Comparative folate metabolism in humans and malaria parasites (part I): pointers for malaria treatment from cancer chemotherapy

New inhibitors are urgently needed to overcome the burgeoning problem of drug resistance in the treatment of Plasmodium falciparum infection. Targeting the folate pathway has proved to be a powerful strategy for drug development against rapidly multiplying systems such as cancer cells and microorganisms. Antifolates have long been used for malaria treatment but, despite their success, much less is known about parasite folate metabolism than about that of the human host. In this article, we focus on folate enzymes used clinically as anticancer drug targets, in addition to those that have potential to be used as drug targets, for which there are inhibitors at various stages of development. We discuss how this information could lead to the identification of new targets in malaria parasites.     

T-iDT : tool for identification of drug target in bacteria and validation by Mycobacterium tuberculosis

With the completion of the Human Genome Project in 2003, many new projects to sequence bacterial genomes were started and soon many complete bacterial genome sequences were available. The sequenced genomes of pathogenic bacteria provide useful information for understanding host-pathogen interactions. These data prove to be a new weapon in fighting against pathogenic bacteria by providing information about potential drug targets. But the limitation of computational tools for finding potential drug targets has hindered the process and further experimental analysis. There are many in silico approaches proposed for finding drug targets but only few have been automated. One such approach finds essential genes in bacterial genomes with no human homologue and predicts these as potential drug targets. The same approach is used in our tool. T-iDT, a tool for the identification of drug targets, finds essential genes by comparing a bacterial gene set against DEG (Database of Essential Genes) and excludes homologue genes by comparing against a human protein database. The tool predicts both the set of essential genes as well as potential target genes for the given genome. The tool was tested with Mycobacterium tuberculosis and results were validated. With default parameters, the tool predicted 236 essential genes and 52 genes to encode potential drug targets. A pathway-based approach was used to validate these potential drug target genes. The pathway in which the products of these genes are involved was determined. Our analysis shows that almost all these pathways are very essential for the bacterial survival and hence these genes encode possible drug targets. Our tool provides a fast method for finding possible drug targets in bacterial genomes with varying stringency level. The tool will be helpful in finding possible drug targets in various pathogenic organisms and can be used for further analysis in novel therapeutic drug development. The tool can be downloaded from http://www.milser.co.in/research.htm and http://www.srmbioinformatics.edu.in/ forum.htm.     

基于网络药理学分析瑞香素抗多种肿瘤的作用机制及体外实验验证

基于网络药理学预测瑞香素抗恶性胶质瘤、肝癌和三阴性乳腺癌的共同靶点及可能机制,并对其进行体外实验验证。利用Swiss Target Prediction和GeneCards等数据库检索瑞香素与恶性胶质瘤、肝癌和三阴性乳腺癌的共同靶点。使用Cytoscape构建瑞香素-三种肿瘤蛋白质相互作用网络图(PPI)并筛选出核心靶点,并对核心靶点进行GO及KEGG富集分析;通过AutoDock Tools对瑞香素与核心靶点进行分子对接。体外实验验证:采用CCK-8和Western blot法行体外实验验证不同浓度瑞香素对U-251 MG、HepG-2和MDA-MB231细胞系细胞抑制率和P53、RRM2蛋白的表达水平的影响。共筛选出瑞香素抗三种肿瘤核心靶点56个,富集分析显示靶点富集在P53通路和癌症通路,参与细胞周期调节、细胞凋亡、DNA生物合成和修复等生物过程;分子对接结果显示瑞香素与P53、RRM2有较好的结合作用。体外验证实验显示,与对照组比较,瑞香素能显著抑制U-251 MG、HepG-2、MDA-MB231的增殖(P<0.01),并显著上调其P53蛋白及下调RRM2蛋白的表达,且呈剂量依赖性(P<0.05)。我们的结果提示瑞香素能抑制U-251 MG、HepG-2和MDA-MB231细胞增殖,其机制可能与调控P53/RRM2通路有关。     

Opportunities for structure-based design of protease-directed drugs

As a result of the recent enormous technological progress, experimental structure determination has become an integral part of the development of drugs against disease-related target proteins. The post-translational modification of proteins is an important regulatory process in living organisms; one such example is lytic processing by peptidases. Many different peptidases represent disease targets and are being used in structure-based drug design approaches. The development of drugs such as aliskiren and tipranavir, which inhibit renin and HIV protease, respectively, testifies to the success of this approach.     

Identification of novel bioactive molecules from garlic bulbs: A special effort to determine the anticancer potential against lung cancer with targeted drugs

Garlic (Allium sativum L.), is a predominant spice, which is used as an herbal medicine and flavoring agent, since ancient times. It has a rich source of various secondary metabolites such as flavonoids, terpenoids and alkaloids, which have various pharmacological properties. Garlic is used in the treatment of various ailments such as cancer, diabetes and cardiovascular diseases. The present study aims to explore the plausible mechanisms of the selected phytocompounds as potential inhibitors against the known drug targets of non-small-cell lung cancer (NSCLC). The phytocompounds of garlic were identified by gas chromatography-mass spectrometry (GC–MS) technique. Subsequently, the identified phytocompounds were subjected to molecular docking to predict the binding with the drug targets, epidermal growth factor receptor (EGFR), human epidermal growth factor receptor 2 (HER2), echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) and group IIa secretory phospholipase A2 (sPLA2-IIA). Molecular dynamics is used to predict the stability of the identified phytocompounds against NSCLC drug targets by refining the intermolecular interactions formed between them. Among the 12 phytocompounds of garlic, three compounds[1,4-dimethyl-7-(1-methylethyl)-2-azulenyl]phenylmethanone, 2,4-bis(1-phenylethyl)-phenol and 4,5–2 h-oxazole-5-one,4-[3,5-di-t-butyl-4-methoxyphenyl] methylene-2-phenyl were identified as potential inhibitors, which might be suitable for targeting the different clinical forms of EGFR and dual inhibition of the studied drug targets to combat NSCLC. The result of this study suggest that these identified phytocompounds from garlic would serve as promising leads for the development of lead molecules to design new multi-targeting drugs to address the different clinical forms of NSCLC.     

Liposome encapsulated tumor-associated antigens elicited humoral and cellular immune responses in mice bearing tumor

Chemically induced tumors in mice provide a system to investigate tumor-associated antigens (TAA). The cell surface glycoprotein antigens on such tumor cells have been identified as suitable targets for immune attack. The induction of immune responses against (TAA) in N-nitrosodiethylamine (DEN) exposed mice has been examined. In order to present antigens to the immune system, the liposome was used as vehicle to deliver the TAA. Liposomal-TAA formulation, elicited both humoral and the cellular immune responses, when administered intramuscularly in DEN-exposed mice. Presence of circulatory antibodies against TAA and the induction of cellular responses in immunized mice were monitored using ELISA and in vitro cell proliferation assay of lymphocytes respectively. Specificity of antibody against TAA in immune sera was analysed using immunoblotting technique. Based on these results, it is proposed that the liposome encapsulated TAA may successfully be used to induce humoral and cellular immune responses against tumor.     

肿瘤放化综合治疗中的靶向研究

放化疗综合应用是癌症治疗中的常用方法。研究表明,放化疗综合应用可以有效地控制杀伤肿瘤,但过程中对正常细胞的毒副作用严重制约着放化疗的剂量和疗效。如何在有效杀伤肿瘤细胞的同时减轻放化疗综合应用中对正常细胞的毒副作用已经成为探索更好的治疗策略的关键。随着研究的不断深入,各种相关的新药和新治疗思路层出不穷,比如针对肿瘤发生及代谢过程的靶向类新药、用于辐射增敏的新的基因靶点等都已进入研究者的视线。另外,近年来关于肿瘤细胞中药物转运蛋白的研究也为综合治疗靶点寻找提供了一定依据。本文根据当前研究现状,着重总结近年来放化疗综合治疗靶向研究在上述几方面的一些新进展。     

肿瘤放化综合治疗中的靶向研究

放化疗综合应用是癌症治疗中的常用方法。研究表明,放化疗综合应用可以有效地控制杀伤肿瘤,但过程中对正常细胞的毒副作用严重制约着放化疗的剂量和疗效。如何在有效杀伤肿瘤细胞的同时减轻放化疗综合应用中对正常细胞的毒副作用已经成为探索更好的治疗策略的关键。随着研究的不断深入,各种相关的新药和新治疗思路层出不穷,比如针对肿瘤发生及代谢过程的靶向类新药、用于辐射增敏的新的基因靶点等都已进入研究者的视线。另外,近年来关于肿瘤细胞中药物转运蛋白的研究也为综合治疗靶点寻找提供了一定依据。本文根据当前研究现状,着重总结近年来放化疗综合治疗靶向研究在上述几方面的一些新进展。     

基于网络药理学的谷糠结合态多酚抗乳腺癌机制研究

本研究旨在探讨谷糠结合态多酚(bound phenol of inner shell,BPIS)发挥抗乳腺癌细胞活性的作用机制。首先采用细胞计数法检测BPIS对乳腺癌细胞以及正常乳腺细胞活性的影响;然后综合运用SEA、SIB以及GeneCards等数据库获得BPIS和乳腺癌的相关靶点,并分析活性成分与作用靶点的互作网络以及通路。本研究筛选得到BPIS抗乳腺癌相关靶点39个,主要涉及糖脂代谢和细胞自噬等生物过程以及MAPK、PI3K/AKT、FoxO等多条信号通,表明BPIS抗乳腺癌是多成分、多靶点、多通路协同作用的过程,而与细胞死亡相关的细胞自噬很可能在BPIS抑制乳腺癌过程中发挥主要作用。     

Vaccines to treat cancer--an old approach whose time has arrived

There are extensive DNA changes in tumor cells and the genes of tumor cells continuously mutate at a high rate. While this can provide therapeutic targets, it makes it unlikely that an agent that is selective for a single target will work against all cells in a tumor. However, it may be possible to use tumor epitopes as sentinels to engage adaptive and innate immunological mechanisms and create a tumor destructive environment effective also against variant cells that have lost a given antigen or their ability to present it. We hypothesize that therapeutic tumor vaccines, in combination with the targeting, to tumors, of costimulatory molecules such as anti-CD137scFv, or lymphokines such as GMCSF, will expand anti-tumor responses for therapeutic benefit when used as an adjunct to surgery and chemotherapy.     

Staphylococci in colonization and disease: prospective targets for drugs and vaccines

Pathogenic staphylococci are now regarded in the scientific community as antibiotic resistant 'superbugs' because they have an amazing capacity to acquire resistance traits. Surprisingly, antibiotic development has decelerated. Promising targets for drug development are enzymes involved in the biosynthesis of cell envelope structures such as peptidoglycan, teichoic acids, membrane lipids, or cell wall associated adhesins. Compounds that inactivate or neutralize the most aggressive toxins such as the superantigens and the pore forming toxins have also been considered. In the past decade, global regulatory systems have been studied that contribute to virulence and might be candidates for target development. Targets that are particularly promising include all enzymatic reactions that are unique to bacteria and that are involved in central metabolism, such as methionine-tRNA(fMet) formyltransferase or the peptide deformylase, which have been successfully used for designing new inhibitors. There are also several known antibiotics that have roused new interest especially if they are active against multi-resistant staphylococci. Various cell wall components are promising candidates for active and passive immunization strategies such as capsule, slime, teichoic acids or cell wall bound adhesins. Several new targets for drugs or vaccines will arise from the functional analysis of the staphylococcal genomes that contain many hitherto unknown targets.     

DNA as a target for antimicrobials

Resistance to antimicrobials is one of the biggest threats to our healthcare. However, in the last few decades very few truly novel antimicrobial compounds have been brought to market, creating the potential threat of a post-antibiotic era in which infections are very difficult to treat. Identification of novel compounds with antimicrobial activity is therefore paramount. Ideally, novel compounds should be designed that are active against targets that are not or barely used, as it is less likely that resistance already exists against such compounds. One example of an underexplored target in the treatment of infections is DNA. In this review we describe a number of DNA binding compounds and discuss potential opportunities and problems.     

Possible implications of biocide accumulation in the environment on the prevalence of bacterial antibiotic resistance

The lethality of biocides depends upon their interaction with a number of distinct biochemical targets. This often reflects reactive chemistry for any given agent, such as thiol oxidation. Susceptibility may vary markedly between different target organisms, and changes within the more sensitive targets can alter the inhibitory effect. The multiplicity of potential targets, however, usually dictates against the development of overt resistance to concentrations used for hygienic applications. Similarly, although changes in cellular permeability toward such agents, mediated either by envelope modification or the induction of efflux-pumps may reduce susceptibility, they rarely influence the outcome of treatments at use-concentration. It has recently been proposed that chronic exposure of the environment to biocides used in a variety of commercial products might expose some microbial communities to subeffective concentrations causing emergence of resistant clones. Such resistance might relate to mutational changes in the most susceptible target or to regulatory mutants that cause the constitutive expression of certain efflux pumps. Although selection of organisms with such modifications is unlikely to influence the effectiveness of the biocides, changes in their susceptibility to third-party antibiotics can be postulated. This is particularly the case where a cellular target is shared between a biocide and an antibiotic, or where induction of efflux is sufficient to confer antibiotic resistance in the clinic. Although such linkage has been demonstrated in the laboratory in pure culture, it has not been documented in environments commonly exposed to biocides. In nature, the effects of chronic stressing with biocides are complicated by competition between microbial community members that may result in clonal expansion of naturally insusceptible clones. Received 11 March 2002/ Accepted in revised form 16 August 2002     

Aptamers against extracellular targets for in vivo applications

Oligonucleotides are multifunctional molecules which can interfere with gene expression by different mechanism such as antisense, RNA interference, ribozymes, etc. For most in vivo diagnostic and therapeutic applications, oligonucleotides need to be delivered to the intracellular compartment of a specific organ, a difficult task which limits considerably their use. However, aptamer oligonucleotides which target extracellular markers obviate this problem. Aptamers are short oligonucleotides (<100 bases) selected from large combinatorial pools of sequences for their capacity to bind to many types of different targets, ranging from small molecules (amino acids, antibiotics...) to proteins or nucleic acid structures. Aptamers present the same high specificity and affinity for their targets as antibodies. In addition to efficient binding, aptamers have been shown in many cases to display an inhibitory activity on their targets. Moreover, they seem to lack immunogenicity and can be chemically modified in order to improve their stability against nucleases or extend their blood circulation time, two properties which are particularly useful for in vivo applications. Recently, aptamers have been selected against whole living cells, opening a new avenue which presents three major advantages 1) direct selection without prior purification of the targets; 2) conservation of membrane proteins in their native conformation similar to the in vivo conditions and 3) identification of (new) targets for a specific phenotype. Many aptamers are now being developed against biomedical relevant extracellular targets: membrane receptor proteins, hormones, neuropeptides, coagulation factors... Among them, one aptamer that inhibits the human VEGF165 has recently been approved by FDA for the treatment of age-related macular degeneration. Here we discuss the recent developments of aptamers against extracellular targets for in vivo therapy and as tools for diagnosis using molecular imaging.     

Human natural cell-mediated cytotoxicity against fetal fibroblasts. II. Isolation and target cell specificity of the effector cells.

Human peripheral Wood lymphocytes were depleted of natural killer cells cytotoxic against human fetal fibroblasts by allowing them to attack the fibroblast targets grown on plastic beads followed by gravity sedimentation under conditions in which single cells floated but the attacker cells sedimented with the carrier beads. The attacker cells could be released from the bead-grown targets and shown to be greatly enriched in natural cytotoxic activity. The effector cells depleted by fibroblast adsorption were also depleted of cytotoxic activity against other monolayer targets whereas suspension grown lymphoma and leukemia cells (MOLT-4, RAJI, and K-562) were killed as effectively as by non-depleted effector cells. In competition assays other monolayer cells inhibited the natural cytotoxicity against fetal fibroblasts but the suspension-grown cells were unable to compete. The results suggested that different effector cell populations were probably involved when monolayer vs suspension targets were used in assays for human natural cell-mediated cytotoxicity. The separation was not, however, functionally complete since in competition assays with suspension-grown target cells also monolayer cells were able to compete. Preliminary morphological characterization of the natural killer cells against fetal fibroblasts is also presented.     

Analytical applications of aptamers

So far, several bio-analytical methods have used nucleic acid probes to detect specific sequences in RNA or DNA targets through hybridisation. More recently, specific nucleic acids, aptamers, selected from random sequence pools, have been shown to bind non-nucleic acid targets, such as small molecules or proteins. The development of in vitro selection and amplification techniques has allowed the identification of specific aptamers, which bind to the target molecules with high affinity. Many small organic molecules with molecular weights from 100 to 10,000 Da have been shown to be good targets for selection. Moreover, aptamers can be selected against difficult target haptens, such as toxins or prions. The selected aptamers can bind to their targets with high affinity and even discriminate between closely related targets.

Aptamers can thus be considered as a valid alternative to antibodies or other bio-mimetic receptors, for the development of biosensors and other analytical methods. The production of aptamers is commonly performed by the SELEX (systematic evolution of ligands by exponential enrichment) process, which, starting from large libraries of oligonucleotides, allows the isolation of large amounts of functional nucleic acids by an iterative process of in vitro selection and subsequent amplification through polymerase chain reaction.

Aptamers are suitable for applications based on molecular recognition as analytical, diagnostic and therapeutic tools. In this review, the main analytical methods, which have been developed using aptamers, will be discussed together with an overview on the aptamer selection process.     

Single-domain antibodies: a versatile and rich source of binders for breast cancer diagnostic approaches

Noninvasive early detection of breast cancer through the use of biomarkers is urgently needed since the risk of recurrence, morbidity, and mortality is closely related to disease stage at the time of primary surgery. A crucial issue in this approach is the availability of relevant markers and corresponding monoclonal antibodies suitable for the development of effective immunodiagnostic modalities. The identification of such markers from human pathological lesions and the isolation of specific antibodies using conventional approaches remain major challenges. Camelids produce functional antibodies devoid of light chains in which the single N-terminal domain of the heavy chain is fully capable of antigen binding. When produced as an independent domain, these so-called single-domain antibody fragments (sdAbs) or nanobodies have several advantages for biotechnological applications owing to their unique properties of size (13 kDa), stability, solubility, and expression yield. In this work, we have generated phage display libraries from animals immunized with breast cancer biopsies. These libraries were used to isolate sdAbs against known and relevant antigens such as HER2, or several cancer-specific sdAbs against unknown targets. We describe the identification of one these targets, cytokeratin 19, using affinity purification in combination with mass spectrometry. Some of these sdAbs were used in several straightforward diagnostic applications such as immunohistochemical analysis of tumor samples, multiplexed cytometric bead array analysis of crude samples, or an immune enrichment procedure of rare cells. Here, we demonstrate that phage display-based selection of single-domain antibodies is an efficient and high-throughput compatible approach to generate binders with excellent characteristics for the fast development of diagnostic and prognostic modalities.     

Monoclonal antibodies in neuro-oncology

Monoclonal antibodies (mAbs) are used with increasing success against many tumors but, for brain tumors, the blood-brain barrier (BBB) is a special concern. The BBB prevents antibody entry to the normal brain; however, its role in brain tumor therapy is more complex. The BBB is closest to normal at micro-tumor sites; its properties and importance change as the tumor grows. In this review, evolving insight into the role of the BBB is balanced against other factors that affect efficacy or interpretation when mAbs are used against brain tumor targets. As specific examples, glioblastoma multiforme (GBM), primary central nervous system lymphoma (PCNSL) and blood-borne metastases from breast cancer are discussed in the context of treatment, respectively, with the mAbs bevacizumab, rituximab, and trastuzumab, each of which is already widely used against tumor outside the brain. It is suggested that success against brain tumors will require getting past the BBB in two senses: physically, to better attack brain tumor targets and conceptually, to give equal attention to problems that are shared with other tumor sites.     

2 型糖尿病治疗药物研究进展

2 型糖尿病（T2DM）是一种代谢障碍性疾病。传统抗糖尿病药物具有不同程度的副作用,如低血糖、胃肠道反应、体重增加、 心血管风险等,因此开发作用于新靶点和新作用机制的T2DM 治疗新药成为当前研究的热点。目前基于新靶点设计的糖尿病治疗新药有 些已上市,且获得良好的降糖效果,但大部分药物仍处于临床或临床前研究阶段,其疗效和安全性有待进一步临床验证。综述传统抗糖 尿病药物、T2DM 药物新靶点及基于新靶点设计的抗糖尿病新药的研究进展。     

Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds

Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.