New progress of protein crystallization and drug design

CHEN Wei-jing; ZHONG Wei-qing

doi:10.3969/j.issn.1006-0111.2012.02.001

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Article Navigation > Journal of Pharmaceutical Practice and Service > 2012 > 30(2): 81-85,136

CHEN Wei-jing, ZHONG Wei-qing. New progress of protein crystallization and drug design[J]. Journal of Pharmaceutical Practice and Service, 2012, 30(2): 81-85,136. doi: 10.3969/j.issn.1006-0111.2012.02.001

Citation:

CHEN Wei-jing, ZHONG Wei-qing. New progress of protein crystallization and drug design[J]. Journal of Pharmaceutical Practice and Service, 2012, 30(2): 81-85,136. doi: 10.3969/j.issn.1006-0111.2012.02.001

New progress of protein crystallization and drug design

doi: 10.3969/j.issn.1006-0111.2012.02.001

School of Pharmacy, Second Military Medical University, Shanghai 200433, China

Received Date: 2010-07-22
Rev Recd Date: 2011-07-11

Abstract

Protein was the foundation of all life, and its function was closely related to its three-dimensional structure. The structure information of proteins was crucial for the determination of drug targets and helped scientists to discover new drug targets according to the structure homology between the protein targets and drugs. Therefore, the availability of protein crystal, which was the basis for its structure information and the drug design, had become an important field in life science. The latest research progresses of protein crystallization technology and its application in the drug design were summarized in this review.
- protein,
- crystallization,
- target,
- drug design

References

[1]	Pastwa E,Somiari SB, Czyz M, et al. Proteomics in human cancer research[J]. Proteom Clin Appl, 2007, 1(1): 4.
[2]	Curcio E, Simone S, Gianluca DP. et al. Memabrane crystallization of lysozyme under forced solution flow[J]. J Membrane Sci, 2005, 257(1-2): 134.
[3]	Zhang XM, Wei KG, Ma RY, et al. Precipitants and additives for membrane crystallization of lysozyme[J]. Biotechnol J, 2006, 1(11): 1302.
[4]	Zhang XM, Zhang P, Ma RY, et al. The study of continuous membrane crystallization on lysozyme[J]. Desalination, 2008, 219(1-3):101.
[5]	庞鸿宇, 刘丽英, 马润宇, 等. 木瓜蛋白酶动态膜结晶的实验研究[J]. 膜科学与技术, 2010, 30(1): 30.
[6]	Xiao T, Takag J, Wang JH, et al. Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics[J]. Nature, 2004, 432(7013): 59.
[7]	李俊君, 陈强, 李刚, 等. 微流控技术应用于蛋白质结晶的研究[J]. 化学进展, 2009, 21(5): 1034.
[8]	马建华, 仓怀兴. 空间蛋白质晶体生长新技术[J]. 生物物理学报, 2009, 25(s1):: 314.
[9]	Koide S. Engineering of recombinant crystallization chaperones[J]. Curr Opin Struct Biol, 2009, 19(4): 449.
[10]	Day PW, Rasmussen SG, Parnot C, et al. A monoclonal antibody for G protein-coupled receptor crystallography[J]. Nat Methods, 2007, 4(11): 927.
[11]	Rasmussen SG, Choi HJ, Rosenbaum DM, et al. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor[J]. Nature, 2007, 450(7168): 383.
[12]	Korotkov KV, Pardon E, Steyaert J, et al. Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody[J]. Structure, 2009, 17(2): 255.
[13]	Lam AY, Pardon E, Korotkov KV, et al. Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus[J]. J Struct Biol, 2009, 166(1): 8.
[14]	Uysal S, Vasquez V, Tereshko V, et al. The crystal structure of fulllength KcsA in its closed conformation[J]. Proc Natl Acad Sci USA, 2009, 106(16): 6644.
[15]	Sennhauser G, Grutter MG. Chaperone-assisted crystallography with DARPins[J]. Structure, 2008, 16(10): 1443.
[16]	Mio K, Maruyama Y, Ogura T, et al. Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules[J]. Progress Biophys Mol Biol, 2010, 103(1): 122.
[17]	Fujiyoshi Y. Structural physiology based on electron crystallography[J]. Protein Sci, 2011, 20(5): 806.
[18]	Bill RM, Henderson PJF, Iwata S, et al. Overcoming barriers to membrane protein structure determination[J]. Nat Biotech, 2011, 29(4): 335.
[19]	Leulliot N, Tresaugues L, Bremang M, et al. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics project: one size fits all[J]. Acta Crystallogr D, 2005, 61(6): 664.
[20]	Kambach C. Pipelines, robots, crystals and biology: What use high throughput solving structures of challenging targets[J]. Curr Protein Pept Sci, 2007, 8(2): 205.
[21]	Luft JR, Snell EH, DeTitta GT. Lessons from high-throughput protein crystallization screening: 10 years of practical experience[J]. Expert Opin Drug Discov, 2011, 6(5): 465.
[22]	Leach AR, Gillet VJ, Lewis RA, et al. Three-dimensional pharmacophore methods in drug discovery[J]. J Med Chem, 2010, 53(2): 539.
[23]	Scapin G. Structural biology and drug discovery[J]. Curr Pharm Des, 2006, 12(17): 2087.
[24]	Arinaminpathy Y, Khurana E, Engelman DM, et al. Computational analysis of membrane proteins: the largest class of drug targets[J]. Drug Discov Today, 2009, 14(23-24): 1130.
[25]	Grey J, Thompson D. Challenges and opportunities for new protein crystallization strategies in structure-based drug design[J]. Expert Opin Drug Discov, 2010, 5(11): 1039.
[26]	甘淋, 刘银坤. Stathm in蛋白:一个潜在的肿瘤标志物[J]. 肿瘤, 2010, 30(1): 73.
[27]	Tabernero L, Aricescu AR, Jones EY, et al. Protein tyrosine phosphatases: structure-function relationships[J]. FEBS J, 2008, 275(5): 867.
[28]	Chrysina ED, Chajistamatiou A, Chegkazi M. From structure-based to knowledge-based drug design through x-ray protein crystallography: sketching glycogen phosphorylase binding sites[J]. Curr Med Chem, 2011, 18(17): 2620.
[29]	Rosano C, Stec-Martyna E, Lappano R. Structure-based approach for the discovery of novel selective estrogen receptor modulators[J]. Curr Med Chem, 2011, 18(8): 1188.
[30]	Morrow JK, Lei DC, Lu C, et al. Recent development of anticancer therapeutics targeting Akt[J]. Rec Pat Anti-Cancer Drug Dis, 2011, 6(1): 146.
[31]	Munikumar RD, Dhanaji AT, Seon HS, et al. Structure based design of heat shock protein 90 inhibitors acting as anticancer agents[J]. Bioorg Med Chem, 2011,19(5): 1714.
[32]	Yuan YX, Pe JF, Lai LH. LigBuilder 2: A practical de novo drug design approach[J]. J Chem Inf Model, 2011, 51(5): 1083.
[33]	Bon RS, Zhong G, Anouk Stigter E, et al. Structure-guided development of selective rabggtase inhibitors[J]. Angew Chem Int Ed, 2011, 50(21): 4957.
[34]	Mai D, Jones J, Rodgers JW, et al. A Screen to Identify Small Molecule Inhibitors of Protein-Protein Interactions in Mycobacteria[J]. ASSAY Drug Dev Tech. 2011, 9(3):299.
[35]	Madabushi S, Yao H, Marsh M, et al. Structural clusters of evolutionary trace residues are statistically significant and common in proteins[J], J Mol Biol, 2002, 316(1): 139.
[36]	Song YL, Qi YP, Zhang WN, et al. Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily: Identification of novel antitumor drug binding site[J]. Sci China Ser C, 2005, 28(4): 375.
[37]	Sheng CQ, Dong GQ, Che XY, et al. Evolutionary trace analysis of CYP51 family: implication for site-directed mutagenesis and novel antifungal drug design[J]. J Mol Mod, 2010, 16(2): 279.

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通讯作者: 陈斌, [email protected]

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沈阳化工大学材料科学与工程学院沈阳 110142

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New progress of protein crystallization and drug design

School of Pharmacy, Second Military Medical University, Shanghai 200433, China

Received Date: 2010-07-22

Rev Recd Date: 2011-07-11

Key words:

protein /
crystallization /
target /
drug design

Abstract: Protein was the foundation of all life, and its function was closely related to its three-dimensional structure. The structure information of proteins was crucial for the determination of drug targets and helped scientists to discover new drug targets according to the structure homology between the protein targets and drugs. Therefore, the availability of protein crystal, which was the basis for its structure information and the drug design, had become an important field in life science. The latest research progresses of protein crystallization technology and its application in the drug design were summarized in this review.

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Reference (37)

[1]	Pastwa E,Somiari SB, Czyz M, et al. Proteomics in human cancer research[J]. Proteom Clin Appl, 2007, 1(1): 4.
[2]	Curcio E, Simone S, Gianluca DP. et al. Memabrane crystallization of lysozyme under forced solution flow[J]. J Membrane Sci, 2005, 257(1-2): 134.
[3]	Zhang XM, Wei KG, Ma RY, et al. Precipitants and additives for membrane crystallization of lysozyme[J]. Biotechnol J, 2006, 1(11): 1302.
[4]	Zhang XM, Zhang P, Ma RY, et al. The study of continuous membrane crystallization on lysozyme[J]. Desalination, 2008, 219(1-3):101.
[5]	庞鸿宇, 刘丽英, 马润宇, 等. 木瓜蛋白酶动态膜结晶的实验研究[J]. 膜科学与技术, 2010, 30(1): 30.
[6]	Xiao T, Takag J, Wang JH, et al. Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics[J]. Nature, 2004, 432(7013): 59.
[7]	李俊君, 陈强, 李刚, 等. 微流控技术应用于蛋白质结晶的研究[J]. 化学进展, 2009, 21(5): 1034.
[8]	马建华, 仓怀兴. 空间蛋白质晶体生长新技术[J]. 生物物理学报, 2009, 25(s1):: 314.
[9]	Koide S. Engineering of recombinant crystallization chaperones[J]. Curr Opin Struct Biol, 2009, 19(4): 449.
[10]	Day PW, Rasmussen SG, Parnot C, et al. A monoclonal antibody for G protein-coupled receptor crystallography[J]. Nat Methods, 2007, 4(11): 927.
[11]	Rasmussen SG, Choi HJ, Rosenbaum DM, et al. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor[J]. Nature, 2007, 450(7168): 383.
[12]	Korotkov KV, Pardon E, Steyaert J, et al. Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody[J]. Structure, 2009, 17(2): 255.
[13]	Lam AY, Pardon E, Korotkov KV, et al. Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus[J]. J Struct Biol, 2009, 166(1): 8.
[14]	Uysal S, Vasquez V, Tereshko V, et al. The crystal structure of fulllength KcsA in its closed conformation[J]. Proc Natl Acad Sci USA, 2009, 106(16): 6644.
[15]	Sennhauser G, Grutter MG. Chaperone-assisted crystallography with DARPins[J]. Structure, 2008, 16(10): 1443.
[16]	Mio K, Maruyama Y, Ogura T, et al. Single particle reconstruction of membrane proteins: A tool for understanding the 3D structure of disease-related macromolecules[J]. Progress Biophys Mol Biol, 2010, 103(1): 122.
[17]	Fujiyoshi Y. Structural physiology based on electron crystallography[J]. Protein Sci, 2011, 20(5): 806.
[18]	Bill RM, Henderson PJF, Iwata S, et al. Overcoming barriers to membrane protein structure determination[J]. Nat Biotech, 2011, 29(4): 335.
[19]	Leulliot N, Tresaugues L, Bremang M, et al. High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics project: one size fits all[J]. Acta Crystallogr D, 2005, 61(6): 664.
[20]	Kambach C. Pipelines, robots, crystals and biology: What use high throughput solving structures of challenging targets[J]. Curr Protein Pept Sci, 2007, 8(2): 205.
[21]	Luft JR, Snell EH, DeTitta GT. Lessons from high-throughput protein crystallization screening: 10 years of practical experience[J]. Expert Opin Drug Discov, 2011, 6(5): 465.
[22]	Leach AR, Gillet VJ, Lewis RA, et al. Three-dimensional pharmacophore methods in drug discovery[J]. J Med Chem, 2010, 53(2): 539.
[23]	Scapin G. Structural biology and drug discovery[J]. Curr Pharm Des, 2006, 12(17): 2087.
[24]	Arinaminpathy Y, Khurana E, Engelman DM, et al. Computational analysis of membrane proteins: the largest class of drug targets[J]. Drug Discov Today, 2009, 14(23-24): 1130.
[25]	Grey J, Thompson D. Challenges and opportunities for new protein crystallization strategies in structure-based drug design[J]. Expert Opin Drug Discov, 2010, 5(11): 1039.
[26]	甘淋, 刘银坤. Stathm in蛋白:一个潜在的肿瘤标志物[J]. 肿瘤, 2010, 30(1): 73.
[27]	Tabernero L, Aricescu AR, Jones EY, et al. Protein tyrosine phosphatases: structure-function relationships[J]. FEBS J, 2008, 275(5): 867.
[28]	Chrysina ED, Chajistamatiou A, Chegkazi M. From structure-based to knowledge-based drug design through x-ray protein crystallography: sketching glycogen phosphorylase binding sites[J]. Curr Med Chem, 2011, 18(17): 2620.
[29]	Rosano C, Stec-Martyna E, Lappano R. Structure-based approach for the discovery of novel selective estrogen receptor modulators[J]. Curr Med Chem, 2011, 18(8): 1188.
[30]	Morrow JK, Lei DC, Lu C, et al. Recent development of anticancer therapeutics targeting Akt[J]. Rec Pat Anti-Cancer Drug Dis, 2011, 6(1): 146.
[31]	Munikumar RD, Dhanaji AT, Seon HS, et al. Structure based design of heat shock protein 90 inhibitors acting as anticancer agents[J]. Bioorg Med Chem, 2011,19(5): 1714.
[32]	Yuan YX, Pe JF, Lai LH. LigBuilder 2: A practical de novo drug design approach[J]. J Chem Inf Model, 2011, 51(5): 1083.
[33]	Bon RS, Zhong G, Anouk Stigter E, et al. Structure-guided development of selective rabggtase inhibitors[J]. Angew Chem Int Ed, 2011, 50(21): 4957.
[34]	Mai D, Jones J, Rodgers JW, et al. A Screen to Identify Small Molecule Inhibitors of Protein-Protein Interactions in Mycobacteria[J]. ASSAY Drug Dev Tech. 2011, 9(3):299.
[35]	Madabushi S, Yao H, Marsh M, et al. Structural clusters of evolutionary trace residues are statistically significant and common in proteins[J], J Mol Biol, 2002, 316(1): 139.
[36]	Song YL, Qi YP, Zhang WN, et al. Evolutionary trace analysis of eukaryotic DNA topoisomerase I superfamily: Identification of novel antitumor drug binding site[J]. Sci China Ser C, 2005, 28(4): 375.
[37]	Sheng CQ, Dong GQ, Che XY, et al. Evolutionary trace analysis of CYP51 family: implication for site-directed mutagenesis and novel antifungal drug design[J]. J Mol Mod, 2010, 16(2): 279.

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New progress of protein crystallization and drug design

doi: 10.3969/j.issn.1006-0111.2012.02.001

Abstract

References

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通讯作者: 陈斌, [email protected]

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