Mudedla Sathish Kumar, Ghosh Boyli, Dhoke Gaurao V, Oh SeKyu, Wu Sangwook
PharmCADD, R&D Center, 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea.
PharmCADD, R&D Center, Workfella Business Center, Floor 5, Western Aqua Kondapur Village, Hyderabad, Telangana 500081, India.
ACS Omega. 2022 Aug 30;7(36):32536-32548. doi: 10.1021/acsomega.2c04116. eCollection 2022 Sep 13.
Human arginase I (HARGI) is a metalloprotein highly expressed in the liver cytosol and catalyzes the hydrolysis of l-arginine to form l-ornithine and urea. Understanding the reaction mechanism would be highly helpful to design new inhibitor molecules for HARGI as it is a target for heart- and blood-related diseases. In this study, we explored the hydrolysis reaction mechanism of HARGI with antiferromagnetic and ferromagnetic coupling between two Mn(II) ions at the catalytic site by employing molecular dynamics simulations coupled with quantum mechanics and molecular mechanics (QM/MM). The spin states, high-spin ferromagnetic couple ( = 5/2, = 5/2), low-spin ferromagnetic couple ( = 1/2, = 1/2), high-spin antiferromagnetic couple ( = 5/2, = -5/2), and low-spin antiferromagnetic couple ( = 1/2, = -1/2) are considered, and the calculated energetics for the complex of the substrate and HARGI are compared. The results show that the high-spin antiferromagnetic couple ( = 5/2, = -5/2) is more stable than other spin states. The low-spin ferromagnetic and antiferromagnetic coupled states are highly unstable compared with the corresponding high-spin states. The high-spin antiferromagnetic couple ( = 5/2, = -5/2) is stabilized by 0.39 kcal/mol compared with the ferromagnetic couple ( = 5/2, = 5/2). The reaction mechanism is independent of spin states; however, the energetics of transition states and intermediates are more stable in the case of the high-spin antiferromagnetic couple ( = 5/2, = -5/2) than the corresponding ferromagnetic state. It is evident that the calculated coupling constants are higher for antiferromagnetic states and, interestingly, superexchange coupling is found to occur between Mn(II) ions via hydroxide ions in a reactant. The hydroxide ion enhances the coupling interaction and initiates the catalytic reaction. It is also noted that the first intermediate structure where there is no superexchange coupling is similar to the known inhibitor 2()-amino-6-boronohexanoic acid.
人精氨酸酶I（HARGI）是一种在肝细胞溶质中高度表达的金属蛋白，催化L-精氨酸水解生成L-鸟氨酸和尿素。了解其反应机制对于设计针对HARGI的新型抑制剂分子非常有帮助，因为它是心脏和血液相关疾病的一个靶点。在本研究中，我们通过结合量子力学和分子力学的分子动力学模拟（QM/MM），探索了HARGI在催化位点两个Mn（II）离子之间具有反铁磁和铁磁耦合的水解反应机制。考虑了自旋态，即高自旋铁磁耦合（S1 = 5/2，S2 = 5/2）、低自旋铁磁耦合（S1 = 1/2，S2 = 1/2）、高自旋反铁磁耦合（S1 = 5/2，S2 = -5/2）和低自旋反铁磁耦合（S1 = 1/2，S2 = -1/2），并比较了底物与HARGI复合物的计算能量。结果表明，高自旋反铁磁耦合（S1 = 5/2，S2 = -5/2）比其他自旋态更稳定。与相应的高自旋态相比，低自旋铁磁和反铁磁耦合态非常不稳定。与铁磁耦合（S1 = 5/2，S2 = 5/2）相比，高自旋反铁磁耦合（S1 = 5/2，S2 = -5/2）稳定了0.39 kcal/mol。反应机制与自旋态无关；然而，在高自旋反铁磁耦合（S1 = 5/2，S2 = -5/2）的情况下，过渡态和中间体的能量比相应的铁磁态更稳定。很明显，反铁磁态的计算耦合常数更高，有趣的是，发现Mn（II）离子之间通过反应物中的氢氧根离子发生超交换耦合。氢氧根离子增强了耦合相互作用并引发了催化反应。还注意到没有超交换耦合的第一个中间体结构与已知抑制剂2-（S）-氨基-6-硼己酸相似。
