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David R, Tuñón I, Laage D. Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J Am Chem Soc 2024; 146:14213-14224. [PMID: 38739765 DOI: 10.1021/jacs.4c03445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.
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Affiliation(s)
- Rolf David
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, 46100 Valencia, Spain
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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2
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Surukonti SR, Manabolu Surya SB, Katari NK, Yerla RR. Investigating Betrixaban Maleate drug degradation profiles, isolation and characterization of unknown degradation products by mass-triggered preparative HPLC, HRMS, and NMR. J Pharm Biomed Anal 2023; 235:115643. [PMID: 37633165 DOI: 10.1016/j.jpba.2023.115643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Betrixaban Maleate, a novel oral, once-daily factor Xa inhibitor drug substance, was subjected to stress testing under a wide range of degradation conditions, including acidic hydrolysis, alkaline hydrolysis, oxidative, thermal, and photolytic, to determine its inherent stability. The drug was biodegradable in acidic and alkaline environments, and three new degradation products were identified. Two degraded products are formed in an acidic environment, while the third is in alkaline conditions. The three degradants were identified using UPLC-ESI/MS and isolated using mass-triggered preparative HPLC, and their structures were unambiguously elucidated using HRMS and 2D NMR techniques. Based on spectral and chromatographic data, it was firmly proven that these distinct degradation products were the betrixaban chemical's hydrolysis components. The formation of the degradants has been hypothesized through several possible mechanisms.
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Affiliation(s)
- Srikanth Reddy Surukonti
- Department of Chemistry, GITAM School of Science, GITAM deemed to be University, Hyderabad, Telangana, 502 329, India
| | - Surendra Babu Manabolu Surya
- Department of Chemistry, GITAM School of Science, GITAM deemed to be University, Hyderabad, Telangana, 502 329, India.
| | - Naresh Kumar Katari
- Department of Chemistry, GITAM School of Science, GITAM deemed to be University, Hyderabad, Telangana, 502 329, India
| | - Rajender Reddy Yerla
- Department of Chemistry, GITAM School of Science, GITAM deemed to be University, Hyderabad, Telangana, 502 329, India
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3
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Tanaka H, Nakamoto M, Yoshida H. Computed ammonia affinity for evaluating Lewis acidity of organoboronates and organoboronamides. RSC Adv 2023; 13:2451-2457. [PMID: 36741141 PMCID: PMC9844674 DOI: 10.1039/d2ra07826k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Lewis acidity of organoboronates [B(pin), B(neop), B(cat), B(eg), B(nad)] and organoboronamides [B(dan), B(aam), B(mdan)] has been found to be unifiedly evaluated by computed ammonia affinity (AA), while other methods [LUMO energies, global electrophilicity index (GEI), fluoride ion affinity (FIA)] were only partially applicable. The relationships between the AA values and such structural characters including the B-X bond lengths, the X-B-X angles, and the changes in the B-X bond lengths in the formation of the ammonia adducts were also described.
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Affiliation(s)
- Hideya Tanaka
- Graduate School of Advanced Science and Engineering, Hiroshima UniversityHigashi-Hiroshima 739-8526Japan
| | - Masaaki Nakamoto
- Graduate School of Advanced Science and Engineering, Hiroshima UniversityHigashi-Hiroshima 739-8526Japan
| | - Hiroto Yoshida
- Graduate School of Advanced Science and Engineering, Hiroshima UniversityHigashi-Hiroshima 739-8526Japan
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4
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Cuesta SA, Rincón L, Torres FJ, Rodríguez V, Mora JR. A computational study of the reaction mechanism involved in the fast cleavage of an unconstrained amide bond assisted by an amine intramolecular nucleophilic attack. J Comput Chem 2021; 42:818-826. [PMID: 33590912 DOI: 10.1002/jcc.26501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/01/2020] [Accepted: 01/31/2021] [Indexed: 12/18/2022]
Abstract
In the present work, the fast amide bond cleavage of [3-((1R,5S,7s)-3-azabicyclo[3.3.1]nonane-7-carbonyl)-3-azabicyclo[3.3.1]nonane-7-carboxylic acid (bi-ATDO)], through an intramolecular nucleophilic attack of an amine group is evaluated. First, six possible peptide bond cleavage mechanisms, two of them including a water molecule, are described at the ωB97XD/6-311 + G(d,p)//MP2/6-311 + G(d,p) level of theory. The reaction consisting of an intramolecular nitrogen nucleophilic attack followed by a proton transfer and the amide bond cleavage is determined as the most favorable mechanism. The activation free energy computed for the latter is 20.5 kcal mol-1 , which agrees with the reported experimental result of 24.8 kcal mol-1 . Inclusion of a water molecule to assist the first step of the reaction results in an activation free energy increase of about 17 kcal mol-1 . All the steps in the most favorable mechanism are studied more in detail employing intrinsic reaction coordinate as well as the reaction force and reaction electronic flux analysis.
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Affiliation(s)
- Sebastián Adolfo Cuesta
- Grupo de Química computacional y teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Luis Rincón
- Grupo de Química computacional y teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - F Javier Torres
- Grupo de Química computacional y teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Vladimir Rodríguez
- Departamento de Matemática, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - José Ramón Mora
- Grupo de Química computacional y teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito, Ecuador
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5
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Li GB, Cheng JQ, Pan RK, Liu SG. Manganese(II) and cobalt(II) complexes based on pyridyl diimide: in situ ligand formation, crystal structures, and sorption properties. TRANSIT METAL CHEM 2016. [DOI: 10.1007/s11243-016-0095-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Phys Chem Chem Phys 2016; 18:24790-24801. [DOI: 10.1039/c6cp02097f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide hydrolysis has been involved in a wide range of biological, biotechnological, and industrial applications.
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Affiliation(s)
- Thomas J. Paul
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Arghya Barman
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Mehmet Ozbil
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | | | - Tingting Zhang
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Gaurav Sharma
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
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7
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Harper LK, Bayse CA. Modeling the chelation of As(III) in lewisite by dithiols using density functional theory and solvent-assisted proton exchange. J Inorg Biochem 2015; 153:60-67. [PMID: 26479948 DOI: 10.1016/j.jinorgbio.2015.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/10/2015] [Accepted: 10/05/2015] [Indexed: 11/29/2022]
Abstract
Dithiols such as British anti-lewisite (BAL, rac-2,3-dimercaptopropanol) are an important class of antidotes for the blister agent lewisite (trans-2-chlorovinyldichloroarsine) and, more generally, are chelating agents for arsenic and other toxic metals. The reaction of the vicinal thiols of BAL with lewisite through the chelation of the As(III) center has been modeled using density functional theory (DFT) and solvent-assisted proton exchange (SAPE), a microsolvation method that uses a network of water molecules to mimic the role of bulk solvent in models of aqueous phase chemical reactions. The small activation barriers for the stepwise SN2-type nucleophilic attack of BAL on lewisite (0.7-4.9kcal/mol) are consistent with the favorable leaving group properties of the chloride and the affinity of As(III) for soft sulfur nucleophiles. Small, but insignificant, differences in activation barriers were found for the initial attack of the primary versus secondary thiol of BAL and the R vs S enantiomer. An examination of the relative stability of various dithiol-lewisite complexes shows that ethanedithiols like BAL form the most favorable chelation complexes because the angles formed in five-membered ring are most consistent with the hybridization of As(III). More obtuse S-As-S angles are required for larger chelate rings, but internal As⋯N or As⋯O interactions can enhance the stability of moderate-sized rings. The low barriers for lewisite detoxification by BAL and the greater stability of the chelation complexes of small dithiols are consistent with the rapid reversal of toxicity demonstrated in previously reported animal models.
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Affiliation(s)
- Lenora K Harper
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, United States
| | - Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, United States.
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8
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Ivanova LV, Anton BJ, Timerghazin QK. On the possible biological relevance of HSNO isomers: a computational investigation. Phys Chem Chem Phys 2015; 16:8476-86. [PMID: 24667901 DOI: 10.1039/c4cp00469h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Thionitrous acid (HSNO), the smallest S-nitrosothiol, has been identified as a potential biologically active molecule that connects the biochemistries of two important gasotransmitters, nitric oxide (NO) and hydrogen sulfide (H2S). Here, we computationally explore possible isomerization reactions of HSNO that may occur under physiological conditions using high-level coupled-cluster as well as density functional theory and composite CBS-QB3 methodology calculations. Gas-phase calculations show that the formation of the tautomeric form HONS and the Y-isomer SN(H)O is thermodynamically feasible, as they are energetically close, within ∼6 kcal mol(-1), to HSNO, while the recently proposed three-membered ring isomer is not thermodynamically or kinetically accessible. The gas-phase intramolecular proton-transfer reactions required for HSNO isomerization into HONS and SN(H)O are predicted to have prohibitively high reaction barriers, 30-50 kcal mol(-1). However, the polar aqueous environment and water-assisted proton shuttle should decrease these barriers to ∼9 kcal mol(-1), which makes these two isomers kinetically accessible under physiological conditions. Our calculations also support the possibility of an aqueous reaction between the Y-isomer SN(H)O and H2S leading to biologically active nitroxyl HNO. These results suggest that the formation of HSNO in biological milieu can lead to various derivative species with their own, possibly biologically relevant, activity.
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Affiliation(s)
- Lena V Ivanova
- Department of Chemistry, Marquette University, P.O. Box 1881, Milwaukee, WI 53201-1881, USA.
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9
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Núñez-Villanueva D, Bonache MÁ, Lozano L, Infantes L, Elguero J, Alkorta I, García-López MT, González-Muñiz R, Martín-Martínez M. Experimental and theoretical studies on the rearrangement of 2-oxoazepane α,α-amino acids into 2'-oxopiperidine β(2,3,3) -amino acids: an example of intramolecular catalysis. Chemistry 2015; 21:2489-500. [PMID: 25522111 DOI: 10.1002/chem.201405640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/07/2022]
Abstract
Enantiopure β-amino acids represent interesting scaffolds for peptidomimetics, foldamers and bioactive compounds. However, the synthesis of highly substituted analogues is still a major challenge. Herein, we describe the spontaneous rearrangement of 4-carboxy-2-oxoazepane α,α-amino acids to lead to 2'-oxopiperidine-containing β(2,3,3) -amino acids, upon basic or acid hydrolysis of the 2-oxoazepane α,α-amino acid ester. Under acidic conditions, a totally stereoselective synthetic route has been developed. The reordering process involved the spontaneous breakdown of an amide bond, which typically requires strong conditions, and the formation of a new bond leading to the six-membered heterocycle. A quantum mechanical study was carried out to obtain insight into the remarkable ease of this rearrangement, which occurs at room temperature, either in solution or upon storage of the 4-carboxylic acid substituted 2-oxoazepane derivatives. This theoretical study suggests that the rearrangement process occurs through a concerted mechanism, in which the energy of the transition states can be lowered by the participation of a catalytic water molecule. Interestingly, it also suggested a role for the carboxylic acid at position 4 of the 2-oxoazepane ring, which facilitates this rearrangement, participating directly in the intramolecular catalysis.
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10
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Barman A, Prabhakar R. Elucidating the catalytic mechanism of β-secretase (BACE1): a quantum mechanics/molecular mechanics (QM/MM) approach. J Mol Graph Model 2013; 40:1-9. [PMID: 23337572 DOI: 10.1016/j.jmgm.2012.12.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/04/2012] [Accepted: 12/17/2012] [Indexed: 12/18/2022]
Abstract
In this quantum mechanics/molecular mechanics (QM/MM) study, the mechanisms of the hydrolytic cleavage of the Met2-Asp3 and Leu2-Asp3 peptide bonds of the amyloid precursor protein (WT-substrate) and its Swedish mutant (SW) respectively catalyzed by β-secretase (BACE1) have been investigated by explicitly including the electrostatic and steric effects of the protein environment in the calculations. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely acknowledged as a promising therapeutic target. The general acid-base mechanism followed by the enzyme proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. The formation of the gem-diol intermediate occurs with the barriers of 19.6 and 16.1 kcal/mol for the WT- and SW-substrate respectively. The QM/MM energetics predict that with the barriers of 21.9 and 17.2 kcal/mol for the WT- and SW-substrate respectively the cleavage of the peptide bond occurs in the rate-determining step. The computed barriers are in excellent agreement with the measured barrier of ∼18.0 kcal/mol for the SW-substrate and in line with the experimental observation that the cleavage of this substrate is sixty times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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11
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CAI JUN, WU ZHIJIAN. SOLVENT AND SUBSTITUENT EFFECTS ON THE INTRAMOLECULAR AMIDE HYDROLYSIS OF N-METHYLMALEAMIC ACID. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df, p)//B3LYP/6-31G(d, p) + ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df, p)//Onsager-B3LYP/6-31G(d, p) + ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.
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Affiliation(s)
- JUN CAI
- School of Nuclear Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - ZHIJIAN WU
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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12
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Antony S, Bayse CA. Modeling the Mechanism of the Glutathione Peroxidase Mimic Ebselen. Inorg Chem 2011; 50:12075-84. [DOI: 10.1021/ic201603v] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Antony
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, United States
| | - Craig A. Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, United States
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13
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Wang B, Cao Z. Acid-catalyzed reactions of twisted amides in water solution: competition between hydration and hydrolysis. Chemistry 2011; 17:11919-29. [PMID: 21901771 DOI: 10.1002/chem.201101274] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/07/2011] [Indexed: 11/12/2022]
Abstract
The acid-catalyzed reactions of twisted amides in water solution were investigated by using cluster-continuum model calculations. In contrast to the previous widely suggested concerted hydration of the C=O group, our calculations show that the reaction proceeds in a practically stepwise manner, and that the hydration and hydrolysis channels of the C-N bond compete. The Eigen ion (H(3)O(+)) is the key species involved in the reaction, and it modulates the hydration and hydrolysis reaction pathways. The phenyl substitution in the twisted amide not only activates the N-CO bond, but also stabilizes the hydrolysis product through n(N)→π(phenyl) delocalization, leading exclusively to the hydrolysis product of the ring-opened carboxylic acid. Generally, the twisted amides are more active than the planar amides, and such a rate acceleration results mainly from the increase in exothermicity in the first N-protonation step; the second step of the nucleophilic attack is less affected by the twisting of the amide bond. The present results show good agreement with the available experimental observations.
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Affiliation(s)
- Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, PR China
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14
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Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry 2011; 50:4337-49. [PMID: 21500768 DOI: 10.1021/bi200081h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In this combined MD simulation and DFT study, interactions of the wild-type (WT) amyloid precursor protein (APP) and its Swedish variant (SW), Lys670 → Asn and Met671 → Leu, with the beta-secretase (BACE1) enzyme and their cleavage mechanisms have been investigated. BACE1 catalyzes the rate-limiting step in the generation of 40-42 amino acid long Alzheimer amyloid beta (Aβ) peptides. All key structural parameters such as position of the flap, volume of the active site, electrostatic binding energy, structures, and positions of the inserts A, D, and F and 10s loop obtained from the MD simulations show that, in comparison to the WT-substrate, BACE1 exhibits greater affinity for the SW-substrate and orients it in a more reactive conformation. The enzyme-substrate models derived from the MD simulations were further utilized to investigate the general acid/base mechanism used by BACE1 to hydrolytically cleave these substrates. This mechanism proceeds through the following two steps: (1) formation of the gem-diol intermediate and (2) cleavage of the peptide bond. For the WT-substrate, the overall barrier of 22.4 kcal/mol for formation of the gem-diol intermediate is 3.3 kcal/mol higher than for the SW-substrate (19.1 kcal/mol). This process is found to be the rate-limiting in the entire mechanism. The computed barrier is in agreement with the measured barrier of ca. 18.00 kcal/mol for the WT-substrate and supports the experimental observation that the cleavage of the SW-substrate is 60 times more efficient than the WT-substrate.
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Affiliation(s)
- Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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15
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Moran EE, Timerghazin QK, Kwong E, English AM. Kinetics and Mechanism of S-Nitrosothiol Acid-Catalyzed Hydrolysis: Sulfur Activation Promotes Facile NO+ Release. J Phys Chem B 2011; 115:3112-26. [DOI: 10.1021/jp1035597] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernesto E. Moran
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Qadir K. Timerghazin
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling, Concordia University, Montreal, Québec H3G 1M8, Canada
| | - Elizabeth Kwong
- Pharmaceutical Research and Development, Merck Frosst Canada Incorporated, Kirkland, Québec H9H 3L1, Canada
| | - Ann M. English
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling, Concordia University, Montreal, Québec H3G 1M8, Canada
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16
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Bayse CA, Pavlou A. Tuning the activity of glutathione peroxidase mimics through intramolecular Se⋯N,O interactions: A DFT study incorporating solvent-assisted proton exchange (SAPE). Org Biomol Chem 2011; 9:8006-15. [DOI: 10.1039/c1ob05827d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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de Barros TC, Filho PB, Loos M, Politi MJ, Chaimovich H, Cuccovia IM. Formation and decomposition of N-alkylnaphthalimides: experimental evidences and ab initio description of the reaction pathways. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1768] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Chen L, Liu T, Ma C. Metal Complexation and Biodegradation of EDTA and S,S-EDDS: A Density Functional Theory Study. J Phys Chem A 2009; 114:443-54. [DOI: 10.1021/jp904296m] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Litao Chen
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Ting Liu
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
| | - Chun’an Ma
- State Key Laboratory Breeding Base for Green Chemistry Synthesis Technology, College of Chemical Engineering and Materials Science, Zhejiang University of Technology, Hangzhou 310014, People’s Republic of China
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19
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Murphy JL, Tenn WJ, Labuda JJ, Nagorski RW. Rapid amidic hydrolysis: a competitive reaction pathway under basic conditions for N-(hydroxymethyl)benzamide derivatives bearing electron-donating groups. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.10.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Singh R, Barman A, Prabhakar R. Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). J Phys Chem B 2009; 113:2990-9. [DOI: 10.1021/jp811154w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rajiv Singh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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21
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Cheong MY, Ariffin A, Khan MN. Effects of Mixed H2O—CH3CN and H2O—HCONMe2 Solvents on the Rate of Cleavage of N-Benzylphthalamic Acid. PROGRESS IN REACTION KINETICS AND MECHANISM 2008. [DOI: 10.3184/146867808x315733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The values of pseudo first-order rate constants, k1, for the O-cyclization and k3 for N-cyclization of N-benzylphthalamic acid 1, obtained at 0.02 M HCl and 35°C, show a respective nonlinear increase from 17.6 × 10−6 to 29.7 × 10−6 s−1 and decrease from 12.5 × 10−7 to 3.75 × 10−7 s−1 with increase in the CH3CN content from 2 to 60% v/v in mixed aqueous solvent. Increase in the CH3CN content from 60 to 90% v/v decreases k1 from 29.7 × 10−6 to 24.4 × 10−6 s−1 and increases k3 from 3.75 × 10−7 to 14.7 × 10−7 s−1. The respective values of k1 and k3 decrease nonlinearly from 16.0 × 10−6 to 3.0 × 10−6 s−1 and 14.0 × 10−7 to ~4.0 × 10−7 s−1 with increase in the content of N,N-dimethylformamide (HCONMe2) from 2 to 80% v/v in mixed aqueous solvents. These results indicate rather mild rate-retarding effects of mixed H2O—CH3CN and H2O—HCONMe2 solvents on the rates of the intramolecular reactions.
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Affiliation(s)
- May-Ye Cheong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Azhar Ariffin
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mohammad Niyaz Khan
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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22
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Hu N, Tu YP, Liu Y, Jiang K, Pan Y. Dissociative Protonation and Proton Transfers: Fragmentation of α, β-Unsaturated Aromatic Ketones in Mass Spectrometry. J Org Chem 2008; 73:3369-76. [DOI: 10.1021/jo702464b] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nan Hu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China, and Drug Metabolism and Pharmacokinetics, Genelabs Technologies, 505 Penobscot Drive, Redwood City, California 94063
| | - Ya-Ping Tu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China, and Drug Metabolism and Pharmacokinetics, Genelabs Technologies, 505 Penobscot Drive, Redwood City, California 94063
| | - Yaqin Liu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China, and Drug Metabolism and Pharmacokinetics, Genelabs Technologies, 505 Penobscot Drive, Redwood City, California 94063
| | - Kezhi Jiang
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China, and Drug Metabolism and Pharmacokinetics, Genelabs Technologies, 505 Penobscot Drive, Redwood City, California 94063
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China, and Drug Metabolism and Pharmacokinetics, Genelabs Technologies, 505 Penobscot Drive, Redwood City, California 94063
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23
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Bayse CA, Antony S. Molecular modeling of bioactive selenium compounds. MAIN GROUP CHEMISTRY 2007. [DOI: 10.1080/10241220801994700] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Modeling the reaction mechanisms for redox regulation of protein tyrosine phosphatase 1B activity. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0343-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Liu N, Ban F, Boyd RJ. Modeling Competitive Reaction Mechanisms of Peroxynitrite Oxidation of Guanine. J Phys Chem A 2006; 110:9908-14. [PMID: 16898693 DOI: 10.1021/jp061297b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant.
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Affiliation(s)
- Ning Liu
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3
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26
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Hudáky P, Perczel A. A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle. Proteins 2005; 62:749-59. [PMID: 16358328 DOI: 10.1002/prot.20827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A model of the catalytic triad of chymotrypsin is built assuring the arrangement and properties as they are within the complete enzyme. The model contains 18 amino acid residues of chymotrypsin and its substrate. A total of 135 atoms (including 70 heavy atoms) were subjected to full ab initio geometry optimizations through 127 individual steps along the reaction coordinate of the complete catalytic mechanism. It was shown that the described model of the catalytic apparatus forms a self-stabilized molecule ensemble without the rest of the enzyme and substrate. According to the calculations, the formations of the first and second tetrahedral intermediates in the model have 20.3 and 15.7 kcal/mol activation energy barriers, respectively. Removing elements of the catalytic apparatus such as the (1) catalytic aspartate or (2) the anion hole, as well as (3) inserting a water molecule "early" in the catalytic process, or (4) introducing conformational rigidity of the substrate, results in an increase of the above energy barrier of the first catalytic step in the model by 6.4, 13.7, 3.7, and 4.1 kcal/mol, respectively. Based on the calculated process one can conclude that the catalytic reaction in this model is much more similar to the reaction in the enzyme than to the reference reaction. To our knowledge, this is the first model system that mimics the complete catalytic mechanism.
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Affiliation(s)
- Péter Hudáky
- Department of Theoretical Chemistry, Eötvös Loránd University, Budapest 112, Hungary
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27
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Gorb L, Asensio A, Tuñón I, Ruiz-López MF. The Mechanism of Formamide Hydrolysis in Water from Ab Initio Calculations and Simulations. Chemistry 2005; 11:6743-53. [PMID: 16130156 DOI: 10.1002/chem.200500346] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The neutral hydrolysis of formamide in water is a suitable reference to quantify the efficiency of proteolytic enzymes. However, experimental data for this reaction has only very recently been obtained and the kinetic constant determined experimentally is significantly higher than that predicted by previous theoretical estimations. In this work, we have investigated in detail the possible mechanisms of this reaction. Several solvent models have been considered that represent a considerable improvement on those used in previous studies. Density functional and ab initio calculations have been carried out on a system which explicitly includes the first solvation shell of the formamide molecule. Its interaction with the bulk has been treated with the aid of a dielectric continuum model. Molecular dynamics simulations at the combined density functional/molecular mechanics level have been carried out in parallel to better understand the structure of the reaction intermediates in aqueous solution. Overall, the most favored mechanism predicted by our study involves two reaction steps. In the first step, the carbonyl group of the formamide molecule is hydrated to form a diol intermediate. The corresponding transition structure involves two water molecules. From this intermediate, a water-assisted proton transfer occurs from one of the hydroxy groups to the amino group. This reaction step may lead either to the formation of a new reaction intermediate with a marked zwitterionic character or to dissociation of the system into ammonia and formic acid. The zwitterionic intermediate dissociates quite easily but its lifetime is not negligible and it could play a role in the hydrolysis of substituted amides or peptides. The predicted pseudo-first-order kinetic constant for the rate-limiting step (the first step) of the hydrolysis reaction at 25 degrees C (3.9x10(-10) s(-1)) is in excellent agreement with experimental data (1.1x10(-10) s(-1)).
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Affiliation(s)
- Leonid Gorb
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, MS 39217, USA
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28
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Ivanova EV, Muchall HM. Influence of the number of water molecules on the mechanism of N-sulfinylaniline hydrolysis. CAN J CHEM 2005. [DOI: 10.1139/v05-171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mechanism of the uncatalyzed hydrolysis of N-sulfinylaniline (Ph-N=S=O) has been studied with B3LYP/6-31+G(2d,2p) in the gas phase, with explicit treatment of water molecules. Hydrolysis involves water attack on sulfur, with a close to perpendicular alignment of a water molecule and the NSO plane in both prereaction complexes and transition states for the rate-determining step. Consequently, the distance of the weak S···O interaction, together with the efficiency of protonation of either nitrogen (attack across the N=S bond) or oxygen (attack across the S=O bond) atoms of the NSO group, determines the height of the activation barrier for hydrolysis. While the reaction with one water molecule is characterized by an unreasonably high enthalpy of activation, a cooperative effect from the weak interactions appears with the inclusion of a second water molecule, where both participate in the reaction, and the activation enthalpy drops significantly. The preference for attack across the S=O bond that is found in the reaction with one water molecule switches to a dominance of attack across the N=S bond in the reaction with three water molecules.Key words: N-sulfinylaniline, hydrolysis, mechanism, density functional theory (DFT).
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29
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Manojkumar TK, Suh SB, Oh KS, Cho SJ, Cui C, Zhang X, Kim KS. Theoretical Studies on the Mechanism of Acid-Promoted Hydrolysis of N-Formylaziridine in Comparison with Formamide. J Org Chem 2005; 70:2651-9. [PMID: 15787556 DOI: 10.1021/jo0493323] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] We present an ab initio study of the acid-promoted hydrolysis reaction mechanism of N-formylaziridine in comparison with formamide. Since the rate of amide hydrolysis reactions depends on the formation of the tetrahedral intermediate, we focused our attention mainly on the reactant complex, the tetrahedral intermediate, and the transition state connecting these two stationary points. Geometries were optimized using the density functional theory, and the energetics were refined using ab initio theory including electron correlation. Solvent effects were investigated by using polarizable continuum method calculations. The proton-transfer reaction between the O-protonated and N-protonated amides was investigated. In acidic media, despite that the N-protonated species is more stable than the O-protonated one, it is predicted that both N-protonated and O-protonated pathways compete in the hydrolysis reaction of N-formylaziridine.
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Affiliation(s)
- Thanathu Krishnan Manojkumar
- National Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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