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Azevedo TSM, Silva LKB, Lima ÁS, Pereira MM, Franceschi E, Faria Soares CM. In Silico Evaluation of Enzymatic Tunnels in the Biotransformation of α-Tocopherol Esters. Front Bioeng Biotechnol 2022; 9:805059. [PMID: 35127674 PMCID: PMC8814584 DOI: 10.3389/fbioe.2021.805059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Motivation: α-Tocopherol is a molecule obtained primarily from plant sources that are important for the pharmaceutical and cosmetics industry. However, this component has some limitations such as sensitivity to oxygen, presence of light, and high temperatures. For this molecule to become more widely used, it is important to carry out a structural modification so that there is better stability and thus it can carry out its activities. To carry out this structural modification, some modifications are carried out, including the application of biotransformation using enzymes as biocatalysts. Thus, the application of a computational tool that helps in understanding the transport mechanisms of molecules in the tunnels present in the enzymatic structures is of fundamental importance because it promotes a computational screening facilitating bench applications. Objective: The aim of this work was to perform a computational analysis of the biotransformation of α-tocopherol into tocopherol esters, observing the tunnels present in the enzymatic structures as well as the energies which correspond to the transport of molecules. Method: To carry out this work, 9 lipases from different organisms were selected; their structures were analyzed by identifying the tunnels (quantity, conformation, and possibility of transport) and later the calculations of substrate transport for the biotransformation reaction in the identified tunnels were carried out. Additionally, the transport of the product obtained in the reaction through the tunnels was also carried out. Results: In this work, the quantity of existing tunnels in the morphological conformational characteristics in the lipases was verified. Thus, the enzymes with fewer tunnels were RML (3 tunnels), LBC and RNL (4 tunnels), PBLL (5 tunnels), CALB (6 tunnels), HLG (7 tunnels), and LCR and LTL (8 tunnels) and followed by the enzyme LPP with the largest number of tunnels (39 tunnels). However, the enzyme that was most likely to transport substrates in terms of α-tocopherol biotransformation (in relation to the Emax and Ea energies of ligands and products) was CALB, as it obtains conformational and transport characteristics of molecules with a particularity. The most conditions of transport analysis were α-tocopherol tunnel 3 (Emax: −4.6 kcal/mol; Ea: 1.1 kcal/mol), vinyl acetate tunnel 1 (Emax: −2.4 kcal/mol; Ea: 0.1 kcal/mol), and tocopherol acetate tunnel 2 (Emax: −3.7 kcal/mol; Ea: 2 kcal/mol).
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Affiliation(s)
- Tamara Stela Mendonça Azevedo
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Lavínia Kelly Barros Silva
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Álvaro Silva Lima
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Matheus Mendonça Pereira
- Department of Materials and Ceramic Engineering, CICECO ‐ Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
| | - Elton Franceschi
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
| | - Cleide Mara Faria Soares
- Graduate Program in Industrial Biotechnology, Tiradentes University (UNIT), Aracaju, Brazil
- Institute of Technology and Research (ITP), Aracaju, Brazil
- *Correspondence: Cleide Mara Faria Soares,
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Doerr M, Romero A, Daza MC. Effect of the acyl-group length on the chemoselectivity of the lipase-catalyzed acylation of propranolol-a computational study. J Mol Model 2021; 27:198. [PMID: 34115202 DOI: 10.1007/s00894-021-04808-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The selective N-acylation of 1,2-amino alcohols has been proposed to occur through the proton shuttle mechanism. However, the O-acetylation of propranolol catalyzed by Candida antarctica lipase B is an exception. We investigated the relation between the chemoselectivity of this reaction and the acyl group length. For this purpose, we compared the acyl groups: ethanoyl, butanoyl, octanoyl, and hexadecanoyl. We studied the Michaelis complexes between serine-acylated Candida antarctica lipase B and propranolol, employing a computational approach that involved sampling Michaelis complex conformations through ensemble docking plus consensus scoring and molecular dynamics simulations. The conformations were then classified as near attack conformations for acylation of the amino or hydroxy group. The relative populations of these two classes of conformations were found to be consistent with the experimentally observed chemoselective O-acetylation. We predict that increasing the length of the hydrocarbon chain of the acyl group will cause O-acylation to be unfavorable with respect to N-acylation. The nucleophilic attack of propranolol to the acylated lipase was found to be more favorable through the classical mechanism when compared with the proton shuttle mechanism.
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Affiliation(s)
- Markus Doerr
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra. 27 Calle 9, Bucaramanga, Colombia.
| | - Alexander Romero
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra. 27 Calle 9, Bucaramanga, Colombia
| | - Martha C Daza
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander, Cra. 27 Calle 9, Bucaramanga, Colombia
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Liu C, Wang Y, Liu J, Chen A, Xu J, Zhang R, Wang F, Nie K, Deng L. One-Step Synthesis of 4-Octyl Itaconate through the Structure Control of Lipase. J Org Chem 2021; 86:7895-7903. [PMID: 34085515 DOI: 10.1021/acs.joc.0c02995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
4-Octyl itaconate is a novel antiviral and immunoregulatory small molecule showing great potential in the treatment of various autoimmune diseases and viral infections. It is difficult to selectively esterify the C4 carboxyl group of itaconate acid via one-step direct esterification using chemical catalysts, while the two-step route with itaconic anhydride as an intermediate is environmentally unfriendly and costly. This research investigated the one-step and green synthesis of 4-octyl itaconate through the structure control of lipase, obtaining 4-octyl itaconate with over 98% yield and over 99% selectivity. Multiscale molecular dynamics simulations were applied to investigate the reaction mechanism. The cavity pocket of lipases resulted in a 4-octyl itaconate selectivity by affecting distribution of substrates toward the catalytic site. Toluene could enhance monoesterification in the C4 carboxyl group and contribute to a nearly 100% conversion from itaconate acid into 4-octyl itaconate by adjusting the catalytic microenvironment around the lipase, producing a shrinkage effect on the channel.
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Affiliation(s)
- Changsheng Liu
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Yilin Wang
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Jiahao Liu
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - An'nan Chen
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Juntao Xu
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Renwei Zhang
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Fang Wang
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Kaili Nie
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
| | - Li Deng
- Beijing Bioprocess Key Laboratory and State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology (BUCT), Beijing 100029, P. R. China
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Borowiecki P, Zdun B, Dranka M. Chemoenzymatic enantioselective and stereo-convergent syntheses of lisofylline enantiomers via lipase-catalyzed kinetic resolution and optical inversion approach. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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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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Yu H, Park KM, Chang PS. Lipase-catalyzed synthesis of lauroyl tripeptide-KHA with multi-functionalities: Its surface-active, antibacterial, and antioxidant properties. Food Chem 2020; 319:126533. [DOI: 10.1016/j.foodchem.2020.126533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/07/2020] [Accepted: 02/29/2020] [Indexed: 01/03/2023]
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Dettori L, Jelsch C, Guiavarc’h Y, Delaunay S, Framboisier X, Chevalot I, Humeau C. Molecular rules for selectivity in lipase-catalysed acylation of lysine. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Dettori L, Ferrari F, Framboisier X, Paris C, Guiavarc'h Y, Hôtel L, Aymes A, Leblond P, Humeau C, Kapel R, Chevalot I, Aigle B, Delaunay S. An aminoacylase activity from Streptomyces ambofaciens catalyzes the acylation of lysine on α-position and peptides on N-terminal position. Eng Life Sci 2018; 18:589-599. [PMID: 32624939 DOI: 10.1002/elsc.201700173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 11/11/2022] Open
Abstract
The presence of aminoacylase activities was investigated in a crude extract of Streptomyces ambofaciens ATCC23877. First activities catalyzing the hydrolysis of N-α or ε-acetyl-L-lysine were identified. Furthermore, the acylation of lysine and different peptides was studied and compared with results obtained with lipase B of Candida antarctica (CALB). Different regioselectivities were demonstrated for the two classes of enzymes. CALB was able to catalyze acylation only on the ε-position whereas the crude extract from S. ambofaciens possessed the rare ability to catalyze the N-acylation on the α-position of the lysine or of the amino-acid in N-terminal position of peptides. Two genes, SAM23877_1485 and SAM23877_1734, were identified in the genome of Streptomyces ambofaciens ATCC23877 whose products show similarities with the previously identified aminoacylases from Streptomyces mobaraensis. The proteins encoded by these two genes were responsible for the major aminoacylase hydrolytic activities. Furthermore, we show that the hydrolysis of N-α-acetyl-L-lysine could be attributed to the product of SAM23877_1734 gene.
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Affiliation(s)
| | | | | | - Cédric Paris
- Université de Lorraine Plateau d'Analyse Structurale et Métabolomique Nancy France
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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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10
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Kuo CH, Lin JA, Chien CM, Tsai CH, Liu YC, Shieh CJ. Formation of amide bond catalyzed by lipase in aqueous phase for peptide synthesis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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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