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A simulation method of combinding boundary element method with generalized Langevin dynamics

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Chinese Science Bulletin 2000年第24期45卷 2227-2231页

作者： CHEN Weizu LU Benzhuo wang cunxin Center tor Biomedical Engineering Beijing Polytechnic UniversityBeijing 100022China School of Life Science University of Science and Technology of ChinaHefei 230026China

A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.

关键词： potential of mean force of solvent boundary element method friction memory function generalized Langevin dynamics.

A novel family of green ionic liquids with surface activities

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Science China Chemistry 2007年第2期50卷 238-242页

作者： ZHANG HaiBo ZHOU XiaoHai DONG JinFeng ZHANG GaoYong wang cunxin Department of Chemistry Wuhan UniversityWuhan 430072China

Ionic liquids have many unique properties as a new and remarkable class of environmental benign solvents,which promises widespread applications in industry and other areas. However,the ionic liq-uids with surface activity are rarely reported. In this work,a series of novel ionic liquids was synthe-sized by using N-methyl-2-pyrrolidone and alkyl bromide. The physical properties of this family of ionic liquids have been characterized,which shows that these compounds have ionic liquids characteristics,surface activity and biocompatibility.

关键词： surface activity ionic liquids N-methyl-2-pyrrolidone biocompatibility

Pharmacophore and Docking-based 3D-QSAR Studies on HIV-1 Integrase Inhibitors

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Chemical Research in Chinese Universities 2014年第2期30卷 297-305页

作者： ZHANG Xiaoyi DENG Dongjie TAN Jianjun HE Yu LI Chunhua wang cunxin College of Life Science and Bioengineering Beijing University of Technology Beijing 100124 P.R.China College of Materials Science and Engineering Beijing University of Technology Beijing 100124 P.R.China

Integrase（IN） plays an essential role in the process of HIV-1 *** inhibitors of diketo acid derivatives（DKAs） were analysed by the Comparative Molecular Field Analysis（CoMFA） and Comparative Molecular Similarity Induces Analysis（CoMSIA） methods.A set of 42 compounds were randomly selected as the training set（35） and test set（7）.Firstly,a good pharmacophore（goodness of hit=0.787） was obtained and used to align ***,predictive models were constructed with the CoMFA and CoMSIA methods based on the pharmacophore *** a result,the CoMS1A method yielded the best model with an r2 of 0.955 and a q2 of 0.665,which can predict the activities of the tested DKAs very well（r2=0.559）.Finally,DKAs were docked into IN,and the predicit modes were superimposed on the contour maps obtained from the best CoMSIA *** superimposed maps gave a visualized and meaningful insight into the inhibitory behaviors,providing significantly useful information for the rational drug design of anti-IN agents.

关键词： HIV-1 integrase Diketo acid Quantitative structure-activity relationship Pharmacophore Molecular docking

A holistic molecular docking approach for predicting protein-protein complex structure

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Science China(Life Sciences) 2010年第9期53卷 1152-1161页

作者： GONG XinQi LIU Bin CHANG Shan LI ChunHua CHEN WeiZu wang cunxin College of Life Science and Bioengineering Beijing University of TechnologyBeijing 100124China

A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure *** article explains the detailed steps and applications for CAPRI Target *** CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures.

关键词： protein-protein complex structure prediction binding site molecular docking CAPRI

Synthesis,Characterization and Calorimetry of Ni(C_4H_8N_2O_3)_2Cl_2

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Wuhan University Journal of Natural Sciences 2007年第3期12卷 511-514页

作者： QU Xiaosheng LI Jie wang Zhiyong wang cunxin College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 Hubei China

A coordination complex was synthesized from NiCl2 and dipeptide glycylglycine（GG）. It was characterized by element analysis, NMR and TG methods, and then was determined to be Ni（C4HsN2O3）2Cl2. Using an isoperibolic reaction calorimeter, the standard molar enthalpy of formation of Ni（GG）2Cl2（solid） has been determined to be -（1 674.66±2.02） kJ · mol^-1 at 298.15 K.

关键词： isoperibolic reaction calorimeter standard molar enthalpy of formation coordination complex glycylglycine Ni(C4HsN203)2Cl2

Salt and pH-dependent properties of native and mutant insulin

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Chinese Science Bulletin 2002年第6期47卷 464-466页

作者： MA Xiaohui LI Chunhua LU Benzhuo CHEN Weizu wang cunxin XU Xiaojie Center for Biomedical Engineering Beijing Polytechnic UniversityBeijing 100022China Department of Astronomy and Applied Physics University of Science and Technology of ChinaHeifei 230026China College of Chemistry&Molecular Engineering Peking UniversityBeijing 100871China

A fast and effective model for predicting the salt and pH dependent properties of protein complexes is presented. It is based on the formal charge parameter sets of ionizable groups and applied in conjunction with the finite difference Poisson-Boltzmann (FDPB) method to calculate the electrostatic interactions. All simulations were performed on the native 2Zn insulin and its fast-acting mutants such as B9D (B9Ser→Asp), B9E (B9Aer→Glu), B9EB10D (B9Ser→ Glu, B10His→Asp), and B10D (B10His→Asp). The salt and pH dependent properties of these dimers were analyzed from the aspect of electrostatic interaction, and the theoretical basis of the fast-acting behavior of these mutants was explained. It is found that the results agree well with experimental observations.

关键词： formal charge electrostatic interaction insulin Pois-son-Boltzmann equation.

Development of a high-throughput assay for the HIV-1 integrase disintegration reaction

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Science China(Life Sciences) 2010年第2期53卷 241-247页

作者： HE HongQiu,LIU Bin,ZHANG XiaoYi,CHEN WeiZu & wang cunxin College of Life Science and Bioengineering,Beijing University of Technology,Beijing 100124,China 1. College of Life Science and Bioengineering Beijing University of Technology Beijing 100124 China

Both HIV-1 integrase (IN) and the central catalytic domain of IN (IN-CCD) catalyze the disintegration reaction in *** this study,IN and IN-CCD proteins were expressed and purified,and a high-throughput format enzyme-linked immunosorbent assay (ELISA) was developed for the disintegration *** exhibited a marked preference for Mn2+ over Mg2+ as the divalent cation cofactor in ***,a known IN inhibitor,was found to be an IN-CCD *** assay is sensitive and specific for the study of disintegration reaction as well as for the in vitro identification of antiviral drugs targeting IN,especially targeting IN-CCD.

关键词： HIV-1 integrase IN-CCD disintegration high-throughput assay

Solvation effects on brain uptakes of isomers of ^(99m)Tc brain imaging agents

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Chinese Science Bulletin 2002年第21期47卷 1786-1791页

作者： JIA Hongmei, MA Xiaohui, wang cunxin & LIU Boli1. Department of Chemistry, Beijing Normal University, Beijing 100875, China 2. Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, China 1. Department of Chemistry Beijing Normal University Beijing 100875 China 2. Center for Biomedical Engineering Beijing Polytechnic University Beijing 100022 China

Analysis of electrostatic hydration free energies of the isomers of the 99mTc-BAT and 99mTc-DADT complexes is carried out using the computer simulation technique. The results show that not only a correlation exists between the logarithm of the brain uptake and the electrostatic hydration free energy for the isomers of 99mTc-brain radiopharmaceu-ticals, but also a linear relationship exists between the logarithm of the ratio of the brain uptake of the syn isomer to that of the anti one and the difference between the electrostatic hydration free energy of the syn-isomer and that of the anti one. Furthermore, the investigation on the important factors influencing the brain uptakes of 99mTc-radiophar-maceuticals and the reasons of the different biodistribution of the isomers of the 99mTc-complexes is explored at the molecular level. The results may provide a reference for the rational drug design of brain imaging agents.

关键词： 99mTc-brain imaging agent isomer brain uptake electro-static hydration free energy.

DESCRIPTION OF A NEW GENUS AND A NEW SPECIES OF A LABROID FISH OF CHINA

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海洋与湖沼 1979年第1期 75-76页

作者： C. T. Cheng and wang cunxin (T. H. wang) (Institute of Oceanology, Academia Sinica)

During the past few years of our investigation on the fish fauna of Xisha Islands, South China Sea, we have collected in three occasions five specimens of a hitherto undiscovered Labroid fish in the vicinity from Dongdao and Yongxingdao, off the coast of Guangdong province. The fish specimens are considered as belonging to a new species and a new genus, the description of which is given below.

关键词： DESCRIPTION OF A NEW GENUS AND A NEW SPECIES OF A LABROID FISH OF CHINA FISH