中文
Announcement
More
Progress in Chemistry 1998, Vol. 10 Issue (04): 427- Previous Articles   Next Articles

• Review •

Computer Modeling for Interaction of Ligands and Receptors and Their Applications in Drug Design

Jiang Hualiang;Hu Zengjian;Chen Jianzhong;Gu Jiande;Zhu Weiliang;Chen Kaixian;Ji Ruyun   

  1. Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200031, China
  • Received: Revised: Online: Published:
PDF ( 3493 ) Cited
Export

EndNote

Ris

BibTeX

The interaction of ligands with their receptor macromolecules are central to most of biological processes. Nowadays, there are accumulating evidences of that ligand-receptor interaction can be simulated with computer modeling and theoretical calculation methods. Some of these methods and their applications in drug design were reviewed in this paper.

CLC Number: 

[1 ] Lybrand T P, Curr. Opin. Struct. Biol. , 1995, 5, 224—228.
[2 ] Kollman P A , Curr. Opin. Struct. Biol. , 1994, 4, 240- 245.
[3 ] 金荫昌等, 分子药理学, 天津科技出版社, 天津, 1989, 75- 100.
[4 ] Kubinyi H, Burger’s Medicinal Chemistry and Drug Discovery , Fifth Edition, Vol. 1: Principlesand Practice (ed. Wolff M E) , John Wiley & Sons, Inc. , New York, 1995, 497- 571.
[5 ] Kenneth M M Jr, Curr. Opin. Struct. Biol. , 1993, 3, 234- 240.
[6 ] Colman P M , Curr. Opin. Struct. Biol. , 1994, 4, 868- 874.
[7 ] Greer J , Erickson J W , Baldwin J J , Varney M D, J. Med. Chem. , 1994, 37, 1035- 1054.
[8 ] Johnson M S, Srinivasan N , Sowdhamini R, Blundell T L , Crit. Rev. Biochem. Mol. Biol. , 1994,29, 1- 68.
[9 ] Kontoyianni M , Lybrand T P, Perspect. Drug Discov. Des. , 1993, 1, 291- 300.
[10 ] Greer J , Method. Enzym. , 1991, 202, 239- 252.
[11 ] Thornton J M , Swindells M B, Molecular Structures in Biology (eds. Diamond R, Koetzle T F,Drout K, Richardson J S) , Oxford, New York, 1993.
[12 ] Spellmeyer D C, Swope W C, Perspect. Drug Discov. Des. , 1993, 1, 359- 370.
[13 ] Olson A J , Morris G M , Perspect. Drug Discov. Des. , 1993, 1, 329- 344.
[14 ] Boyd D B, Milosevich S A F, Perspect. Drug Discov. Des. , 1993, 1, 345- 358.
[15 ] Andrews P R, Craik D J , Martin J L , J. Med. Chem. , 1984, 27, 1648- 1657.
[16 ] Blaney J M , Dixon J S , Perspect. Drug Discov. Des. , 1993, 1, 301- 320.
[17 ] SYBYL [分子模拟与分子设计软件包], Version 6. 2, St. Louis (MO ) : Tripos Associates, 1995.
[18 ] Insight II[分子模拟与分子设计软件包], Version 95, San Diego: Molucular Simulation, Inc. , 1995.
[19 ] Whittle P J , Annu. Rev. Biophys. Biomol. Struct. , 1994, 23, 349- 375.
[20 ] Kuntz I D, Blaney J M , Oatley S J , Langridge R, Ferrin T E, J. Mol. Biol. , 1982, 161, 269-288.
[21 ] Connolly M L , Science, 1983, 221, 709- 713.
[22 ] Lewis R A , Method. Enzym. , 1991, 202, 126- 156.
[23 ] Allen F H, Bellard S, Brice M D, Cartwright B A , Doubleday A , Higgs H, Hummelink T ,Hummelink-Peters B G, Kennard O , Motherwell W D S, Rodgers J R, Watson D G, Acta Crystallogr. , 1979, B 35, 2331- 2339.
[24 ] Bolin J T , Fellman D J , Matthews D A , Hamlin R C, Hraut J , J. Biol. Chem. , 1982, 257, 13650- 13662.
[25 ] Bobhm H J , J. Comput. -Aided Mol. Des. , 1992, 6, 593- 606.
[26 ] Fersht A R, Shi J , Knill-Jones J , Lowe D M , Willkinson A J , Blow D M , Brick P, Carter P, Waye M M Y, Winter G, Nature, 1985, 314, 235- 238.
[27 ] Bohacek R S, McMartin C, J. Med. Chem. , 1992, 35, 1671- 1684.
[28 ] 蒋华良, 陈凯先, 陈建忠, 顾健德等, 中国科学(B 辑) , 1997, 27, 411- 418.
[29 ] Jiang H L , Chen K X, Tang Y, Chen J Z, Li Q , Yang Y S, Wang Q M , Ji R Y , J. Med. Chem. ,1997, 40, 3085- 3090.
[30 ] Jiang H L , Chen K X, Tang Y, Chen J Z, Li Q , Wang Q M , JiR Y, Acta Pharmacol. Sin. , 1997,18 (1) , 36- 44.
[31 ] Jiang H L , Chen K X, Tang Y, Chen J Z, Li Q , Wang Q M , Ji R Y, Chin. Chem. Lett. , 1996, 7(3) , 252- 256.
[32 ] Blaney J M , Weiner P K, J. Am. Chem. Soc. , 1982, 104, 6424- 6434.
[33 ] Darden T , Blaney J M , Ann. N . Y. Acad. Sci. , 1986, 482, 249- 250.
[34 ] Kuyper L , Davis S, LeBlanc H, Advancesin Gene Technology: Protein Engineering and Production,ICSU Short Receptors ,vol. 8 (ed. Brew K) , IRL Press, Oxford, 1988, 190.
[35 ] Kollman P, Chem. Rev. , 1993, 93, 2395- 2417.
[36 ] Lee C, Curr. Opin. Struct. Biol. , 1992, 2, 217- 222.
[37 ] Gerber P R, Mark A E, Van Gausteren W F, J. Computer-Aided Mol. Des. , 1993, 7, 305- 323.
[38 ] Van Gunsteren W F, King P M , Mark A E, Quart. Rev. Biophys. , 1994, 27, 435- 481.
[39 ] Wong C F, McCammon J A , J. Am. Chem. Soc. , 1986, 108, 3830- 3832.
[40 ] Bash P A , Singh U C, Langridge R, Kollman P A , Science, 1987, 236, 564- 568.
[41 ] Merz K M , Kollman P A , J. Am. Chem. Soc. , 1989; 111, 5649- 5658.
[42 ] Morgan B P, Scholtz J M , Ballinger M D et al. , J. Am. Chem. Soc. , 1991, 113, 197- 307.
[43 ] Merz K M , Murcko M A , Kollman P A , J. Am. Chem. Soc. , 1991, 113, 4484- 4490.
[44 ] Menziam M C, Reynolds C A , Richards W G, J. Chem. Soc. , Chem. Commun. , 1989, 853- 855.
[45 ] Hoops S C, Anderson K W , Merz K M , J. Am. Chem. Soc. , 1991, 113, 8262- 8270.
[46 ] Rao B G, Singh U C, J. Am. Chem. Soc. , 1991, 113, 6735- 6750.
[47 ] Reddy M R, Viswanadhan V N , Weinstein J N , Proc. Natl. Acad. Sci. USA , 1991, 88, 10287-10291.
[48 ] Reddy M R, Kalish V , Palmer C et al. , Paper Presented at Spring ACS Meeting in Denver, 1993.
[49 ] Ferguson D M , Radmer R J , Kollman P A , J. Med. Chem. , 1991, 34, 2654- 2659.
[50 ] Tropsha A , Hermans J , J. Protein Eng. , 1992, 5, 29- 33.
[51 ] Cieplak P, Kollman P A , J. Comput.-Aided. Mol. Des. , 1993, 7, 291- 304.
[52 ] Cummins P L , Ramnarayan K, Singh U C et al. , J. Am. Chem. Soc. , 1991, 113, 8247- 8256.
[53 ] Fleischman S H, Brooks C L , Proteins, 1990, 7, 52- 61.
[54 ] Brooks C L , Fleischman S H, J. Am. Chem. Soc. , 1990, 112, 3307- 3312.
[55 ] McDonald J J , Brooks C L , J. Am. Chem. Soc. , 1991, 113, 2295- 2301.
[56 ] McDonald J J , Brooks C L , J. Am. Chem. Soc. , 1992, 114, 2062- 2072.
[57 ] Caldwell J W , Agard D A , Kollman P A , Proteins, 1991, 10, 140- 148.
[58 ] Hirono S, Kollman P A , J. Mol. Biol. , 1990, 212, 193- 207.
[59 ] Rao S N , Singh U C, Bash P A , Kollman P A , Nature, 1987, 328, 551- 553.
[60 ] Hwang J K, Warshel A , Biochemistry , 1987, 26, 2669- 2673.
[61 ] Mizushima N , Spellmeger D, J. Biol. Chem. , 1991, 266, 11801- 11809.
[62 ] Computer Simulation of Biomolecular Systems; Theoretical and Experimental Applications, Vol. 2,Part 4: Computationof Free Energy (eds. Van Gunsteren W F, Weiner P K) , ESCOM , New York,1990.
[63 ] WarshelA , Levitt M , J. Mol. Biol. , 1976, 103, 227- 249.
[64 ] Field M J , Bash P A , Karplus M , J. Comput. Chem. , 1990, 11, 700- 733.
[65 ] Gao J , Xia X, Science, 1992, 258, 631- 635.
[66 ] 蒋华良, 陈凯先, 嵇汝运, 化学通报, 1995, (4) , 1- 6.
[67 ] WarshelA , Computer Modeling of Chemical Reactions in Enzymes and Solutions, John Wiley and Sons, Inc. , New York, 1991.
[68 ] Aqvist J , Warshel A , Chem. Rev. , 1993, 93, 2523- 2544.
[69 ] Gresh N , Caverle P, Pullman A , Theoret. Chim. Acta, 1984, 20, 1- 20.
[70 ] Elock A H, Lyne P D, Mulholland A J , Mandra A , Richards W G, J. Am. Chem. Soc. , 1995,117, 4706- 4707.
[71 ] Waszowycz B, Hillier I H, Gensmantel N , Payling D W , J. Chem. Soc. , Perkin Trans. , ê 1991,(2) , 225- 230.
[72 ] Waszowycz B, Hillier I H, Gensmantel N , Payling D W , J. Chem. Soc. , Perkin Trans. ê , 1991,(12) , 2025- 2032.
[73 ] Bash P A , Field M J , Davenport R C, Petako G A et al. , Biochemistry , 1991, 30, 5826- 5832.
[74 ] Knowles J R, Albery W J , Acc. Chem. Rev. , 1977, 10, 105- 111.
[75 ] Aqvist J , WarshelA , J. Mol. Biol. , 1992, 224, 7- 14.
[76 ] Aqvist J , Fothergill M , Warshel A , J. Am. Chem. Soc. , 1993, 115, 631- 635.
[77 ] Jann J , Protein: Struct. , Funct. ,and Genet. , 1995, 21, 20- 39.
[78 ] DeWitte R S, Shakhnovich E I, J. Am. Chem. Soc. , 1997, 118, 11733- 11744

[1] Zhang Xiaofei, Li Shenhao, Wang Zhen, Yan Jian, Liu Jiaqin, Wu Yucheng. Review on the First-Principles Calculation in Lithium-Sulfur Battery [J]. Progress in Chemistry, 2023, 35(3): 375-389.
[2] Guoyong Huang, Xi Dong, Jianwei Du, Xiaohua Sun, Botian Li, Haimu Ye. High-Voltage Electrolyte for Lithium-Ion Batteries [J]. Progress in Chemistry, 2021, 33(5): 855-867.
[3] Tong Wang, Wenjiao Zhao, Liangchun Li, Renlin Zheng, Dequn Sun. Synthesis of Dehydroamino Acids and Their Applications in the Drug Research and Development [J]. Progress in Chemistry, 2020, 32(1): 55-71.
[4] Zhan Peng, Wang Xueshun, Liu Xinyong. Contemporary Molecular Targeted Drug in the Context of “Precision Medicine”: An Attempting Discussion of “Precision Drug Design” [J]. Progress in Chemistry, 2016, 28(9): 1363-1386.
[5] Yuan Shuo, Sun Dequn. The Conformational Restriction of β-Peptidomimetics in Drug Design [J]. Progress in Chemistry, 2016, 28(7): 1084-1098.
[6] Hou hui, Sun Dequn. Conformational Restriction of Peptidomimetics in Drug Design [J]. Progress in Chemistry, 2015, 27(9): 1260-1274.
[7] Zhang Lingling, Ma Yulin, Du Chunyu, Yin Geping. Research on the High-Voltage Electrolyte for Lithium Ion Batteries [J]. Progress in Chemistry, 2014, 26(04): 553-559.
[8] Ren Yanrong, Tian Feifei, Zhou Peng. Computational Peptidology [J]. Progress in Chemistry, 2012, (9): 1674-1682.
[9] Jia Jianfeng, Wu Haishun. Stability Rule of Ⅲ-ⅤPolyhedral Clusters [J]. Progress in Chemistry, 2012, 24(06): 1008-1022.
[10] . Theoretical Calculation of Cyclodextrins [J]. Progress in Chemistry, 2010, 22(05): 803-811.
[11] . "Click Chemistry" and Its Growing Applications in Biomedical Field [J]. Progress in Chemistry, 2010, 22(0203): 417-426.
[12] Xu Mengqing Xing Lidan Li Weishan. Additives of Interphase Film Formation for Lithium Ion Batteries [J]. Progress in Chemistry, 2009, 21(10): 2017-2027.
[13] . Reactive Halogen Chemistry [J]. Progress in Chemistry, 2009, 21(0203): 307-334.
[14] 刘幸海 XingHai Liu. Progress in KARI and its Inhibitors [J]. Progress in Chemistry, 2008, 20(11): 1788-1797.
[15] Han Chunyan|Li Yan|Liu Gang**

. Drug-likeness: Predication and Practice [J]. Progress in Chemistry, 2008, 20(09): 1335-1344.