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化学进展 2016, Vol. 28 Issue (9): 1328-1340 DOI: 10.7536/PC160343 前一篇   后一篇

• 综述与评论 •

聚酰胺类多肽二级结构模拟物的结构设计与性质分析

王志鹏1,2, 田长麟1, 郑基深1*   

  1. 1. 中国科学技术大学生命科学学院 合肥 230026;
    2. 美国德克萨斯农工大学化学系 德州 77840
  • 收稿日期:2016-03-01 修回日期:2016-07-01 出版日期:2016-09-15 发布日期:2016-08-16
  • 通讯作者: 郑基深 E-mail:jszheng@ustc.edu.cn
  • 基金资助:
    国家自然科学基金项目(No.21402206)、安徽省自然科学基金(No.1508085QB30)和北京分子科学国家实验室资助(No.20140124)

The Structural Designs and Property Analysis of Polyamide Based Structures as Peptide Secondary Structure Mimics

Wang Zhipeng1,2, Tian Changlin1, Zheng Jishen1*   

  1. 1. School of Life Science, University of Science and Technology of China, Hefei 230026, China;
    2. Department of Chemistry, Texas A & M University, College Station 77840, United States
  • Received:2016-03-01 Revised:2016-07-01 Online:2016-09-15 Published:2016-08-16
  • Supported by:
    The work was supported by the National Natural Science Foundation of China (No. 21402206), the Anhui Provincial Natural Science Foundation (No. 1508085QB30), and the Beijing National Laboratory for Molecular Sciences (No. 20140124).
多肽与蛋白质具有结构支持、酶促催化、蛋白-蛋白相互作用等一系列功能。其中,二级结构作为少数氨基酸参与的相对局域性的结构,是一切高级结构的基础。为了模拟天然多肽的结构与功能,人们成功设计并合成了多种非天然的寡聚物结构。这些拟肽或类肽结构能有效地模拟以α-螺旋、转角为主体的多肽二级结构。二级结构模拟物具有重要的理论意义,并被进一步用于蛋白-蛋白相互作用的抑制剂研究与新药设计中。本文从分析多肽的二级结构特征入手,分类阐述了目前的各类多肽二级结构模拟物,并重点分析了最为主要的基于酰胺键型的模拟物的设计与结构多样性。同时,本文提出一系列形象化的命名手段进行分类,如χ肽、ζ/ξ-肽及ζ-ξ-肽等。
The peptides and proteins lay the foundation of diverse functions including structural supporting, enzymatic catalysis, protein-protein interactions etc. Specifically, secondary structures are essential elements for any possible higher structures, as rather localized motifs with limited amino acid residues involved. Nowadays, different non-natural oligomers have been developed for the peptide structural and functional mimicking, such as α-helix and turns. Protein secondary structure mimics are a group of organic compounds with theoretical importance, which can be further applied to protein-protein inhibitor study as well as drug design. This manuscript starts with the property analysis of typical protein secondary structures, followed by the introduction of current peptide secondary structure mimics. These foldamers are divided into three main groups, and the design principles as well as the structural diversity of oligo/poly-amide based peptide secondary structure mimics are emphasized. Additionally, the draft provides several visualizable nomenclature, including χ-peptides, ζ/ξ-peptides, and ζ-ξ-peptides.

Contents
1 Introduction
2 Analysis on the peptide secondary structures
2.1 α-helix
2.2 β-strain/sheet
2.3 Turns
3 Oligo/poly-amide based peptide secondary structure mimics
3.1 β-peptide & its analogs
3.2 γ-peptide & its analogs
3.3 χ-peptides
3.4 ζ/ξ-peptides
3.5 ζ-ξ-peptides
3.6 Peptoids
3.7 Other unnatural oligo/poly-amides
4 Helix mimics based on the stick structures
5 Turn mimics based on the introduction of non-natural structures
6 Conclusion

中图分类号: 

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[1] Rual J F, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz G F, Gibbons F D, Dreze M, Ayivi-Guedehoussou N. Nature,2005, 437:1173.
[2] Ou H D, May A P, O' Shea C C. Wiley Interdisciplinary Reviews:Systems Biology and Medicine,2011, 3:48.
[3] Chang H N, Liu B Y, Qi Y K, Zhou Y, Chen Y P, Pan K M, Li W W, Zhou X M, Ma W W, Fu C Y, Liu L. Angew. Chem. Int. Ed., 2015, 127:11926.
[4] Conte L L, Chothia C, Janin J. J. Mol. Biol.,1999, 285:2177.
[5] Wells J A, McClendon C L. Nature,2007, 450:1001.
[6] Arkin M R, Wells J A. Nat. Rev. Drug Discov.,2004, 3:301.
[7] Luque I, Freire E. Proteins:Structure, Function, and Bioinformatics,2000, 41:63.
[8] Sundberg E J, Mariuzza R A. Structure,2000, 8:137.
[9] Egrie J C, Browne J K. Nephrology Dialysis Transplantation,2001, 16:3.
[10] Teague S J. Nat. Rev. Drug Discov.,2003, 2:527.
[11] Kochendoerfer G G, Chen S Y, Mao F, Cressman S, Traviglia S, Shao H, Hunter C L, Low D W, Cagle E N, Carnevali M. Science,2003, 299:884.
[12] Liu L, Guo Q X. Chem. Rev.,2001, 101:673.
[13] Walensky L D, Kung A L, Escher I, Malia T J, Barbuto S, Wright R D, Wagner G, Verdine G L, Korsmeyer S J. Science,2004, 305:1466.
[14] Cui H K, Guo Y, He Y, Wang F L, Chang H N, Wang Y J, Wu F M, Tian C L, Liu L. Angew. Chem. Int. Ed.,2013, 52:9558.
[15] Walensky L D, Bird G H. J. Med. Chem., 2014, 57:6275.
[16] Verdine G L, Hilinski G J. Drug Discov. Today:Technologies,2012, 9:41.
[17] Khakshoor O, Nowick J S. Org. Lett.,2009, 11:3000.
[18] Clackson T, Wells J A. Science,1995, 267:383.
[19] Bogan A A, Thorn K S. J. Mol. Biol.,1998, 280:1.
[20] Robinson J A. Curr. Opin. Chem. Biol.,2011, 15:379.
[21] Wang L, Xie J, Schultz P G. Annu. Rev. Biophys. Biomol. Struct.,2006, 35:225.
[22] Wang Z A, Ding X, Tian C, Zheng J S. RSC Adv., 2016, 6:61599.
[23] Sun T, Lin F H, Campbell R L, Allingham J S, Davies P L. Science,2014, 343:795.
[24] Azzarito V, Long K, Murphy N S, Wilson A J. Nature Chemistry,2013, 5:161.
[25] Ou H D, May A P, O' Shea C C. Wiley Interdisciplinary Reviews:Systems Biology and Medicine,2011, 3:48.
[26] Moebius U, Clayton L K, Abraham S, Diener A, Yunis J J, Harrison S C, Reinherz E L. Proc. Natl. Acad. Sci. U. S. A.,1992, 89:12008.
[27] Somers W S, Phillips S E V. Nature,1992, 359:387.
[28] Mattson M P. Nature,2004, 430:631.
[29] Rufo C M, Moroz Y S, Moroz O V, St hr J, Smith T A, Hu X, de Grado W F, Korendovych I V. Nat. Chem.,2014, 6:303.
[30] Rose G D, Gierasch L M, Smith J A. Adv. Protein Chem.,1985, 37:1.
[31] Stigers K D, Soth M J, Nowick J S. Curr. Opin. Chem. Biol.,1999, 3:714.
[32] Toniolo C. Crc. Cr. Rev. Bioch. Mol.,1980, 9:1.
[33] Chou K C. Anal. Biochem.,2000, 286:1.
[34] Venkatachalam C. Biopolymers,1968, 6:1425.
[35] Richardson J. Adv. Protein Chem.,1981, 34:167.
[36] Burgess K. Acc. Chem. Res.,2001, 34:826.
[37] Li L, Zhong W, Zacharias N, Gibbs C, Lester H A, Dougherty D A. Chem. Biol.,2001, 8:47.
[38] Steer D L, Lew R A, Perlmutter P, Smith A, Aguilar M I. Curr. Med. Chem.,2002, 9:811.
[39] Seebach D, Ciceri P E, Overhand M, Jaun B, Rigo D, Oberer L, Hommel U, Amstutz R, Widmer H. Helv. Chim. Acta.,1996, 79:2043.
[40] Appella D H, Christianson L A, Karle I L, Powell D R, Gellman S H. J. Am. Chem. Soc.,1996, 118:13071.
[41] Appella D H, Christianson L A, Karle I L, Powell D R, Gellman S H. J. Am. Chem. Soc.,1999, 121:6206.
[42] Li X, Wu Y D, Yang D. Acc. Chem. Res.,2008, 41:1428.
[43] Yang D, Qu J, Li B, Ng F F, Wang X C, Cheung K K, Wang D P, Wu Y D. J. Am. Chem. Soc.,1999, 121:589.
[44] 王志鹏(Wang Z P), 冯天师(Feng T S), 崔丽嘉(Cui L J),石玉洁(Shi Y J), 沙耀武(Sha Y W).中国科学:生命科学(Scientia Sinica Vitae), 2013, 43(9):778.
[45] de Bont D, Moree W J, Liskamp R M J. Bioorg. Med. Chem.,1996, 4:667.
[46] Cheng R P, Gellman S H, DeGrado W F. Chem. Rev.,2001, 101:3219.
[47] Sharma G V M, Manohar V, Dutta S K, Subash V, Kunwar A C. J. Org. Chem.,2008, 73:3689.
[48] Seebach D, Beck A K, Bierbaum D J. Chem. Biodivers., 2004, 1:1111.
[49] Hanessian S, Luo X, Schaum R, Michnick S. J. Am. Chem. Soc.,1998, 120:8569.
[50] Hanessian S, Luo X H, Schaum R. Tetrahedron Lett.,1999, 40:4925.
[51] Hintermann T, Gademann K, Jaun B, Seebach D. Helv. Chim. Acta.,1998, 81:983.
[52] Woll M G, Lai J R, Guzei I A, Taylor S J C, Smith M E B, Gellman S H. J. Am. Chem. Soc.,2001, 123:11077.
[53] Hanessian S, Luo X H, Schaum R. Tetrahedron Lett.,1999, 40:4925.
[54] Gennari C, Salom B, Potenza D, Williams A. Angew. Chem. Int. Ed.,1994, 33:2067.
[55] Gennari C, Salom B, Potenza D, Longari C, Fioravanzo E, Carugo O, Sardone N. Chem.-Eur. J.,1996, 2:644.
[56] Gellman S H. Acc. Chem. Res., 1998, 31:173.
[57] Volchkova V A, Klenk H D, Volchkov V E. Virology, 1999, 265:164.
[58] Baldauf C, Günther R, Hofmann H J. J. Org. Chem., 2004, 69:6214.
[59] Arndt H D, Ziemer B, Koert U. Org. Lett., 2004, 6:3269.
[60] Roy R S, Gopi H N, Raghothama S, Karle I L, Balaram P. Chem.-Eur. J., 2006, 12:3295.
[61] van der Want G, Peters H, Inklaar P. Recueil des Travaux Chimiques des Pays-Bas, 1952, 71:1221.
[62] Huang D, Korolev N, Eom K D, Tam J P, Nordenski ld L. Biomacromolecules, 2007, 9:321.
[63] Zhao X, Jia M X, Jiang X K, Wu L Z, Li Z T, Chen G J. J. Org. Chem., 2004, 69:270.
[64] Roviello G N, Di Gaetano S, Capasso D, Franco S, Crescenzo C, Bucci E M, Pedone C. J. Med. Chem., 2011, 54:2095.
[65] Yan J, Korolev N, Eom K D, Tam J P, Nordenski ld L. Biomacromolecules, 2011, 13:124.
[66] Cooper H J, Hudgins R R, Marshall A G. Int. J. Mass Spectrom., 2004, 234:23.
[67] Schramm P, Sharma G V, Hofmann H J. J. Pept. Sci., 2010, 94:279.
[68] Schramm P, Hofmann H J. J. Mol. Struc. THEOCHEM, 2009, 907:109.
[69] Guo L, Almeida A M, Zhang W, Reidenbach A G, Choi S H, Guzei I A, Gellman S H. J. Am. Chem. Soc., 2010, 132:7868.
[70] Brea R J, Castedo L, Granja J R, Herranz M Á, Sánchez L, Martín N, Seitz W, Guldi D M. Proc. Natl. Acad. Sci. U. S. A., 2007, 104:5291.
[71] Pilsl L K, Reiser O. Amino Acids, 2011, 41:709.
[72] Cheloha R W, Maeda A, Dean T, Gardella T J, Gellman S H. Nat. Biotechnol., 2014, 32:653.
[73] Vasudev P G, Chatterjee S, Shamala N, Balaram P. Chem. Rev., 2010, 111:657.
[74] Sawada T, Gellman S H. J. Am. Chem. Soc., 2011, 133:7336.
[75] 梁妍钰(Liang Y Y),唐姗(Tang S),郑基深(Zheng J S). 化学进展(Progress in Chemistry), 2014, 26(11):1793.
[76] Kawakami T, Ishizawa T, Murakami H. J. Am. Chem. Soc., 2013, 135:12297.
[77] Machetti F, Ferrali A, Menchi G, Occhiato E G, Guarna A. Org. Lett.,2000, 2:3987.
[78] Lummis S C R, Beene D L, Lee L W, Lester H A, Broadhurst R W, Dougherty D A. Nature,2005, 438:248.
[79] Hanessian S, Auzzas L. Acc. Chem. Res.,2008, 41:1241.
[80] Hosoya M, Otani Y, Kawahata M, Yamaguchi K, Ohwada T. J. Am. Chem. Soc., 2010, 132:14780.
[81] Zuckermann R N, Kerr J M, Kent S B H, Moos W H. J. Am. Chem. Soc.,1992, 114:10646.
[82] Simon R J, Kania R S, Zuckermann R N, Huebner V D, Jewell D A, Banville S, Ng S, Wang L, Rosenberg S, Marlowe C K, Spellmeyer D C, Tan R Y, Frankel A D, Santi D V, Cohen F E, Bartlett P A. Proc. Natl. Acad. Sci. U. S. A.,1992, 89:9367.
[83] Miller S M, Simon R J, Ng S, Zuckermann R N, Kerr J M, Moos W H. Drug Develop Res.,1995, 35:20.
[84] Sanborn T J, Wu C W, Zuckerman R N, Barron A E. Biopolymers,2002, 63:12.
[85] Wu C W, Sanborn T J, Zuckermann R N, Barron A E. J. Am. Chem. Soc.,2001, 123:2958.
[86] Wu C W, Kirshenbaum K, Sanborn T J, Patch J A, Huang K, Dill K A, Zuckermann R N, Barron A E. J. Am. Chem. Soc.,2003, 125:13525.
[87] Shin S B Y, Yoo B, Todaro L, Kirshenbaum K. Biopolymers,2007, 88:636.
[88] Hamper B C, Kolodziej S A, Scates A M, Smith R G, Cortez E. J. Org. Chem.,1998, 63:708.
[89] Roy O, Faure S, Thery V, Didierjean C, Taillefumier C. Org. Lett.,2008, 10:921.
[90] Olsen C A. Biopolymers,2011, 96:561.
[91] Zuckermann R N, Martin E J, Spellmeyer D C, Stauber G B, Shoemaker K R, Kerr J M, Figliozzi G M, Goff D A, Siani M A. J. Med. Chem., 1994, 37:2678.
[92] Udugamasooriya D G, Dineen S P, Brekken R A, Kodadek T. J. Am. Chem. Soc., 2008, 130:5744.
[93] Yaroslavov A A, Kuchenkova O Y, Okuneva I B, Melik-Nubarov N S, Kozlova N O, Lobyshev V I, Menger F M, Kabanov V A. Biochim. Biophys. Acta. Biomembr.,2003, 1611:44.
[94] Kramer J R, Deming T J. J. Am. Chem. Soc.,2014, 136:5547.
[95] Reichelt A, Martin S F. Acc. Chem. Res.,2006, 39:433.
[96] Szabo L, Smith B L, McReynolds K D, Parrill A L, Morris E R, Gervay J. J. Org. Chem.,1998, 63:1074.
[97] Smith M, Claridge T W, Fleet G J, Tranter G, Sansom M P. Chem. Comm.,1998:2041.
[98] Ilin S, Schl nvogt I, Ebert M O, Jaun B, Schwalbe H. ChemBioChem.,2002, 3:93.
[99] Roviello G N, Musumeci D, Castiglione M, Bucci E M, Pedone C, Benedetti E. J. Pept. Sci.,2009, 15:155.
[100] Karig G, Fuchs A, Buesing A, Brandstetter T, Scherer S, Bats J W, Eschenmoser A, Quinkert G. Helvetica Chimica Acta,2000, 83:1049.
[101] Fletcher M D, Campbell M M. Chem. Rev.,1998, 98:763.
[102] Hou J L, Shao X B, Chen G J, Zhou Y X, Jiang X K, Li Z T. J. Am. Chem. Soc.,2004, 126:12386.
[103] Lelais G, Seebach D. Helv. Chim. Acta.,2003, 86:4152.
[104] Lee H J, Song J W, Choi Y S, Park H M, Lee K B. J. Am. Chem. Soc.,2002, 124:11881.
[105] Dyker H, Scherkenbeck J, Gondol D, Goehrt A, Harder A. J. Org. Chem.,2001, 66:3760.
[106] Avan I, Hall C D, Katritzky A R. Chem. Soc. Rev.,2014, 43:3575.
[107] Ernst J T, Becerril J, Park H S, Yin H, Hamilton A D. Angew. Chem. Int. Ed.,2003, 115:553.
[108] Becerril J, Hamilton A D. Angew. Chem. Int. Ed.,2007, 119:4555.
[109] Rodriguez J M, Hamilton A D. Tetrahedron Lett.,2006, 47:7443.
[110] Dewal M B, Firestine S M. Curr. Med. Chem.,2011, 18:2420.
[111] Zheng J S, Tang S, Qi Y K, Wang Z P, Liu L. Nat. Protoc.,2013, 8:2483.
[112] Chen X, Tang S, Zheng J S, Zhao R, Wang Z P, Shao W, Chang H N, Cheng J Y, Zhao H, Liu L. Nat. Comm., 2015, 6:1.
[113] Zheng J S, Yu M, Qi Y K, Tang S, Shen F, Wang Z P, Xiao L, Zhang L, Tian C L, Liu L. J. Am. Chem. Soc.,2014, 136:3695.
[114] McGinty R K, Kohn M, Chatterjee C, Chiang K P, Pratt M R, Muir T W. ACS Chem. Biol.,2009, 4:958.
[115] Liu C C, Schultz P G. Annu. Rev. Biochem.,2010, 79:413.
[116] Chitnumsub P, Fiori W R, Lashuel H A, Diaz H, Kelly J W. Bioorg. Med. Chem.,1999, 7:39.
[117] Tsang K Y, Diaz H, Graciani N, Kelly J W. J. Am. Chem. Soc.,1994, 116:3988.
[118] Ranganathan D, Haridas V, Kurur S, Thomas A, Madhusudanan K P, Nagaraj R, Kunwar A C, Sarma A V S, Karle I L. J. Am. Chem. Soc.,1998, 120:8448.
[119] Jones I G, Jones W, North M. J. Org. Chem.,1998, 63:1505.
[120] Soth M J, Nowick J S. J. Org. Chem.,1999, 64:276.
[121] Nowick J S, Brower J O. J. Am. Chem. Soc.,2003, 125:876.
[122] 卢雁(Lu Y),李向荣(Li X R). 化学进展(Progress in Chemistry), 2005, 17(5):905.
[123] 王志鹏(Wang Z P),袁金颖(Yuan J Y). 化学进展(Progress in Chemistry), 2012, 24(12):2342.
[124] 王志鹏(Wang Z P), 邓耿(Deng G), 席婵娟(Xi C J). 科学通报(Chinese Science Bulletin), 2015, 60:3099.
[125] Wang Z P, Ding X, Wang J, Li Y. RSC Advances, 2015, 5:28258.
[126] 任锦(Ren J), 钦传光(Qin C G), 徐春兰(Xu C L), 王秋雨(Wang Q Y), 左晓佳(Zuo X J). 药学学报(Acta Pharmaceutica Sinica), 2010, 45:17.
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