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Mudedla S, Ghosh B, Dhoke GV, Oh S, Wu S. QM/MM Simulations for the Broken-Symmetry Catalytic Reaction Mechanism of Human Arginase I. ACS OMEGA 2022; 7:32536-32548. [PMID: 36119997 PMCID: PMC9475637 DOI: 10.1021/acsomega.2c04116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
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.
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Affiliation(s)
- Sathish
Kumar Mudedla
- PharmCADD, R&D Center, 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea
| | - Boyli Ghosh
- PharmCADD, R&D Center, Workfella Business Center, Floor
5, Western Aqua Kondapur Village, Hyderabad, Telangana 500081, India
| | - Gaurao V. Dhoke
- PharmCADD, R&D Center, Workfella Business Center, Floor
5, Western Aqua Kondapur Village, Hyderabad, Telangana 500081, India
| | - SeKyu Oh
- KYNOGEN
Co., Suwon 16229, Republic of Korea
| | - Sangwook Wu
- PharmCADD, R&D Center, 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea
- Department
of Physics, Pukyong National University, Busan 48513, Republic of Korea
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Maruyama T, Ohnari J, Tada K, Hinuma Y, Kawakami T, Yamanaka S, Okumura M. Extension of the Linear Response Function of Electron Density to a Plane-wave Basis and the First Application to Periodic Surface Systems. CHEM LETT 2021. [DOI: 10.1246/cl.210375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Maruyama
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jinta Ohnari
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kohei Tada
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoyo Hinuma
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Center for Quantum Information and Quantum Biology, Osaka University, 1-2 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, 1-30 Goryo Ohara, Nishikyo, Kyoto 615-8245, Japan
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