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Burke JR, La Clair JJ, Philippe RN, Pabis A, Corbella M, Jez JM, Cortina GA, Kaltenbach M, Bowman ME, Louie GV, Woods KB, Nelson AT, Tawfik DS, Kamerlin SC, Noel JP. Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jason R. Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J. La Clair
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Ryan N. Philippe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph M. Jez
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - George A. Cortina
- Department of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Miriam Kaltenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Gordon V. Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Katherine B. Woods
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Andrew T. Nelson
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shina C.L. Kamerlin
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
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Zhang R, Bhattacharjee A, Field MJ, Salahub DR. Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model. Proteins 2014; 83:268-81. [DOI: 10.1002/prot.24732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rui Zhang
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Anirban Bhattacharjee
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Martin J. Field
- DYNAMOP; Institut de Biologie Structurale, Jean-Pierre Ebel; Grenoble France
| | - Dennis R. Salahub
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
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3
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Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study. J Mol Model 2013; 19:4753-61. [DOI: 10.1007/s00894-013-1975-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
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Ruiz-Pernía JJ, Martí S, Moliner V, Tuñón I. A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition. J Chem Theory Comput 2012; 8:1532-5. [DOI: 10.1021/ct300064f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Javier Ruiz-Pernía
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Sergio Martí
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- Departament de Química
Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
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Kosugi T, Hayashi S. QM/MM Reweighting Free Energy SCF for Geometry Optimization on Extensive Free Energy Surface of Enzymatic Reaction. J Chem Theory Comput 2011; 8:322-34. [DOI: 10.1021/ct2005837] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Takahiro Kosugi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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ZHANG ZHIQIANG, CHOW RAYMONDKWOKKEI, ZHOU HONGWEI, LI JIELIANG, CHEUNG HONYEUNG. AN AB INITIO STUDY ON THE STRUCTURE–CYTOTOXICITY RELATIONSHIP OF TERPENOID LACTONES BASED ON THE MICHAEL REACTION BETWEEN THEIR PHARMACOPHORES AND L-CYSTEINE-METHYLESTER-1. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608003794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The cytotoxic effects of terpenoid lactones are attributed to the alkylation of biological nucleophiles, especially sulfhydryl groups in proteins, by the α,β-unsaturated carbonyl moiety of lactones through Michael reaction. Therefore, the cytotoxicity could be reflected by the reactivity of the pharmacophores. In this work, the Michael reaction between 12 α,β-unsaturated-carbonyl-containing small species, i.e. 10 analogues of the alpha methylene gamma butyrolactone moiety of andrographolide, one cyclopentenone, and one methylene–pentanolide, and L-cysteine-methylester-1 were investigated by ab initio methods to mimic the alkylation of proteins by terpenoid lactones. The trend in the calculated reaction free energies of the small species is qualitatively in accordance with the reported cytotoxicity of corresponding terpenoid lactones.
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Affiliation(s)
- ZHI QIANG ZHANG
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - RAYMOND KWOK KEI CHOW
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - HONG WEI ZHOU
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - JIE LIANG LI
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - HON-YEUNG CHEUNG
- Research Group for Bioactive Products, Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
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Tuñón I, Hynes JT. A Simple Model for Barrier Frequencies for Enzymatic Reactions. Chemphyschem 2010; 12:184-90. [DOI: 10.1002/cphc.201000774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Indexed: 11/10/2022]
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8
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Domínguez de María P, van Gemert RW, Straathof AJJ, Hanefeld U. Biosynthesis of ethers: unusual or common natural events? Nat Prod Rep 2010; 27:370-92. [PMID: 20179877 DOI: 10.1039/b809416k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ether bonds are found in a wide variety of natural products--mainly secondary metabolites--including lipids, oxiranes, terpenoids, flavonoids, polyketides, and carbohydrate derivatives, to name some representative examples. To furnish such a biodiversity of structures, a large number of different enzymes are involved in several different biosynthetic pathways. Depending on the compound and on the (micro) environment in which the reaction is performed, ethers are produced by very different (enzymatic) reactions, thus providing an impressive display of how Nature has combined evolution and thermodynamics to be able to produce a vast number of compounds. In addition, many of these compounds possess different biological activities of pharmacological interest. Moreover, some of these ethers (i.e., epoxides) have high chemical reactivity, and can be useful starting materials for further synthetic processes. This review aims to provide an overview of the different strategies that are found in Nature for the formation of these "bioethers". Both fundamental and practical insights of the biosynthetic processes will be discussed.
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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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Ruiz-Pernía JJ, Tuñón I, Moliner V, Hynes JT, Roca M. Dynamic Effects on Reaction Rates in a Michael Addition Catalyzed by Chalcone Isomerase. Beyond the Frozen Environment Approach. J Am Chem Soc 2008; 130:7477-88. [DOI: 10.1021/ja801156y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- J. Javier Ruiz-Pernía
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Vicente Moliner
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - James T. Hynes
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Maite Roca
- Departamento de Química Física, Universidad de Valencia, 46100 Burjassot, Spain, Departamento de Química Física y Analítica, Universidad Jaume I, 12071 Castellón, Spain, Département de Chimie, UMR 8640 Pasteur, Ecole Normale Supérieure, 75005 Paris, France, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
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Higashi M, Truhlar DG. Electrostatically Embedded Multiconfiguration Molecular Mechanics Based on the Combined Density Functional and Molecular Mechanical Method. J Chem Theory Comput 2008; 4:790-803. [DOI: 10.1021/ct800004y] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Masahiro Higashi
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant Street SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
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van der Kamp MW, Mulholland AJ. Computational enzymology: insight into biological catalysts from modelling. Nat Prod Rep 2008; 25:1001-14. [DOI: 10.1039/b600517a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ma S, Devi-Kesavan LS, Gao J. Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. J Am Chem Soc 2007; 129:13633-45. [PMID: 17935329 PMCID: PMC2556303 DOI: 10.1021/ja074222+] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Lakshmi S. Devi-Kesavan
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
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