人源可溶性环氧化物水解酶与抑制剂相互作用的分子动力学模拟研究
|
摘要
蛋白质-配体相互作用几乎是生物体或细胞内一切生化过程的基础,在所有生命过程中起着重要的作用。深入地了解蛋白质与生物学相关的配体或小分子抑制剂之间的相互作用,将对分子识别和药物分子的设计产生深刻的影响。
本论文应用分子对接和分子动力学模拟方法,研究了人源可溶性环氧化物水解酶结合酰胺类和脲类抑制剂的相互作用情况。
(1)基于苯并恶唑的酰胺类抑制剂结合人源可溶性环氧化物水解酶的分子对接和分子动力学模拟研究。
可溶性环氧化物水解酶已成为治疗人类多种疾病的新靶点。采用分子对接和分子动力学模拟相结合的方法研究了抑制剂抑制人源可溶性环氧化物水解活性的作用机理。通过分子对接、动力学模拟、结合自由能计算和能量分解等分析方法研究六个基于苯并恶唑的酰胺类抑制剂与sEH的结合特征。基于分子力学-广义波恩/面积区域计算和正则模分析结果表明计算获得的这些抑制剂结合自由能排序与实验测量的生物活性数据IC50值排序相吻合,具有很好的相关性,相关系数为0.88。在所有组成结合自由能的能量项中,范德华相互作用能对结合能的贡献最大；熵对体系结合自由能的贡献也不可忽略。通过对接和结合自由能确定了抑制剂的合理结合模式。自由能分解结果表明在所有残基中(?)rp334残基对体系的结合贡献最大,这些抑制剂的结合强度与氢键没有直接的关系,结合强度由结合口袋中多个残基共同决定,主要是范德华相互作用的结果。
(2)含哌嗪环的金刚烷1,3-二取代脲类抑制剂结合人源可溶性环氧化物水解酶的分子动力学模拟研究。
采用分子对接、动力学模拟、结合自由能计算和自由能分解分析研究了一系列基于金刚烷基1,3-二取代脲类抑制剂结合sEH蛋白酶的结合模式和抑制机理。根据结合亲和力分析,确定了抑制剂的最佳结合模式。结合自由能计算表明总结合自由能与实验IC50有很好的相关性,相关系数达到0.99。在结合能的各能量项中,范德华作用对结合自由能贡献最大。详细讨论了抑制剂与活性口袋上残基之间的相互作用方式和氢键的形成情况。结合自由能分解,发现在所有模拟体系中残基Asp333和残基Trp334贡献的结合自由能最大。此外,质子化残基Hip523对抑制剂的空间取向起到了决定作用。
Protein-ligand interactions are the basis of all the biochemical processes in living systems. A deep understanding of protein-small molecule interactions is of great interest as it provides opportunities for understanding function and therapeutic intervention. It will cause a profound impact on molecular recognition and drug molecules design.
We employed a method combined with molecular docking and molecular dynamics simulations to study the interaction of human epoxide hydrolase with amide and urea inhibitors in current thesis.
(1) Probing Ligand-binding modes and binding mechanisms of benzoxazole-based amide inhibitors with soluble Epoxide Hydrolase by molecular docking and molecular dynamics simulation.
Soluble epoxide hydrolase (sEH) has become a new therapeutic target for treating a variety of human diseases. The inhibition of human sEH hydrolase activity was studied by molecular docking and molecular dynamics (MD) simulation techniques. A set of six benzoxazole-based amide inhibitors binding to sEH has been studied through molecular docking, MD simulation, free energy calculations, and energy decomposition analysis. On the basis of molecular mechanics-generalized Born/surface area (MM-GB/SA) computation and normal mode analysis (NMA), the obtained results indicate that the rank of calculated binding free energies (ΔΔGTOT) of these inhibitors is in excellent agreement with that of experimental bioactivity data (IC50). The correlation coefficient (r2) between the predicted ΔΔGTOT and IC50is0.88. van der Waals energies are the largest component of the total energies and the entropy changes play an indispensable role in determining the ΔΔGTOT.Rational binding modes were discussed and determined by the docking results and binding free energies. The free energy decomposition of each residue reveals that the residue Trp334dominates the most binding free energies among all residues and the activities for these molecules to the sEH are not decided by hydrogen bonds or a certain residue but by the common effect of multiple side chains in the active site.
(2) Insight into the Binding Modes and Inhibition Mechanisms of Adamantyl-based1,3-disubstituted Urea Inhibitors in the Active Site of the Human Soluble Epoxide Hydrolase.
The binding modes and interaction mechanisms of a series of adamantyl-based1,3-disubstituted urea inhibitors were investigated by combining molecular docking, molecular dynamics simulations, binding free energy calculations, and binding energy decomposition analysis. Based on binding affinity, those favorable binding modes had been determined. The binding free energy calculations indicated that the total binding free energies present a good correlation with the experimental inhibitory activity (IC50, r2=0.99). van der Waals energies are the largest component contributed to the total energies. The electrostatic energies are the major reasons for distinct binding affinity in different binding modes. A detailed discussion of the interaction mechanisms of inhibitors with residues in the active pocket was made based on hydrogen bond and binding modes analysis. According to binding energy decomposition, the residues Asp333and Trp334contributed the most binding free energies in all systems. Furthermore, Hip523play a major role in determining this class of inhibitor-binding orientations. These obtained results in this works will provide valuable information for the design of high potency sEH inhibitors in the future.
本论文应用分子对接和分子动力学模拟方法,研究了人源可溶性环氧化物水解酶结合酰胺类和脲类抑制剂的相互作用情况。
(1)基于苯并恶唑的酰胺类抑制剂结合人源可溶性环氧化物水解酶的分子对接和分子动力学模拟研究。
可溶性环氧化物水解酶已成为治疗人类多种疾病的新靶点。采用分子对接和分子动力学模拟相结合的方法研究了抑制剂抑制人源可溶性环氧化物水解活性的作用机理。通过分子对接、动力学模拟、结合自由能计算和能量分解等分析方法研究六个基于苯并恶唑的酰胺类抑制剂与sEH的结合特征。基于分子力学-广义波恩/面积区域计算和正则模分析结果表明计算获得的这些抑制剂结合自由能排序与实验测量的生物活性数据IC50值排序相吻合,具有很好的相关性,相关系数为0.88。在所有组成结合自由能的能量项中,范德华相互作用能对结合能的贡献最大；熵对体系结合自由能的贡献也不可忽略。通过对接和结合自由能确定了抑制剂的合理结合模式。自由能分解结果表明在所有残基中(?)rp334残基对体系的结合贡献最大,这些抑制剂的结合强度与氢键没有直接的关系,结合强度由结合口袋中多个残基共同决定,主要是范德华相互作用的结果。
(2)含哌嗪环的金刚烷1,3-二取代脲类抑制剂结合人源可溶性环氧化物水解酶的分子动力学模拟研究。
采用分子对接、动力学模拟、结合自由能计算和自由能分解分析研究了一系列基于金刚烷基1,3-二取代脲类抑制剂结合sEH蛋白酶的结合模式和抑制机理。根据结合亲和力分析,确定了抑制剂的最佳结合模式。结合自由能计算表明总结合自由能与实验IC50有很好的相关性,相关系数达到0.99。在结合能的各能量项中,范德华作用对结合自由能贡献最大。详细讨论了抑制剂与活性口袋上残基之间的相互作用方式和氢键的形成情况。结合自由能分解,发现在所有模拟体系中残基Asp333和残基Trp334贡献的结合自由能最大。此外,质子化残基Hip523对抑制剂的空间取向起到了决定作用。
Protein-ligand interactions are the basis of all the biochemical processes in living systems. A deep understanding of protein-small molecule interactions is of great interest as it provides opportunities for understanding function and therapeutic intervention. It will cause a profound impact on molecular recognition and drug molecules design.
We employed a method combined with molecular docking and molecular dynamics simulations to study the interaction of human epoxide hydrolase with amide and urea inhibitors in current thesis.
(1) Probing Ligand-binding modes and binding mechanisms of benzoxazole-based amide inhibitors with soluble Epoxide Hydrolase by molecular docking and molecular dynamics simulation.
Soluble epoxide hydrolase (sEH) has become a new therapeutic target for treating a variety of human diseases. The inhibition of human sEH hydrolase activity was studied by molecular docking and molecular dynamics (MD) simulation techniques. A set of six benzoxazole-based amide inhibitors binding to sEH has been studied through molecular docking, MD simulation, free energy calculations, and energy decomposition analysis. On the basis of molecular mechanics-generalized Born/surface area (MM-GB/SA) computation and normal mode analysis (NMA), the obtained results indicate that the rank of calculated binding free energies (ΔΔGTOT) of these inhibitors is in excellent agreement with that of experimental bioactivity data (IC50). The correlation coefficient (r2) between the predicted ΔΔGTOT and IC50is0.88. van der Waals energies are the largest component of the total energies and the entropy changes play an indispensable role in determining the ΔΔGTOT.Rational binding modes were discussed and determined by the docking results and binding free energies. The free energy decomposition of each residue reveals that the residue Trp334dominates the most binding free energies among all residues and the activities for these molecules to the sEH are not decided by hydrogen bonds or a certain residue but by the common effect of multiple side chains in the active site.
(2) Insight into the Binding Modes and Inhibition Mechanisms of Adamantyl-based1,3-disubstituted Urea Inhibitors in the Active Site of the Human Soluble Epoxide Hydrolase.
The binding modes and interaction mechanisms of a series of adamantyl-based1,3-disubstituted urea inhibitors were investigated by combining molecular docking, molecular dynamics simulations, binding free energy calculations, and binding energy decomposition analysis. Based on binding affinity, those favorable binding modes had been determined. The binding free energy calculations indicated that the total binding free energies present a good correlation with the experimental inhibitory activity (IC50, r2=0.99). van der Waals energies are the largest component contributed to the total energies. The electrostatic energies are the major reasons for distinct binding affinity in different binding modes. A detailed discussion of the interaction mechanisms of inhibitors with residues in the active pocket was made based on hydrogen bond and binding modes analysis. According to binding energy decomposition, the residues Asp333and Trp334contributed the most binding free energies in all systems. Furthermore, Hip523play a major role in determining this class of inhibitor-binding orientations. These obtained results in this works will provide valuable information for the design of high potency sEH inhibitors in the future.
引文
[1]Dunn Michael F. Protein-Ligand Interactions:General Description.2001.
[2]HARDER D. R., CAMPBELL W. B., ROMAN R. J. ROLE OF CYTOCHROME-P-450 ENZYMES AND METABOLITES OF ARACHIDONIC-ACID IN THE CONTROL OF VASCULAR TONE. JOURNAL OF VASCULAR RESEARCH.1995.32 (2).79-92
[3]Perozzo R., Folkers G., Scapozza L. Thermodynamics of protein-ligand interactions:History, presence, and future aspects. JOURNAL OF RECEPTORS AND SIGNAL. TRANSDUCTION.2004.24(1-2).1-52
[4]Freire Ernesto. Do enthalpy and entropy distinguish first in class from best in class? DRUG DISCOVERY TODAY.2008.13(19-20).869-874
[5]Gohlke H., Hendlich M., Klebe G. Predicting binding modes, binding affinities and'hot spots' for protein-ligand complexes using a knowledge-based scoring function. PERSPECTIVES IN DRUG DISCOVERY AND DESIGN.2000.20(1).115-144
[6]Gohlke H., Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION.2002.41(15).2645-2676
[7]Rich R. L., Myszka D. G. Advances in surface plasmon resonance biosensor analysis. CURRENT OPINION IN BIOTECHNOLOGY.2000.11(1).54-61
[8]Bissantz Caterina, Kuhn Bernd, Stahl Martin. A Medicinal Chemist's Guide to Molecular Interactions. JOURNAL OF MEDICINAL CHEMISTRY.2010.53(14).5061-5084
[9]B6hm H. J. Prediction of Non-bonded Interactions in Drug Design.2003.3-20
[10]Hubbard Roderick E., Kamran Haider Muhammad. Hydrogen Bonds in Proteins:Role and Strength.2001.
[11]RICHARDS F. M. AREAS, VOLUMES, PACKING, AND PROTEIN-STRUCTURE. ANNUAL REVIEW OF BIOPHYSICS AND BIOENGINEERING.1977.6.151-176
[12]SHARP K. A., NICHOLLS A., FRIEDMAN R., HONIG B. EXTRACTING HYDROPHOBIC FREE-ENERGIES FROM EXPERIMENTAL-DATA-RELATIONSHIP TO PROTEIN FOLDING AND THEORETICAL-MODELS. BIOCHEMISTRY.1991. 30(40).9686-9697
[13]Meyer E. A., Castellano R K., Diederich F. Interactions with aromatic rings in chemical and biological recognition. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION,2003. 42(11).1210-1250
[14]McGiaughey G. B., Gragne M., Rappe A. K. pi-stacking interactions-Alive and well in proteins. JOURNAL OF BIOLOGICAL CHEMISTRY.1998.273(25).15458-15463
[15]Desiraju G. R. C-H center dot center dot center dot O and other weak hydrogen bonds. From crystal engineering to virtual screening. CHEMICAL COMMUNICATIONS.2005. (24). 2995-3001
[16]Tsuzuki S., Honda K., Uchimaru T., Mikami M., Tanabe K. The magnitude of the CH/pi interaction between benzene and some model hydrocarbons. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.2000.122(15).3746-3753
[17]Mobley David L., Dill Ken A. Binding of Small-Molecule Ligands to Proteins:"What You See" Is Not Always "What You Get". STRUCTURE.2009.17(4).489-498
[18]Cozzini Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., Orozco Modesto, Pertinhez Thelma A., Rizzi Menico, Sotriffer Christoph A. Target Flexibility:An Emerging Consideration in Drug Discovery and Design. JOURNAL OF MEDICINAL CHEMISTRY.2008.51(20).6237-6255
[19]Gutteridge A., Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. JOURNAL OF MOLECULAR BIOLOGY.2005.346(1).21-28
[20]Butcher J. C. Numerical Methods for Ordinary Differential Equations.2nd Edition. Hoboken. Wiley.2003.
[21]Humphreys P. Extending Ourselves:Computati onal Science, Empiricism, and Scientific Method.1st Edition. Oxford University Press.
[22]J. L. McClean, M. E. Maltrud And F. O. Bryan. Measures of the fidelity of eddying ocean models. Oceanography.2006.19(1).104-117
[23]Chourasia Amit, Cutchin Steve, Aagaard Brad. Visualizing the ground motions of the 1906 San Francisco earthquake. COMPUTERS & amp; GEOSCIENCES.2008.34(12).1798-1805
[24]Haile J. M. Molecular Dynamics Simulation:Elementary Methods.1st Edition. New York. Wiley-Interscience.1997.
[25]Allen M. P., Tildesley D. J. Computer Simulation of Liquids. Oxford. Clarendon Press. 1987.
[26]Frenkel D., Smit B. Understanding Molecular Simulation-From Algorithms to Applications. San Diego. Academic Press.2002.
[27]Hill T. L. An Introduction to Statistical Thermodynamics. New York. Dover Publications Inc.1986.
[28]MCCAMMON J. A., GELIN B. R., KARPLUS M. DYNAMICS OF FOLDED PROTEINS. NATURE.1977.267(5612).585-590
[29]KARPLUS M., MCCAMMON J. A. PROTEIN STRUCTURAL FLUCTUATIONS DURING A PERIOD OF 100-PS. NATURE.1979.277(5697).578
[30]Van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A. E., Berendsen HJC. GROMACS:Fast, flexible, and free. JOURNAL OF COMPUTATIONAL CHEMISTRY. 2005.26(16).1701-1718
[31]Case David A., Cheatham Thomas E., Darden Tom, Gohlke Holger, Luo Ray, Merz Kenneth M., Onufriev Alexey, Simmerling Carlos, Wang Bing, Woods Robert J. The Amber biomolecular simulation programs. Journal of Computational Chemistry.2005.26(16). 1668-1688
[32]Phillips J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kale L., Schulten K. Scalable molecular dynamics with NAMD. JOURNAL OF COMPUTATIONAL CHEMISTRY.2005.26(16).1781-1802
[33]Alvarez J. C. High-throughput docking as a source of novel drug leads. CURRENT OPINION IN CHEMICAL BIOLOGY.2004.8(4).365-370
[34]Fretland Adrian J., Omiecinski Curtis J. Epoxide hydrolases:biochemistry and molecular biology. Chemico-Biological Interactions.2000.129(1-2).41-59
[35]Yu Z. G., Xu F. Y., Huse L. M., Morisseau C., Draper A. J., Newman J. W., Parker C., Graham L., Engler M. M., Hammock B. D., Zeldin D. C., Kroetz D. L. Soluble epoxide hydrolase regulates hydrolysis of vasoactive epoxyeicosatrienoic acids. CIRCULATION RESEARCH.2000.87(11).992-998
[36]VANROLLINS M., KADUCE T. L., KNAPP H. R., SPECTOR A. A. 14,15-EPOXYEICOSATRIENOIC ACID METABOLISM IN ENDOTHELIAL-CELLS. JOURNAL OF LIPID RESEARCH.1993.34(11).1931-1942
[37]FANG X., VANROLLINS M., KADUCE T. L., SPECTOR A. A. EPOXYEICOSATRIENOIC ACID METABOLISM IN ARTERIAL SMOOTH-MUSCLE CELLS. JOURNAL OF LIPID RESEARCH.1995.36(6).1236-1246
[38]JOHANSSON C., STARK A., SANDBERG M., EK B., RASK L., MEIJER J. TISSUE-SPECIFIC BASAL EXPRESSION OF SOLUBLE MURINE EPOXIDE HYDROLASE AND EFFECTS OF CLOFIBRATE ON THE MESSENGER-RNA LEVELS IN EXTRAHEPATIC TISSUES AND LIVER. ARCHIVES OF TOXICOLOGY.1995. 70(1).61-63
[39]Enayetallah A. E., French R. A., Thibodeau M. S., Grant D. F. Distribution of soluble epoxide hydrolase and of cytochrome P4502C8,2C9, and 2J2 in human tissues. JOURNAL OF HISTOCHEMISTRY & amp; CYTOCHEMISTRY.2004.52(4).447-454.
[40]HOLLINSHEAD M., MEIJER J. IMMUNOCYTOCHEMICAL ANALYSIS OF SOLUBLE EPOXIDE HYDROLASE AND CATALASE IN MOUSE AND RAT HEPATOCYTES DEMONSTRATES A PEROXISOMAL LOCALIZATION BEFORE AND AFTER CLOFIBRATE TREATMENT. EUROPEAN JOURNAL OF CELL BIOLOGY.1988.46(3). 394-402
[41]ERIKSSON A. M., ZETTERQVIST M. A., LUNDGREN B.,ANDERSSON K., BEIJE B., DEPIERRE J. W. STUDIES ON THE INTRACELLULAR DISTRIBUTIONS OF SOLUBLE EPOXIDE HYDROLASE AND OF CATALASE BY DIGITONIN-PERMEABILIZATION OF HEPATOCYTES ISOLATED FROM CONTROL AND CLOFIBRATE-TREATED MICE. EUROPEAN JOURNAL OF BIOCHEMISTRY. 1991.198(2).471-476
[42]Mullen R. T., Trelease R. N., Duerk H., Arand M., Hammock B. D., Oesch F., Grant D. F. Differential subcellular localization of endogenous and transfected soluble epoxide hydrolase in mammalian cells:evidence for isozyme variants. FEBS LETTERS.1999.445(2-3). 301-305
[43]SCHLADT L., THOMAS H., HARTMANN R., OESCH F. HUMAN-LIVER CYTOSOLIC EPOXIDE HYDROLASES. EUROPEAN JOURNAL OF BIOCHEMISTRY.1988.176(3). 715-723
[44]Sandberg M., Hassett C., Adman E. T., Meijer J., Omiecinski C. J. Identification and functional characterization of human soluble epoxide hydrolase genetic polymorphisms. JOURNAL OF BIOLOGICAL CHEMISTRY.2000.275(37).28873-28881
[45]Saito S., Iida A., Sekine A., Eguchi C., Miura Y., Nakamura Y. Seventy genetic variations in human microsomal and soluble epoxide hydrolase genes (EPHX1 and EPHX2) in the Japanese population. JOURNAL OF HUMAN GENETICS.2001.46(6).325-329
[46]CATELLA F., LAWSON J. A., FITZGERALD D. J., FITZGERALD G. A. ENDOGENOUS BIOSYNTHESIS OF ARACHIDONIC-ACID EPOXIDES IN HUMANS-INCREASED FORMATION IN PREGNANCY-INDUCED HYPERTENSION. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.1990. 87(15).5893-5897
[47]Morisseau Christophe, Schebb Nils Helge, Dong Hua, Ulu Arzu, Aronov Pavel A., Hammock Bruce D. Role of soluble epoxide hydrolase phosphatase activity in the metabolism of lysophosphatidic acids. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS.2012.419(4).796-800
[48]Newman J. W., Morisseau C., Harris T. R., Hammock B. D. The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2003.100(4).1558-1563
[49]Tran K. L., Aronov P. A., Tanaka H., Newman J. W., Hammock B. D., Morisseau C. Lipid sulfates and sulfonates are allosteric competitive inhibitors of the N-terminal phosphatase activity of the mammalian soluble epoxide hydrolase. BIOCHEMISTRY.2005.44(36). 12179-12187
[50]Spector Arthur A. Arachidonic acid cytochrome P450 epoxygenase pathway. JOURNAL OF LIPID RESEARCH.2009.50. S52-S56
[51]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY.2007.292(3). C996-C1012
[52]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY.2007.292(3). C996-C1012
[53]HAMMOCK B. D., PINOT F., BEETHAM J. K., GRANT D. F., ARAND M. E., OESCH F. ISOLATION OF A PUTATIVE HYDROXYACYL ENZYME INTERMEDIATE OF AN EPOXIDE HYDROLASE. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS.1994.198(3).850-856
[54]BORHAN B., JONES A. D., PINOT F., GRANT D. F., KURTH M. J., HAMMOCK B. D. MECHANISM OF SOLUBLE EPOXIDE HYDROLASE-FORMATION OF AN ALPHA-HYDROXY ESTER-ENZYME INTERMEDIATE THROUGH ASP-333. JOURNAL OF BIOLOGICAL CHEMISTRY.1995.270(45).26923-26930
[55]Arand M., Wagner H., Oesch F. Asp(333), Asp(495), and His(523) form the catalytic triad of rat soluble epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.1996.271(8). 4223-4229
[56]PINOT F., GRANT D. F., BEETHAM J. K., PARKER A. G., BORHAN B., LANDT S., JONES A. D., HAMMOCK B. D. MOLECULAR AND BIOCHEMICAL-EVIDENCE FOR THE INVOLVEMENT OF THE ASP-333-HIS-523 PAIR IN CATALYTIC MECHANISM OF SOLUBLE EPOXIDE HYDROLASE. JOURNAL OF BIOLOGICAL CHEMISTRY. 1995.270(14).7968-7974
[57]Arand M., Wagner H., Oesch F. Asp(333), Asp(495), and His(523) form the catalytic triad of rat soluble epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.1996.271(8).
[58]Yamada T., Morisseau C., Maxwell J. E., Argiriadi M. A., Christianson D. W., Hammock B. D. Biochemical evidence for the involvement of tyrosine in epoxide activation during the catalytic cycle of epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.2000. 275(30).23082-23088
[59]MULLIN C. A., HAMMOCK B. D. CHALCONE OXIDES-POTENT SELECTIVE INHIBITORS OF CYTOSOLIC EPOXIDE HYDROLASE. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS.1982.216(2).423-439
[60]DIETZE E. C., KUWANO E., CASAS J., HAMMOCK B. D. INHIBITION OF CYTOSOLIC EPOXIDE HYDROLASE BY TRANS-3-PHENYLGLYCIDOLS. BIOCHEMICAL PHARMACOLOGY.1991.42(6).1163-1175
[61]Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna, Zheng Jiang, Greene Jessica F., Sanborn James R., Hammock Bruce D. Potent urea and carbamate inhibitors of soluble epoxide hydrolases. Proceedings of the National Academy of Sciences.1999.96(16). 8849-8854
[62]黄少胥,王勇,龙亚秋.人类可溶性环氧化物水解酶抑制剂的研究进展.有机化学.2012.32.877-888
[63]Kim In-Hae, Morisseau Christophe, Watanabe Takaho, Hammock Bruce D. Design, Synthesis, and Biological Activity of 1,3-Disubstituted Ureas as Potent Inhibitors of the Soluble Epoxide Hydrolase of Increased Water Solubility. Journal of Medicinal Chemistry. 2004.47(8).2110-2122
[64]Kasagami Takeo, Kim In-Hae, Tsai Hsing-Ju, Nishi Kosuke, Hammock Bruce D., Morisseau Christophe. Salicylate-urea-based soluble epoxide hydrolase inhibitors with high metabolic and chemical stabilities. BIOORGANIC & amp; MEDICINAL CHEMISTRY LETTERS. 2009.19(6).1784-1789
[65]Kim I. H., Heirtzler F. R., Morisseau C., Nishi K., Tsai H. J., Hammock B. D. Optimization of amide-based inhibitors of soluble epoxide hydrolase with improved water solubility. Journal of medicinal chemistry.2005.48(10).3621-3629
[66]Li Hui-Yuan, Jin Yi, Morisseau Christophe, Hammock Bruce D., Long Ya-Qiu. The 5-substituted piperazine as a novel secondary pharmacophore greatly improving the physical properties of urea-based inhibitors of soluble epoxide hydrolase. BIOORGANIC& MEDICINAL CHEMISTRY.2006.14(19).6586-6592
[67]Jones P. D., Tsai H. J., Do Z. N., Morisseau C., Hammock B. D. Synthesis and SAR of conformationally restricted inhibitors of soluble epoxide hydrolase. Bioorganic and Medicinal Chemistry Letters.2006.16(19).5212-5216
[68]Huang Shao-Xu, Li Hui-Yuan, Liu Jun-Yan, Morisseau Christophe, Hammock Bruce D., Long Ya-Qiu. Incorporation of Piperazino Functionality into 1,3-Disubstituted Urea as the Tertiary Pharmacophore Affording Potent Inhibitors of Soluble Epoxide Hydrolase with Improved Pharmacokinetic Properties. Journal of Medicinal Chemistry.2010.53(23). 8376-8386
[69]Huang Shao-Xu, Cao Bin, Morisseau Christophe, Jin Yi, Hammock Bruce D., Long Ya-Qiu. Structure-based optimization of the piperazino-containing 1,3-disubstituted ureas affording sub-nanomolar inhibitors of soluble epoxide hydrolase. MedChemComm.2012.3(3). 379-384
[70]Eldrup Anne B., Soleymanzadeh Fariba, Taylor Steven J., Muegge Ingo, Farrow Neil A., Joseph David, McKellop Keith, Man Chuk C., Kukulka Alison, De Lombaert Ste phane. Structure-Based Optimization of Arylamides as Inhibitors of Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2009.52(19).5880-5895
[71]Eldrup Anne B., Soleymanzadeh Fariba, Farrow Neil A., Kukulka Alison, De Lombaert St閜 hane. Optimization of piperidyl-ureas as inhibitors of soluble epoxide hydrolase. Bioorganic & Medicinal Chemistry Letters.2010.20(2).571-575
[72]Shen Hong C., Ding Fa-Xiang, Wang Siyi, Xu Suoyu, Chen Hsuan-shen, Tong Xinchun, Tong Vincent, Mitra Kaushik, Kumar Sanjeev, Zhang Xiaoping, Chen Yuli, Zhou Gaochao, Pai Lee-Yuh, Alonso-Galicia Magdalena, Chen Xiaoli, Zhang Bei, Tata James R., Berger Joel P., Colletti Steven L. Discovery of spirocyclic secondary amine-derived tertiary ureas as highly potent, selective and bioavailable soluble epoxide hydrolase inhibitors. BIOORGANIC & amp; MEDICINAL CHEMISTRY LETTERS.2009.19(13).3398-3404
[73]Xing Li, McDonald Joseph J., Kolodziej Steve A., Kurumbail Ravi G., Williams Jennifer M., Warren Chad J., O Neal Janet M., Skepner Jill E., Roberds Steven L. Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening. Journal of Medicinal Chemistry.2011.54(5).1211-1222
[74]Marino Jr. J. P. Soluble epoxide hydrolase, a target with multiple opportunities for cardiovascular drug discovery. Current Topics in Medicinal Chemistry.2009.9(5).452-463
[75]Iliff Jeffrey J., Alkayed Nabil J. Soluble epoxide hydrolase inhibition:targeting multiple mechanisms of ischemic brain injury with a single agent. Future Neurology.2009.4(2). 179-199
[76]Imig J. D., Hammock B. D. Soluble epoxide hydrolase as a therapeutic target for cardiovascular diseases. Nature Reviews Drug Discovery.2009.8(10).794-805
[77]Shen H. C. Soluble epoxide hydrolase inhibitors:A patent review. Expert Opinion on Therapeutic Patents.2010.20(7).941-956
[78]Morisseau C., Hammock B. D. Impact of Soluble Epoxide Hydrolase and Epoxyeicosanoids on Human Health. Annual review of pharmacology and toxicology.2012.
[79]H Ingraham R., D Gless R., Y Lo H. Soluble Epoxide Hydrolase Inhibitors and their Potential for Treatment of Multiple Pathologic Conditions. Current Medicinal Chemistry.2011.18. 587-603
[80]Node K., Huo Y. Q., Ruan X. L., Yang B. C., Spiecker M., Ley K., Zeldin D. C., Liao J. K. Anti-inflammatory properties of cytochrome P450 epoxygenase-derived eicosanoids. SCIENCE.1999.285(5431).1276-1279
[81]Spector A. A., Fang X., Snyder G. D., Weintraub N. L. Epoxyeicosatrienoic acids (EETs): metabolism and biochemical function. PROGRESS IN LIPID RESEARCH.2004.43(1). 55-90
[82]Inceoglu Bora, Jinks Steven L., Schmelzer Kara R., Waite Troy, Kim In Hae, Hammock Bruce D. Inhibition of soluble epoxide hydrolase reduces LPS-induced thermal hyperalgesia and mechanical allodynia in a rat model of inflammatory pain. LIFE SCIENCES.2006. 79(24).2311-2319
[83]Schmelzer K. R., Kubala L., Newman J. W., Kim I. H., Eiserich J. P., Hammock B. D. Soluble epoxide hydrolase is a therapeutic target for acute inflammation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2005.102(28).9772-9777
[84]Xu Danyan, Li Ning, He Yuxia, Timofeyev Valeriy, Lu Ling, Tsai Hsing-Ju, Kim In-Hae, Tuteja Dipika, Mateo Robertino Karlo P., Singapuri Anil, Davis Benjamin B., Low Reginald, Hammock Bruce D., Chiamvimonvat Nipavan. Prevention and reversal of cardiac hypertrophy by soluble epoxide hydrolase inhibitors. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2006.103(49). 18733-18738
[85]Fisslthaler B., Popp R., Kiss L., Potente M., Harder D. R., Fleming I., Busse R. Cytochrome P4502C is an EDHF synthase in coronary arteries. NATURE.1999.401(6752).493-497
[86]Imig J. D., Zhao X. Y., Capdevila J. H., Hammock B. D. Soluble epoxide hydrolase inhibition lowers arterial blood pressure in angiotensin Ⅱ hypertension. HYPERTENSION 2002.39 (2 S).690-694
[87]Jung O., Brandes R. P., Kim I. H., Schmidt R., Busse R. Soluble epoxide hydrolase is a main effector of angiotensin Ⅱ-induced hypertension. HYPERTENSION.2005.45(4).759-765
[88]Sinal Christopher J., Miyata Masaaki, Tohkin Masahiro, Nagata Kiyoshi, Bend John R., Gonzalez Frank J. Targeted Disruption of Soluble Epoxide Hydrolase Reveals a Role in Blood Pressure Regulation. Journal of Biological Chemistry.2000.275(51).40504-40510
[89]Zeldin D. C., Foley J., Cook M. E., Ma J. X., Tomer K. B., Wu S. CYP2J subfamily cytochrome P450s in the gastrointestinal tract:Expression, localization, and potential functional significance. MOLECULAR PHARMACOLOGY.1997.51 (6)
[90]Fang X., Moore S. A., Stoll L. L., Kaduce T. L., Spector A. A.14,15-epoxyeicosatrienoic acid inhibits prostaglandin E-2 production in vascular smooth muscle cells. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.1998.275 (6)
[91]Munzenmaier D. H., Harder D. R. Cerebral microvascular endothelial cell tube formation: role of astrocytic epoxyeicosatrienoic acid release. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.2000.278 (4)
[92]Sun Jianxin, Sui XinXin, Bradbury J. Alyce, Zeldin Darryl C., Conte Michael S., Liao James K. Inhibition of Vascular Smooth Muscle Cell Migration by Cytochrome P450 Epoxygenase-Derived Eicosanoids. Circulation Research.2002.90(9).1020-1027
[93]Node K., Ruan X. L., Dai J. W., Graham L., Liao J. K. Activation of G alpha(s) mediates induction of tissue-type plasminogen activator gene transcription by epoxyeicosatrienoic acids. JOURNAL OF BIOLOGICAL CHEMISTRY.2001.276 (19).15983-15989
[94]Snyder G. D., Krishna U. M., Falck J. R. Evidence for a membrane site of action for 14,15-EET on expression of aromatase in vascular smooth muscle. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.2002.283 (5). H1936-H1942
[95]GOODFORD P. J. A COMPUTATIONAL-PROCEDURE FOR DETERMINING ENERGETICALLY FAVORABLE BINDING-SITES ON BIOLOGICALLY IMPORTANT MACROMOLECULES. JOURNAL OF MEDICINAL CHEMISTRY.1985.28(7).849-857
[96]Kastenholz M. A., Pastor M., Cruciani G., Haaksma EEJ, Fox T. GRID/CPCA:A new computational tool to design selective ligands. JOURNAL OF MEDICINAL CHEMISTRY. 2000.43(16).3033-3044
[97]LEVITT D. G., BANASZAK L. J. POCKET-A COMPUTER-GRAPHICS METHOD FOR IDENTIFYING AND DISPLAYING PROTEIN CAVITIES AND THEIR SURROUNDING AMINO-ACIDS. JOURNAL OF MOLECULAR GRAPHICS.1992.10(4).229-234
[98]LASKOWSKI R. A. SURFNET-A PROGRAM FOR VISUALIZING MOLECULAR-SURFACES, CAVITIES, AND INTERMOLECULAR INTERACTIONS. JOURNAL OF MOLECULAR GRAPHICS.1995.13(5).323
[99]Glaser F., Morris R. J., Najmanovich R. J., Laskowski R. A., Thornton J. M. A method for localizing ligand binding pockets in protein structures. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS.2006.62(2).479-488
[100]Mezei M. A new method for mapping macromolecular topography. JOURNAL OF MOLECULAR GRAPHICS & MODELLING.2003.21(5).463-472
[101]Fischer Emil. Einfluss der Configuration auf die Wirkung der Enzyme. Berichte der deutschen chemischen Gesellschaft.1894.27(3).2985-2993
[102]KOSHLAND D. E. CORRELATION OF STRUCTURE AND FUNCTION IN ENZYME ACTION. SCIENCE.1963.142(359).1533
[103]Hammes G. G. Multiple conformational changes in enzyme catalysis. BIOCHEMISTRY. 2002.41(26).8221-8228
[104]Sherman W., Day T., Jacobson M. P., Friesner R. A., Farid R. Novel procedure for modeling ligand/receptor induced fit effects. JOURNAL OF MEDICINAL CHEMISTRY. 2006.49(2).534-553
[105]JIANG F., KIM S. H. SOFT DOCKING-MATCHING OF MOLECULAR-SURFACE CUBES. JOURNAL OF MOLECULAR BIOLOGY.1991.219(1).79-102
[106]Claussen H., Buning C., Rarey M., Lengauer T. FlexE:Efficient molecular docking considering protein structure variations. JOURNAL OF MOLECULAR BIOLOGY.2001. 308(2).377-395
[107]Alonso Hernan, Bliznyuk Andrey A., Gready Jill E. Combining docking and molecular dynamic simulations in drug design. MEDICINAL RESEARCH REVIEWS.2006. 26(5). 531-568
[108]Sander Tommy, Lijefors Tommy, Balle Thomas. Prediction of the receptor conformation for iGluR2 agonist binding:QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. JOURNAL OF MOLECULAR GRAPHICS & amp; MODELLING.2008.26(8).1259-1268
[109]Subramanian Jyothi, Sharma Somesh, B-Rao Chandrika. A novel computational analysis of ligand-induced conformational changes in the ATP binding sites of cyclin dependent kinases. JOURNAL OF MEDICINAL CHEMISTRY.2006.49(18).5434-5441
[110]Subramanian Jyothi, Sharma Somesh, B-Rao Chandrika. Modeling and selection of flexible proteins for structure-based drug design:Backbone and side chain movements in p38 MAPK. CHEMMEDCHEM.2008.3(2).336-344
[111]Moitessier N., Englebienne P., Lee D., Lawandi J., Corbeil C. R. Towards the development of universal, fast and highly accurate docking/scoring methods:a long way to go. BRITISH JOURNAL OF PHARMACOLOGY.2008.153. S7-S26
[112]KUNTZ I. D., BLANEY J. M., OATLEY S. J., LANGRIDGE R., FERRIN T. E. A GEOMETRIC APPROACH TO MACROMOLECULE-LIGAND INTERACTIONS. JOURNAL OF MOLECULAR BIOLOGY.1982.161(2).269-288
[113]MILLER M. D., KEARSLEY S. K., UNDERWOOD D. J., SHERIDAN R. P. FLOG-A SYSTEM TO SELECT QUASI-FLEXIBLE LIGANDS COMPLEMENTARY TO A RECEPTOR OF KNOWN 3-DIMENSIONAL STRUCTURE. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1994.8(2).153-174
[114]Diller D. J., Merz K. M. High throughput docking for library design and library prioritization. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2001.43(2). 113-124
[115]Burkhard P., Taylor P., Walkinshaw M. D. An example of a protein ligand found by database mining:Description of the docking method and its verification by a 2.3 angstrom X-ray structure of a thrombin-ligand complex. JOURNAL OF MOLECULAR BIOLOGY. 1998.277(2).449-466
[116]Ewing TJA, Makino S., Skillman A. G., Kuntz I. D. DOCK 4.0:Search strategies for automated molecular docking of flexible molecule databases. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.2001.15(5).411-428
[117]Rarey M., Kramer B., Lengauer T., Klebe G. A fast flexible docking method using an incremental construction algorithm. JOURNAL OF MOLECULAR BIOLOGY.1996.261(3). 470-489
[118]Welch W., Ruppert J., Jain A. N. Hammerhead:Fast, fully automated docking of flexible ligands to protein binding sites. CHEMISTRY & amp; BIOLOGY.1996.3(6).449-462
[119]Schnecke V., Kuhn L. A. Virtual screening with solvation and ligand-induced complementarity. PERSPECTIVES IN DRUG DISCOVERY AND DESIGN.2000.20(1). 171-190
[120]Zsoldos Zsolt, Reid Darryl, Simon Aniko, Sadjad Bashir S., Johnson A. Peter. eHITS:An innovative approach to the docking and scoring function problems. CURRENT PROTEIN & PEPTIDE SCIENCE.2006.7(5).421-435
[121]GOODSELL D. S., OLSON A. J. AUTOMATED DOCKING OF SUBSTRATES TO PROTEINS BY SIMULATED ANNEALING. PROTEINS-STRUCTURE FUNCTION AND GENETICS.1990.8(3).195-202
[122]ABAGYAN R., TOTROV M., KUZNETSOV D. ICM-A NEW METHOD FOR PROTEIN MODELING AND DESIGN-APPLICATIONS TO DOCKING AND STRUCTURE PREDICTION FROM THE DISTORTED NATIVE CONFORMATION. JOURNAL OF COMPUTATIONAL CHEMISTRY.1994.15(5).488-506
[123]Verdonk M. L., Cole J. C., Hartshorn M. J., Murray C. W., Taylor R. D. Improved protein-ligand docking using GOLD. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2003.52(4).609-623
[124]CLARK K. P., AJAY. FLEXIBLE LIGAND DOCKING WITHOUT PARAMETER ADJUSTMENT ACROSS 4 LIGAND-RECEPTOR COMPLEXES. JOURNAL OF COMPUTATIONAL CHEMISTRY.1995.16(10).1210-1226
[125]Taylor J. S., Burnett R. M. DARWIN:A program for docking flexible molecules. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2000.41(2).173-191
[126]Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(14). 1639-1662
[127]Rosin M. P., Epstein J. B., Berean K., Durham S., Hay J., Cheng X., Zeng T., Huang Y. Q., Zhang L. W. The use of exfoliative cell samples to map clonal genetic alterations in the oral epithelium of high-risk patients. CANCER RESEARCH.1997.57(23).5258-5260
[128]Hart William Eugene. Adaptive Global Optimization with Local Search.
[129]Kitchen D. B., Decornez H., Furr J. R., Bajorath J. Docking and scoring in virtual screening for drug discovery:Methods and applications. NATURE REVIEWS DRUG DISCOVERY. 2004.3(11).935-949
[130]Bohm H. J. Prediction of binding constants of protein ligands:A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1998.12(4).309-323
[131]GEHLHAAR D. K., VERKHIVKER G. M., REJTO P. A., SHERMAN C. J., FOGEL D. B., FOGEL L. J., FREER S. T. MOLECULAR RECOGNITION OF THE INHIBITOR AG-1343 BY HIV-1 PROTEASE-CONFORMATIONALLY FLEXIBLE DOCKING BY EVOLUTIONARY PROGRAMMING. CHEMISTRY & amp; BIOLOGY.1995.2(5). 317-324
[132]Verkhivker G. M., Bouzida D., Gehlhaar D. K., Rejto P. A., Arthurs S., Colson A. B., Freer S. T., Larson V., Luty B. A., Marrone T., Rose P. W. Deciphering common failures in molecular docking of ligand-protein complexes. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.2000.14(8).731-751
[133]Jain A. N. Scoring noncovalent protein-ligand interactions:A continuous differentiable function tuned to compute binding affinities. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1996.10(5).427-440
[134]Head R. D., Smythe M. L., Oprea T. I., Waller C. L., Green S. M., Marshall G. R. VALIDATE:A new method for the receptor-based prediction of binding affinities of novel ligands. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.1996.118(16). 3959-3969
[135]BOHM H. J. LUDI-RULE-BASED AUTOMATIC DESIGN OF NEW SUBSTITUENTS FOR ENZYME-INHIBITOR LEADS. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1992.6(6).593-606
[136]GEHLHAAR D. K., MOERDER K. E., ZICHI D., SHERMAN C. J., OGDEN R. C., FREER S. T. DE-NOVO DESIGN OF ENZYME-INHIBITORS BY MONTE-CARLO LIGAND GENERATION. JOURNAL OF MEDICINAL CHEMISTRY.1995.38(3). 466-472
[137]Eldridge M. D., Murray C. W., Auton T. R., Paolini G. V., Mee R. P. Empirical scoring functions.1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1997.11(5).425-445
[138]KOLLMAN P. FREE-ENERGY CALCULATIONS-APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA. CHEMICAL REVIEWS.1993.93(7).2395-2417
[139]Aqvist J., Luzhkov V. B., Brandsdal B. O. Ligand binding affinities from MD simulations. ACCOUNTS OF CHEMICAL RESEARCH.2002.35(6).358-365
[140]CARLSON H. A., JORGENSEN W. L. AN EXTENDED LINEAR-RESPONSE METHOD FOR DETERMINING FREE-ENERGIES OF HYDRATION. JOURNAL OF PHYSICAL CHEMISTRY.1995.99(26).10667-10673
[141]LEACH A. R., KUNTZ I. D. CONFORMATIONAL-ANALYSIS OF FLEXIBLE LIGANDS IN MACROMOLECULAR RECEPTOR-SITES. JOURNAL OF COMPUTATIONAL CHEMISTRY.1992.13(6).730-748
[142]SHOICHET B. K., STROUD R. M., SANTI D. V., KUNTZ I. D., PERRY K. M. STRUCTURE-BASED DISCOVERY OF INHIBITORS OF THYMIDYLATE SYNTHASE. SCIENCE.1993.259(5100).1445-1450
[143]Verdonk M. L., Cole J. C., Hartshorn M. J., Murray C. W., Taylor R. D. Improved protein-ligand docking using GOLD. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2003.52(4).609-623
[144]Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(14). 1639-1662
[145]Michel Julien, Verdonk Marcel L., Essex Jonathan W. Protein-ligand binding affinity predictions by implicit solvent simulations:A tool for lead optimization? JOURNAL OF MEDICINAL CHEMISTRY.2006.49(25).7427-7439
[146]KOLLMAN P. FREE-ENERGY CALCULATIONS-APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA. CHEMICAL REVIEWS.1993.93(7).2395-2417
[147]Briggs J. M., Marrone T. J., McCammon J. A. Computational science new horizons and relevance to pharmaceutical design. TRENDS IN CARDIOVASCULAR MEDICINE.1996. 6(6).198-204
[148]Canutescu A. A., Shelenkov A. A., Dunbrack R. L. A graph-theory algorithm for rapid protein side-chain prediction. PROTEIN SCIENCE.2003.12(9).2001-2014
[149]Petrella R. J., Lazaridis T., Karplus M. Protein sidechain conformer prediction:a test of the energy function (vol 3, pg 353,1998). FOLDING & DESIGN.1998.3(6).588
[150]WILSON C., GREGORET L. M., AGARD D. A. MODELING SIDE-CHAIN CONFORMATION FOR HOMOLOGOUS PROTEINS USING AN ENERGY-BASED ROTAMER SEARCH. JOURNAL OF MOLECULAR BIOLOGY.1993.229(4).996-1006
[151]Wawak R. J., Pillardy J., Liwo A., Gibson K. D., Scheraga H. A. Diffusion equation and distance scaling methods of global optimization:Applications to crystal structure prediction. JOURNAL OF PHYSICAL CHEMISTRY A.1998.102(17).2904-2918
[152]Andricioaei I., Straub J. E. Global optimization using bad derivatives:Derivative-free method for molecular energy minimization. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(13).1445-1455
[153]PILLARDY J., PIELA L. MOLECULAR-DYNAMICS ON DEFORMED POTENTIAL-ENERGY HYPERSURFACES. JOURNAL OF PHYSICAL CHEMISTRY. 1995.99(31).11805-11812
[154]Lazaridis T., Karplus M. Thermodynamics of protein folding:a microscopic view. BIOPHYSICAL CHEMISTRY.2003.100(1-3).367-395
[155]Duan Yong, Wu Chun, Chowdhury Shibasish, Lee Mathew C., Xiong Guoming, Zhang Wei, Yang Rong, Cieplak Piotr, Luo Ray, Lee Taisung, Caldwell James, Wang Junmei, Kollman Peter. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 2003.24(16).1999-2012
[156]Ryckaert Jean-Paul, Ciccotti Giovanni, Berendsen Herman J. C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. Journal of Computational Physics.1977.23(3).327-341
[157]Tsui V., Case D. A. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.2000. 122(11).2489-2498
[158]Spector Arthur A., Fang Xiang, Snyder Gary D., Weintraub Neal L. Epoxyeicosatrienoic acids (EETs):metabolism and biochemical function. Progress in Lipid Research.2004.43(1). 55-90
[159]Newman John W., Morisseau Christophe, Hammock Bruce D. Epoxide hydrolases:their roles and interactions with lipid metabolism. Progress in Lipid Research.2005.44(1).1-51
[160]Yu Zhigang, Xu Fengyun, Huse Linn M., Morisseau Christophe, Draper Alison J., Newman John W., Parker Carol, Graham LeRae, Engler Marguerite M., Hammock Bruce D., Zeldin Darryl C., Kroetz Deanna L. Soluble Epoxide Hydrolase Regulates Hydrolysis of Vasoactive Epoxyeicosatrienoic Acids. Circulation Research.2000.87(11).992-998
[161]Schmelzer Kara R., Kubala Lukas, Newman John W., Kim In-Hae, Eiserich Jason P., Hammock Bruce D. Soluble epoxide hydrolase is a therapeutic target for acute inflammation. Proceedings of the National Academy of Sciences of the United States of America.2005. 102(28).9772-9777
[162]Node Koichi, Huo Yuqing, Ruan Xiulu, Yang Baichun, Spiecker Martin, Ley Klaus, Zeldin Darryl C., Liao James K. Anti-inflammatory Properties of Cytochrome P450 Epoxygenase-Derived Eicosanoids. Science.1999.285(5431).1276-1279
[163]Katragadda D., Batchu S. N., Cho W. J., Chaudhary K. R., Falck J. R., Seubert J. M. Epoxyeicosatrienoic acids limit damage to mitochondrial function following stress in cardiac cells. Journal of Molecular and Cellular Cardiology.2009.46(6).867-875
[164]Yousif M. H. M., Benter I. F., Roman R. J. Cytochrome P450 metabolites of arachidonic acid play a role in the enhanced cardiac dysfunction in diabetic rats following ischaemic reperfusion injury. Autonomic and Autacoid Pharmacology.2009.29(1-2).33-41
[165]Xu Danyan, Li Ning, He Yuxia, Timofeyev Valeriy, Lu Ling, Tsai Hsing-Ju, Kim In-Hae, Tuteja Dipika, Mateo Robertino Karlo P., Singapuri Anil, Davis Benjamin B., Low Reginald, Hammock Bruce D., Chiamvimonvat Nipavan. Prevention and reversal of cardiac hypertrophy by soluble epoxide hydrolase inhibitors. Proceedings of the National Academy of Sciences.2006.103(49).18733-18738
[166]Sudhahar V., Shaw S., Imig J. D. Epoxyeicosatrienoic acid analogs and vascular function. Current Medicinal Chemistry.2010.17(12).1181-1190
[167]Zeldin D. C., Kobayashi J., Falck J. R., Winder B. S., Hammock B. D., Snapper J. R., Capdevila J. H. Regio-and enantiofacial selectivity of epoxyeicosatrienoic acid hydration by cytosolic epoxide hydrolase. Journal of Biological Chemistry.1993.268(9).6402-6407
[168]Zeldin D. C., Wei S. Z., Falck J. R., Hammock B. D., Snapper J. R., Capdevila J. H. Metabolism of Epoxyeicosatrienoic Acids by Cytosolic Epoxide Hydrolase:Substrate Structural Determinants of Asymmetric Catalysis. Archives of Biochemistry and Biophysics. 1995.316(1).443-451
[169]Zeldin Darryl C. Epoxygenase Pathways of Arachidonic Acid Metabolism. Journal of Biological Chemistry.2001.276(39).36059-36062
[170]Roman Richard J. P-450 Metabolites of Arachidonic Acid in the Control of Cardiovascular Function. Physiological Reviews.2002.82(1).131-185
[171]Imig John D. Cardiovascular Therapeutic Aspects of Soluble Epoxide Hydrolase Inhibitors. Cardiovascular Drug Reviews.2006.24(2).169-188
[172]Qiu Hong, Li Ning, Liu Jun-Yan, Harris Todd R., Hammock Bruce D., Chiamvimonvat Nipavan. Soluble Epoxide Hydrolase Inhibitors and Heart Failure. Cardiovascular Therapeutics.2011.29(2).99-111
[173]Fang Xiang. Soluble Epoxide Hydrolase:A Novel Target for the Treatment of Hypertension. Recent Patents on Cardiovascular Drug Discovery.2006.1.67-72
[174]Anandan Sampath-Kumar, Webb Heather Kay, Chen Dawn, Wang Yi-Xin Jim, Aavula Basker R., Cases Sylvaine, Cheng Ying, Do Zung N., Mehra Upasana, Tran Vinh, Vincelette Jon, Waszczuk Joanna, White Kathy, Wong Kenneth R., Zhang Le-Ning, Jones Paul D., Hammock Bruce D., Patel Dinesh V., Whitcomb Randall, Maclntyre D. Euan, Sabry James, Gless Richard. 1-(1-Acetyl-piperidin-4-yl)-3-adamantan-1-yl-urea (AR9281) as a potent, selective, and orally available soluble epoxide hydrolase inhibitor with efficacy in rodent models of hypertension and dysglycemia. Bioorganic & Medicinal Chemistry Letters.2011. 21(3).983-988
[175]Kim In-Hae, Park Yong-Kyu, Hammock Bruce D., Nishi Kosuke. Structure-Activity Relationships of Cycloalkylamide Derivatives as Inhibitors of the Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2011.54(6).1752-1761
[176]Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna, Zheng Jiang, Greene Jessica F., Sanborn James R., Hammock Bruce D. Potent urea and carbamate inhibitors of soluble epoxide hydrolases. Proceedings of the National Academy of Sciences.1999.96(16). 8849-8854
[177]Rose Tristan E., Morisseau Christophe, Liu Jun-Yan, Inceoglu Bora, Jones Paul D., Sanborn James R., Hammock Bruce D. 1-Aryl-3-(1-acylpiperidin-4-yl)urea Inhibitors of Human and Murine Soluble Epoxide Hydrolase:Structure-Activity Relationships, Pharmacokinetics, and Reduction of Inflammatory Pain. Journal of Medicinal Chemistry.2010.53(19).7067-7075
[178]Shen Hong C., Ding Fa-Xiang, Deng Qiaolin, Xu Suoyu, Tong Xinchun, Zhang Xiaoping, Chen Yuli, Zhou Gaochao, Pai Lee-Yuh, Alonso-Galicia Magdalena, Roy Sophie, Zhang Bei, Tata James R., Berger Joel P., Colletti Steven L. A strategy of employing aminoheterocycles as amide mimics to identify novel, potent and bioavailable soluble epoxide hydrolase inhibitors. Bioorganic & Medicinal Chemistry Letters.2009.19(19).5716-5721
[179]Chen Dawn, Whitcomb Randall, MacIntyre Euan, Tran Vinh, Do Zung N., Sabry James, Patel Dinesh V., Anandan Sampath K., Gless Richard, Webb Heather K. Pharmacokinetics and Pharmacodynamics of AR9281, an Inhibitor of Soluble Epoxide Hydrolase, in Single-and Multiple-Dose Studies in Healthy Human Subjects. The Journal of Clinical Pharmacology.2012.52(3).319-328
[180]Singh Dipali, Tripathi Anushree, Kumar Gautam. An Overview of Computational Approaches in Structure Based Drug Design. Nepal Journal of Biotechnology.2012.2(1). 53-61
[181]Kubinyi H. Structure-based design of enzyme inhibitors and receptor ligands. Current Opinion in Drug Discovery and Development.1998.1(1).4-15
[182]Alonso Hernan, Bliznyuk Andrey A., Gready Jill E. Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews.2006.26(5).531-568
[183]Hao Ming, Li Yan, Wang Yonghua, Yan Yulian, Zhang Shuwei. Combined 3D-QSAR, Molecular Docking, and Molecular Dynamics Study on Piperazinyl-Glutamate-Pyridines/Pyrimidines as Potent P2Y12 Antagonists for Inhibition of Platelet Aggregation. Journal of Chemical Information and Modeling.2011.51(10). 2560-2572
[184]AbdulHameed Mohamed Diwan M., Hamza Adel, Zhan Chang-Guo. Microscopic Modes and Free Energies of 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Binding with Celecoxib and Other Inhibitors. Journal of Physical Chemistry B.2006.110(51). 26365-26374
[185]Ertl Peter. JME Molecular Editor.
[186]Schuttelkopf Alexander W., van Aalten Daan M. F. PRODRG:a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D.2004.60(8). 1355-1363
[187]Frisch M. J., Al. Et. Gaussian 09.
[188]Huey Ruth, Morris Garrett M., Olson Arthur J., Goodsell David S. A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry.2007. 28(6).1145-1152
[189]Gomez German A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Human soluble epoxide hydrolase:Structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids. Protein Science.2006.15(1).58-64
[190]Argiriadi Maria A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Detoxification of Environmental Mutagens and Carcinogens:Structure, Mechanism, and Evolution of Liver Epoxide Hydrolase. Proceedings of the National Academy of Sciences of the United States of America.1999.96(19).10637-10642
[191]Argiriadi Maria A., Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna L., Hammock Bruce D., Christianson David W. Binding of Alkylurea Inhibitors to Epoxide Hydrolase Implicates Active Site Tyrosines in Substrate Activation. Journal of Biological Chemistry.2000.275(20).15265-15270
[192]Gomez German A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Structure of Human Epoxide Hydrolase Reveals Mechanistic Inferences on Bifunctional Catalysis in Epoxide and Phosphate Ester Hydrolysis,. Biochemistry.2004.43(16). 4716-4723
[193]Sanner. Michel F. Python:a programming language for software integration and development. J. Mol. Graphics Mod.1999.17(1).57-61
[194]Morris Garrett M., Huey Ruth, Lindstrom William, Sanner Michel F., Belew Richard K., Goodsell David S., Olson Arthur J. AutoDock4 and AutoDockTools4:Automated docking with selective receptor flexibility. Journal of Computational Chemistry.2009.30(16). 2785-2791
[195]Case D. A., Darden T. A., T. E. Cheatham Ⅲ, Simmerling C. L., Wang J., Duke R. E., Luo R., Crowley M., Walker R. C., Zhang W., Merz K. M., Wang B., Hayik S., Roitberg A., Seabra G., Kolossvary I., Wong K. F., Paesani F., Vanicek J., Wu X., Brozell S. R., Steinbrecher T., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Mathews D. H., Seetin M. G., Sagui C., Babin V., Kollman P. A. AMBER10.
[196]Lee Mathew C., Duan Yong. Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins:Structure, Function, and Bioinformatics.2004.55(3).620-634
[197]Wang Junmei, Wolf Romain M., Caldwell James W., Kollman Peter A., Case David A. Development and testing of a general amber force field. Journal of Computational Chemistry. 2004.25(9).1157-1174
[198]Ryckaert Jean-Paul, Ciccotti Giovanni, Berendsen Herman J. C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. Journal of Computational Physics.1977.23(3).327-341
[199]Darden Tom, York Darrin, Pedersen Lee. Particle mesh Ewald:An N [center-dot] log(N) method for Ewald sums in large systems. Journal of Chemical Physics.1993.98(12). 10089-10092
[200]Feig M. Implicit solvation based on generalized Born theory in different dielectric environments. Journal of Chemical Physics.2004.120(2).903
[201]Kollman Peter A., Massova Irina, Reyes Carolina, Kuhn Bernd, Huo Shuanghong, Chong Lillian, Lee Matthew, Lee Taisung, Duan Yong, Wang Wei, Donini Oreola, Cieplak Piotr, Srinivasan Jaysharee, Case David A., Cheatham Thomas E. Calculating Structures and Free Energies of Complex Molecules:Combining Molecular Mechanics and Continuum Models. Accounts of Chemical Research.2000.33(12).889-897
[202]Onufriev Alexey, Bashford Donald, Case David A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Structure, Function, and Bioinformatics.2004.55(2).383-394
[203]SITKOFF D., SHARP K. A., HONIG B. ACCURATE CALCULATION OF HYDRATION FREE-ENERGIES USING MACROSCOPIC SOLVENT MODELS. JOURNAL OF PHYSICAL CHEMISTRY.1994.98(7).1978-1988
[204]Weiser Jorg, Shenkin Peter S., Still W. Clark. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry.1999.20(2). 217-230
[205]Gohlke Holger, Kiel Christina, Case David A. Insights into Protein-Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes. Journal of Molecular Biology.2003.330(4).891-913
[206]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. American Journal of Physiology-Cell Physiology.2007.292(3). C996-C1012
[207]Spector Arthur A. Arachidonic acid cytochrome P450 epoxygenase pathway. Journal of Lipid Research.2009.50(Supplement). S52-S56
[208]Newman John W., Morisseau Christophe, Hammock Bruce D. Epoxide hydrolases:their roles and interactions with lipid metabolism. Progress in Lipid Research.2005.44(1).1-51
[209]Behm David J., Ogbonna Andrea, Wu Charlene, Burns-Kurtis Cynthia L., Douglas Stephen A. Epoxyeicosatrienoic Acids Function as Selective, Endogenous Antagonists of Native Thromboxane Receptors:Identification of a Novel Mechanism of Vasodilation. Journal of Pharmacology and Experimental Therapeutics.2009.328(1).231-239
[210]Wang Zhen-He, B Davis Benjamin, Jiang De-Qian, Zhao Ting-Ting, Xu Dan-Yan. Soluble Epoxide Hydrolase Inhibitors and Cardiovascular Diseases.105-111
[211]Pecic Stevan, Deng Shi-Xian, Morisseau Christophe, Hammock Bruce D., Landry Donald W. Design, synthesis and evaluation of non-urea inhibitors of soluble epoxide hydrolase. Bioorganic & Medicinal Chemistry Letters.2012.22(1).601-605
[212]Hwang Sung Hee, Wagner Karen M., Morisseau Christophe, Liu Jun-Yan, Dong Hua, Wecksler Aaron T., Hammock Bruce D. Synthesis and Structure-Activity Relationship Studies of Urea-Containing Pyrazoles as Dual Inhibitors of Cyclooxygenase-2 and Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2011.54(8).3037-3050
[213]Morisseau Christophe, Hammock Bruce D. Epoxide Hydrolases:Mechanisms, Inhibitor Designs, and Biological Roles. ChemInform.2005.36(39). no-no
[214]Morisseau Christophe, Goodrow Marvin H., Newman John W., Wheelock Craig E., Dowdy Deanna L., Hammock Bruce D. Structural refinement of inhibitors of urea-based soluble epoxide hydrolases. Biochemical Pharmacology.2002.63(9).1599-1608
[215]Cronin Annette, Mowbray Sherry, Diirk Heike, Homburg Shirli, Fleming Ingrid, Fisslthaler Beate, Oesch Franz, Arand Michael. The N-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase. Proceedings of the National Academy of Sciences.2003.100(4). 1552-1557
[216]Cornell Wendy D., Cieplak Piotr, Bayly Christopher I., Gould Ian R., Merz Kenneth M., Ferguson David M., Spellmeyer David C, Fox Thomas, Caldwell James W., Kollman Peter A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. Journal of the American Chemical Society.1995.117(19).5179-5197
[217]Gordon John C., Myers Jonathan B., Folta Timothy, Shoja Valia, Heath Lenwood S., Onufriev Alexey. H++:a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research.2005.33(suppl 2). W368-W371
[218]Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. Journal of Chemical Physics.1983. 79(2).926-935
[219]Pettersen Eric F., Goddard Thomas D., Huang Conrad C., Couch Gregory S., Greenblatt Daniel M., Meng Elaine C., Ferrin Thomas E. UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry.2004.25(13). 1605-1612
[220]Feig M., Im W., Brooks C. L. Implicit solvation based on generalized Born theory in different dielectric environments. Journal of Chemical Physics.2004.120(2).903-911
[221]Kollman P. A., Massova I., Reyes C., Kuhn B., Huo S. H., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D. A., Cheatham T. E. Calculating structures and free energies of complex molecules:Combining molecular mechanics and continuum models. Accounts of Chemical Research.2000.33(12).889-897
[222]STILL W. C., TEMPCZYK A., HAWLEY R. C., HENDRICKSON T. SEMIANALYTICAL TREATMENT OF SOLVATION FOR MOLECULAR MECHANICS AND DYNAMICS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.1990. 112(16).6127-6129
[223]SITKOFF D., SHARP K. A., HONIG B. ACCURATE CALCULATION OF HYDRATION FREE-ENERGIES USING MACROSCOPIC SOLVENT MODELS. JOURNAL OF PHYSICAL CHEMISTRY.1994.98(7).1978-1988
[224]Sanner M. F., Olson A. J., Spehner J. C. Reduced surface:An efficient way to compute molecular surfaces. Biopolymers.1996.38(3).305-320
[225]Whitlow M., Howard A. J., Stewart D., Hardman K. D., Chan J. H., Baccanari D. P., Tansik R. L., Hong J. S., Kuyper L. F. X-ray crystal structures of Candida albicans dihydrofolate reductase:High resolution ternary complexes in which the dihydronicotinamide moiety of NADPH is displaced by an inhibitor. JOURNAL OF MEDICINAL CHEMISTRY.2001. 44(18).2928-2932
[226]Kelley Lawrence A., Gardner Stephen P., Sutcliffe Michael J. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Engineering.1996.9(11).1063-1065
[227]Jain A. K., Murty M. N., Flynn P. J. Data clustering:a review. ACM Comput. Surv.1999. 31(3).264-323
[228]Imig John, Carpenter Margaret, Shaw Sean. The Soluble Epoxide Hydrolase Inhibitor AR9281 Decreases Blood Pressure, Ameliorates Renal Injury and Improves Vascular Function in Hypertension. Pharmaceuticals.2009.2(3).217-227
[229]Karthikeyan S., Nagase S. Origins of the Stability of Imidazole-Imidazole, Benzene-Imidazole, and Benzene-Indole Dimers:CCSD(T)/CBS and SAPT Calculations. Journal of Physical Chemistry A.2012.116(7).1694-1700
[230]Zhuravlev A. V., Shchegolev B. F., Savvateeva-Popova E. V., Popov A. V. Molecular mechanisms of imidazole and benzene ring binding in proteins.2009.74(8).925-932
[2]HARDER D. R., CAMPBELL W. B., ROMAN R. J. ROLE OF CYTOCHROME-P-450 ENZYMES AND METABOLITES OF ARACHIDONIC-ACID IN THE CONTROL OF VASCULAR TONE. JOURNAL OF VASCULAR RESEARCH.1995.32 (2).79-92
[3]Perozzo R., Folkers G., Scapozza L. Thermodynamics of protein-ligand interactions:History, presence, and future aspects. JOURNAL OF RECEPTORS AND SIGNAL. TRANSDUCTION.2004.24(1-2).1-52
[4]Freire Ernesto. Do enthalpy and entropy distinguish first in class from best in class? DRUG DISCOVERY TODAY.2008.13(19-20).869-874
[5]Gohlke H., Hendlich M., Klebe G. Predicting binding modes, binding affinities and'hot spots' for protein-ligand complexes using a knowledge-based scoring function. PERSPECTIVES IN DRUG DISCOVERY AND DESIGN.2000.20(1).115-144
[6]Gohlke H., Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION.2002.41(15).2645-2676
[7]Rich R. L., Myszka D. G. Advances in surface plasmon resonance biosensor analysis. CURRENT OPINION IN BIOTECHNOLOGY.2000.11(1).54-61
[8]Bissantz Caterina, Kuhn Bernd, Stahl Martin. A Medicinal Chemist's Guide to Molecular Interactions. JOURNAL OF MEDICINAL CHEMISTRY.2010.53(14).5061-5084
[9]B6hm H. J. Prediction of Non-bonded Interactions in Drug Design.2003.3-20
[10]Hubbard Roderick E., Kamran Haider Muhammad. Hydrogen Bonds in Proteins:Role and Strength.2001.
[11]RICHARDS F. M. AREAS, VOLUMES, PACKING, AND PROTEIN-STRUCTURE. ANNUAL REVIEW OF BIOPHYSICS AND BIOENGINEERING.1977.6.151-176
[12]SHARP K. A., NICHOLLS A., FRIEDMAN R., HONIG B. EXTRACTING HYDROPHOBIC FREE-ENERGIES FROM EXPERIMENTAL-DATA-RELATIONSHIP TO PROTEIN FOLDING AND THEORETICAL-MODELS. BIOCHEMISTRY.1991. 30(40).9686-9697
[13]Meyer E. A., Castellano R K., Diederich F. Interactions with aromatic rings in chemical and biological recognition. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION,2003. 42(11).1210-1250
[14]McGiaughey G. B., Gragne M., Rappe A. K. pi-stacking interactions-Alive and well in proteins. JOURNAL OF BIOLOGICAL CHEMISTRY.1998.273(25).15458-15463
[15]Desiraju G. R. C-H center dot center dot center dot O and other weak hydrogen bonds. From crystal engineering to virtual screening. CHEMICAL COMMUNICATIONS.2005. (24). 2995-3001
[16]Tsuzuki S., Honda K., Uchimaru T., Mikami M., Tanabe K. The magnitude of the CH/pi interaction between benzene and some model hydrocarbons. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.2000.122(15).3746-3753
[17]Mobley David L., Dill Ken A. Binding of Small-Molecule Ligands to Proteins:"What You See" Is Not Always "What You Get". STRUCTURE.2009.17(4).489-498
[18]Cozzini Pietro, Kellogg Glen E., Spyrakis Francesca, Abraham Donald J., Costantino Gabriele, Emerson Andrew, Fanelli Francesca, Gohlke Holger, Kuhn Leslie A., Morris Garrett M., Orozco Modesto, Pertinhez Thelma A., Rizzi Menico, Sotriffer Christoph A. Target Flexibility:An Emerging Consideration in Drug Discovery and Design. JOURNAL OF MEDICINAL CHEMISTRY.2008.51(20).6237-6255
[19]Gutteridge A., Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. JOURNAL OF MOLECULAR BIOLOGY.2005.346(1).21-28
[20]Butcher J. C. Numerical Methods for Ordinary Differential Equations.2nd Edition. Hoboken. Wiley.2003.
[21]Humphreys P. Extending Ourselves:Computati onal Science, Empiricism, and Scientific Method.1st Edition. Oxford University Press.
[22]J. L. McClean, M. E. Maltrud And F. O. Bryan. Measures of the fidelity of eddying ocean models. Oceanography.2006.19(1).104-117
[23]Chourasia Amit, Cutchin Steve, Aagaard Brad. Visualizing the ground motions of the 1906 San Francisco earthquake. COMPUTERS & amp; GEOSCIENCES.2008.34(12).1798-1805
[24]Haile J. M. Molecular Dynamics Simulation:Elementary Methods.1st Edition. New York. Wiley-Interscience.1997.
[25]Allen M. P., Tildesley D. J. Computer Simulation of Liquids. Oxford. Clarendon Press. 1987.
[26]Frenkel D., Smit B. Understanding Molecular Simulation-From Algorithms to Applications. San Diego. Academic Press.2002.
[27]Hill T. L. An Introduction to Statistical Thermodynamics. New York. Dover Publications Inc.1986.
[28]MCCAMMON J. A., GELIN B. R., KARPLUS M. DYNAMICS OF FOLDED PROTEINS. NATURE.1977.267(5612).585-590
[29]KARPLUS M., MCCAMMON J. A. PROTEIN STRUCTURAL FLUCTUATIONS DURING A PERIOD OF 100-PS. NATURE.1979.277(5697).578
[30]Van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A. E., Berendsen HJC. GROMACS:Fast, flexible, and free. JOURNAL OF COMPUTATIONAL CHEMISTRY. 2005.26(16).1701-1718
[31]Case David A., Cheatham Thomas E., Darden Tom, Gohlke Holger, Luo Ray, Merz Kenneth M., Onufriev Alexey, Simmerling Carlos, Wang Bing, Woods Robert J. The Amber biomolecular simulation programs. Journal of Computational Chemistry.2005.26(16). 1668-1688
[32]Phillips J. C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kale L., Schulten K. Scalable molecular dynamics with NAMD. JOURNAL OF COMPUTATIONAL CHEMISTRY.2005.26(16).1781-1802
[33]Alvarez J. C. High-throughput docking as a source of novel drug leads. CURRENT OPINION IN CHEMICAL BIOLOGY.2004.8(4).365-370
[34]Fretland Adrian J., Omiecinski Curtis J. Epoxide hydrolases:biochemistry and molecular biology. Chemico-Biological Interactions.2000.129(1-2).41-59
[35]Yu Z. G., Xu F. Y., Huse L. M., Morisseau C., Draper A. J., Newman J. W., Parker C., Graham L., Engler M. M., Hammock B. D., Zeldin D. C., Kroetz D. L. Soluble epoxide hydrolase regulates hydrolysis of vasoactive epoxyeicosatrienoic acids. CIRCULATION RESEARCH.2000.87(11).992-998
[36]VANROLLINS M., KADUCE T. L., KNAPP H. R., SPECTOR A. A. 14,15-EPOXYEICOSATRIENOIC ACID METABOLISM IN ENDOTHELIAL-CELLS. JOURNAL OF LIPID RESEARCH.1993.34(11).1931-1942
[37]FANG X., VANROLLINS M., KADUCE T. L., SPECTOR A. A. EPOXYEICOSATRIENOIC ACID METABOLISM IN ARTERIAL SMOOTH-MUSCLE CELLS. JOURNAL OF LIPID RESEARCH.1995.36(6).1236-1246
[38]JOHANSSON C., STARK A., SANDBERG M., EK B., RASK L., MEIJER J. TISSUE-SPECIFIC BASAL EXPRESSION OF SOLUBLE MURINE EPOXIDE HYDROLASE AND EFFECTS OF CLOFIBRATE ON THE MESSENGER-RNA LEVELS IN EXTRAHEPATIC TISSUES AND LIVER. ARCHIVES OF TOXICOLOGY.1995. 70(1).61-63
[39]Enayetallah A. E., French R. A., Thibodeau M. S., Grant D. F. Distribution of soluble epoxide hydrolase and of cytochrome P4502C8,2C9, and 2J2 in human tissues. JOURNAL OF HISTOCHEMISTRY & amp; CYTOCHEMISTRY.2004.52(4).447-454.
[40]HOLLINSHEAD M., MEIJER J. IMMUNOCYTOCHEMICAL ANALYSIS OF SOLUBLE EPOXIDE HYDROLASE AND CATALASE IN MOUSE AND RAT HEPATOCYTES DEMONSTRATES A PEROXISOMAL LOCALIZATION BEFORE AND AFTER CLOFIBRATE TREATMENT. EUROPEAN JOURNAL OF CELL BIOLOGY.1988.46(3). 394-402
[41]ERIKSSON A. M., ZETTERQVIST M. A., LUNDGREN B.,ANDERSSON K., BEIJE B., DEPIERRE J. W. STUDIES ON THE INTRACELLULAR DISTRIBUTIONS OF SOLUBLE EPOXIDE HYDROLASE AND OF CATALASE BY DIGITONIN-PERMEABILIZATION OF HEPATOCYTES ISOLATED FROM CONTROL AND CLOFIBRATE-TREATED MICE. EUROPEAN JOURNAL OF BIOCHEMISTRY. 1991.198(2).471-476
[42]Mullen R. T., Trelease R. N., Duerk H., Arand M., Hammock B. D., Oesch F., Grant D. F. Differential subcellular localization of endogenous and transfected soluble epoxide hydrolase in mammalian cells:evidence for isozyme variants. FEBS LETTERS.1999.445(2-3). 301-305
[43]SCHLADT L., THOMAS H., HARTMANN R., OESCH F. HUMAN-LIVER CYTOSOLIC EPOXIDE HYDROLASES. EUROPEAN JOURNAL OF BIOCHEMISTRY.1988.176(3). 715-723
[44]Sandberg M., Hassett C., Adman E. T., Meijer J., Omiecinski C. J. Identification and functional characterization of human soluble epoxide hydrolase genetic polymorphisms. JOURNAL OF BIOLOGICAL CHEMISTRY.2000.275(37).28873-28881
[45]Saito S., Iida A., Sekine A., Eguchi C., Miura Y., Nakamura Y. Seventy genetic variations in human microsomal and soluble epoxide hydrolase genes (EPHX1 and EPHX2) in the Japanese population. JOURNAL OF HUMAN GENETICS.2001.46(6).325-329
[46]CATELLA F., LAWSON J. A., FITZGERALD D. J., FITZGERALD G. A. ENDOGENOUS BIOSYNTHESIS OF ARACHIDONIC-ACID EPOXIDES IN HUMANS-INCREASED FORMATION IN PREGNANCY-INDUCED HYPERTENSION. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.1990. 87(15).5893-5897
[47]Morisseau Christophe, Schebb Nils Helge, Dong Hua, Ulu Arzu, Aronov Pavel A., Hammock Bruce D. Role of soluble epoxide hydrolase phosphatase activity in the metabolism of lysophosphatidic acids. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS.2012.419(4).796-800
[48]Newman J. W., Morisseau C., Harris T. R., Hammock B. D. The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2003.100(4).1558-1563
[49]Tran K. L., Aronov P. A., Tanaka H., Newman J. W., Hammock B. D., Morisseau C. Lipid sulfates and sulfonates are allosteric competitive inhibitors of the N-terminal phosphatase activity of the mammalian soluble epoxide hydrolase. BIOCHEMISTRY.2005.44(36). 12179-12187
[50]Spector Arthur A. Arachidonic acid cytochrome P450 epoxygenase pathway. JOURNAL OF LIPID RESEARCH.2009.50. S52-S56
[51]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY.2007.292(3). C996-C1012
[52]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY.2007.292(3). C996-C1012
[53]HAMMOCK B. D., PINOT F., BEETHAM J. K., GRANT D. F., ARAND M. E., OESCH F. ISOLATION OF A PUTATIVE HYDROXYACYL ENZYME INTERMEDIATE OF AN EPOXIDE HYDROLASE. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS.1994.198(3).850-856
[54]BORHAN B., JONES A. D., PINOT F., GRANT D. F., KURTH M. J., HAMMOCK B. D. MECHANISM OF SOLUBLE EPOXIDE HYDROLASE-FORMATION OF AN ALPHA-HYDROXY ESTER-ENZYME INTERMEDIATE THROUGH ASP-333. JOURNAL OF BIOLOGICAL CHEMISTRY.1995.270(45).26923-26930
[55]Arand M., Wagner H., Oesch F. Asp(333), Asp(495), and His(523) form the catalytic triad of rat soluble epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.1996.271(8). 4223-4229
[56]PINOT F., GRANT D. F., BEETHAM J. K., PARKER A. G., BORHAN B., LANDT S., JONES A. D., HAMMOCK B. D. MOLECULAR AND BIOCHEMICAL-EVIDENCE FOR THE INVOLVEMENT OF THE ASP-333-HIS-523 PAIR IN CATALYTIC MECHANISM OF SOLUBLE EPOXIDE HYDROLASE. JOURNAL OF BIOLOGICAL CHEMISTRY. 1995.270(14).7968-7974
[57]Arand M., Wagner H., Oesch F. Asp(333), Asp(495), and His(523) form the catalytic triad of rat soluble epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.1996.271(8).
[58]Yamada T., Morisseau C., Maxwell J. E., Argiriadi M. A., Christianson D. W., Hammock B. D. Biochemical evidence for the involvement of tyrosine in epoxide activation during the catalytic cycle of epoxide hydrolase. JOURNAL OF BIOLOGICAL CHEMISTRY.2000. 275(30).23082-23088
[59]MULLIN C. A., HAMMOCK B. D. CHALCONE OXIDES-POTENT SELECTIVE INHIBITORS OF CYTOSOLIC EPOXIDE HYDROLASE. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS.1982.216(2).423-439
[60]DIETZE E. C., KUWANO E., CASAS J., HAMMOCK B. D. INHIBITION OF CYTOSOLIC EPOXIDE HYDROLASE BY TRANS-3-PHENYLGLYCIDOLS. BIOCHEMICAL PHARMACOLOGY.1991.42(6).1163-1175
[61]Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna, Zheng Jiang, Greene Jessica F., Sanborn James R., Hammock Bruce D. Potent urea and carbamate inhibitors of soluble epoxide hydrolases. Proceedings of the National Academy of Sciences.1999.96(16). 8849-8854
[62]黄少胥,王勇,龙亚秋.人类可溶性环氧化物水解酶抑制剂的研究进展.有机化学.2012.32.877-888
[63]Kim In-Hae, Morisseau Christophe, Watanabe Takaho, Hammock Bruce D. Design, Synthesis, and Biological Activity of 1,3-Disubstituted Ureas as Potent Inhibitors of the Soluble Epoxide Hydrolase of Increased Water Solubility. Journal of Medicinal Chemistry. 2004.47(8).2110-2122
[64]Kasagami Takeo, Kim In-Hae, Tsai Hsing-Ju, Nishi Kosuke, Hammock Bruce D., Morisseau Christophe. Salicylate-urea-based soluble epoxide hydrolase inhibitors with high metabolic and chemical stabilities. BIOORGANIC & amp; MEDICINAL CHEMISTRY LETTERS. 2009.19(6).1784-1789
[65]Kim I. H., Heirtzler F. R., Morisseau C., Nishi K., Tsai H. J., Hammock B. D. Optimization of amide-based inhibitors of soluble epoxide hydrolase with improved water solubility. Journal of medicinal chemistry.2005.48(10).3621-3629
[66]Li Hui-Yuan, Jin Yi, Morisseau Christophe, Hammock Bruce D., Long Ya-Qiu. The 5-substituted piperazine as a novel secondary pharmacophore greatly improving the physical properties of urea-based inhibitors of soluble epoxide hydrolase. BIOORGANIC& MEDICINAL CHEMISTRY.2006.14(19).6586-6592
[67]Jones P. D., Tsai H. J., Do Z. N., Morisseau C., Hammock B. D. Synthesis and SAR of conformationally restricted inhibitors of soluble epoxide hydrolase. Bioorganic and Medicinal Chemistry Letters.2006.16(19).5212-5216
[68]Huang Shao-Xu, Li Hui-Yuan, Liu Jun-Yan, Morisseau Christophe, Hammock Bruce D., Long Ya-Qiu. Incorporation of Piperazino Functionality into 1,3-Disubstituted Urea as the Tertiary Pharmacophore Affording Potent Inhibitors of Soluble Epoxide Hydrolase with Improved Pharmacokinetic Properties. Journal of Medicinal Chemistry.2010.53(23). 8376-8386
[69]Huang Shao-Xu, Cao Bin, Morisseau Christophe, Jin Yi, Hammock Bruce D., Long Ya-Qiu. Structure-based optimization of the piperazino-containing 1,3-disubstituted ureas affording sub-nanomolar inhibitors of soluble epoxide hydrolase. MedChemComm.2012.3(3). 379-384
[70]Eldrup Anne B., Soleymanzadeh Fariba, Taylor Steven J., Muegge Ingo, Farrow Neil A., Joseph David, McKellop Keith, Man Chuk C., Kukulka Alison, De Lombaert Ste phane. Structure-Based Optimization of Arylamides as Inhibitors of Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2009.52(19).5880-5895
[71]Eldrup Anne B., Soleymanzadeh Fariba, Farrow Neil A., Kukulka Alison, De Lombaert St閜 hane. Optimization of piperidyl-ureas as inhibitors of soluble epoxide hydrolase. Bioorganic & Medicinal Chemistry Letters.2010.20(2).571-575
[72]Shen Hong C., Ding Fa-Xiang, Wang Siyi, Xu Suoyu, Chen Hsuan-shen, Tong Xinchun, Tong Vincent, Mitra Kaushik, Kumar Sanjeev, Zhang Xiaoping, Chen Yuli, Zhou Gaochao, Pai Lee-Yuh, Alonso-Galicia Magdalena, Chen Xiaoli, Zhang Bei, Tata James R., Berger Joel P., Colletti Steven L. Discovery of spirocyclic secondary amine-derived tertiary ureas as highly potent, selective and bioavailable soluble epoxide hydrolase inhibitors. BIOORGANIC & amp; MEDICINAL CHEMISTRY LETTERS.2009.19(13).3398-3404
[73]Xing Li, McDonald Joseph J., Kolodziej Steve A., Kurumbail Ravi G., Williams Jennifer M., Warren Chad J., O Neal Janet M., Skepner Jill E., Roberds Steven L. Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening. Journal of Medicinal Chemistry.2011.54(5).1211-1222
[74]Marino Jr. J. P. Soluble epoxide hydrolase, a target with multiple opportunities for cardiovascular drug discovery. Current Topics in Medicinal Chemistry.2009.9(5).452-463
[75]Iliff Jeffrey J., Alkayed Nabil J. Soluble epoxide hydrolase inhibition:targeting multiple mechanisms of ischemic brain injury with a single agent. Future Neurology.2009.4(2). 179-199
[76]Imig J. D., Hammock B. D. Soluble epoxide hydrolase as a therapeutic target for cardiovascular diseases. Nature Reviews Drug Discovery.2009.8(10).794-805
[77]Shen H. C. Soluble epoxide hydrolase inhibitors:A patent review. Expert Opinion on Therapeutic Patents.2010.20(7).941-956
[78]Morisseau C., Hammock B. D. Impact of Soluble Epoxide Hydrolase and Epoxyeicosanoids on Human Health. Annual review of pharmacology and toxicology.2012.
[79]H Ingraham R., D Gless R., Y Lo H. Soluble Epoxide Hydrolase Inhibitors and their Potential for Treatment of Multiple Pathologic Conditions. Current Medicinal Chemistry.2011.18. 587-603
[80]Node K., Huo Y. Q., Ruan X. L., Yang B. C., Spiecker M., Ley K., Zeldin D. C., Liao J. K. Anti-inflammatory properties of cytochrome P450 epoxygenase-derived eicosanoids. SCIENCE.1999.285(5431).1276-1279
[81]Spector A. A., Fang X., Snyder G. D., Weintraub N. L. Epoxyeicosatrienoic acids (EETs): metabolism and biochemical function. PROGRESS IN LIPID RESEARCH.2004.43(1). 55-90
[82]Inceoglu Bora, Jinks Steven L., Schmelzer Kara R., Waite Troy, Kim In Hae, Hammock Bruce D. Inhibition of soluble epoxide hydrolase reduces LPS-induced thermal hyperalgesia and mechanical allodynia in a rat model of inflammatory pain. LIFE SCIENCES.2006. 79(24).2311-2319
[83]Schmelzer K. R., Kubala L., Newman J. W., Kim I. H., Eiserich J. P., Hammock B. D. Soluble epoxide hydrolase is a therapeutic target for acute inflammation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2005.102(28).9772-9777
[84]Xu Danyan, Li Ning, He Yuxia, Timofeyev Valeriy, Lu Ling, Tsai Hsing-Ju, Kim In-Hae, Tuteja Dipika, Mateo Robertino Karlo P., Singapuri Anil, Davis Benjamin B., Low Reginald, Hammock Bruce D., Chiamvimonvat Nipavan. Prevention and reversal of cardiac hypertrophy by soluble epoxide hydrolase inhibitors. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA.2006.103(49). 18733-18738
[85]Fisslthaler B., Popp R., Kiss L., Potente M., Harder D. R., Fleming I., Busse R. Cytochrome P4502C is an EDHF synthase in coronary arteries. NATURE.1999.401(6752).493-497
[86]Imig J. D., Zhao X. Y., Capdevila J. H., Hammock B. D. Soluble epoxide hydrolase inhibition lowers arterial blood pressure in angiotensin Ⅱ hypertension. HYPERTENSION 2002.39 (2 S).690-694
[87]Jung O., Brandes R. P., Kim I. H., Schmidt R., Busse R. Soluble epoxide hydrolase is a main effector of angiotensin Ⅱ-induced hypertension. HYPERTENSION.2005.45(4).759-765
[88]Sinal Christopher J., Miyata Masaaki, Tohkin Masahiro, Nagata Kiyoshi, Bend John R., Gonzalez Frank J. Targeted Disruption of Soluble Epoxide Hydrolase Reveals a Role in Blood Pressure Regulation. Journal of Biological Chemistry.2000.275(51).40504-40510
[89]Zeldin D. C., Foley J., Cook M. E., Ma J. X., Tomer K. B., Wu S. CYP2J subfamily cytochrome P450s in the gastrointestinal tract:Expression, localization, and potential functional significance. MOLECULAR PHARMACOLOGY.1997.51 (6)
[90]Fang X., Moore S. A., Stoll L. L., Kaduce T. L., Spector A. A.14,15-epoxyeicosatrienoic acid inhibits prostaglandin E-2 production in vascular smooth muscle cells. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.1998.275 (6)
[91]Munzenmaier D. H., Harder D. R. Cerebral microvascular endothelial cell tube formation: role of astrocytic epoxyeicosatrienoic acid release. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.2000.278 (4)
[92]Sun Jianxin, Sui XinXin, Bradbury J. Alyce, Zeldin Darryl C., Conte Michael S., Liao James K. Inhibition of Vascular Smooth Muscle Cell Migration by Cytochrome P450 Epoxygenase-Derived Eicosanoids. Circulation Research.2002.90(9).1020-1027
[93]Node K., Ruan X. L., Dai J. W., Graham L., Liao J. K. Activation of G alpha(s) mediates induction of tissue-type plasminogen activator gene transcription by epoxyeicosatrienoic acids. JOURNAL OF BIOLOGICAL CHEMISTRY.2001.276 (19).15983-15989
[94]Snyder G. D., Krishna U. M., Falck J. R. Evidence for a membrane site of action for 14,15-EET on expression of aromatase in vascular smooth muscle. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY.2002.283 (5). H1936-H1942
[95]GOODFORD P. J. A COMPUTATIONAL-PROCEDURE FOR DETERMINING ENERGETICALLY FAVORABLE BINDING-SITES ON BIOLOGICALLY IMPORTANT MACROMOLECULES. JOURNAL OF MEDICINAL CHEMISTRY.1985.28(7).849-857
[96]Kastenholz M. A., Pastor M., Cruciani G., Haaksma EEJ, Fox T. GRID/CPCA:A new computational tool to design selective ligands. JOURNAL OF MEDICINAL CHEMISTRY. 2000.43(16).3033-3044
[97]LEVITT D. G., BANASZAK L. J. POCKET-A COMPUTER-GRAPHICS METHOD FOR IDENTIFYING AND DISPLAYING PROTEIN CAVITIES AND THEIR SURROUNDING AMINO-ACIDS. JOURNAL OF MOLECULAR GRAPHICS.1992.10(4).229-234
[98]LASKOWSKI R. A. SURFNET-A PROGRAM FOR VISUALIZING MOLECULAR-SURFACES, CAVITIES, AND INTERMOLECULAR INTERACTIONS. JOURNAL OF MOLECULAR GRAPHICS.1995.13(5).323
[99]Glaser F., Morris R. J., Najmanovich R. J., Laskowski R. A., Thornton J. M. A method for localizing ligand binding pockets in protein structures. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS.2006.62(2).479-488
[100]Mezei M. A new method for mapping macromolecular topography. JOURNAL OF MOLECULAR GRAPHICS & MODELLING.2003.21(5).463-472
[101]Fischer Emil. Einfluss der Configuration auf die Wirkung der Enzyme. Berichte der deutschen chemischen Gesellschaft.1894.27(3).2985-2993
[102]KOSHLAND D. E. CORRELATION OF STRUCTURE AND FUNCTION IN ENZYME ACTION. SCIENCE.1963.142(359).1533
[103]Hammes G. G. Multiple conformational changes in enzyme catalysis. BIOCHEMISTRY. 2002.41(26).8221-8228
[104]Sherman W., Day T., Jacobson M. P., Friesner R. A., Farid R. Novel procedure for modeling ligand/receptor induced fit effects. JOURNAL OF MEDICINAL CHEMISTRY. 2006.49(2).534-553
[105]JIANG F., KIM S. H. SOFT DOCKING-MATCHING OF MOLECULAR-SURFACE CUBES. JOURNAL OF MOLECULAR BIOLOGY.1991.219(1).79-102
[106]Claussen H., Buning C., Rarey M., Lengauer T. FlexE:Efficient molecular docking considering protein structure variations. JOURNAL OF MOLECULAR BIOLOGY.2001. 308(2).377-395
[107]Alonso Hernan, Bliznyuk Andrey A., Gready Jill E. Combining docking and molecular dynamic simulations in drug design. MEDICINAL RESEARCH REVIEWS.2006. 26(5). 531-568
[108]Sander Tommy, Lijefors Tommy, Balle Thomas. Prediction of the receptor conformation for iGluR2 agonist binding:QM/MM docking to an extensive conformational ensemble generated using normal mode analysis. JOURNAL OF MOLECULAR GRAPHICS & amp; MODELLING.2008.26(8).1259-1268
[109]Subramanian Jyothi, Sharma Somesh, B-Rao Chandrika. A novel computational analysis of ligand-induced conformational changes in the ATP binding sites of cyclin dependent kinases. JOURNAL OF MEDICINAL CHEMISTRY.2006.49(18).5434-5441
[110]Subramanian Jyothi, Sharma Somesh, B-Rao Chandrika. Modeling and selection of flexible proteins for structure-based drug design:Backbone and side chain movements in p38 MAPK. CHEMMEDCHEM.2008.3(2).336-344
[111]Moitessier N., Englebienne P., Lee D., Lawandi J., Corbeil C. R. Towards the development of universal, fast and highly accurate docking/scoring methods:a long way to go. BRITISH JOURNAL OF PHARMACOLOGY.2008.153. S7-S26
[112]KUNTZ I. D., BLANEY J. M., OATLEY S. J., LANGRIDGE R., FERRIN T. E. A GEOMETRIC APPROACH TO MACROMOLECULE-LIGAND INTERACTIONS. JOURNAL OF MOLECULAR BIOLOGY.1982.161(2).269-288
[113]MILLER M. D., KEARSLEY S. K., UNDERWOOD D. J., SHERIDAN R. P. FLOG-A SYSTEM TO SELECT QUASI-FLEXIBLE LIGANDS COMPLEMENTARY TO A RECEPTOR OF KNOWN 3-DIMENSIONAL STRUCTURE. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1994.8(2).153-174
[114]Diller D. J., Merz K. M. High throughput docking for library design and library prioritization. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2001.43(2). 113-124
[115]Burkhard P., Taylor P., Walkinshaw M. D. An example of a protein ligand found by database mining:Description of the docking method and its verification by a 2.3 angstrom X-ray structure of a thrombin-ligand complex. JOURNAL OF MOLECULAR BIOLOGY. 1998.277(2).449-466
[116]Ewing TJA, Makino S., Skillman A. G., Kuntz I. D. DOCK 4.0:Search strategies for automated molecular docking of flexible molecule databases. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.2001.15(5).411-428
[117]Rarey M., Kramer B., Lengauer T., Klebe G. A fast flexible docking method using an incremental construction algorithm. JOURNAL OF MOLECULAR BIOLOGY.1996.261(3). 470-489
[118]Welch W., Ruppert J., Jain A. N. Hammerhead:Fast, fully automated docking of flexible ligands to protein binding sites. CHEMISTRY & amp; BIOLOGY.1996.3(6).449-462
[119]Schnecke V., Kuhn L. A. Virtual screening with solvation and ligand-induced complementarity. PERSPECTIVES IN DRUG DISCOVERY AND DESIGN.2000.20(1). 171-190
[120]Zsoldos Zsolt, Reid Darryl, Simon Aniko, Sadjad Bashir S., Johnson A. Peter. eHITS:An innovative approach to the docking and scoring function problems. CURRENT PROTEIN & PEPTIDE SCIENCE.2006.7(5).421-435
[121]GOODSELL D. S., OLSON A. J. AUTOMATED DOCKING OF SUBSTRATES TO PROTEINS BY SIMULATED ANNEALING. PROTEINS-STRUCTURE FUNCTION AND GENETICS.1990.8(3).195-202
[122]ABAGYAN R., TOTROV M., KUZNETSOV D. ICM-A NEW METHOD FOR PROTEIN MODELING AND DESIGN-APPLICATIONS TO DOCKING AND STRUCTURE PREDICTION FROM THE DISTORTED NATIVE CONFORMATION. JOURNAL OF COMPUTATIONAL CHEMISTRY.1994.15(5).488-506
[123]Verdonk M. L., Cole J. C., Hartshorn M. J., Murray C. W., Taylor R. D. Improved protein-ligand docking using GOLD. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2003.52(4).609-623
[124]CLARK K. P., AJAY. FLEXIBLE LIGAND DOCKING WITHOUT PARAMETER ADJUSTMENT ACROSS 4 LIGAND-RECEPTOR COMPLEXES. JOURNAL OF COMPUTATIONAL CHEMISTRY.1995.16(10).1210-1226
[125]Taylor J. S., Burnett R. M. DARWIN:A program for docking flexible molecules. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2000.41(2).173-191
[126]Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(14). 1639-1662
[127]Rosin M. P., Epstein J. B., Berean K., Durham S., Hay J., Cheng X., Zeng T., Huang Y. Q., Zhang L. W. The use of exfoliative cell samples to map clonal genetic alterations in the oral epithelium of high-risk patients. CANCER RESEARCH.1997.57(23).5258-5260
[128]Hart William Eugene. Adaptive Global Optimization with Local Search.
[129]Kitchen D. B., Decornez H., Furr J. R., Bajorath J. Docking and scoring in virtual screening for drug discovery:Methods and applications. NATURE REVIEWS DRUG DISCOVERY. 2004.3(11).935-949
[130]Bohm H. J. Prediction of binding constants of protein ligands:A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1998.12(4).309-323
[131]GEHLHAAR D. K., VERKHIVKER G. M., REJTO P. A., SHERMAN C. J., FOGEL D. B., FOGEL L. J., FREER S. T. MOLECULAR RECOGNITION OF THE INHIBITOR AG-1343 BY HIV-1 PROTEASE-CONFORMATIONALLY FLEXIBLE DOCKING BY EVOLUTIONARY PROGRAMMING. CHEMISTRY & amp; BIOLOGY.1995.2(5). 317-324
[132]Verkhivker G. M., Bouzida D., Gehlhaar D. K., Rejto P. A., Arthurs S., Colson A. B., Freer S. T., Larson V., Luty B. A., Marrone T., Rose P. W. Deciphering common failures in molecular docking of ligand-protein complexes. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.2000.14(8).731-751
[133]Jain A. N. Scoring noncovalent protein-ligand interactions:A continuous differentiable function tuned to compute binding affinities. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1996.10(5).427-440
[134]Head R. D., Smythe M. L., Oprea T. I., Waller C. L., Green S. M., Marshall G. R. VALIDATE:A new method for the receptor-based prediction of binding affinities of novel ligands. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.1996.118(16). 3959-3969
[135]BOHM H. J. LUDI-RULE-BASED AUTOMATIC DESIGN OF NEW SUBSTITUENTS FOR ENZYME-INHIBITOR LEADS. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1992.6(6).593-606
[136]GEHLHAAR D. K., MOERDER K. E., ZICHI D., SHERMAN C. J., OGDEN R. C., FREER S. T. DE-NOVO DESIGN OF ENZYME-INHIBITORS BY MONTE-CARLO LIGAND GENERATION. JOURNAL OF MEDICINAL CHEMISTRY.1995.38(3). 466-472
[137]Eldridge M. D., Murray C. W., Auton T. R., Paolini G. V., Mee R. P. Empirical scoring functions.1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN.1997.11(5).425-445
[138]KOLLMAN P. FREE-ENERGY CALCULATIONS-APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA. CHEMICAL REVIEWS.1993.93(7).2395-2417
[139]Aqvist J., Luzhkov V. B., Brandsdal B. O. Ligand binding affinities from MD simulations. ACCOUNTS OF CHEMICAL RESEARCH.2002.35(6).358-365
[140]CARLSON H. A., JORGENSEN W. L. AN EXTENDED LINEAR-RESPONSE METHOD FOR DETERMINING FREE-ENERGIES OF HYDRATION. JOURNAL OF PHYSICAL CHEMISTRY.1995.99(26).10667-10673
[141]LEACH A. R., KUNTZ I. D. CONFORMATIONAL-ANALYSIS OF FLEXIBLE LIGANDS IN MACROMOLECULAR RECEPTOR-SITES. JOURNAL OF COMPUTATIONAL CHEMISTRY.1992.13(6).730-748
[142]SHOICHET B. K., STROUD R. M., SANTI D. V., KUNTZ I. D., PERRY K. M. STRUCTURE-BASED DISCOVERY OF INHIBITORS OF THYMIDYLATE SYNTHASE. SCIENCE.1993.259(5100).1445-1450
[143]Verdonk M. L., Cole J. C., Hartshorn M. J., Murray C. W., Taylor R. D. Improved protein-ligand docking using GOLD. PROTEINS-STRUCTURE FUNCTION AND GENETICS.2003.52(4).609-623
[144]Morris G. M., Goodsell D. S., Halliday R. S., Huey R., Hart W. E., Belew R. K., Olson A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(14). 1639-1662
[145]Michel Julien, Verdonk Marcel L., Essex Jonathan W. Protein-ligand binding affinity predictions by implicit solvent simulations:A tool for lead optimization? JOURNAL OF MEDICINAL CHEMISTRY.2006.49(25).7427-7439
[146]KOLLMAN P. FREE-ENERGY CALCULATIONS-APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA. CHEMICAL REVIEWS.1993.93(7).2395-2417
[147]Briggs J. M., Marrone T. J., McCammon J. A. Computational science new horizons and relevance to pharmaceutical design. TRENDS IN CARDIOVASCULAR MEDICINE.1996. 6(6).198-204
[148]Canutescu A. A., Shelenkov A. A., Dunbrack R. L. A graph-theory algorithm for rapid protein side-chain prediction. PROTEIN SCIENCE.2003.12(9).2001-2014
[149]Petrella R. J., Lazaridis T., Karplus M. Protein sidechain conformer prediction:a test of the energy function (vol 3, pg 353,1998). FOLDING & DESIGN.1998.3(6).588
[150]WILSON C., GREGORET L. M., AGARD D. A. MODELING SIDE-CHAIN CONFORMATION FOR HOMOLOGOUS PROTEINS USING AN ENERGY-BASED ROTAMER SEARCH. JOURNAL OF MOLECULAR BIOLOGY.1993.229(4).996-1006
[151]Wawak R. J., Pillardy J., Liwo A., Gibson K. D., Scheraga H. A. Diffusion equation and distance scaling methods of global optimization:Applications to crystal structure prediction. JOURNAL OF PHYSICAL CHEMISTRY A.1998.102(17).2904-2918
[152]Andricioaei I., Straub J. E. Global optimization using bad derivatives:Derivative-free method for molecular energy minimization. JOURNAL OF COMPUTATIONAL CHEMISTRY.1998.19(13).1445-1455
[153]PILLARDY J., PIELA L. MOLECULAR-DYNAMICS ON DEFORMED POTENTIAL-ENERGY HYPERSURFACES. JOURNAL OF PHYSICAL CHEMISTRY. 1995.99(31).11805-11812
[154]Lazaridis T., Karplus M. Thermodynamics of protein folding:a microscopic view. BIOPHYSICAL CHEMISTRY.2003.100(1-3).367-395
[155]Duan Yong, Wu Chun, Chowdhury Shibasish, Lee Mathew C., Xiong Guoming, Zhang Wei, Yang Rong, Cieplak Piotr, Luo Ray, Lee Taisung, Caldwell James, Wang Junmei, Kollman Peter. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 2003.24(16).1999-2012
[156]Ryckaert Jean-Paul, Ciccotti Giovanni, Berendsen Herman J. C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. Journal of Computational Physics.1977.23(3).327-341
[157]Tsui V., Case D. A. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.2000. 122(11).2489-2498
[158]Spector Arthur A., Fang Xiang, Snyder Gary D., Weintraub Neal L. Epoxyeicosatrienoic acids (EETs):metabolism and biochemical function. Progress in Lipid Research.2004.43(1). 55-90
[159]Newman John W., Morisseau Christophe, Hammock Bruce D. Epoxide hydrolases:their roles and interactions with lipid metabolism. Progress in Lipid Research.2005.44(1).1-51
[160]Yu Zhigang, Xu Fengyun, Huse Linn M., Morisseau Christophe, Draper Alison J., Newman John W., Parker Carol, Graham LeRae, Engler Marguerite M., Hammock Bruce D., Zeldin Darryl C., Kroetz Deanna L. Soluble Epoxide Hydrolase Regulates Hydrolysis of Vasoactive Epoxyeicosatrienoic Acids. Circulation Research.2000.87(11).992-998
[161]Schmelzer Kara R., Kubala Lukas, Newman John W., Kim In-Hae, Eiserich Jason P., Hammock Bruce D. Soluble epoxide hydrolase is a therapeutic target for acute inflammation. Proceedings of the National Academy of Sciences of the United States of America.2005. 102(28).9772-9777
[162]Node Koichi, Huo Yuqing, Ruan Xiulu, Yang Baichun, Spiecker Martin, Ley Klaus, Zeldin Darryl C., Liao James K. Anti-inflammatory Properties of Cytochrome P450 Epoxygenase-Derived Eicosanoids. Science.1999.285(5431).1276-1279
[163]Katragadda D., Batchu S. N., Cho W. J., Chaudhary K. R., Falck J. R., Seubert J. M. Epoxyeicosatrienoic acids limit damage to mitochondrial function following stress in cardiac cells. Journal of Molecular and Cellular Cardiology.2009.46(6).867-875
[164]Yousif M. H. M., Benter I. F., Roman R. J. Cytochrome P450 metabolites of arachidonic acid play a role in the enhanced cardiac dysfunction in diabetic rats following ischaemic reperfusion injury. Autonomic and Autacoid Pharmacology.2009.29(1-2).33-41
[165]Xu Danyan, Li Ning, He Yuxia, Timofeyev Valeriy, Lu Ling, Tsai Hsing-Ju, Kim In-Hae, Tuteja Dipika, Mateo Robertino Karlo P., Singapuri Anil, Davis Benjamin B., Low Reginald, Hammock Bruce D., Chiamvimonvat Nipavan. Prevention and reversal of cardiac hypertrophy by soluble epoxide hydrolase inhibitors. Proceedings of the National Academy of Sciences.2006.103(49).18733-18738
[166]Sudhahar V., Shaw S., Imig J. D. Epoxyeicosatrienoic acid analogs and vascular function. Current Medicinal Chemistry.2010.17(12).1181-1190
[167]Zeldin D. C., Kobayashi J., Falck J. R., Winder B. S., Hammock B. D., Snapper J. R., Capdevila J. H. Regio-and enantiofacial selectivity of epoxyeicosatrienoic acid hydration by cytosolic epoxide hydrolase. Journal of Biological Chemistry.1993.268(9).6402-6407
[168]Zeldin D. C., Wei S. Z., Falck J. R., Hammock B. D., Snapper J. R., Capdevila J. H. Metabolism of Epoxyeicosatrienoic Acids by Cytosolic Epoxide Hydrolase:Substrate Structural Determinants of Asymmetric Catalysis. Archives of Biochemistry and Biophysics. 1995.316(1).443-451
[169]Zeldin Darryl C. Epoxygenase Pathways of Arachidonic Acid Metabolism. Journal of Biological Chemistry.2001.276(39).36059-36062
[170]Roman Richard J. P-450 Metabolites of Arachidonic Acid in the Control of Cardiovascular Function. Physiological Reviews.2002.82(1).131-185
[171]Imig John D. Cardiovascular Therapeutic Aspects of Soluble Epoxide Hydrolase Inhibitors. Cardiovascular Drug Reviews.2006.24(2).169-188
[172]Qiu Hong, Li Ning, Liu Jun-Yan, Harris Todd R., Hammock Bruce D., Chiamvimonvat Nipavan. Soluble Epoxide Hydrolase Inhibitors and Heart Failure. Cardiovascular Therapeutics.2011.29(2).99-111
[173]Fang Xiang. Soluble Epoxide Hydrolase:A Novel Target for the Treatment of Hypertension. Recent Patents on Cardiovascular Drug Discovery.2006.1.67-72
[174]Anandan Sampath-Kumar, Webb Heather Kay, Chen Dawn, Wang Yi-Xin Jim, Aavula Basker R., Cases Sylvaine, Cheng Ying, Do Zung N., Mehra Upasana, Tran Vinh, Vincelette Jon, Waszczuk Joanna, White Kathy, Wong Kenneth R., Zhang Le-Ning, Jones Paul D., Hammock Bruce D., Patel Dinesh V., Whitcomb Randall, Maclntyre D. Euan, Sabry James, Gless Richard. 1-(1-Acetyl-piperidin-4-yl)-3-adamantan-1-yl-urea (AR9281) as a potent, selective, and orally available soluble epoxide hydrolase inhibitor with efficacy in rodent models of hypertension and dysglycemia. Bioorganic & Medicinal Chemistry Letters.2011. 21(3).983-988
[175]Kim In-Hae, Park Yong-Kyu, Hammock Bruce D., Nishi Kosuke. Structure-Activity Relationships of Cycloalkylamide Derivatives as Inhibitors of the Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2011.54(6).1752-1761
[176]Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna, Zheng Jiang, Greene Jessica F., Sanborn James R., Hammock Bruce D. Potent urea and carbamate inhibitors of soluble epoxide hydrolases. Proceedings of the National Academy of Sciences.1999.96(16). 8849-8854
[177]Rose Tristan E., Morisseau Christophe, Liu Jun-Yan, Inceoglu Bora, Jones Paul D., Sanborn James R., Hammock Bruce D. 1-Aryl-3-(1-acylpiperidin-4-yl)urea Inhibitors of Human and Murine Soluble Epoxide Hydrolase:Structure-Activity Relationships, Pharmacokinetics, and Reduction of Inflammatory Pain. Journal of Medicinal Chemistry.2010.53(19).7067-7075
[178]Shen Hong C., Ding Fa-Xiang, Deng Qiaolin, Xu Suoyu, Tong Xinchun, Zhang Xiaoping, Chen Yuli, Zhou Gaochao, Pai Lee-Yuh, Alonso-Galicia Magdalena, Roy Sophie, Zhang Bei, Tata James R., Berger Joel P., Colletti Steven L. A strategy of employing aminoheterocycles as amide mimics to identify novel, potent and bioavailable soluble epoxide hydrolase inhibitors. Bioorganic & Medicinal Chemistry Letters.2009.19(19).5716-5721
[179]Chen Dawn, Whitcomb Randall, MacIntyre Euan, Tran Vinh, Do Zung N., Sabry James, Patel Dinesh V., Anandan Sampath K., Gless Richard, Webb Heather K. Pharmacokinetics and Pharmacodynamics of AR9281, an Inhibitor of Soluble Epoxide Hydrolase, in Single-and Multiple-Dose Studies in Healthy Human Subjects. The Journal of Clinical Pharmacology.2012.52(3).319-328
[180]Singh Dipali, Tripathi Anushree, Kumar Gautam. An Overview of Computational Approaches in Structure Based Drug Design. Nepal Journal of Biotechnology.2012.2(1). 53-61
[181]Kubinyi H. Structure-based design of enzyme inhibitors and receptor ligands. Current Opinion in Drug Discovery and Development.1998.1(1).4-15
[182]Alonso Hernan, Bliznyuk Andrey A., Gready Jill E. Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews.2006.26(5).531-568
[183]Hao Ming, Li Yan, Wang Yonghua, Yan Yulian, Zhang Shuwei. Combined 3D-QSAR, Molecular Docking, and Molecular Dynamics Study on Piperazinyl-Glutamate-Pyridines/Pyrimidines as Potent P2Y12 Antagonists for Inhibition of Platelet Aggregation. Journal of Chemical Information and Modeling.2011.51(10). 2560-2572
[184]AbdulHameed Mohamed Diwan M., Hamza Adel, Zhan Chang-Guo. Microscopic Modes and Free Energies of 3-Phosphoinositide-Dependent Kinase-1 (PDK1) Binding with Celecoxib and Other Inhibitors. Journal of Physical Chemistry B.2006.110(51). 26365-26374
[185]Ertl Peter. JME Molecular Editor.
[186]Schuttelkopf Alexander W., van Aalten Daan M. F. PRODRG:a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D.2004.60(8). 1355-1363
[187]Frisch M. J., Al. Et. Gaussian 09.
[188]Huey Ruth, Morris Garrett M., Olson Arthur J., Goodsell David S. A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry.2007. 28(6).1145-1152
[189]Gomez German A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Human soluble epoxide hydrolase:Structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids. Protein Science.2006.15(1).58-64
[190]Argiriadi Maria A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Detoxification of Environmental Mutagens and Carcinogens:Structure, Mechanism, and Evolution of Liver Epoxide Hydrolase. Proceedings of the National Academy of Sciences of the United States of America.1999.96(19).10637-10642
[191]Argiriadi Maria A., Morisseau Christophe, Goodrow Marvin H., Dowdy Deanna L., Hammock Bruce D., Christianson David W. Binding of Alkylurea Inhibitors to Epoxide Hydrolase Implicates Active Site Tyrosines in Substrate Activation. Journal of Biological Chemistry.2000.275(20).15265-15270
[192]Gomez German A., Morisseau Christophe, Hammock Bruce D., Christianson David W. Structure of Human Epoxide Hydrolase Reveals Mechanistic Inferences on Bifunctional Catalysis in Epoxide and Phosphate Ester Hydrolysis,. Biochemistry.2004.43(16). 4716-4723
[193]Sanner. Michel F. Python:a programming language for software integration and development. J. Mol. Graphics Mod.1999.17(1).57-61
[194]Morris Garrett M., Huey Ruth, Lindstrom William, Sanner Michel F., Belew Richard K., Goodsell David S., Olson Arthur J. AutoDock4 and AutoDockTools4:Automated docking with selective receptor flexibility. Journal of Computational Chemistry.2009.30(16). 2785-2791
[195]Case D. A., Darden T. A., T. E. Cheatham Ⅲ, Simmerling C. L., Wang J., Duke R. E., Luo R., Crowley M., Walker R. C., Zhang W., Merz K. M., Wang B., Hayik S., Roitberg A., Seabra G., Kolossvary I., Wong K. F., Paesani F., Vanicek J., Wu X., Brozell S. R., Steinbrecher T., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Mathews D. H., Seetin M. G., Sagui C., Babin V., Kollman P. A. AMBER10.
[196]Lee Mathew C., Duan Yong. Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins:Structure, Function, and Bioinformatics.2004.55(3).620-634
[197]Wang Junmei, Wolf Romain M., Caldwell James W., Kollman Peter A., Case David A. Development and testing of a general amber force field. Journal of Computational Chemistry. 2004.25(9).1157-1174
[198]Ryckaert Jean-Paul, Ciccotti Giovanni, Berendsen Herman J. C. Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. Journal of Computational Physics.1977.23(3).327-341
[199]Darden Tom, York Darrin, Pedersen Lee. Particle mesh Ewald:An N [center-dot] log(N) method for Ewald sums in large systems. Journal of Chemical Physics.1993.98(12). 10089-10092
[200]Feig M. Implicit solvation based on generalized Born theory in different dielectric environments. Journal of Chemical Physics.2004.120(2).903
[201]Kollman Peter A., Massova Irina, Reyes Carolina, Kuhn Bernd, Huo Shuanghong, Chong Lillian, Lee Matthew, Lee Taisung, Duan Yong, Wang Wei, Donini Oreola, Cieplak Piotr, Srinivasan Jaysharee, Case David A., Cheatham Thomas E. Calculating Structures and Free Energies of Complex Molecules:Combining Molecular Mechanics and Continuum Models. Accounts of Chemical Research.2000.33(12).889-897
[202]Onufriev Alexey, Bashford Donald, Case David A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Structure, Function, and Bioinformatics.2004.55(2).383-394
[203]SITKOFF D., SHARP K. A., HONIG B. ACCURATE CALCULATION OF HYDRATION FREE-ENERGIES USING MACROSCOPIC SOLVENT MODELS. JOURNAL OF PHYSICAL CHEMISTRY.1994.98(7).1978-1988
[204]Weiser Jorg, Shenkin Peter S., Still W. Clark. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry.1999.20(2). 217-230
[205]Gohlke Holger, Kiel Christina, Case David A. Insights into Protein-Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras-Raf and Ras-RalGDS Complexes. Journal of Molecular Biology.2003.330(4).891-913
[206]Spector Arthur A., Norris Andrew W. Action of epoxyeicosatrienoic acids on cellular function. American Journal of Physiology-Cell Physiology.2007.292(3). C996-C1012
[207]Spector Arthur A. Arachidonic acid cytochrome P450 epoxygenase pathway. Journal of Lipid Research.2009.50(Supplement). S52-S56
[208]Newman John W., Morisseau Christophe, Hammock Bruce D. Epoxide hydrolases:their roles and interactions with lipid metabolism. Progress in Lipid Research.2005.44(1).1-51
[209]Behm David J., Ogbonna Andrea, Wu Charlene, Burns-Kurtis Cynthia L., Douglas Stephen A. Epoxyeicosatrienoic Acids Function as Selective, Endogenous Antagonists of Native Thromboxane Receptors:Identification of a Novel Mechanism of Vasodilation. Journal of Pharmacology and Experimental Therapeutics.2009.328(1).231-239
[210]Wang Zhen-He, B Davis Benjamin, Jiang De-Qian, Zhao Ting-Ting, Xu Dan-Yan. Soluble Epoxide Hydrolase Inhibitors and Cardiovascular Diseases.105-111
[211]Pecic Stevan, Deng Shi-Xian, Morisseau Christophe, Hammock Bruce D., Landry Donald W. Design, synthesis and evaluation of non-urea inhibitors of soluble epoxide hydrolase. Bioorganic & Medicinal Chemistry Letters.2012.22(1).601-605
[212]Hwang Sung Hee, Wagner Karen M., Morisseau Christophe, Liu Jun-Yan, Dong Hua, Wecksler Aaron T., Hammock Bruce D. Synthesis and Structure-Activity Relationship Studies of Urea-Containing Pyrazoles as Dual Inhibitors of Cyclooxygenase-2 and Soluble Epoxide Hydrolase. Journal of Medicinal Chemistry.2011.54(8).3037-3050
[213]Morisseau Christophe, Hammock Bruce D. Epoxide Hydrolases:Mechanisms, Inhibitor Designs, and Biological Roles. ChemInform.2005.36(39). no-no
[214]Morisseau Christophe, Goodrow Marvin H., Newman John W., Wheelock Craig E., Dowdy Deanna L., Hammock Bruce D. Structural refinement of inhibitors of urea-based soluble epoxide hydrolases. Biochemical Pharmacology.2002.63(9).1599-1608
[215]Cronin Annette, Mowbray Sherry, Diirk Heike, Homburg Shirli, Fleming Ingrid, Fisslthaler Beate, Oesch Franz, Arand Michael. The N-terminal domain of mammalian soluble epoxide hydrolase is a phosphatase. Proceedings of the National Academy of Sciences.2003.100(4). 1552-1557
[216]Cornell Wendy D., Cieplak Piotr, Bayly Christopher I., Gould Ian R., Merz Kenneth M., Ferguson David M., Spellmeyer David C, Fox Thomas, Caldwell James W., Kollman Peter A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. Journal of the American Chemical Society.1995.117(19).5179-5197
[217]Gordon John C., Myers Jonathan B., Folta Timothy, Shoja Valia, Heath Lenwood S., Onufriev Alexey. H++:a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research.2005.33(suppl 2). W368-W371
[218]Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. Journal of Chemical Physics.1983. 79(2).926-935
[219]Pettersen Eric F., Goddard Thomas D., Huang Conrad C., Couch Gregory S., Greenblatt Daniel M., Meng Elaine C., Ferrin Thomas E. UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry.2004.25(13). 1605-1612
[220]Feig M., Im W., Brooks C. L. Implicit solvation based on generalized Born theory in different dielectric environments. Journal of Chemical Physics.2004.120(2).903-911
[221]Kollman P. A., Massova I., Reyes C., Kuhn B., Huo S. H., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D. A., Cheatham T. E. Calculating structures and free energies of complex molecules:Combining molecular mechanics and continuum models. Accounts of Chemical Research.2000.33(12).889-897
[222]STILL W. C., TEMPCZYK A., HAWLEY R. C., HENDRICKSON T. SEMIANALYTICAL TREATMENT OF SOLVATION FOR MOLECULAR MECHANICS AND DYNAMICS. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY.1990. 112(16).6127-6129
[223]SITKOFF D., SHARP K. A., HONIG B. ACCURATE CALCULATION OF HYDRATION FREE-ENERGIES USING MACROSCOPIC SOLVENT MODELS. JOURNAL OF PHYSICAL CHEMISTRY.1994.98(7).1978-1988
[224]Sanner M. F., Olson A. J., Spehner J. C. Reduced surface:An efficient way to compute molecular surfaces. Biopolymers.1996.38(3).305-320
[225]Whitlow M., Howard A. J., Stewart D., Hardman K. D., Chan J. H., Baccanari D. P., Tansik R. L., Hong J. S., Kuyper L. F. X-ray crystal structures of Candida albicans dihydrofolate reductase:High resolution ternary complexes in which the dihydronicotinamide moiety of NADPH is displaced by an inhibitor. JOURNAL OF MEDICINAL CHEMISTRY.2001. 44(18).2928-2932
[226]Kelley Lawrence A., Gardner Stephen P., Sutcliffe Michael J. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Engineering.1996.9(11).1063-1065
[227]Jain A. K., Murty M. N., Flynn P. J. Data clustering:a review. ACM Comput. Surv.1999. 31(3).264-323
[228]Imig John, Carpenter Margaret, Shaw Sean. The Soluble Epoxide Hydrolase Inhibitor AR9281 Decreases Blood Pressure, Ameliorates Renal Injury and Improves Vascular Function in Hypertension. Pharmaceuticals.2009.2(3).217-227
[229]Karthikeyan S., Nagase S. Origins of the Stability of Imidazole-Imidazole, Benzene-Imidazole, and Benzene-Indole Dimers:CCSD(T)/CBS and SAPT Calculations. Journal of Physical Chemistry A.2012.116(7).1694-1700
[230]Zhuravlev A. V., Shchegolev B. F., Savvateeva-Popova E. V., Popov A. V. Molecular mechanisms of imidazole and benzene ring binding in proteins.2009.74(8).925-932
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |