过渡态类似物

过渡态类似物为在酵素催化反应中，和基质分子的过渡状态有相似化学结构的化合物。^[1] 理论显示酵素抑制剂像过渡态的结构。^[2]过渡态类似物可借由键结于酵素活化位，作为酵素反应的酵素抑制剂。像是药物就是过渡态的类似物抑制剂，包含流感药物，像是神经胺酸酶抑制剂，奥司他韦；蛋白酶抑制剂，沙奎那韦。

过渡状态

过渡状态的结构可以透过统计力学描述，统计力学是在描述键的打断或形成，使过渡状态回到反应物，或是变成产物。在酵素催化反应中，当酵素可以稳定高能的过渡状态中间物时，反应的活化能会很低。过渡态类似物模仿这些高能的中间物，但是没有走这些催化反应，且会比基质和产物的类似物和酵素键结的更紧。

设计过渡状态类似物

要设计过渡状态类似物，其关键步骤为决定和酵素作用下，基质的过渡状态结构。像是，动力学同位素效应。此外，其过渡态类似物的结构，也可以透过类似和动力学的同位素互补的计算方法预测出来。以下两个简单的方法介绍。

动力学同位素效应

动力学同位素效应就是，利用同位素标志反应物，取代自然基质和反应物的键结。动力学同位素效应的值为turnover number和所有反应步骤的比例。^[3] 固有的动力学同位素效应的值来自于，原子在过渡状态和基态之间的键的震动环境的不同。^[3]透过动力学同位素效应的角度，可以了解酵素催化反应的过渡态，且也可以用来发展过渡的类似物。

电脑模拟器

电脑模拟器被视为可以表示出酵素行为机制最有用的工具。^[4]分子力学本身无法预测电子转移；电子转移为有机反应的基础，但是分子力学可以模拟在酵素催化反应时蛋白质分子的多变性提供了足够的讯息。互补的方法，结合了分子力学和量子力学模拟的方法。^[5]根据这个办法，只有酵素催化反应的原子用于量子力学中，而剩下的原子，则用于分子力学中。^[6]

设计过渡状态类似物例子

在利用KIE或是电脑模拟器决定过渡态的结构后，抑制剂就可以根据过渡态的结构以及中间产物设计出来。接下来的例子说明，抑制剂如何借由改变官能基所对应的过渡态的几何结构和电子分布，模仿过渡态的结构。

甲硫核苷酶抑制剂

甲硫核苷酶为一种酵素，可以催化5'-methylthioadenosine 和S-adenosylhomocysteine的水解脱腺苷酸化的反应。甲硫核苷酶也被视为抗细菌药物发现的目标，因为甲硫核苷酶对于细菌代谢系统是非常重要的，且也只有细菌会产生。^[7]视腺嘌呤的氮和核糖的碳距离不同，过渡态的结构可借由早期或晚期的解离程度决定。根据找到不同的过渡态结构，Schramm和他的同事设计了两个过渡态类似物，模仿早期即晚期的解离过渡态。早期即晚期的解离过渡态展现了个别的解离常数，约在360~140pM。^[8]

嗜热菌蛋白酶抑制剂

嗜热菌为一种酵素，可以水解由芽孢杆菌属所产生的疏水性氨基酸，所含有的肽酰胺键。^[9]因此，他也是一种设计抗菌的目标媒介。这个酵素反应的机制，从小的多肽分子取代水分子的锌键结朝向嗜热菌的Glu143。水分子可被锌离子和Glu143活化，攻击四面体过渡态的羰基碳。Holden和他的伙伴，就开始设计模仿一系列的磷酸酰胺化肽类似物。在这些合成的类似物中，R = L-Leu为具有最有效的抑制剂活性(Ki = 9.1 nM)。^[10]

精氨酸酶抑制剂

精氨酸酶是一种有双核的锰金属蛋白，可以催化水解L型的精胺酸到L型的鸟胺酸以及尿素。他也被视为治疗哮喘的药物标靶。^[11]这个水解左旋精胺酸的机制是借由水分子的亲和攻击，而形成一四面体过渡态。研究显示，硼酸的部分采用四面体结构，作为一种抑制剂。此外，磺酰胺官能基，也可以模仿过渡态的结构。^[12]硼酸模仿过渡态类似物抑制剂，是借由X光照射人类精胺酸所产生的金体结构所证明。^[13]

参见

酵素
结构类似, 化合物具有相似的结构。
酵素抑制剂
基质类似
自杀抑制剂

参考资料

[1]
Silverman, Richard B. The Organic Chemistry of Drug Design and Drug Action. San Diego, CA: Elsevier Academic Press. 2004. ISBN 0-12-643732-7.
[2]
Copeland, R.A.; Davis, J.P.; Cain, G.A.; Pitts, W.J.; Magolda, R.L. The Immunosuppressive Metabolite of Leflunomide is a Potent Inhibitor of Human Dihydroorotate Dehydrogenase. Biochemistry. 1996, 35 (4): 1270. doi:10.1021/bi952168g.
[3]
Schramm, Vern L>. Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes. Annu. Rev. Biochem. 2011, 80: 703–732. PMID 21675920. doi:10.1146/annurev-biochem-061809-100742.
[4]
Peter, Kollman; Kuhn, B. & Peräkylä, M. Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?. J. Phys. Chem. B. 2002, 106 (7): 1537–1542. doi:10.1021/jp012017p.
[5]
Hou, G; Hou, G. & Cui, Q. QM/MM Analysis Suggests that Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily. J. Am. Chem. Soc. 2011, 134 (1): 229–246. doi:10.1021/ja205226d.
[6]
Schwartz, S; Saen-oon, S.; Quaytman-Machleder, S.; Schramm, V. L. & Schwartz, S. D. Atomic Detail of Chemical Transformation at the Transition State of an Enzymatic Reaction. PNAS. 2008, 105 (43): 16543–16545. Bibcode:2008PNAS..10516543S. doi:10.1073/pnas.0808413105.
[7]
Singh, Vipender; Singh V, Lee JE, Núñez S, Howell PL, Schramm VL. Transition state structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli and its similarity to transition state analogues. Biochemistry. 2005, 44 (35): 11647–11659. PMID 16128565. doi:10.1021/bi050863a.
[8]
Guitierrez, Jemy; Luo, M., Singh, V., Li, L., Brown, R. L., Norris, G. E. Picomolar Inhibitors as Transition-State Probes of 5′-Methylthioadenosine Nucleosidases. ACS chemical biology. 2007, 2 (11): 725–734. PMID 18030989. doi:10.1021/cb700166z.
[9]
S, Endo. Studies on protease produced by thermophilic bacteria. J. Ferment. Technol. 1962, 40: 346–353.
[10]
Holden, Hazel; Tronrud, D. E., Monzingo, A. F., & Weaver, L. H. Slow-and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphoramidate transition-state analogs. Biochemistry. 1987, 26 (26): 8542–8553. doi:10.1021/bi00400a008.
[11]
Maarsingh, Harm; Johan Zaagsma, Herman Meurs. Arginase: a key enzyme in the pathophysiology of allergic asthma opening novel therapeutic perspectives. Br J Pharmacol. October 2009, 158 (3): 652–664. PMC 2765587 . doi:10.1111/j.1476-5381.2009.00374.x.
[12]
E, Cama; Shin H, Christianson DW. Design of amino acid sulfonamides as transition-state analogue inhibitors of arginase. J Am Chem Soc. 2003, 125 (43): 13052–7. doi:10.1021/ja036365b.
[13]
Shishova, Ekaterina; Luigi Di Costanzo, David E. Cane, and David W. Christianson. Probing the Specificity Determinants of Amino Acid Recognition by Arginase. Biochemistry. 2009, 48 (1): 121–131. doi:10.1021/bi801911v.

[1] [1]
Silverman, Richard B. The Organic Chemistry of Drug Design and Drug Action. San Diego, CA: Elsevier Academic Press. 2004. ISBN 0-12-643732-7.

[2] [2]
Copeland, R.A.; Davis, J.P.; Cain, G.A.; Pitts, W.J.; Magolda, R.L. The Immunosuppressive Metabolite of Leflunomide is a Potent Inhibitor of Human Dihydroorotate Dehydrogenase. Biochemistry. 1996, 35 (4): 1270. doi:10.1021/bi952168g.

[Schramm2011-3] [3]
Schramm, Vern L>. Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes. Annu. Rev. Biochem. 2011, 80: 703–732. PMID 21675920. doi:10.1146/annurev-biochem-061809-100742.

[4] [4]
Peter, Kollman; Kuhn, B. & Peräkylä, M. Computational Studies of Enzyme-Catalyzed Reactions: Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?. J. Phys. Chem. B. 2002, 106 (7): 1537–1542. doi:10.1021/jp012017p.

[5] [5]
Hou, G; Hou, G. & Cui, Q. QM/MM Analysis Suggests that Alkaline Phosphatase (AP) and Nucleotide Pyrophosphatase/Phosphodiesterase Slightly Tighten the Transition State for Phosphate Diester Hydrolysis Relative to Solution: Implication for Catalytic Promiscuity in the AP Superfamily. J. Am. Chem. Soc. 2011, 134 (1): 229–246. doi:10.1021/ja205226d.

[6] [6]
Schwartz, S; Saen-oon, S.; Quaytman-Machleder, S.; Schramm, V. L. & Schwartz, S. D. Atomic Detail of Chemical Transformation at the Transition State of an Enzymatic Reaction. PNAS. 2008, 105 (43): 16543–16545. Bibcode:2008PNAS..10516543S. doi:10.1073/pnas.0808413105.

[7] [7]
Singh, Vipender; Singh V, Lee JE, Núñez S, Howell PL, Schramm VL. Transition state structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli and its similarity to transition state analogues. Biochemistry. 2005, 44 (35): 11647–11659. PMID 16128565. doi:10.1021/bi050863a.

[8] [8]
Guitierrez, Jemy; Luo, M., Singh, V., Li, L., Brown, R. L., Norris, G. E. Picomolar Inhibitors as Transition-State Probes of 5′-Methylthioadenosine Nucleosidases. ACS chemical biology. 2007, 2 (11): 725–734. PMID 18030989. doi:10.1021/cb700166z.

[9] [9]
S, Endo. Studies on protease produced by thermophilic bacteria. J. Ferment. Technol. 1962, 40: 346–353.

[10] [10]
Holden, Hazel; Tronrud, D. E., Monzingo, A. F., & Weaver, L. H. Slow-and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphoramidate transition-state analogs. Biochemistry. 1987, 26 (26): 8542–8553. doi:10.1021/bi00400a008.

[11] [11]
Maarsingh, Harm; Johan Zaagsma, Herman Meurs. Arginase: a key enzyme in the pathophysiology of allergic asthma opening novel therapeutic perspectives. Br J Pharmacol. October 2009, 158 (3): 652–664. PMC 2765587 . doi:10.1111/j.1476-5381.2009.00374.x.

[12] [12]
E, Cama; Shin H, Christianson DW. Design of amino acid sulfonamides as transition-state analogue inhibitors of arginase. J Am Chem Soc. 2003, 125 (43): 13052–7. doi:10.1021/ja036365b.

[13] [13]
Shishova, Ekaterina; Luigi Di Costanzo, David E. Cane, and David W. Christianson. Probing the Specificity Determinants of Amino Acid Recognition by Arginase. Biochemistry. 2009, 48 (1): 121–131. doi:10.1021/bi801911v.

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