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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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Velázquez-Libera JL, Caballero J, Tuñón I, Hernández-Rodríguez EW, Ruiz-Pernía JJ. On the Nature of the Enzyme–Substrate Complex and the Reaction Mechanism in Human Arginase I. A Combined Molecular Dynamics and QM/MM Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Velázquez-Libera
- Doctorado en Ciencias Aplicadas, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - Erix W. Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca 3460000, Chile
| | - J. Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
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Saito T, Kawakami T, Yamanaka S, Okumura M. QM/MM study of hydrolysis of arginine catalysed by arginase. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1078506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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