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Huang Z, Ni D, Chen Z, Zhu Y, Zhang W, Mu W. Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37485919 DOI: 10.1080/10408398.2023.2238054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.
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Affiliation(s)
- Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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2
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Rincón D, Doerr M, Daza MC. Hydrogen Bonds and n → π* Interactions in the Acetylation of Propranolol Catalyzed by Candida antarctica Lipase B: A QTAIM Study. ACS OMEGA 2021; 6:20992-21004. [PMID: 34423207 PMCID: PMC8375099 DOI: 10.1021/acsomega.1c02559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Enzyme-substrate interactions play a crucial role in enzymatic catalysis. Quantum theory of atoms in molecules (QTAIM) calculations are extremely useful in computational studies of these interactions because they provide very detailed information about the strengths and types of molecular interactions. QTAIM also provides information about the intramolecular changes that occur in the catalytic reaction. Here, we analyze the enzyme-substrate interactions and the topological properties of the electron density in the enantioselective step of the acylation of (R,S)-propranolol, an aminoalcohol with therapeutic applications, catalyzed by Candida antarctica lipase B. Eight reaction paths (four for each enantiomer) are investigated and the energies, atomic charges, hydrogen bonds, and n → π* interactions of propranolol, the catalytic triad (composed of D187, H224, and S105), and the oxyanion hole are analyzed. It is found that D187 acts as an electron density reservoir for H224, and H224 acts as an electron density reservoir for the active site of the protein. It releases electron density when the tetrahedral intermediate is formed from the Michaelis complex and receives it when the enzyme-product complex is formed. Hydrogen bonds can be grouped into noncovalent and covalent hydrogen bonds. The latter are stronger and more important for the reaction than the former. We also found weak n → π* interactions, which are characterized by QTAIM and the natural bond orbital (NBO) analysis.
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Valderrama DIB, Daza MC, Doerr M. Finite-temperature effect in the O-acylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B. J Mol Graph Model 2021; 107:107951. [PMID: 34111759 DOI: 10.1016/j.jmgm.2021.107951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022]
Abstract
CalB is a triacylglycerol hydrolase (E.C.3.1.1.3) used in the O-acylation of the beta-adrenergic blocking agent (R,S)-propranolol. The catalytic mechanism involves two steps: enzyme acylation and enzyme deacylation. The enantioselectivity of the O-acylation of (R,S)-propranolol originates from the second step, where the acyl-enzyme transfers the acyl group to the racemic substrate. This step occurs via an initial Michaelis complex (MCC) and a tetrahedral intermediate (TI-2). To gain more insight into the molecular basis of this reaction, we performed an exhaustive conformational sampling along the reaction coordinate of the enantioselective step of the reaction (MCC→TI-2→EPC) applying a QM/MM MD protocol (SCC-DFTB/CHARMM) in combination with umbrella sampling and the weighted histogram analysis method. To identify finite temperature effects we compare the PMF and the potential energy pathway. It is found that the effect of the finite temperature in this reaction is a destabilization of the tetrahedral intermediate and an increase of the barrier height of its formation. This increase is higher for the S-enantiomer.
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Affiliation(s)
- Daniel I Barrera Valderrama
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia; Departamento de Química, Universidad de Pamplona, Km 1 Vía Bucaramanga, Pamplona, Colombia
| | - Martha C Daza
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Markus Doerr
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia.
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Chałupka J, Sikora A, Kozicka A, Marszałł MP. Overview: Enzyme-catalyzed Enantioselective Biotransformation of Chiral Active Compounds Used in Hypertension Treatment. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201020204256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enzymatic kinetic resolution is one of the methods which allows for the synthesis
of enantiomerically pure various active pharmaceutical ingredients. In contrast to chemical
routes, enzymatic reactions have characteristics, including mild reaction conditions, a few byproducts,
and relatively high activity of the used enzymes. β-adrenolytic drugs are widely
used in the treatment of hypertension and cardiovascular disorders. Due to the fact that β-
blockers possess an asymmetric carbon atom in their structure, they are presented in two
enantiomeric forms. It was reported by many studies that only the (S)-enantiomers of these
drugs possess the desired therapeutic effect, whereas the administration of the racemate may
cause dangerous side effects, such as bronchoconstriction or diabetes. Nevertheless, β-
blockers are still commercially available drugs mainly used in medicine as racemates, whereas there are several
methods that are widely used in order to obtain enantiomerically pure compounds.
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Affiliation(s)
- Joanna Chałupka
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Adam Sikora
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Aleksandra Kozicka
- Department of Medical Genetics, University in Cambridge, Lv 6 Addenbrooke’s Treatment Centre, Cambridge, United Kingdom
| | - Michał Piotr Marszałł
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
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5
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Borowiecki P, Młynek M, Dranka M. Chemoenzymatic synthesis of enantiomerically enriched diprophylline and xanthinol nicotinate. Bioorg Chem 2020; 106:104448. [PMID: 33229120 DOI: 10.1016/j.bioorg.2020.104448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/01/2023]
Abstract
A concise chemoenzymatic route toward enantiomerically enriched active pharmaceutical ingredients (API) - diprophylline and xanthinol nicotinate - is reported for the first time. The decisive step is an enantioselective lipase-mediated methanolysis of racemic chlorohydrin-synthon acetate, namely 1-chloro-3-(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)propan-2-yl acetate, performed under kinetically-controlled conditions on a preparative 500 mg-scale. The best results in terms of reaction enantioselectivity (E = 14) were obtained for the enantiomers resolution performed with lipase type B from Candida antarctica immobilized on acrylic resin (CAL-B, Novozym 435) suspended in homophasic acetonitrile-methanol mixture. The elaborated biocatalytic system furnished the key chlorohydrin intermediate (in 71% ee and 38% yield), which was then smoothly converted into enantioenriched active agents: (R)-(-)-diprophylline (57% ee) and (S)-(+)-xanthinol nicotinate (65% ee). To support the assignment of absolute configurations of EKR-products as well as to confirm the stereochemical outcome of the remaining reaction steps, docking studies toward the prediction of enantiomers binding selectivity in CAL-B active site as well as the respective chemical correlations with enantiomerically enriched analytical standards obtained from commercially available (R)-(-)-epichlorohydrin, were applied. In addition, single-crystal X-ray diffraction (XRD) analyses were performed for the synthesized optically active APIs furnishing by this manner a first crystal structures of nicotinic acid salt of xanthinol.
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Affiliation(s)
- Paweł Borowiecki
- Warsaw University of Technology, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformations, Koszykowa St. 75, 00-662 Warsaw, Poland.
| | - Mateusz Młynek
- Warsaw University of Technology, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformations, Koszykowa St. 75, 00-662 Warsaw, Poland
| | - Maciej Dranka
- Warsaw University of Technology, Faculty of Chemistry, Department of Inorganic Chemistry and Solid State Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W. Molecular dynamics study of taxadiene synthase catalysis. J Comput Chem 2018; 39:1215-1225. [PMID: 29450907 DOI: 10.1002/jcc.25184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Andrés M Escorcia
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | | | - Gui-Juan Cheng
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | - Patrick Schrepfer
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Thomas B Brück
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Walter Thiel
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
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7
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Barrera Valderrama DI, Doerr M, Daza Espinosa MC. Función de los confórmeros de ataque cercano en la acilación enantioselectiva del (R,S)-propranolol catalizada por lipasa B de Candida antarctica. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n1.73652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
La lipasa B de Candida antarctica (CalB) se ha utilizado en la acilación quimio- y enantioselectiva del racemato (R,S)-propranolol. CalB tiene enantioselectividad moderada (E=63) por el R-propranolol. La enantioselectividad, se origina en la reacción de transferencia del grupo acilo desde la serina catalítica, acilada, al propranolol. La fase inicial de esta reacción involucra la formación de complejos de Michaelis y posteriormente conformaciones de ataque cercano. El análisis de las conformaciones de ataque cercano ha permitido en varios casos explicar el origen de la catálisis o reproducir el efecto catalítico. En este trabajo se profundiza en la comprensión la función de las conformaciones de ataque cercano en la enantioselectividad de la acilación del (R,S)-propranolol catalizada por CalB. Para lo anterior se realizó un estudio detallado de los complejos de Michaelis y de las conformaciones de ataque cercano del paso enantioselectivo de la reacción de acilación del (R,S)-propranolol utilizando un protocolo de dinámica molecular QM/MM (SCCDFTB/CHARMM) utilizando 6 distribuciones de velocidades iniciales y simulaciones de 2,5 ns. Se estudiaron 7 complejos CalB-propranolol. Los enlaces de hidrógeno del sitio activo de CalB acilada relevantes para la actividad catalítica fueron estables en todas las simulaciones. Las poblaciones de los complejos de Michaelis y de las conformaciones de ataque cercano son dependientes de la distribución de las velocidades iniciales de la dinámica molecular. La enantioselectividad moderada de CalB acilada, encontrada experimentalmente, puede ser parcialmente atribuida a la alta población de conformaciones de ataque cercano observada para el S-propranolol.
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8
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Escorcia AM, Sen K, Daza MC, Doerr M, Thiel W. Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrés M. Escorcia
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Kakali Sen
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | - Martha C. Daza
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Markus Doerr
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
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Borowiecki P, Paprocki D, Dudzik A, Plenkiewicz J. Chemoenzymatic Synthesis of Proxyphylline Enantiomers. J Org Chem 2016; 81:380-95. [DOI: 10.1021/acs.joc.5b01840] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Paweł Borowiecki
- Warsaw University of Technology, Faculty of Chemistry,
Institute of Biotechnology, Koszykowa St. 3, 00-664 Warsaw, Poland
| | - Daniel Paprocki
- Warsaw University of Technology, Faculty of Chemistry,
Institute of Biotechnology, Koszykowa St. 3, 00-664 Warsaw, Poland
| | - Agnieszka Dudzik
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek St. 8, 30-239 Cracow, Poland
| | - Jan Plenkiewicz
- Warsaw University of Technology, Faculty of Chemistry,
Institute of Biotechnology, Koszykowa St. 3, 00-664 Warsaw, Poland
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