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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.
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Bortoli M, Zaccaria F, Dalla Tiezza M, Bruschi M, Fonseca Guerra C, Bickelhaupt FM, Orian L. Oxidation of organic diselenides and ditellurides by H 2O 2 for bioinspired catalyst design. Phys Chem Chem Phys 2019; 20:20874-20885. [PMID: 30066704 DOI: 10.1039/c8cp02748j] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.
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Affiliation(s)
- Marco Bortoli
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy.
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Qiu S, Azofra LM, MacFarlane DR, Sun C. Hydrogen bonding effect between active site and protein environment on catalysis performance in H 2-producing [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:6735-6743. [PMID: 29457815 DOI: 10.1039/c7cp07685a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H+/e- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S- in cysteine residues shows a larger influence on the energy profile than that via the CN- ligands on Fe.
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Affiliation(s)
- Siyao Qiu
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia.
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Bortoli M, Torsello M, Bickelhaupt FM, Orian L. Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site. Chemphyschem 2017; 18:2990-2998. [DOI: 10.1002/cphc.201700743] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Marco Bortoli
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35129 Padova Italy
| | | | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 J Nijmegen The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35129 Padova Italy
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Jiang JH, Zhou H, Li HJ, Wang YC, Tian M, Huang YL, Deng P. Comprehensive modeling of the antioxidant mechanism of ebselen. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615500534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three possible catalytic cycles for ebselen have been comprehensively modeled by theoretical calculations using density functional theory (DFT) at a mixed basis set level; the 6-31G(d) basis set for hydrocarbon fragments and the 6-31[Formula: see text]G(d,p) basis set for other atoms. The 2[Formula: see text] cycle is the main pathway in the glutathione peroxidase (GPx) cycle (cycle A), and IM3[Formula: see text]TS3 is the rate controlling process. The 1[Formula: see text]1 cycle is the main pathway for the oxidation cycle (cycle B), and the rate controlling step is the [Formula: see text] step. Ebselen reacts with the selenol 3 to form the diselenide 9, and this is the rate controlling step for cycle C. The extremely high energy barrier for the IM9[Formula: see text]TS9 process indicates that cycle C is unlikely to occur in vivo. Although cycle B is favored based on the energy analysis, with a maximum energy barrier of only 26.68[Formula: see text]kcal/mol at the mixed basis set level, it is generally unlikely to have very high concentrations of peroxides present in vivo. The results indicate that in order to improve the antioxidant activity of ebselen, it would be necessary to suitably modify the molecular structure of ebselen to reduce the energy barrier of the IM3[Formula: see text]TS3 process.
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Affiliation(s)
- Jun-Hao Jiang
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Hui Zhou
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Hui-Jie Li
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Yu-Chun Wang
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Mei Tian
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Ya-Lin Huang
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Ping Deng
- School of Pharmacy, Chongqing Medical University, Chongqing, 400016, P. R. China
- Chongqing Key Laboratory of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, P. R. China
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Orian L, Mauri P, Roveri A, Toppo S, Benazzi L, Bosello-Travain V, De Palma A, Maiorino M, Miotto G, Zaccarin M, Polimeno A, Flohé L, Ursini F. Selenocysteine oxidation in glutathione peroxidase catalysis: an MS-supported quantum mechanics study. Free Radic Biol Med 2015; 87:1-14. [PMID: 26163004 DOI: 10.1016/j.freeradbiomed.2015.06.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/18/2015] [Accepted: 06/09/2015] [Indexed: 12/31/2022]
Abstract
Glutathione peroxidases (GPxs) are enzymes working with either selenium or sulfur catalysis. They adopted diverse functions ranging from detoxification of H(2)O(2) to redox signaling and differentiation. The relative stability of the selenoenzymes, however, remained enigmatic in view of the postulated involvement of a highly unstable selenenic acid form during catalysis. Nevertheless, density functional theory calculations obtained with a representative active site model verify the mechanistic concept of GPx catalysis and underscore its efficiency. However, they also allow that the selenenic acid, in the absence of the reducing substrate, reacts with a nitrogen in the active site. MS/MS analysis of oxidized rat GPx4 complies with the predicted structure, an 8-membered ring, in which selenium is bound as selenenylamide to the protein backbone. The intermediate can be re-integrated into the canonical GPx cycle by glutathione, whereas, under denaturing conditions, its selenium moiety undergoes β-cleavage with formation of a dehydro-alanine residue. The selenenylamide bypass prevents destruction of the redox center due to over-oxidation of the selenium or its elimination and likely allows fine-tuning of GPx activity or alternate substrate reactions for regulatory purposes.
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Affiliation(s)
- Laura Orian
- Department of Chemistry, University of Padova, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies, National Research Council, Milano, Italy
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Italy
| | - Louise Benazzi
- Institute for Biomedical Technologies, National Research Council, Milano, Italy
| | | | - Antonella De Palma
- Institute for Biomedical Technologies, National Research Council, Milano, Italy
| | | | - Giovanni Miotto
- Department of Molecular Medicine, University of Padova, Italy
| | - Mattia Zaccarin
- Department of Molecular Medicine, University of Padova, Italy
| | | | - Leopold Flohé
- Department of Molecular Medicine, University of Padova, Italy.
| | - Fulvio Ursini
- Department of Molecular Medicine, University of Padova, Italy
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8
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 758] [Impact Index Per Article: 84.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Orian L, Toppo S. Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled. Free Radic Biol Med 2014; 66:65-74. [PMID: 23499840 DOI: 10.1016/j.freeradbiomed.2013.03.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 12/14/2022]
Abstract
Organochalcogen compounds have attracted the interest of a multitude of studies to design potential therapeutic agents mimicking the peroxidase activity of selenium-based glutathione peroxidases (GPx's). Starting from the pioneering ebselen, various compounds have been synthesized over the years, which may be traced in three major classes of molecules: cyclic selenenyl amides, diaryl diselenides, and aromatic or aliphatic monoselenides. These compounds share common features and determinants needed to exert an efficient GPx-like activity, such as polarizing groups in close proximity to selenium and steric effects. Nonetheless, the reactivity of selenium, and tellurium as well, poses serious problems for the predictability of the biological effects of these compounds in vivo when used as potential drugs. These molecules, indeed, interfere with thiols of redox-regulated proteins and enzymes, leading to unexpected biological effects. The various chemical aspects of the reaction mechanism of peroxidase mimetics are surveyed here, focusing on experimental evidence and quantum mechanics calculations of organochalcogen representatives of the various classes.
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Affiliation(s)
- Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, 35129 Padova, Italy.
| | - Stefano Toppo
- Dipartimento di Medicina Molecolare, Università degli Studi di Padova, 35121 Padova, Italy.
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Akyüz MA, Erdem SS. Computational modeling of the direct hydride transfer mechanism for the MAO catalyzed oxidation of phenethylamine and benzylamine: ONIOM (QM/QM) calculations. J Neural Transm (Vienna) 2013; 120:937-45. [PMID: 23619993 DOI: 10.1007/s00702-013-1027-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/15/2013] [Indexed: 11/28/2022]
Abstract
Monoamine oxidases are two isozymic flavoenzymes which are the important targets for drugs used in the treatment of depression, Parkinson and Alzheimer's diseases. The catalytic reaction taking place between the cofactor FAD and amine substrate is still not completely understood. Herein we employed quantum chemical methods on the recently proposed direct hydride transfer mechanism including full active site residues of MAO isoforms in the calculations. Activation free energy barriers of direct hydride transfer mechanism for MAO-A and MAO-B were calculated by ONIOM (our own n-layered integrated molecular orbital + molecular mechanics) method with QM/QM (quantum mechanics:quantum mechanics) approach employing several density functional theory functionals, B3LYP, WB97XD, CAM-B3LYP and M06-2X, for the high layer. The formation of very recently proposed αC-flavin N5 adduct inside the enzyme has been investigated. ONIOM (M06-2X/6-31+G(d,p):PM6) results revealed that such an adduct may form only in MAO-B suggesting slightly different hydride transfer mechanisms for MAO-A and MAO-B.
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Affiliation(s)
- Mehmet Ali Akyüz
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Göztepe, 34722, Istanbul, Turkey
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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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Kóňa J, Fabian WMF. Hybrid QM/MM Calculations on the First Redox Step of the Catalytic Cycle of Bovine Glutathione Peroxidase GPX1. J Chem Theory Comput 2011; 7:2610-6. [DOI: 10.1021/ct200129q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Juraj Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Walter M. F. Fabian
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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Erdem SS, Büyükmenekşe B. Computational investigation on the structure-activity relationship of the biradical mechanism for monoamine oxidase. J Neural Transm (Vienna) 2011; 118:1021-9. [PMID: 21476070 DOI: 10.1007/s00702-011-0635-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
Abstract
Although a considerable amount of mechanistic data has accumulated in literature, the detailed mechanism for amine oxidation by monoamine oxidase is still controversial. The single electron transfer mechanism (SET) has been widely discussed, but not completely understood yet. In the present study, the modified SET mechanism, proposed by Silverman et al., was explored by quantum chemical calculations. The ONIOM method was applied with UDFT/B3LYP/6-31 + G(d,p) for the higher layer and with UHF/6-31G(d) for the lower layer. Isoalloxazin heterocyclic ring and benzylamine were employed in the calculations to represent flavin and the substrate, respectively. The substituents CH(3), OH, OCH(3), H, F, Cl, Br, CF(3) and NO(2) were incorporated at the para position of benzylamine to explore structure-activity relationships. The structures of the reactant complex, transition state and product complex were fully optimized. Activation energies and rate constants of all the reactions were calculated. The results obtained from the linear regression analysis showed that electron-donating groups at the para position of benzylamine increase the reaction rate. A linear but inverse correlation between the log of the calculated rate constants (log k) and the electronic parameter of the substituent was observed (R = 0.93). In accordance with this result, a relatively weak inverse correlation between the calculated log k and the experimental log k was obtained (R = 0.78). The results are contrary to the previous kinetic experiments and the computational study on the effect of p-substituents in the flavin reduction of MAO A by p-substituted benzylamine analogs. Therefore, they present negative evidence for the modeled biradical mechanism.
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Affiliation(s)
- Safiye S Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Göztepe, Istanbul, Turkey.
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Hricovíni M. Effect of Solvent and Counterions upon Structure and NMR Spin−Spin Coupling Constants in Heparin Disaccharide. J Phys Chem B 2011; 115:1503-11. [DOI: 10.1021/jp1098552] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovakia
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Kawatsu T, Lundberg M, Morokuma K. Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS). J Chem Theory Comput 2010; 7:390-401. [DOI: 10.1021/ct1005592] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsutomu Kawatsu
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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16
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Ali ST, Karamat S, Kóňa J, Fabian WMF. Theoretical Prediction of pKa Values of Seleninic, Selenenic, Sulfinic, and Carboxylic Acids by Quantum-Chemical Methods. J Phys Chem A 2010; 114:12470-8. [DOI: 10.1021/jp102266v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S. Tahir Ali
- Institut für Chemie, Karl Franzens Universität Graz, Heinrichstrasse 28, A-8010 Graz, Austria, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
| | - Sajjad Karamat
- Institut für Chemie, Karl Franzens Universität Graz, Heinrichstrasse 28, A-8010 Graz, Austria, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
| | - Juraj Kóňa
- Institut für Chemie, Karl Franzens Universität Graz, Heinrichstrasse 28, A-8010 Graz, Austria, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
| | - Walter M. F. Fabian
- Institut für Chemie, Karl Franzens Universität Graz, Heinrichstrasse 28, A-8010 Graz, Austria, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
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Chung LW, Li X, Sugimoto H, Shiro Y, Morokuma K. ONIOM Study on a Missing Piece in Our Understanding of Heme Chemistry: Bacterial Tryptophan 2,3-Dioxygenase with Dual Oxidants. J Am Chem Soc 2010; 132:11993-2005. [DOI: 10.1021/ja103530v] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Hiroshi Sugimoto
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
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18
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Ali ST, Jahangir S, Karamat S, Fabian WMF, Nawara K, Kóňa J. Theoretical Study on the Redox Cycle of Bovine Glutathione Peroxidase GPx1: pKa Calculations, Docking, and Molecular Dynamics Simulations. J Chem Theory Comput 2010; 6:1670-81. [DOI: 10.1021/ct9003355] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Syed Tahir Ali
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Sajid Jahangir
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Sajjad Karamat
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Walter M. F. Fabian
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Krzysztof Nawara
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
| | - Juraj Kóňa
- Institute of Chemistry, Karl Franzens University, Graz, Heinrichstrasse 28, A-8010 Graz, Austria, Department of Chemistry, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Science Campus, Karachi, Sindh, Pakistan, and Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravska cesta 9, 845 38 Bratislava, Slovak Republic
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19
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Heverly-Coulson GS, Boyd RJ. Reduction of Hydrogen Peroxide by Glutathione Peroxidase Mimics: Reaction Mechanism and Energetics. J Phys Chem A 2009; 114:1996-2000. [DOI: 10.1021/jp910368u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
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20
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Tao P, Fisher JF, Shi Q, Vreven T, Mobashery S, Schlegel HB. Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue. Biochemistry 2009; 48:9839-47. [PMID: 19754151 DOI: 10.1021/bi901118r] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computationally. The inhibition mechanism involves C-H deprotonation with concomitant opening of the three-membered heterocycle. SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine the reaction of these two inhibitors in the active site of MMP2. The calculations show that the reaction barrier for transformation of SB-3CT is 1.6 kcal/mol lower than its oxirane analogue, and the ring-opening reaction energy of SB-3CT is 8.0 kcal/mol more exothermic than that of its oxirane analogue. Calculations also show that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. A six-step partial charge fitting procedure is introduced for the QM/MM calculations to update atomic partial charges of the quantum mechanics region and to ensure consistent electrostatic energies for reactants, transition states, and products.
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Affiliation(s)
- Peng Tao
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
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21
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Rauschnot JC, Yang C, Yang V, Bhattacharyya S. Theoretical Determination of the Redox Potentials of NRH:Quinone Oxidoreductase 2 Using Quantum Mechanical/Molecular Mechanical Simulations. J Phys Chem B 2009; 113:8149-57. [DOI: 10.1021/jp901854a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James C. Rauschnot
- Department of Chemistry, University of Wisconsin-Eau Claire, 105 Garfield Avenue, Eau Claire, Wisconsin 54702
| | - Chee Yang
- Department of Chemistry, University of Wisconsin-Eau Claire, 105 Garfield Avenue, Eau Claire, Wisconsin 54702
| | - Vang Yang
- Department of Chemistry, University of Wisconsin-Eau Claire, 105 Garfield Avenue, Eau Claire, Wisconsin 54702
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, 105 Garfield Avenue, Eau Claire, Wisconsin 54702
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22
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Smith AJT, Li Y, Houk KN. Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2. Org Biomol Chem 2009; 7:2716-24. [PMID: 19532987 DOI: 10.1039/b901429b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanisms of enzyme-catalyzed phosphate transfer and hydrolysis reactions are of great interest due to their importance and abundance in biochemistry. The reaction may proceed in a stepwise fashion, with either a pentavalent phosphorane or a metaphosphate anion intermediate, or by a concerted SN2 mechanism. Despite much theoretical work focused on a few key enzymes, a consensus for the mechanism has not been reached, and examples of all three possibilities have been demonstrated. We have investigated the mechanism of human uridine-cytidine kinase 2 (UCK2, EC 2.7.1.48), which catalyzes the transfer of a phosphate group from ATP to the ribose 5'-hydroxyl of cytidine and uridine. UCK2 is normally expressed in human placenta, but is overexpressed in certain cancer cells, where it is responsible for activating a class of antitumor prodrugs. The UCK2 mechanism was investigated by generating a 2D potential energy surface as a function of the P-O bonds forming and breaking, with energies calculated using a quantum mechanics/molecular mechanics potential (B3LYP/6-31G(d):AMBER). The mechanism of phosphate transfer is shown to be concerted, and is accompanied by concerted proton transfer from the 5'-hydroxyl to a conserved active site aspartic acid that serves as a catalytic base. The calculated barrier for this reaction is 15.1 kcal/mol, in relatively good agreement with the experimental barrier of 17.5 kcal/mol. The interactions of the enzyme active site with the reactant, transition state, and product are examined for their implications on the design of anticancer prodrugs or positron emission tomography (PET) reporter probes for this enzyme.
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Affiliation(s)
- Adam J T Smith
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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23
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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25
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Lundberg M, Kawatsu T, Vreven T, Frisch MJ, Morokuma K. Transition States in a Protein Environment − ONIOM QM:MM Modeling of Isopenicillin N Synthesis. J Chem Theory Comput 2008; 5:222-34. [DOI: 10.1021/ct800457g] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Tsutomu Kawatsu
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Thom Vreven
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Michael J. Frisch
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan, and Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492
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27
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Banás P, Rulísek L, Hánosová V, Svozil D, Walter NG, Sponer J, Otyepka M. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B 2008; 112:11177-87. [PMID: 18686993 DOI: 10.1021/jp802592z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In contrast, some mechanistic studies support the role of C75 acting as general acid and thus being protonated before the reaction. We report combined quantum chemical/molecular mechanical calculations for the C75 general base pathway, utilizing the available structural data for the wild type HDV genomic ribozyme as a starting point. Several starting configurations differing in magnesium ion placement were considered and both one-dimensional and two-dimensional potential energy surface scans were used to explore plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. We identify a most likely position for the magnesium ion, which also suggests it acts as a Lewis acid. The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data.
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Affiliation(s)
- Pavel Banás
- Department of Physical Chemistry and Center for Biomolecules and Complex Molecular Systems, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
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Suresh CH, Vargheese AM, Vijayalakshmi KP, Mohan N, Koga N. Role of structural water molecule in HIV protease-inhibitor complexes: A QM/MM study. J Comput Chem 2008; 29:1840-9. [DOI: 10.1002/jcc.20961] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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Jacob CR, Neugebauer J, Visscher L. A flexible implementation of frozen-density embedding for use in multilevel simulations. J Comput Chem 2008; 29:1011-8. [DOI: 10.1002/jcc.20861] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Morokuma K. Theoretical Studies of Chemical Reactions—A Fascinating World of Chemistry from Gas-Phase Elementary Reactions through Nanostructure Formation and Homogeneous Catalysis to Reactions of Metalloenzymes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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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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Lundberg M, Morokuma K. Protein Environment Facilitates O2 Binding in Non-Heme Iron Enzyme. An Insight from ONIOM Calculations on Isopenicillin N Synthase (IPNS). J Phys Chem B 2007; 111:9380-9. [PMID: 17637052 DOI: 10.1021/jp071878g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O2 binding is close to zero. Two major factors consistently stabilize O2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O2 (side-on or end-on). The second major factor that stabilizes O2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.
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Affiliation(s)
- Marcus Lundberg
- Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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