标的相互作用为基础的，对药物-靶点相互作用的定性分析与定量检测贯穿于从新药筛选发现到走向临床的整个过程。经过几十年的发展，研究药物分子与靶蛋白间相互作用的手段已经从传统的生化实验方法转变为以先进的分子生物学、生物物理学理论为支撑的高效、准确、多样化的技术体系。笔者从靶点发现与验证、亲和力测定、相互作用位点与结构分析几个方面对代表性的方法和技术进行介绍，以期为药物研发与机制探索提供参考。     

Peptide aptamers as guides for small-molecule drug discovery

Peptide aptamers are combinatorial protein reagents that bind to target proteins with a high specificity and a strong affinity. By so doing, they can modulate the function of their cognate targets. Because peptide aptamers introduce perturbations that are similar to those caused by therapeutic molecules, their use identifies and/or validates therapeutic targets with a higher confidence level than is typically provided by methods that act upon protein expression levels. The unbiased combinatorial nature of peptide aptamers enables them to 'decorate' numerous polymorphic protein surfaces, whose biological relevance can be inferred through characterization of the peptide aptamers. Bioactive aptamers that bind druggable surfaces can be used in displacement screening assays to identify small-molecule hits to the surfaces. The peptide aptamer technology has a positive impact on drug discovery by addressing major causes of failure and by offering a seamless, cost-effective process from target validation to hit identification.     

Targeting disease, not disease targets: Innovative approaches in tackling neurodegenerative disorders

Preclinical drug investigation entails identifying and optimizing drug candidates to yield effective therapeutics with an acceptable level of adverse side effects. Inevitably, this investigation phase is bound to using model systems that mimic crucial aspects of disease biology in order to assess drug efficacy. The quality or predictability of these disease models is therefore of utmost importance to the development of successful drugs. Models should also be cost-effective and, from a biological point of view, sufficiently simple to enable molecules that act specifically (ie, that modulate a single, pre-defined target) to be identified easily and to allow for HTS. To meet these demands, typical drug discovery approaches rely heavily on biochemical assays in which the activity of a pre-defined target is reconstituted artificially. However, such a rational reductionist approach may compromise the predictability of a model because targets are assessed in an artificial environment that is deprived of any relevant biological context. Moreover, given the pre-established limits on target space and mode of action in a model, efficient and innovative drug discovery programs may be hampered. This feature article considers alternative or complementary approaches that advocate the introduction of biological context early in the drug discovery process. A case study of how NV reMYND has implemented 'biology-driven' drug discovery is presented.     

Molecular approaches to target discovery:--evaluating targets for anti-tuberculosis drug discovery programmes

Selection of appropriate targets for launching antituberculosis drug discovery programmes is challenging. This challenge is magnified by the limited repertoire of 'validated targets' and the paucity of clinically successful drugs. However, continued understanding of the biology of the microbe and its interaction with the host has enabled detailed evaluation of several interesting pathways and novel targets. The value of a target that is suitable for antituberculosis drug discovery needs to be defined not only in the context of its 'essentiality' for survival in vitro but also against a variety of properties relevant to activities in the drug discovery process, e.g.; selectivity, vulnerability, suitability for structural studies, ability to monitor inhibition in whole cells etc. It is also rarely feasible to obtain all the relevant information on the target prior to the launch of a discovery programme. Thus, there is a continuous confidence-building exercise on the validity of a target. Several novel approaches have enabled exploitation of the mycobacterial genome and prioritisation of putative targets; the concept of 'sterilisation' is now being evaluated not only through the availability of structurally diverse probe compounds but also by the ability to characterise metabolic pathways in vivo. The impact of the current knowledge base on the different facets of 'target validation' relevant to antituberculosis drug discovery is discussed in this article with emphasis on developing appropriate matrix systems to prioritise them. The article also discusses the influence of lead generation approaches with specific reference to antibacterial drug discovery.     

反义技术在新型抗菌药物研发中的应用

抗生素耐药菌株的出现及迅速蔓延对人类生命安全构成了严重威胁,为解决这一问题,迫切需要研发新型抗菌药物。反义技术在这一领域中发挥着越来越重要的作用。本文重点综述了反义技术在以下几个方面的应用,包括寻找新的抗菌药物作用靶点、利用反义技术构建敏感菌从天然化合物库中筛选新型抗菌药物、采用反义技术抑制耐药基因的表达从而逆转耐药菌对现有抗生素的敏感性。另外,本文还讨论了人工合成的反义核酸的抗菌活性,并分析了其作为抗菌药物存在的问题及今后的发展前景。     

Emerging techniques for the discovery and validation of therapeutic targets for skeletal diseases

Advances in genomics and proteomics have revolutionised the drug discovery process and target validation. Identification of novel therapeutic targets for chronic skeletal diseases is an extremely challenging process based on the difficulty of obtaining high-quality human diseased versus normal tissue samples. The quality of tissue and genomic information obtained from the sample is critical to identifying disease-related genes. Using a genomics-based approach, novel genes or genes with similar homology to existing genes can be identified from cDNA libraries generated from normal versus diseased tissue. High-quality cDNA libraries are prepared from uncontaminated homogeneous cell populations harvested from tissue sections of interest. Localised gene expression analysis and confirmation are obtained through in situ hybridisation or immunohistochemical studies. Cells overexpressing the recombinant protein are subsequently designed for primary cell-based high-throughput assays that are capable of screening large compound banks for potential hits. Afterwards, secondary functional assays are used to test promising compounds. The same overexpressing cells are used in the secondary assay to test protein activity and functionality as well as screen for small-molecule agonists or antagonists. Once a hit is generated, a structure-activity relationship of the compound is optimised for better oral bioavailability and pharmacokinetics allowing the compound to progress into development. Parallel efforts from proteomics, as well as genetics/transgenics, bioinformatics and combinatorial chemistry, and improvements in high-throughput automation technologies, allow the drug discovery process to meet the demands of the medicinal market. This review discusses and illustrates how different approaches are incorporated into the discovery and validation of novel targets and, consequently, the development of potentially therapeutic agents in the areas of osteoporosis and osteoarthritis. While current treatments exist in the form of hormone replacement therapy, antiresorptive and anabolic agents for osteoporosis, there are no disease-modifying therapies for the treatment of the most common human joint disease, osteoarthritis. A massive market potential for improved options with better safety and efficacy still remains. Therefore, the application of genomics and proteomics for both diseases should provide much needed novel therapeutic approaches to treating these major world health problems.     

Validation strategies for identifying drug targets in dermal fibrotic disorders

Fibrotic skin disorders, such as keloid disease (KD), are common clinically challenging disorders with unknown etiopathogenesis and ill-defined treatment strategies that affect millions of people worldwide. Thus, there is an urgent need to discover novel therapeutics. The validation of potential drug targets is an obligatory step in discovering and developing new therapeutic agents for the successful treatment of dermal fibrotic conditions, such as KD. The integration of multi-omics data with traditional and modern technological approaches, such as RNA interference (RNAi) and genome-editing tools, would provide unique opportunities to identify and validate novel targets in KD during early drug development. Thus, in this review, we summarize the current and emerging drug discovery process with a focus on validation strategies of potential drug targets identified in dermal fibrosis.     

Genetically engineered mouse models for drug discovery: new chemical genetic approaches

While standard transgenic and knockout mouse technologies have provided a wealth of information for target selection and validation, there have been great advances in using more sophisticated modeling techniques to achieve temporal and spatial regulation of individual genes in adult animals. Recent developments in RNA interference (RNAi) technology in in vivo models promise to further improve upon the static and irreversible features of gene knockouts. Chemical genetic approaches create novel functional alleles of targets and allow fine modulation of protein function in vivo by small molecules, providing the most pharmacologically relevant target validation. Using these advanced models, one can not only ask whether the function of the target is critical for the initiation and maintenance of the disease, but also whether therapies designed to alter the function of the target would be safe and efficacious. In this review, we describe various in vivo tools for target validation in mouse models, discuss advantages and disadvantages of each approach, and give examples of their impact on drug discovery.     

Genomics in the real world

The term genomics has evolved into a catch-all term for a variety of information intensive biological methodologies. While the promise of genomics in the bio/pharmaceutical industry is great, its impact on the drug discovery pipeline has not yet been realized, excluding a few notable exceptions. As companies acquire several years of experience in working with genomic data, it is likely that the impact on the discovery process will slowly emerge as we learn to integrate these new technologies into individual discovery programs. It is clear that extracting novel biologically valid targets targets from exponentially growing amounts of sequence data requires time and considerable investment in biological research infrastructure. In order to accelerate the process of target validation, a variety of functional genomics technologies are also being developed to try to predict the effect of inhibitory compounds in advance of development. Resources spent on early stage exploratory efforts such as these can pay off by improving the success rate for screening and medicinal chemistry.