Who will develop new antibacterial agents?

The golden age of antimicrobial drug development is a distant memory, and the likelihood of there being another seems slim. In part, this is because the pharmaceutical industry, which has now adopted an unsustainable business model, abandoned the anti-infective sector, and the pipeline is almost empty. The contribution to this crisis of national governments, health agencies and funders also merits discussion. Much of the basis for drug discovery is funded by the public sector, thereby generating intellectual property and leads for drug development that are often not pursued owing to funding gaps. In particular, the cost of testing drug efficacy in clinical trials is beyond the means of most companies and organizations. Lack of a concerted international effort to develop new antimicrobials is particularly alarming at a time when multidrug-resistant bacteria threaten all areas of human medicine globally. Here, the steps that led to this situation are retraced, and some possible solutions to the dilemma are proposed.     

The integration of investigative toxicology in the drug discovery process

Summary— Integrating toxicology early in the drug discovery process adds value by providing the earliest possible identification of a compound's potential for toxicological and pathological effects relevant to intended clinical use. With this approach true ‘lead’ candidates, with a high probability of clinical success, are identified and advanced while reducing effort and resources expended on compounds without the requisite therapeutic index. Resources are focussed on the speed of getting a discovery ‘lead’ into early clinical development, defining the mechanisms of observed preclinical toxicity and their relevance to human use, and developing early safety data with in vitro test systems ahead of in vivo systems where possible, thus reducing animal use.     

可持续性科学研究热点及其知识基础——以Sustainability Science载文数据为例

以Sustainability Science 2006—2015年间刊载的论文为基础数据,应用Cite Space软件,采取文献共被引分析、关键词共现分析、突现词分析等方法对可持续性科学研究现状进行可视化分析。研究发现,Sustainability Science载文质量和国际影响力逐年上升;日、美、德、澳、加5国及东京大学、联合国大学、亚利桑那州立大学、茨城大学、京都大学、大阪大学、中国科学院等研究机构发文量位居前列,具有较强的研究实力。Komiyama H、Lang D J、Miller T R、Talwar S、Clark W S等是期刊载文引用较多的作者,显示了这些学者在可持续性科学领域的权威性。可持续性科学研究主要聚焦"可持续性"、"气候变化"、"概念框架"、"管治"、"脆弱性"、"适应性"、"恢复力"等热点问题。可持续性科学研究的知识基础主要包括"学科发展"、"跨学科研究"、"规划机制"、"灾害管控"、"信息管理"、"海岛环境"、"沿海脆弱性评估"、"土地利用"和"生态景观"等研究领域。     

A personal account of the role of peptide research in drug discovery: the case of hepatitis C.

Although peptides themselves are not usually the end products of a drug discovery effort, peptide research often plays a key role in many aspects of this process. This will be illustrated by reviewing the experience of peptide research carried out at IRBM in the course of our study of hepatitis C virus (HCV). The target of our work is the NS3/4A protease, which is essential for maturation of the viral polyprotein. After a thorough examination of its substrate specificity we fine-tuned several substrate-derived peptides for enzymology studies, high-throughput screening and as fluorescent probes for secondary binding assays. In the course of these studies we made the key observation: that the protease is inhibited by its own cleavage products. Single analog and combinatorial optimization then derived potent peptide inhibitors. The crucial role of the NS4A cofactor was also addressed. NS4A is a small transmembrane protein, whose central domain is the minimal region sufficient for enzyme activation. Structural studies were performed with a peptide corresponding to the minimal activation domain, with a series of product inhibitors and with both. We found that NS3/4A is an induced fit enzyme, requiring both the cofactor and the substrate to acquire its bioactive conformation; this explained some puzzling results of 'serine-trap' type inhibitors. A more complete study on NS3 activation, however, requires the availability of the full-length NS4A protein. This was prepared by native chemical ligation, after sequence engineering to enhance its solubility; structural studies are in progress. Current work is focused on the P' region of the substrate, which, at variance with the P region, is not used for ground state binding to the enzyme and might give rise to inhibitors showing novel interactions with the enzyme.     

Microarray technology GEM microarrays and drug discovery

Incyte Genomics' GEM™ Gene Expression Microarray is a proven genomics tool used by a large number of pharmaceutical companies to speed up the drug discovery and development process. The development and integration of this technology, together with Incyte's sequence databases and clone resources, have resulted in GEM microarrays that span approximately 60,000 human genes as well as approximately 60,000 plant, rat, mouse, yeast, and bacterial genes. The technology underlying the use of these arrays and their application to the drug discovery process is highlighted. Journal of Industrial Microbiology & Biotechnology (2002) 28, 180–185 DOI: 10.1038/sj/jim/7000136 Received 16 November 2000/ Accepted in revised form 01 March 2001     

中国新药研究开发现状

随着国民经济的持续发展和生活水平的不断提高,健康状况与生命质量已经成为我国新时期社会发展的重大课题。人口老龄化和农村医药市场的拓展为生物医药产业提供了前所未有的成长空间。经过多年的不懈努力,我国自主的创新药物研究体系已经初步形成,以提升国际竞争力为导向,医药产业正在实现由仿制为主向创新为主的历史性转变。     

A solid-phase glycosyltransferase assay for high-throughput screening in drug discovery research

Glycosyltransferases mediate changes in glycosylation patterns which, in turn, may affect the function of glycoproteins and/or glycolipids and, further downstream, processes of development, differentiation, transformation and cell-cell recognition. Such enzymes, therefore, represent valid targets for drug discovery. We have developed a solid-phase glycosyltransferase assay for use in a robotic high-throughput format. Carbohydrate acceptors coupled covalently to polyacrylamide are coated onto 96-well plastic plates. The glycosyltransferase reaction is performed with recombinant enzymes and radiolabeled sugar-nucleotide donor at 37°C, followed by washing, addition of scintillation counting fluid, and measurement of radioactivity using a 96-well -counter. Glycopolymer construction and coating of the plastic plates, enzyme and substrate concentrations, and linearity with time were optimized using recombinant Core 2 1-6-N-acetylglucosaminyltransferase (Core 2 GlcNAc-T). This enzyme catalyzes a rate-limiting reaction for expression of polylactosamine and the selectin ligand sialyl-Lewis^x in -glycans. A glycopolymer acceptor for 1-6-N-acetylglucosaminyltransferase V was also designed and shown to be effective in the solid-phase assay. In a high-throughput screen of a microbial extract library, the coefficient of variance for positive controls was 9.4%, and high concordance for hit validation was observed between the Core 2 GlcNAc-T solid-phase assay and a standard solution-phase assay. The solid-phase assay format, which can be adapted for a variety of glycosyltransferase enzymes, allowed a 5–6 fold increase in throughput compared to the corresponding solution-phase assay.     

Simultaneous Determination of Patulin and Penicillic Acid in Grains by Gas Chromatographic Method

Changes in aggregation and properties of alkali-treated soybean 7S and 11S globulins depend upon protein concentration during alkali-treatment. Such variables were investigated by viscosity, electrophoresis, circular dichroism, pulsed NMR, emulsion capacity and CaCl₂ precipitation measurements. In lower protein concentrations, the intrinsic viscosity decreased and the penetrative fractions into electrophoresis gel increased. The reduced contacts of proteins during neutralization resulted in smaller aggregates. Also specific fractions which were more sensitive to protein concentration on aggregation were observed for 11S globulin. The quantity of bound water depended only on pH at 7% concentration treatment. When the gel was formed, the bound water of protein increased, e.g., 0.085 g and 0.135 g/g protein at pH 10.6 and 13.2 treatment, respectively, whereas at 1% treatment, bound water showed almost no pH dependence (about 0.13 g/g protein). Furthermore, proteins prepared at higher protein concentrations were characterized by higher emulsion capacity and CaCI₂ precipitation ability. However, no protein concentration dependence was seen in the secondary structure of the aggregates.     

Computational estimation of quality and clinical relevance of cancer cell lines

Immortal cancer cell lines (CCLs) are the most widely used system for investigating cancer biology and for the preclinical development of oncology therapies. Pharmacogenomic and genome‐wide editing screenings have facilitated the discovery of clinically relevant gene–drug interactions and novel therapeutic targets via large panels of extensively characterised CCLs. However, tailoring pharmacological strategies in a precision medicine context requires bridging the existing gaps between tumours and in vitro models. Indeed, intrinsic limitations of CCLs such as misidentification, the absence of tumour microenvironment and genetic drift have highlighted the need to identify the most faithful CCLs for each primary tumour while addressing their heterogeneity, with the development of new models where necessary. Here, we discuss the most significant limitations of CCLs in representing patient features, and we review computational methods aiming at systematically evaluating the suitability of CCLs as tumour proxies and identifying the best patient representative in vitro models. Additionally, we provide an overview of the applications of these methods to more complex models and discuss future machine‐learning‐based directions that could resolve some of the arising discrepancies.     

Computational Fragment-Based Design of Phytochemical Derivatives as EGFR Inhibitors

Epidermal growth factor receptor (EGFR) is a potential target with disease modifying benefits against Alzheimer's disease (AD). Repurposing of FDA approved drugs against EGFR have shown beneficial effect against AD but are confined to quinazoline, quinoline and aminopyrimidines. Futuristically, the possibility of acquiring drug resistance mutation as seen in the case of cancer could also hamper AD treatment. To identify novel chemical scaffolds, we rooted on phytochemicals identified from plants such as Acorus calamus, Bacopa monnieri, Convolvulus pluricaulis, Tinospora cordifloia, and Withania somnifera that have well-established records in the treatment of brain disorders. The rationale was to mimic the biosynthetic metabolite extension process observed in the plants for synthesizing new phytochemical derivates. Thus, novel compounds were designed computationally by fragment-based method followed by extensive in silico analysis to pick potential phytochemical derivates. PCD1, 8 and 10 were predicted to have better blood brain barrier permeability. ADMET and SoM analysis suggested that these PCDs exhibited druglike properties. Further simulation studies showed that PCD1 and PCD8 stably interact with EGFR and have the potential to be used even in cases of drug-resistance mutations. With further experimental evidence, these PCDs could be leveraged as potential inhibitors of EGFR.     

A proposed bioactive form of peptide T and the design of peptidomimetics

Peptide T is a non-natural octapeptide of sequence Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr, taken from the sequence of the protein gp120 of HIV. The peptide has been shown to bind competitively to the CD4 receptors of the helper/inducer lymphocytes T. The peptide is presently used for the treatment of AIDS-associated dementia and has been proven useful for the treatment of psoriasis. Using molecular modeling procedures, we studied the conformational profile of this peptide as well as those of several active and inactive analogs. The analysis of these results gave rise to the proposal of a bioactive conformation of the peptide, which can be described as a pseudo -turn structure, involving the last four residues at the C-terminus of the peptide. The secondary structure is stabilized by a hydrogen bond between the hydroxyl hydrogen of the side chain of Thr⁵ and the carbonyl oxygen of Tyr⁷. From the bioactive form and different structure–activity relationship studies, a pharmacophore was proposed. This hypothesis was used to search on several 3D data bases. One of the hits obtained was the natural compound amigdalin, which was tested and exhibited moderate activity.     

A proposed bioactive form of peptide T and the design of peptidomimetics

Summary Peptide T is a non-natural octapeptide of sequence Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr, taken from the sequence of the protein gp 120 of HIV. The peptide has been shown to bind competitively to the CD4 receptors of the helper/inducer lymphocytes T. The peptide is presently used for the treatment of AIDS-associated dementia and has been proven useful for the treatment of psoriasis. Using molecular modeling procedures, we studied the conformational profile of this peptide as well as those of several active and inactive analogs. The analysis of these results gave rise to the proposal of a bioactive conformation of the peptide, which can be described as a pseudo β-turn structure, involving the last four residues at the C-terminus of the peptide. The secondary structure is stabilized by a hydrogen bond between the hydroxyl hydrogen of the side chain of Thr⁵ and the carbonyl oxygen of Tyr⁷. From the bioactive form and different structure-activity relationship studies, a pharmacophore was proposed. This hypothesis was used to search on several 3D data bases. One of the hits obtained was the natural compound amigdalin, which was tested and exhibited moderate activity.     

当地生态知识在海洋哺乳动物研究中的应用与展望

当地生态知识(local ecological knowledge,LEK)是指人们在长期的生活体验和生产实践中,获得的有关周边环境、生物资源及其相互关系的经验和知识。近几十年来,LEK在海洋哺乳动物研究中得到了广泛的应用和发展,尤其是在基础相对薄弱的发展中国家或地区,LEK作为一种低成本、短周期且适合大范围调查的手段,日益成为研究人员获取目标物种生态信息的重要渠道。LEK与野外实地调查等获得的数据可以互补,从而为评估海洋哺乳动物的生存状况和环境变化提供多维度的信息来源;该方法还往往是了解目标物种生存状况历史变动的有效手段,回答传统方法很难甚至无法回答的科学问题,如目标物种在较长时间尺度上的生态信息历史变化趋势等。本文介绍了LEK的定义及特征、海洋哺乳动物及其传统生态调查方法、LEK在海洋哺乳动物中的研究进展、应用LEK开展海洋哺乳动物研究的步骤,还讨论了LEK在我国海洋哺乳动物研究中的应用前景和推广价值,旨在为今后相关研究提供参考资料。     

Ubiquitinomics: History,methods, and applications in basic research and drug discovery

The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. Ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition, and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research.     

Interrogating 7TM receptors: Does texture in the question yield greater texture in the answer?

The key to detecting and classifying drug effect at seven transmembrane (7TM) receptors is the pharmacological assay. Drug discovery had been rooted in testing of molecules on intact animal tissue until technology provided high-throughput binding assays for screening. While this allowed for the testing of large numbers of molecules, it also limited detection to molecules that interfere with the interaction of the receptor with a defined probe (i.e., radioligand). The ability to monitor functional changes in cells (recombinant or natural) provided a huge leap forward. Earlier functional assays were tied to specific signaling pathways (i.e., cyclic AMP and calcium) but now label-free assays in live cells provide the opportunity to detect more ligands and more fully characterize their efficacy. These ideas will be discussed in terms of harnessing the phenomenon of “functional selectivity” for therapeutic advantage.