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中国化学会第28届学术年会

作者： Dong-Sheng Cao1 Mao-Mao Zeng2 Jun Yan1 Jian-Hua Huang1 Qian-Nan Hu4 Qing-Song Xu3 Yi-Zeng Liang*1 1research center of modernization of traditional Chinese medicines Central South University Changsha 410083 p.r.china 2State key laboratory of Food Science and Technology School of Food Science and Technology Jiangnan Univesity Wuxi 214122 p.r.china 3School of Mathematical Sciences and Computing Technology Central South University Changsha 410083 p.r.china 4key laboratory of combinatorial biosynthesis and drug discovery (Wuhan University) Ministry of Education and Wuhan University School of pharmaceutical Sciences Wuhan 430071 p.r.china research center of modernization of traditional Chinese medicines Central South UniversityChangsha 410083 P. R. China State Key Laboratory of Food Science and Technology School of Food Science and Technology Jiangnan Univesity Wuxi 214122 P.R.China Research center of modernization of traditional Chinese medicines Central South UniversityChangsha 410083 P.R. China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery(Wuhan University)Ministry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071 P.R.China School of Mathematical Sciences and Computing Technology Central South UniversityChangsha 410083 P.R.China

Large amounts of data from high-throughput metabolomics experiments become commonly more and more complex,which brings an enormous amount of challenges to existing statistical *** there is a need to develop statistically efficient approach for mining the underlying metabolite information contained by metabolomics data under *** the work,we developed a novel kernel Fisher discriminant analysis （KFDA） algorithm by constructing an informative kernel based on decision tree *** constructed kernel can effectively encode the similarities of metabolomics samples between informative metabolites/biomarkers in specific parts of the measurement ***,informative metabolites or potential biomarkers can be successfully discovered by variable importance ranking in the process of building ***,KFDA can also deal with nonlinear relationship in the metabolomics data by such a kernel to some ***,two real metabolomics datasets together with a simulated data were used to demonstrate the performance of the proposed approach through the comparison of different approaches.

关键词： metabolomics kernel methods Fisher discriminant analysis (FDA) biomarker discovery decision tree classification and regression tree (CArT)

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predicting drug-Target Interaction Networks by Fusing drug and Target Kernel Measures

Predicting Drug-Target Interaction Networks by Fusing Drug a...

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中国化学会第28届学术年会

作者： Dong-Sheng Cao1 Jian-Hua Huang1 Jun Yan1 Nai-ping Dong1 Qian-Nan Hu4 Shao Liu3 Qing-Song Xu2 Yi-Zeng Liang1 1research center of modernization of traditional Chinese medicines Central South University Changsha 410083 p.r.china 2School of Mathematical Sciences and Computing Technology Central South University Changsha 410083 p.r.china 3Xiangya Hospital Central South University Changsha 410008 p.r.china 4key laboratory of combinatorial biosynthesis and drug discovery (Wuhan University) Ministry of Education and Wuhan University School of pharmaceutical Sciences Wuhan 430071 p.r.china research center of modernization of traditional Chinese medicines Central South UniversityChangsha 410083 P.R. China Key Laboratory of Combinatorial Biosynthesis and Drug Discovery(Wuhan University)Ministry of Education and Wuhan University School of Pharmaceutical SciencesWuhan 430071 P.R.China Xiangya Hospital Central South University Changsha 410008 P. R. China School of Mathematical Sciences and Computing Technology Central South UniversityChangsha 410083 P.R.China

The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug *** is both consuming and costly to determine drug-target interactions by experiments ***,there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug-target interactions in a timely manner.A key issue for predicting drug-target interactions is how to represent the interaction relationship between drugs and target proteins by using a certain numeric *** the work,we aim at addressing such an issue by using some basic properties of kernel *** means of different kernel representations,drug similarity can be represented by constructing a drug kernel matrix,and protein similarity a protein kernel *** interactions between drugs and target proteins are represented by some certain combination of drug kernel and target *** can be considered as a new interaction kernel representing complex interaction relationships between drugs and targets,strictly under the framework of basic kernel ***,we redesigned the question as a binary classification one by support vector machines （SVMs） with an interaction kernel as an *** classes of drug-target interaction networks in humans involving enzymes,ion channels,G-protein-coupled receptors （GpCrs） and nuclear receptors,are independently used for establishing predictive models using SVM as their operation engine,with each to predict the interactions between drugs and one of the four protein *** conclusion,the results demonstrate the ability of our proposed method to predict the drug-target interactions.

关键词： drug-target interaction data fusion molecular fingerprint networks genomic drug discovery kernel methods.

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Separation,identification,and quantification of active constituents in Fructus psoraleae by high-performance liquid chromatography with UV,ion trap mass spectrometry,and electrochemical detection

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Journal of pharmaceutical Analysis 2012年第2期2卷 143-151页

作者： Qinhua Chen,Yuan Li,Zilin Chen key laboratory of combinatorial biosynthesis and drug discovery (Wuhan University),Ministry of Education,and Wuhan University School of pharmaceutical Sciences,Wuhan,430071,china key laboratory of combinatorial biosynthesis and drug discovery (Wuhan University) Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China

The qualitative and quantitative analysis of active constituents in Fructus psoraleae is presented by high-performance liquid chromatography (HpLC) coupled with different *** of Fructus psoraleae were examined by HpLC with ion trap mass spectrometry (IT-MS) and 18 major compounds of coumarins,benzofuran glycosides,flavonoids,and meroterpene were *** determination of four major constituents including bavachin,isobavachalcone,bavachinin,and bakuchiol was accomplished by HpLC with UV,MS,and electrochemical detection (ECD).These methods were evaluated for a number of validation characteristics (repeatability,LOD,calibration range,and recovery).ECD obtained a high sensitivity for analysis of the four components;MS provided a high selectivity and sensitivity for determination of bavachin,isobavachalcone,and bavachinin in negative-ion *** optimization of the methods,separation,*** quantification of the four components in Fructus psoraleae were comprehensively tested by HpLC with UV,MS,and ECD.

关键词： HpLC-UV HpLC-MS HpLC-ECD Fructus psoraleae Chinese medicine

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New developments in small molecular compounds for anti-hepatitis C virus(HCV) therapy

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2012年第1期13卷 56-82页

作者： Jing TONG1,2,You-wei WANG2,Yuan-an LU1,2(1Department of public Health Sciences,University of Hawaii,Honolulu,Hawaii 96822,USA)(2key laboratory of combinatorial biosynthesis and drug discovery,Ministry of Education,Institute of Traditional Chinese Medicine & Natural products,School of pharmaceutical Sciences,Wuhan University,Wuhan 430071,china) Department of public Health Sciences University of Hawaii Honolulu Hawaii 96822 USA

Infection with hepatitis C virus （HCV） affects approximately 170 million people worldwide. However, no vaccine or immunoglobulin is currently available for the prevention of HCV infection. The standard of care （SOC） involving pegylated interferon-（] （pEG-IFN a） plus ribavirin （rBV） for 48 weeks results in a sustained virologic re- sponse in less than 50% of patients with chronic hepatitis C genotype 1, the most prevalent type of HCV in North America and Europe. recently, reliable in vitro culture systems have been developed for accelerating antiviral therapy research, and many new specifically targeted antiviral therapies for hepatitis C （STAT-C） and treatment strategies are being evaluated in clinical trials. These new antiviral agents are expected to improve present treatment significantly and may potentially shorten treatment duration. The aim of this review is to summarize the current developments in new anti-HCV drugs.

关键词： Hepatitis C virus (HCV) Clinical trial Small molecular compounds review

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Organocatalytic asymmetric allylic alkylation of sulfonylimidates with Morita-Baylis-Hillman carbonates

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Science china Chemistry 2011年第1期54卷 81-86页

作者： pENG Jing,CUI HaiLei & CHEN YingChun key laboratory of drug-Targeting and drug Delivery System,Ministry of Education Department of Medicinal Chemistry,West china School of pharmacy,Sichuan University,Chengdu 610041,china 1. key laboratory of drug-Targeting and drug Delivery System Ministry of Education Department of Medicinal Chemistry West China School of Pharmacy Sichuan University Chengdu 610041 China

The asymmetric allylic alkylation reaction of sulfonylimidates with various Morita-Baylis-Hillman (MBH) carbonates was accomplished by the catalysis of commercially available cinchona alkaloids catalyst (DHQD)*** corresponding allylic alkylation products were obtained in good yields with high stereoselectivities (up to 99% ee,89:11 dr).

关键词： organocatalysis asymmetric allylic alkylation sulfonylimidates Morita-Baylis-Hillman carbonates cinchona alkaloids

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Conformational flexibility of β-secretase: molecular dynamics simulation and essential dynamics analysis

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Acta pharmacologica Sinica 2004年第6期25卷 3-11页

作者： Bing XIONG, Xiao-qin HUANG, Ling-ling SHEN, Jian-hua SHEN 2,Xiao-min LUO, Xu SHEN, Hua-liang JIANG2, Kai-xian CHENdrug discovery and Design Center, State key laboratory of drug research, Shanghai Institute of Materia Medica,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, china drug discovery and Design Center State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 201203 China

AIM: Based on the structural analysis to reveal the mechanism of ligand binding to b-secretase and the specificityof each binding sub-site. METHODS: Molecular dynamics was used to simulate on the ligand free b-secretase andligand bound b-secretase. The trajectories were analyzed using the essential dynamics, and the significant confor-mational change was illustrated employing the DynDom program. rESULTS: The essential dynamics and DynDomanalyses clearly showed that the b-secretase experienced a large conformational change upon the substrate orinhibitor binding. The flap structure adopted a swing motion, gradually covering the active site to facilitate theligand binding process. residues Ser86 and Ile87 served as the hinge point. Inhibitor-enzyme interaction analysisrevealed that residues at p2, p1, and p1 positions of the inhibitor were very important for the binding, and residuesat p2 and p3 positions may be modified to improve the binding specificity. S3 subsite of the enzyme still hadspace to modify the inhibitors in increasing the binding affinity. CONCLUSION: The information presented hereis valuable and could be used to identify small molecular inhibitors of b-secretase.

关键词： molecular dynamics secretase essential dynamics computer simulation Alzheimer disease

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Advances of multiplex and high throughput biomolecular detection technologies based on encoding microparticles

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Science china Chemistry 2011年第8期54卷 1185-1201页

作者： ZHAO XiangWei, ZHAO YuanJin & GU ZhongZe State key laboratory of Bioelectronics Southeast University, Nanjing 210096, china 1. State key laboratory of Bioelectronics Southeast University Nanjing 210096 China

The rapid developments of genomics and proteomics have driven the demand for multiplex and high throughput analysis of large numbers of biomolecules in the fields of medical diagnostics, drug discovery, and environmental monitoring. Encoding the biomolecular binding events is the key technique to fulfill this demand, in which microparticles play the most important roles. This review outlines the development of multiplex and high throughput biodetections, and highlights the most recent advances in the field of encoding microparticles, together with problems that need to be resolved.

关键词： multiplex bioassays multiplex labels encoded microcarrier binding assays high throughput screening

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Detailed Conformational Dynamics of Juxtamembrane region and Activation Loop in c-Kit Kinase Activating process

Detailed Conformational Dynamics of Juxtamembrane Region and...

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第九届全国计算（机）化学学术会议

作者： Jun Zou Sheng-Yong Yang Lab of Molecular Modeling and Computer-Aided drug discovery,State key laboratory of Biotherapy,West china Hospital,Sichuan University,Chengdu,p.r.china,610041.

＜正＞The stem--cell factor receptor（c-Kit）plays critical roles in initiating cell growth and *** kinase functional abnormity has been thought to associate with some human *** of the kinase activity is achieved by the phosphorylation of residues Tyr568 and Tyr570 in juxtamembrane region（JMr）and subsequent eonformational changes of JMr and activation loop（A-Loop）of ***,the detailed conformational changes of JMr and A-Loop are far from clear,especially the conformational changes are coupled or not during the kinase activity *** this investigation,the whole conformational transition pathway is explored using a series of nanosecond conventional molecular dynamics and targeted molecular dynamics simulations[programs used:Insight Ⅱ（Accelrys Inc.）and NAMD].The dynamics simulation results show that phosphorylation of residues Tyr568 and Tyr570 in JMr weakens the interaction between the JMr and kinase domain,thus initiating the kinase activating process. During the autoinhibitory-to-activated TMD simulation,the JMr departs firstly from the autoinhibitory binding site,and then undergoes a rapid dissociation process and drift into the solvent ultimately.A large conformational change of the A-Loop and the orientational flexibility of helix aC in the N-lobe of the kinase domain take place after the dissociation of JMr,which indicates that the eonformational transition of A-loop is not coupled to the changes of *** results might be helpful for the rational drug discovery targeting c-Kit and other related kinases.

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The role of Smad signaling in vascular and hematopoietic development revealed by studies using genetic mouse models

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Science china(Life Sciences) 2010年第4期53卷 485-489页

作者： LAN Yu & YANG Xiao State key laboratory of proteomics, Genetic laboratory of Development and Diseases, Institute of Biotechnology, Beijing 100071, china 1. State key laboratory of proteomics Genetic Laboratory of Development and Diseases Institute of Biotechnology Beijing 100071 China

Smads are intracellular mediators of transforming growth factor β (TGF-β) superfamily signaling. In this review, we focus on the genetic mouse models for Smad pathways, which have provided functional evidence regarding the complex circuitry in angiogenesis and hematopoiesis during development. In the early stages of vascular development, TGF-β signaling is a contri buting factor in angiogenesis and vascular maturation. Whereas in the later embryogenesis, selected molecules of Smad pathways, such as TGF-β type II receptor (TbrII), ALK5, and Smad5, seem to be dispensable for vessel morphogenesis and integrity. TGF-β signaling is not required in the induction of hematopoietic precursors from mesoderm, but inhibits the subsequent expansion of committed hematopoietic precursors. By contrast, bone morphogenetic protein 4 (BMp4) has long been acknowledged pivotal in mesoderm induction and hematopoietic commitment during development. However, recent genetic evidence shows the BMp4-ALK3 axis is not crucial for the formation of hematopoietic cells from FLK1+ mesoderm. Because of the highly redundant mechanisms within the Smad pathways, the precise role of the Smad signaling involved in vascular and hematopoietic development remains nebulous. The generation of novel cell lineage restricted Cre transgenes would shed new light on the future relevant investigations.

关键词： Smad transforming growth factor β (TGF-β) bone morphogenetic protein (BMp) angiogenesis hematopoiesis knockout development

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Synthesis of N^(11)-anchoring biotinylated artemisinin derivatives and their preliminary biological assessment

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Science china Chemistry 2010年第1期53卷 119-124页

作者： pAN QiYu1,2,WANG ShaoZhong1,LU JinJian3,MENG LingHua3 & YAO ZhuJun1,2 1Nanjing National laboratory of Microstructures(NNLM),School of Chemistry and Chemical Engineering,Nanjing University,Nanjing 210093,china 2Joint laboratory of Green Chemistry,Department of Chemistry,University of Science and Technology of china,Hefei 230026,china 3State key laboratory of drug research,Shanghai Institute of Materia Medica,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,Shanghai 201203,china. 1. Nanjing National laboratory of Microstructures (NNLM) School of Chemistry and Chemical Engineering Nanjing University Nanjing 210093 China2. Joint Laboratory of Green Chemistry Department of Chemistry University of Science and Technology of China Hefei 230026 China3. State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 201203 China

Unique endoperoxide moiety of artemisinin and its derivatives has been considered the functionality exhibiting highly potent antimalarial and anticancer *** investigate the mechanisms of their biological actions,development of suitable molecular probes including biotinylated derivatives is of extreme *** synthesis and preliminary biological assessment of four new biotinylated artemisinin derivatives have been reported in this work.

关键词： artemisinin endoperoxide biotinylated derivative synthesis anticancer activity

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