QM/MM Simulations for the Broken-Symmetry Catalytic Reaction Mechanism of Human Arginase I

Sathish Kumar Mudedla; Boyli Ghosh; Gaurao V Dhoke; SeKyu Oh; Sangwook Wu

doi:10.1021/acsomega.2c04116

QM/MM Simulations for the Broken-Symmetry Catalytic Reaction Mechanism of Human Arginase I

ACS Omega. 2022 Aug 30;7(36):32536-32548. doi: 10.1021/acsomega.2c04116. eCollection 2022 Sep 13.

Authors

Sathish Kumar Mudedla¹, Boyli Ghosh², Gaurao V Dhoke², SeKyu Oh³, Sangwook Wu^{1

4}

Affiliations

¹ PharmCADD, R&D Center, 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea.
² PharmCADD, R&D Center, Workfella Business Center, Floor 5, Western Aqua Kondapur Village, Hyderabad, Telangana 500081, India.
³ KYNOGEN Co., Suwon 16229, Republic of Korea.
⁴ Department of Physics, Pukyong National University, Busan 48513, Republic of Korea.

Abstract

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 (S _Mn1 = 5/2, S _Mn2 = 5/2), low-spin ferromagnetic couple (S _Mn1 = 1/2, S _Mn2 = 1/2), high-spin antiferromagnetic couple (S _Mn1 = 5/2, S _Mn2 = -5/2), and low-spin antiferromagnetic couple (S _Mn1 = 1/2, S _Mn2 = -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 (S _Mn1 = 5/2, S _Mn2 = -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 (S _Mn1 = 5/2, S _Mn2 = -5/2) is stabilized by 0.39 kcal/mol compared with the ferromagnetic couple (S _Mn1 = 5/2, S _Mn2 = 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 (S _Mn1 = 5/2, S _Mn2 = -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(S)-amino-6-boronohexanoic acid.