A pathway profile-based method for drug repositioning

Finding new applications for existing pharmaceuticals,known as drug repositioning,is a validated strategy for resolving the problem of high expenditure but low productivity in drug discovery.Currently,the prevalent computational methods for drug repositioning are focused mainly on the similarity or relevance between known drugs based on their "features",including chemical structure,side effects,gene expression profile,and/or chemical-protein interactome.However,such drug-oriented methods may constrain the newly predicted functions to the pharmacological functional space of the existing drugs.Clinically,many drugs have been found to bind "off-target"(i.e.to receptors other than their primary targets),which can lead to undesirable effects.In this study,which integrates known drug target information,we propose a disease-oriented strategy for evaluating the relationship between drugs and disease based on their pathway profile.The basic hypothesis of this method is that drugs exerting a therapeutic effect may not only directly target the disease-related proteins but also modulate the pathways involved in the pathological process.Upon testing eight of the global best-selling drugs in 2010(each with more than three targets),the FDA(Food and Drug Administration,USA)-approved therapeutic function of each was included in the top 10 predicted indications.On average,60% of predicted results made using our method are proved by literature.This approach could be used to complement existing methods and may provide a new perspective in drug repositioning and side effect evaluation.     

基于流形正则化非负矩阵分解预测药物-靶蛋白作用关系

识别药物-靶蛋白作用关系是当前药物研究的重要内容,其可帮助识别已有药物的新功能,发现药物的"偏靶蛋白"等。现有预测算法对新药物的作用靶蛋白,及新靶蛋白的作用药物预测存在困难,由此提出一种新奇的基于流形正则化非负矩阵分解的新药物/新靶蛋白作用关系预测算法,该方法首先通过聚类算法构建新药物/新靶蛋白的初始作用标签,然后设计引入流形学习正则化约束的非负矩阵分解算法预测药物-靶蛋白作用关系,最后在四个经典数据集中测试,并与最新预测算法BLM-NII、RLS-WNN和WKNKN+WGRMF算法进行比较,证明本文算法可获取较高的预测精度。     

Enhanced urease inhibition activity of Ag nanomaterials capped with N-substituted methyl 5-acetamido-β-resorcylate

Medically, bacterial ureases are important virulent factors and are used for treatment of peptic ulcers and urinary tones. Reported urease inhibitors are associated with various side effects including antibiotic resistance as a major one. Still there is an urgent need to synthesize new urease inhibitors. In this context we have synthesized new urease inhibitor i.e. AgL that is composed of Ag nanomaterials capped with N-substituted methyl 5-acetamido-β-resorcylate(L). The conjugation of L to silver was confirmed through FTIR, UV–vis and TEM analysis.Bare silver nanomaterials(Ag) were also prepared. The stability of AgL nanostructures was determined against various parameters(temperature, high salt concentration, pH) and found to be stable. The in vitro antimicrobial(antibacterial, antifungal), enzyme inhibition(xanthine oxidase, urease, carbonic anhydrase, α-chymotrypsin,cholinesterase) and antioxidant activities of AgL were investigated and compared with Ag, L and standard drugs.In comparison to other bioactivities, AgL shows statistically enhanced selective enzyme inhibition activity against urease enzyme. Urease inhibition activity of AgL was significantly greater than standard drug(thiourea),L and Ag. On a per weight basis, AgL required about 11–18 times less amount of L for inhibition of urease enzyme.     

Paternal cyclophosphamide treatment of rats causes fetal loss and malformations without affecting male fertility

The use of cytotoxic, mutagenic and carcinogenic agents as treatment for various types of cancer may be particularly hazardous in men of reproductive age as there exists the possibility that this may lead to congenital malformations in the progeny. Such agents can affect fertility and other aspects of male reproductive function, for example, treatment with anti-cancer drugs such as cyclophosphamide has been associated with oligozoospermia, azoospermia and increased levels of serum follicle-stimulating hormone (FSH). Depending on the cumulative dose and the duration of treatment, spermatogenesis often returns but this may take years. The relevance of the effects of such chemicals on the male reproductive system to the offspring is poorly understood. We have set out to determine whether present tests of male reproductive function (that is, endocrine status, numbers of spermatozoa, fertility) can predict deleterious effects of a paternally administered agent on the offspring. Here, we report that chronic administration in rats of low doses of the widely used drug cyclophosphamide had minimal effects on the male reproductive system and fertility, but resulted in malformations and retardation of growth in the surviving fetuses and a high frequency of fetal death. Thus, adverse effects on the fetus cannot be predicted from the effects of a drug on the male reproductive system.     

The application of Tau protein testing to gastric cancer patients treated with paclitaxel

Paclitaxel is one of the main drugs used to treat gastric cancer, but many tumors develop drug resistance, resulting in treatment failure. The levels of expression of Tan protein in breast tumors have been found to be related to paclitaxel resistance, suggesting that Tau protein expression may predict breast cancer sensitivity to paclitaxel treatment. To determine whether Tan protein ex- pression can predict gastric cancer sensitivity to paclitaxel, we assayed Tan protein expression levels in gastric cancer specimens from 70 patients. We observed Tan protein expression in 54 of 70 （77.1%） specimens. Assays in gastric cancer cell lines showed that Tan protein expression was significantly lower in BGC823 than in MKN45 cells （P -- 0.0147）. MTT assays showed that dif- ferent concentrations of paclitaxel inhibited the growth of MKN45 and BGC823 cells, but inhibition and apoptosis were more obvious in cells expressing low levels of Tau protein. Paclitaxel chemotherapy was effective in 34 of the 70 patients （48.6%） and was significantly correlated with low expression of Tau protein （P 〈 0.01）. These findings indicate that Tau protein is expressed in a high percentage of gastric cancers, with paclitaxel being more effective in tumors with low Tau expression.     

基于网络药理学研究黄芪-半枝莲药对治疗肺癌机制

探讨黄芪-半枝莲药对治疗肺癌的机制。通过数据库检索黄芪-半枝莲有效活性成分、靶蛋白和肺癌相关疾病靶点,分别构建药物-化合物-靶点和化合物-靶点-疾病网络。构建关键靶点蛋白质-蛋白质相互作用(protein-protein interaction,PPI)网络,用R软件进行基因本体（gene ontology,GO）和京都基因和基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG）的关键靶点的富集分析。得到黄芪-半枝莲药对的16个有效活性成分,作用于111个肺癌相关靶点,关键靶点包括TP53、AKT1、MAPK、TNF、VEGFA、IL-6等。GO富集分析主要涉及RNA转录、炎症、胞外和胞核,KEGG信号通路主要有TLR、NLR、HIF-1、FoxO、PI3K-Akt等信号通路,黄芪-半枝莲药对通过抑制炎症、信号转导、血管生成等过程共同起到治疗肺癌的作用。研究结果初步预测了黄芪-半枝莲药对治疗肺癌的分子机制,为该药对药理作用的深入研究奠定了基础。     

基于网络药理学研究黄芪-半枝莲药对治疗肺癌机制

探讨黄芪-半枝莲药对治疗肺癌的机制。通过数据库检索黄芪-半枝莲有效活性成分、靶蛋白和肺癌相关疾病靶点,分别构建药物-化合物-靶点和化合物-靶点-疾病网络。构建关键靶点蛋白质-蛋白质相互作用(protein-protein interaction,PPI)网络,用R软件进行基因本体（gene ontology,GO）和京都基因和基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG）的关键靶点的富集分析。得到黄芪-半枝莲药对的16个有效活性成分,作用于111个肺癌相关靶点,关键靶点包括TP53、AKT1、MAPK、TNF、VEGFA、IL-6等。GO富集分析主要涉及RNA转录、炎症、胞外和胞核,KEGG信号通路主要有TLR、NLR、HIF-1、FoxO、PI3K-Akt等信号通路,黄芪-半枝莲药对通过抑制炎症、信号转导、血管生成等过程共同起到治疗肺癌的作用。研究结果初步预测了黄芪-半枝莲药对治疗肺癌的分子机制,为该药对药理作用的深入研究奠定了基础。     

Synthesis of thrombin-inhibiting heparin mimetics without side effects

Unwanted side effects of pharmacologically active compounds can usually be eliminated by structural modifications. But the complex heterogeneous structure of the polysaccharide heparin has limited this approach to fragmentation, leading to slightly better-tolerated heparin preparations of low molecular mass. Despite this improvement, heparin-induced thrombocytopaenia (HIT), related to an interaction with platelet factor 4 (PF4) and, to a lesser extent, haemorrhages, remain significant side effects of heparinotherapy. Breakthroughs in oligosaccharide chemistry made possible the total synthesis of the pentasaccharide antithrombin-binding site of heparin. This pentasaccharide represents a new family of potential antithrombotic drugs, devoid of thrombin inhibitory properties, and free of undesired interactions with blood and vessel components. To obtain more potent and well-tolerated antithrombotic drugs, we wished to synthesize heparin mimetics able to inhibit thrombin, that is, longer oligosaccharides. Like thrombin inhibition, undesired interactions are directly correlated to the charge and the size of the molecules, so we had to design structures that were able to discriminate between thrombin and other proteins, particularly PF4. Here we describe the use of multistep converging synthesis to obtain sulphated oligosaccharides that meet these requirements.     

相关向量机模型在边坡稳定性预测中的应用

近年来,边坡稳定性预测得到了广泛的研究,及时、准确的预测可以有效的预防边坡破坏灾害的发生。本文提出了一种基于相关向量机(RVM)的边坡稳定性预测模型,结合京-新高速公路高堑边坡工程实例,通过对比支持向量机（RVM）模型、RBF神经网络模型和支持向量机(SVM)模型的拟合及预测结果来分析其可行性。结果表明:相较于SVM模型和RBF神经网络模型,RVM模型的三种预测指标值均是最小的。其中,平均绝对误差（MAE）分别降低了86.02%和22.11%,均方根误差（RMSE）分别降低了72.05%和1.09%,相对均方误差（RRMSE）也分别降低了75.89%和21.13%,表明RVM是一种预测边坡稳定性的稳健工具,该方法能较为准确地预测出不同指标下的边坡安全系数。     

Platensimycin is a selective FabF inhibitor with potent antibiotic properties

Bacterial infection remains a serious threat to human lives because of emerging resistance to existing antibiotics. Although the scientific community has avidly pursued the discovery of new antibiotics that interact with new targets, these efforts have met with limited success since the early 1960s. Here we report the discovery of platensimycin, a previously unknown class of antibiotics produced by Streptomyces platensis. Platensimycin demonstrates strong, broad-spectrum Gram-positive antibacterial activity by selectively inhibiting cellular lipid biosynthesis. We show that this anti-bacterial effect is exerted through the selective targeting of beta-ketoacyl-(acyl-carrier-protein (ACP)) synthase I/II (FabF/B) in the synthetic pathway of fatty acids. Direct binding assays show that platensimycin interacts specifically with the acyl-enzyme intermediate of the target protein, and X-ray crystallographic studies reveal that a specific conformational change that occurs on acylation must take place before the inhibitor can bind. Treatment with platensimycin eradicates Staphylococcus aureus infection in mice. Because of its unique mode of action, platensimycin shows no cross-resistance to other key antibiotic-resistant strains tested, including methicillin-resistant S. aureus, vancomycin-intermediate S. aureus and vancomycin-resistant enterococci. Platensimycin is the most potent inhibitor reported for the FabF/B condensing enzymes, and is the only inhibitor of these targets that shows broad-spectrum activity, in vivo efficacy and no observed toxicity.     

改进的基于“当前”统计模型自适应滤波算法及其在航迹预测中的应用

基于"当前"统计模型的模糊自适应(FACS)滤波算法利用机动目标"当前"加速度调整加速度极限值,实现了对一般机动目标的有效预测;但是在预测强机动目标时却存在较大的预测误差。为了解决这一问题,引入强跟踪滤波器(STF),提出了一种新的自适应滤波算法STF-FACS。该算法根据滤波残差实时调整卡尔曼滤波增益,提高了对强机动目标的预测能力;同时保留了FACS算法对于一般机动目标的预测性能。最后,对强机动目标分直线机动和转弯机动,分别进行航迹预测仿真。仿真结果表明,对弱机动目标进行航迹预测时,两种算法的预测效果相当;对强机动目标进行航迹预测时,STF-FACS算法无论是在动态时延和预测精度方面都比FACS算法要好。     

肿瘤精准药物治疗研究进展

 随着新一代基因测序技术以及癌生物学的迅猛发展，基于基因组生物标志物的抗肿瘤精准药物开发成为药物研发的重要方向。介绍了抗肿瘤精准药物在非小细胞肺癌、乳腺癌、黑色素瘤以及白血病等肿瘤领域表现出的优异治疗效果，剖析了目前已上市以及处于研发阶段的“泛癌种”药物，表明基于生物标志物而非肿瘤组织的治疗药物将成为抗肿瘤药物研发的方向之一。介绍了以“篮子试验”和“雨伞试验”为代表的抗肿瘤药物新型临床试验设计以及PROTACs药物开发新技术，指出新理念新技术的出现将进一步推动抗肿瘤精准药物发展，促进针对耐药或“不可成药靶点”的靶向药物的开发。     

基于异质信息网络元路径的药物‒靶标相互作用预测模型

提出一种融合元路径信息的图神经网络模型, 用于预测药物-靶标相互作用(GMDTI)。首先根据8个数据集中的药物、靶标、疾病和副作用数据以及它们之间的8种作用关系, 构建药物-靶标异质信息网络(HIN); 然后定义两条元路径来捕获药物-靶标HIN 中的不同子结构信息和不同节点间隐藏的语义信息, 并应用图神经网络的方法聚合节点的一阶邻居信息和元路径中节点间的语义信息; 最后利用端到端的学习方法完成DTIs预测。该方法同时考虑药物-靶标HIN的结构特性和元路径语义信息, 有助于学习到更多潜在的药物-靶标作用关系。实验结果表明, GMDTI的预测准确率高于所有基线模型, AUC达到98.6%, AUPR达到94.5%。同时通过调整数据的稀疏度和降噪实验, 证明GMDTI具备优于所有基线模型的鲁棒性。     

Endothelial cells and VEGF in vascular development

The intricate patterning processes that establish the complex vascular system during development depend on a combination of intrinsic pre-patterning and extrinsic responses to environmental parameters. Mutational studies in mice and fish have shown that the vascular system is highly sensitive to genetic disruption and have identified potential targets for therapeutic interventions. New insights into non-vascular roles of vascular endothelial growth factor and the requirement for endothelial cells in adult organs and stem-cell niches highlight possible side effects of anti-angiogenic therapy and the need for new targets.     

基于数据挖掘及网络药理学探讨中药治疗消化性溃疡的用药规律及作用机制

运用数据挖掘和网络药理学方法探讨中药治疗消化性溃疡(peptic ulcer, PU)的用药规律,筛选核心药对潜在靶点并研究其治疗PU的作用机制。通过频数分析、关联规则分析得出核心药对,筛选核心药对活性成分及靶点;将核心药对治疗PU的关键靶点进行基因本体(gene ontology, GO)和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)富集分析;建立药对成分-靶点-信号通路网络。233份治疗PU的处方中含216味中药,其中茯苓-白术为核心药对。核心药对的22个化学成分对应的143个潜在靶点中与PU交集的靶点有41个。通过GO分析,得到相关的92个生物学过程,5个分子功能及11个细胞组成,KEGG分析得出15条信号通路。核心药对茯苓-白术能通过JUN、IL6、TP53、AKT1、VEGFA、MAPK1、CASP3、EGFR、RB1、IL1B靶点调控IL-17、PI3K-AKT、NF-κB、幽门螺杆菌感染中的上皮细胞信号转导等相关通路发挥对PU的治疗作用。通过探讨中药治疗PU的用药规律,初步阐述了治疗PU的核心药对茯苓-白术的药理作用,为临床用药和新药研究提供思路。     

Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry

Hepatitis C virus (HCV) is a leading cause of cirrhosis and liver cancer worldwide. A better understanding of the viral life cycle, including the mechanisms of entry into host cells, is needed to identify novel therapeutic targets. Although HCV entry requires the CD81 co-receptor, and other host molecules have been implicated, at least one factor critical to this process remains unknown (reviewed in refs 1-3). Using an iterative expression cloning approach we identified claudin-1 (CLDN1), a tight junction component that is highly expressed in the liver, as essential for HCV entry. CLDN1 is required for HCV infection of human hepatoma cell lines and is the first factor to confer susceptibility to HCV when ectopically expressed in non-hepatic cells. Discrete residues within the first extracellular loop (EL1) of CLDN1, but not protein interaction motifs in intracellular domains, are critical for HCV entry. Moreover, antibodies directed against an epitope inserted in the CLDN1 EL1 block HCV infection. The kinetics of this inhibition indicate that CLDN1 acts late in the entry process, after virus binding and interaction with the HCV co-receptor CD81. With CLDN1 we have identified a novel key factor for HCV entry and a new target for antiviral drug development.     

PHBV/葡聚糖纳米药物载体的制备及表征

两亲性聚合物纳米颗粒作为疏水性抗肿瘤药物载体因其能够增强化疗效率并降低毒副作用而受到广泛关注.采用双乳液溶剂挥发法制备了聚(3-羟基丁酸酯-co-3-羟基戊酸酯)(PHBV)/葡聚糖纳米颗粒,测得平均粒径为205.0±6.9nm,Zeta电势为-1.59±0.12mV,纳米颗粒具有明显的壳核结构,粒径均一,分散性良好.将疏水性化疗药物顺铂包载后,其粒径及电势均无明显变化,载药量达19.3±2.9%.顺铂在模拟肿瘤细胞环境pH=5.5的磷酸盐缓冲液(PBS)中比正常细胞环境pH=7.4时释放更快,且累计释放周期均长达7d以上,表明该药物载体具有一定的pH响应性以及优异的缓释性能.细胞集落形成实验表明PHBV/葡聚糖纳米药物载体具有良好的生物相容性,而载药纳米颗粒对肿瘤细胞的毒性明显高于正常细胞,表明该纳米颗粒对肿瘤细胞具有更强的杀伤作用.综上所述,PHBV/葡聚糖纳米颗粒具有两亲性分子结构,合适的粒径及Zeta电势,显著的缓释效果,对肿瘤细胞具有pH响应性及更强的杀伤作用等优势,有望成为一种新型纳米药物载体,在癌症化疗中显著提高药物利用率并降低毒副作用.     

Distinct functions of the two isoforms of dopamine D2 receptors

Signalling through dopamine D2 receptors governs physiological functions related to locomotion, hormone production and drug abuse. D2 receptors are also known targets of antipsychotic drugs that are used to treat neuropsychiatric disorders such as schizophrenia. By a mechanism of alternative splicing, the D2 receptor gene encodes two molecularly distinct isoforms, D2S and D2L, previously thought to have the same function. Here we show that these receptors have distinct functions in vivo; D2L acts mainly at postsynaptic sites and D2S serves presynaptic autoreceptor functions. The cataleptic effects of the widely used antipsychotic haloperidol are absent in D2L-deficient mice. This suggests that D2L is targeted by haloperidol, with implications for treatment of neuropsychiatric disorders. The absence of D2L reveals that D2S inhibits D1 receptor-mediated functions, uncovering a circuit of signalling interference between dopamine receptors.     

Drosophila RNAi screen identifies host genes important for influenza virus replication

All viruses rely on host cell proteins and their associated mechanisms to complete the viral life cycle. Identifying the host molecules that participate in each step of virus replication could provide valuable new targets for antiviral therapy, but this goal may take several decades to achieve with conventional forward genetic screening methods and mammalian cell cultures. Here we describe a novel genome-wide RNA interference (RNAi) screen in Drosophila that can be used to identify host genes important for influenza virus replication. After modifying influenza virus to allow infection of Drosophila cells and detection of influenza virus gene expression, we tested an RNAi library against 13,071 genes (90% of the Drosophila genome), identifying over 100 for which suppression in Drosophila cells significantly inhibited or stimulated reporter gene (Renilla luciferase) expression from an influenza-virus-derived vector. The relevance of these findings to influenza virus infection of mammalian cells is illustrated for a subset of the Drosophila genes identified; that is, for three implicated Drosophila genes, the corresponding human homologues ATP6V0D1, COX6A1 and NXF1 are shown to have key functions in the replication of H5N1 and H1N1 influenza A viruses, but not vesicular stomatitis virus or vaccinia virus, in human HEK 293 cells. Thus, we have demonstrated the feasibility of using genome-wide RNAi screens in Drosophila to identify previously unrecognized host proteins that are required for influenza virus replication. This could accelerate the development of new classes of antiviral drugs for chemoprophylaxis and treatment, which are urgently needed given the obstacles to rapid development of an effective vaccine against pandemic influenza and the probable emergence of strains resistant to available drugs.     

Selective inhibition of cotranslational translocation of vascular cell adhesion molecule 1

Increased expression of vascular cell adhesion molecule 1 (VCAM1) is associated with a variety of chronic inflammatory conditions, making its expression and function a target for therapeutic intervention. We have recently identified CAM741, a derivative of a fungus-derived cyclopeptolide that acts as a selective inhibitor of VCAM1 synthesis in endothelial cells. Here we show that the compound represses the biosynthesis of VCAM1 in cells by blocking the process of cotranslational translocation, which is dependent on the signal peptide of VCAM1. CAM741 does not inhibit targeting of the VCAM1 nascent chains to the translocon channel but prevents translocation to the luminal side of the endoplasmic reticulum (ER), through a process that involves the translocon component Sec61beta. Consequently, the VCAM1 precursor protein is synthesized towards the cytosolic compartment of the cells, where it is degraded. Our results indicate that the inhibition of cotranslational translocation with low-molecular-mass compounds, using specificity conferred by signal peptides, can modulate the biosynthesis of certain secreted and/or membrane proteins. In addition, they highlight cotranslational translocation at the ER membrane as a potential target for drug discovery.