Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115.
Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115.
复制标题
OV 329和CPP-115灭活GABA氨基转移酶的全局动力学参数的理论和机制验证。
DOI：
10.1021/acschembio.0c00784
复制
发表时间：
2021-04-16
影响因子：
4
通讯作者：
Silverman RB
中科院分区：
文献类型：
--
作者：
Weerawarna PM;Moschitto MJ;Silverman RB
（（S）-3-氨基-（二氟亚甲基）环戊二烯-1-羧酸（OV 329）是最近发现的γ-氨基丁酸氨基转移酶（GABA-AT）的灭活剂，其灭活效率比其前身CPP-115高10倍，尽管OV 329中唯一的结构差异是内环双键。这两种化合物都是基于机制的酶灭活剂（MBEI），其通过相似的机制抑制GABA-AT。在这里，各种计算化学工具和实验方法的组合，包括量子力学（QM）计算，分子动力学模拟，进度曲线分析，和氘动力学同位素效应（KIE）实验，被用来全面研究GABA-AT的CPP-115和OV 329的失活机制，并解释其实验获得的全局动力学参数kinact和KI。我们的第一个关键发现是，失活机制的限速步骤是去质子化步骤，并且，根据QM计算和KIE实验，kinact准确地代表了给定机制的限速步骤的增强。其次，本研究表明，广泛使用的简单QM模型不能准确地代表几何标准，存在于酶的去质子化步骤。相比之下，QM集团模型成功地代表了基态不稳定和过渡态稳定，所揭示的自然键轨道分析。此外，根据进展曲线分析和观察到的结合同位素效应，两种灭活剂的全局推导KI值代表初始结合复合物的抑制剂常数（Kd），并表明灭活剂与底物的竞争。构型熵损失解释了失活剂之间KI值的差异。我们在这项工作中描述的方法可以用来确定的MBEI优化过程中给定的失活机制的全局导出的参数的有效性。
((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEI), which inactivate GABA-AT by a similar mechanism. Here, a combination of a variety of computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, and deuterium kinetic isotope effect (KIE) experiments, are utilized to comprehensively study the mechanism of inactivation of GABA-AT by CPP-115 and OV329 and account for their experimentally obtained global kinetic parameters kinact and KI. Our first key finding is that the rate-limiting step of the inactivation mechanism is the deprotonation step, and, according to QM calculations and the KIE experiments, kinact accurately represents the enhancement of the rate-limiting step for the given mechanism. Secondly, the present study shows that the widely-used simple QM models do not accurately represent the geometric criteria that are present in the enzyme for the deprotonation step. In contrast, QM cluster models successfully represent both the ground state destabilization and the transition state stabilization, as revealed by natural bond orbital analysis. Furthermore, the globally derived KI values for both of the inactivators represent the inhibitor constants for the initial binding complexes (Kd) and indicate the inactivator competition with the substrate according to progress curve analysis and the observed binding isotope effect. The configurational entropy loss accounts for the difference in KI values between the inactivators. The approach we describe in this work can be employed to determine the validity of globally-derived parameters in the process of MBEI optimization for given inactivation mechanisms.
登录
查看更多内容
影响因子：
2.2
作者：
Ghalami-Choobar, Bahram;Dezhampanah, Hamid;Ghiami-Shomami, Ali
通讯作者：
Ghiami-Shomami, Ali
影响因子：
5.8
作者：
Pronk, Sander;Pall, Szilard;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
15
作者：
Eiden, Carter G.;Maize, Kimberly M.;Aldrich, Courtney C.
通讯作者：
Aldrich, Courtney C.
DOI：
10.1007/978-1-61779-465-0_20
发表时间：
2012-01-01
期刊：
COMPUTATIONAL DRUG DISCOVERY AND DESIGN
影响因子：
--
作者：
Guitierrez-de-Teran, Hugo;Aqvist, Johan
通讯作者：
Aqvist, Johan
影响因子：
15
作者：
Juncosa JI;Takaya K;Le HV;Moschitto MJ;Weerawarna PM;Mascarenhas R;Liu D;Dewey SL;Silverman RB
通讯作者：
Silverman RB