From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways

Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail.     

寻找微生物基因组中适合高通量药物筛选靶点的功能未知基因

开发有新作用机制的抗生素迫在眉睫。刚发现青霉素时 ,几乎所有的金黄色链球菌都是药物敏感型 ;异烟肼和链霉素刚用来治疗结核病时 ,效果几乎 1 0 0 % ,但 90年代中期 ,几乎 90 %的金黄色链球菌和 50 %以上的结核分枝杆菌都耐药 ,耐多药菌株也日益普遍。现有抗生素的作用机制比较单一 ,是细菌产生耐药性的一个主要原因。解决日益严重的细菌耐药性、交叉耐药性、毒性和难以根除条件致病菌感染最有效的途径是开发新作用机制的抗生素。1 .微生物基因组及其功能未知基因中蕴涵了开发新型抗生素的大量有用靶点抗生素开发首先往往需要鉴定靶点。靶…     

Searching for drug targets in microbial genomes

Comparative analysis of the complete genome sequences of 10 bacterial pathogens available in the public databases offers the first insights into the drug discovery approaches of the near future. Genes that are conserved in different genomes often turn out to be essential, which makes them attractive targets for new broad-spectrum antibiotics. Subtractive genome analysis reveals the genes that are conserved in all or most of the pathogenic bacteria but not in eukaryotes; these are the most obvious candidates for drug targets. Species-specific genes, on the other hand, may offer the possibility to design drugs against a particular, narrow group of pathogens.     

From cancer metabolism to new biomarkers and drug targets

Great interest is presently given to the analysis of metabolic changes that take place specifically in cancer cells. In this review we summarize the alterations in glycolysis, glutamine utilization, fatty acid synthesis and mitochondrial function that have been reported to occur in cancer cells and in human tumors. We then propose considering cancer as a system-level disease and argue how two hallmarks of cancer, enhanced cell proliferation and evasion from apoptosis, may be evaluated as system-level properties, and how this perspective is going to modify drug discovery. Given the relevance of the analysis of metabolism both for studies on the molecular basis of cancer cell phenotype and for clinical applications, the more relevant technologies for this purpose, from metabolome and metabolic flux analysis in cells by Nuclear Magnetic Resonance and Mass Spectrometry technologies to positron emission tomography on patients, are analyzed. The perspectives offered by specific changes in metabolism for a new drug discovery strategy for cancer are discussed and a survey of the industrial activity already going on in the field is reported.     

Oxidized phospholipids as potential novel drug targets

The interactions of three therapeutic agents, viz. the antipsychotics HPD and CPZ, and the antineoplastic anthracycline DOX, with oxidatively modified phospholipids were studied by monitoring the quenching of fluorescence of an incorporated pyrene-labeled lipid derivative. All three drugs bound avidly to the two oxidized PCs bearing either an aldehyde or carboxylic function at the end of the sn-2 nonanoyl chain, with the highest affinity measured between CPZ and the latter oxidized lipid. Subsequent dissociation of the above drugs from the oxidized lipids by DNA, acidic phospholipids, and NaCl revealed the binding of these drugs with the aldehyde lipid to be driven by hydrophobicity similarly to their binding to lysophosphatidylcholine, whereas a significant contribution of electrostatics was evident for the lipid with the carboxylic moiety. These results connect to previous experimental data, demonstrating the induction by these drugs of oxidative stress and binding to membrane phospholipids. These issues are elaborated with reference to their clinical use and side effects.     

Affinity capillary electrophoresis for the screening of novel antimicrobial targets

The increasing number of multiantibiotic-resistant organisms, including methicillin-resistant Staphylococcus aureus (MRSA), requires the development of novel chemotherapies that are structurally distinct and exempt from current resistance mechanisms. Bioinformatics data mining of microbial genomes has revealed numerous previously unexploited essential open reading frames (ORFs) of unknown biochemical function. The potential of these proteins as screening targets is not readily apparent because most screening technologies rely on knowledge of biological function. To address this problem, the authors employed affinity capillary electrophoresis (ACE) to identify antimicrobial compounds that bound the novel target YihA. Screening a small-molecule library of 44,000 compounds initially identified 115 binders, of which 76% were confirmed. Furthermore, the ACE assay distinguished diverse compounds that possessed drug-like properties and antimicrobial activity against drug-resistant clinical isolates. These data validate ACE as a valuable tool for the fast, efficient detection of specific binding molecules that possess biological activity.     

Mining nematode genome data for novel drug targets

Expressed sequence tag projects have currently produced over 400 000 partial gene sequences from more than 30 nematode species and the full genomic sequences of selected nematodes are being determined. In addition, functional analyses in the model nematode Caenorhabditis elegans have addressed the role of almost all genes predicted by the genome sequence. This recent explosion in the amount of available nematode DNA sequences, coupled with new gene function data, provides an unprecedented opportunity to identify pre-validated drug targets through efficient mining of nematode genomic databases. This article describes the various information sources available and strategies that can expedite this process.     

新的抗真菌药物靶点研究进展

近30年来,侵袭性真菌感染发病率持续上升,病死率居高不下,而治疗药物十分有限是造成其高致死率的重要因素之一。因此,发现新的抗真菌靶点和药物,已成为迫切需要。正在研究的新的抗真菌靶点如下：一是信号通路介导的抗真菌靶点,包括钙调神经磷酸酶及其分子伴侣Hsp90、3-磷酸肌醇依赖性蛋白激酶（PKH）以及参与Ras蛋白修饰的相关酶等,其拮抗剂包括传统免疫抑制剂的类似物以及Hsp90抗体、KP-372-1和PS77以及手霉素A等;二是GPI锚定蛋白合成通路的催化酶,其抑制剂有E1210和M720等化合物;三是分泌型天冬氨酸蛋白酶,肽类、逆转录病毒抑制剂,以及砜类的衍生物等均可以抑制这一靶点;四是海藻糖的合成的两个关键酶Tps1和Tps2。鉴于侵袭性真菌感染严重影响人类公共健康安全,而新型抗真菌药物的研发又依赖于新靶点的探索,因此,本文靶向这一核心真菌临床问题,系统介绍了当前新的抗真菌药物靶点发展概况,并在靶点选择可行性以及针对靶点的药物研发策略上提出见解。     

New antibiotic discovery, novel screens, novel targets and impact of microbial genomics

The clinical need for new classes of antibiotic continues to grow, as drug resistance erodes the efficacy of current therapies. Historically, most antibiotics were discovered by random screening campaigns, but over the past 20 years, this strategy has largely failed to deliver a sufficient range of chemical diversity to keep pace with changing clinical profiles. A more rational approach to drug hunting has been greatly potentiated by the availability of bacterial genomic information. The rapid progress in sequencing and analysis of these small, prokaryotic genomes has enabled the concomitant development of powerful new technologies that are already enhancing the potential utility of genomic information. The future promises versatile and precise tools to understand what makes a successful antibiotic and moreover the means to identify and evaluate novel classes of drug.     

Molecular engineering of antimicrobial peptides: microbial targets,peptide motifs and translation opportunities

The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.     

Using siclopps for the discovery of novel antimicrobial peptides and their targets

High throughput screening of SICLOPPS libraries afforded six distinct cyclic peptides that inhibit Escherichia coli growth both in liquid and solid media. One of these peptides (LN05) reduced both bacterial growth rate and caused cell aggregation in liquid media. Mutant bacteria immune to LN05 action were obtained at a frequency of 10(-7). Over-expression of an E. coli genomic library in the presence of LN05 production resulted in enrichment of a single genomic construct, a fragment of the NarZ gene.     

Drug resistance mechanisms and novel drug targets for tuberculosis therapy

Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.     

Human monogenic disorders - a source of novel drug targets

The decrease in new drug applications and approvals over the past several years results from an underlying crisis in drug target identification and validation. Model organisms are being used to address this problem, in combination with novel approaches such as the International HapMap Project. What has been underappreciated is that discovery of new drug targets can also be revived by traditional Mendelian genetics. A large fraction of the human gene repertoire remains phenotypically uncharacterized, and is likely to encode many unanticipated and novel phenotypes that will be of interest to pharmaceutical and biotechnological drug developers.     

Sirtuins: novel targets for metabolic disease in drug development

Calorie restriction extends lifespan and produces a metabolic profile desirable for treating diseases such as type 2 diabetes. SIRT1, an NAD⁺-dependent deacetylase, is a principal modulator of pathways downstream of calorie restriction that produces beneficial effects on glucose homeostasis and insulin sensitivity. Activation of SIRT1 leads to enhanced activity of multiple proteins, including peroxisome proliferator-activated receptor coactivator-1α (PGC-1α) and FOXO which helps to mediate some of the in vitro and in vivo effects of sirtuins. Resveratrol, a polyphenolic SIRT1 activator, mimics the effects of calorie restriction in lower organisms and in mice fed a high-fat diet ameliorates insulin resistance. In this review, we summarize recent research advances in unveiling the molecular mechanisms that underpin sirtuin as therapeutic candidates and discuss the possibility of using resveratrol as potential drug for treatment of diabetes.     

A metabolic network approach for the identification and prioritization of antimicrobial drug targets

For many infectious diseases, novel treatment options are needed in order to address problems with cost, toxicity and resistance to current drugs. Systems biology tools can be used to gain valuable insight into pathogenic processes and aid in expediting drug discovery. In the past decade, constraint-based modeling of genome-scale metabolic networks has become widely used. Focusing on pathogen metabolic networks, we review in silico strategies used to identify effective drug targets and highlight recent successes as well as limitations associated with such computational analyses. We further discuss how accounting for the host environment and even targeting the host may offer new therapeutic options. These systems-level approaches are beginning to provide novel avenues for drug targeting against infectious agents.