Enzyme models: design and selection

There are two approaches to the discovery of enzyme mimics, that is identifying molecules that are able to bind substrate(s) and then catalyze reactions. The first approach, often inspired by enzymes themselves, utilises chemical knowledge and experience to design the catalyst. The other approach is to create a library and select the best host of a transition state analogue of the required reaction.     

Peptide-cleaving catalyst selective for melanin-concentrating hormone: oxidative decarboxylation of N-terminal aspartate catalyzed by Co(III)cyclen

To provide a firm basis for the new paradigm of drug discovery based on catalysts for oxidative cleavage of N-terminal aspartate (Asp) residues of oligopeptides, oligopeptide-cleaving catalysts were searched by using melanin-concentrating hormone (MCH) as the substrate. MCH is a target for designing drugs to reduce obesity. Catalyst candidates containing the Co(III) complex of cyclen as the catalytic center were prepared by multicomponent condensation reactions. From three kinds of chemical libraries containing about 19,000 catalyst candidates, one compound was identified as the MCH-cleaving catalyst. On incubation with the catalyst, the N-terminal Asp residue of MCH was converted to the pyruvate residue by oxidative decarboxylation. Detailed kinetics analysis revealed the catalytic nature of the action of the catalyst. In addition, the kinetics data indicated that MCH can be cleaved with half-lives of 3 h or less with submicromolar catalyst concentrations if the structure of the catalyst is further improved.     

Fragment-based lead discovery: a chemical update

Fragment-based lead discovery constructs drug leads from small molecular fragments. In theory, this is a highly efficient method for drug discovery, and the technique has become enormously popular in the past few years. In this review, I describe how a variety of approaches in fragment-based lead discovery--including NMR, X-ray crystallography, mass spectrometry, functional screening, and in silico screening--have produced drug leads. Although the examples show that the technique can reliably generate potent molecules, there is still much work to be done to maintain the efficiency of molecules' binding affinities as fragments are linked, expanded, and otherwise improved.     

Genotyping by Genome Reducing and Sequencing for Outbred Animals

Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.     

Recent advances in the discovery of organometallic catalysts using high-throughput screening assays

Combinatorial techniques were developed initially to accelerate the identification of molecules with biological activity. The successes of these techniques inspired the design of high-throughput methods to assist in the discovery of new catalysts. Over the past year, many groups in academia and industry have utilized high-throughput screening assays to reduce the time required to identify catalysts for asymmetric processes, cross-coupling reactions and other metal-catalyzed transformations. The continued success of combinatorial techniques in organometallic chemistry should propagate the development of new and improved methods to facilitate catalyst discovery.     

High Throughput Screening for Anti–Trypanosoma cruzi Drug Discovery

The discovery of new therapeutic options against Trypanosoma cruzi, the causative agent of Chagas disease, stands as a fundamental need. Currently, there are only two drugs available to treat this neglected disease, which represents a major public health problem in Latin America. Both available therapies, benznidazole and nifurtimox, have significant toxic side effects and their efficacy against the life-threatening symptomatic chronic stage of the disease is variable. Thus, there is an urgent need for new, improved anti–T. cruzi drugs. With the objective to reliably accelerate the drug discovery process against Chagas disease, several advances have been made in the last few years. Availability of engineered reporter gene expressing parasites triggered the development of phenotypic in vitro assays suitable for high throughput screening (HTS) as well as the establishment of new in vivo protocols that allow faster experimental outcomes. Recently, automated high content microscopy approaches have also been used to identify new parasitic inhibitors. These in vitro and in vivo early drug discovery approaches, which hopefully will contribute to bring better anti–T. cruzi drug entities in the near future, are reviewed here.     

现代生物学对药物发现的影响

随着后基因组时代的到来,药物发现研究领域不断涌现出一系列新思路、新技术、新方法,从而迅速推进药物发现的多元化发展。一方面,基因组学、蛋白质组学、转录组学、代谢组学、生物信息学、系统生物学等新兴学科的崛起与发展,为药物发现提供更为广泛而深刻的理论基础;另一方面,计算机辅助药物设计、高通量筛选、高内涵筛选、生物芯片、转基因和RNA干扰等高新技术的发展和完善,为药物发现提供了新的技术手段和有力工具,极大地拓宽了药物发现的途径。本文结合近年来现代生物学的研究进展,综述现代生物学对药物发现过程的影响。     

microRNA计算发现方法的研究进展

microRNA (miRNA)是近几年发现的一类长度为～21 nt的内源非编码小RNA, 在植物和动物中发挥着重要而广泛的调控功能。它的发现主要有cDNA克隆测序和计算发现两条途径。由于cDNA克隆测序方法受miRNA表达的时间和组织特异性以及表达水平的影响, 而计算发现可以弥补其不足, 因此miRNA的计算发现方法研究受到了广泛的重视。文章对近几年计算发现miRNA的研究进展进行了综述, 根据计算发现方法的本质, 将计算发现方法归纳为5类, 分别是同源片段搜索方法、基于比较基因组学的预测方法、基于序列和结构特征打分的预测方法、结合作用靶标的预测方法和基于机器学习的预测方法, 并对各类方法的原理、核心思想、优点和局限性进行了分析, 最后探讨了进一步的发展方向。     

Proton-activated fluorescence as a tool for simultaneous screening of combinatorial chemical reactions

In recent years, combinatorial chemistry has had a significant impact on catalyst discovery in diverse fields. Proton-activated fluorescence (PAF) has been successfully demonstrated as a technique for effective screening of catalysts for electro-oxidation, enzymatic ester hydrolysis and nonenzymatic acyl transfer reactions. Among the working prototypes are screens for high-throughput assays of arrayed solid-state catalysts, dissolved enzymatic and small-molecule catalysts, as well as catalysts immobilized in solid-phase synthesis beads or polymeric gels. Given the range of reactions that may be set up to provide a change in local pH, the potential of PAF to facilitate catalyst discovery and process development is significant.     

Lessons learned from the transformation of natural product discovery to a genome-driven endeavor

Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as “reverse-discovered” natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs.     

Iridium Oxide‐Assisted Plasmon‐Induced Hot Carriers: Improvement on Kinetics and Thermodynamics of Hot Carriers

Plasmonic nanostructures are capable of driving photocatalysis through absorbing photons in the visible region of the solar spectrum. Unfortunately, the short lifetime of plasmon‐induced hot carriers and sluggish surface chemical reactions significantly limit their photocatalytic efficiencies. Moreover, the thermodynamically favored excitation mechanism of plasmonic photocatalytic reactions is unclear. The mechanism of how the plasmonic catalyst could enhance the performance of chemical reaction and the limitation of localized surface plasmon resonance devices is proposed. In addition, a design is demonstrated through co‐catalyst decorated plasmonic nanoparticles Au/IrO_X upon a semiconductor nanowire‐array TiO₂ electrode that are able to considerably improve the lifetime of plasmon‐induced charge‐carriers and further facilitate the kinetics of chemical reaction. A thermodynamically favored excitation with improved kinetics of hot carriers is revealed through electrochemical studies and characterization of X‐ray absorption spectrum. This discovery provides an opportunity to efficiently manage hot carriers that are generated from metal nanostructures through surface plasmon effects for photocatalysis applications.     

Synthetic biology enabling access to designer polyketides

The full potential of polyketide discovery has yet to be reached owing to a lack of suitable technologies and knowledge required to advance engineering of polyketide biosynthesis. Recent investigations on the discovery, enhancement, and non-natural use of these biosynthetic gene clusters via computational biology, metabolic engineering, structural biology, and enzymology-guided approaches have facilitated improved access to designer polyketides. Here, we discuss recent successes in gene cluster discovery, host strain engineering, precursor-directed biosynthesis, combinatorial biosynthesis, polyketide tailoring, and high-throughput synthetic biology, as well as challenges and outlooks for rapidly generating useful target polyketides.     

Discovery of novel sodium channel inhibitors—A gene family-based approach

Voltage-gated sodium (Na_V) channel inhibitors are an important class of drugs that are used to treat a number of CNS indications including pain, local anaesthesia, epilepsy and bipolar disorder. These drugs all have their origins in traditional “empirical” pharmacology, and it was only some time after discovery that they were found to inhibit Na_V channels. The basis for therapeutic selectivity of these drugs within different disease indications is currently unknown. However, the subsequent discovery of a multi-gene family of Na_V channels suggests a possible mechanism and has opened the way for more targeted approaches to finding improved therapeutic inhibitors. This article describes some ongoing approaches to systematically clone, express and characterise the entire family of Na_V subtypes in order to better understand their properties and define their individual physiological and pathophysiological roles. As well as providing specific disease validation for individual subtypes, this also provides a panel of reagents for comprehensively exploring the efficacy, selectivity and potency relationships of existing Na_V-blocking drugs. In this way, a gene family-based approach to Na_V channels has enabled a “drug-to-target” approach, reversing the more usual “gene-to-target-to-drug” paradigm. Together with recent advances in assay technology, gene family-based approaches are increasing the tractability of these targets and are re-invigorating Na_V drug discovery within the pharmaceutical industry.     

Clinical Proteomics and OMICS clues useful in Translational Medicine Research

ABSTRACT: Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems, spanning areas of basic biological research, clinical diagnostics, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage. Proteomic signatures, specific for multiple diseases, including cancer and pre-invasive lesions, are emerging. This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus helping to improve applications of clinical proteomic strategies for translational medicine research.     

Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa

Probiotic bacteria can modulate immune responses in the host gastrointestinal tract to promote health. The genomics era has provided novel opportunities for the discovery and characterization of bacterial probiotic effector molecules that elicit specific responses in the intestinal system. Furthermore, nutrigenomic analyses of the response to probiotics have unravelled the signalling and immune response pathways which are modulated by probiotic bacteria. Together, these genomic approaches and nutrigenomic analyses have identified several bacterial factors that are involved in modulation of the immune system and the mucosal barrier, and have revealed that a molecular 'bandwidth of human health' could represent a key determinant in an individual's physiological responsiveness to probiotics. These approaches may lead to improved stratification of consumers and to subpopulation-level probiotic supplementation to maintain or improve health, or to reduce the risk of disease.     

Emerging methods for the rapid determination of enantiomeric excess

Methods for enantiomeric excess determination using a variety of spectroscopic techniques are summarized. Particular attention is paid to techniques that have promise for application to problems of combinatorial catalyst discovery but have not yet been so employed.     

Functional proteomics: The goalposts are moving

Holistic understanding of protein function is a primary goal of the post-genome sequencing era. Functional genomic approaches are powerful and relatively straightforward but produce an incomplete picture at the protein level. Proteomics offers physiologically enriched insights to protein function, and ongoing advances are enabling proteome analyses to proceed with increased depth and efficiency. Exciting discoveries have emerged recently amidst growing awareness of the power of proteomics. However, while proven as a potent discovery tool, proteomics is under pressure to provide improved functional value particularly in concert with other investigative approaches. As reviewed here for ERp29, a recently discovered endoplasmic reticulum protein, the role of novel proteins can remain elusive even after substantial information has accrued. Thousands more proteins of uncertain function will be unveiled in the near future. Consequently, the goalposts are moving for proteomics both through increasing demand for high-value functional information and improving capacity to deliver.