1
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Ludwig J, Curado-Carballada C, Hammer SC, Schneider A, Diether S, Kress N, Ruiz-Barragán S, Osuna S, Hauer B. Controlling Monoterpene Isomerization by Guiding Challenging Carbocation Rearrangement Reactions in Engineered Squalene-Hopene Cyclases. Angew Chem Int Ed Engl 2024; 63:e202318913. [PMID: 38270537 DOI: 10.1002/anie.202318913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024]
Abstract
The interconversion of monoterpenes is facilitated by a complex network of carbocation rearrangement pathways. Controlling these isomerization pathways is challenging when using common Brønsted and Lewis acid catalysts, which often produce product mixtures that are difficult to separate. In contrast, natural monoterpene cyclases exhibit high control over the carbocation rearrangement reactions but are reliant on phosphorylated substrates. In this study, we present engineered squalene-hopene cyclases from Alicyclobacillus acidocaldarius (AacSHC) that catalyze the challenging isomerization of monoterpenes with unprecedented precision. Starting from a promiscuous isomerization of (+)-β-pinene, we first demonstrate noticeable shifts in the product distribution solely by introducing single point mutations. Furthermore, we showcase the tuneable cation steering by enhancing (+)-borneol selectivity from 1 % to >90 % (>99 % de) aided by iterative saturation mutagenesis. Our combined experimental and computational data suggest that the reorganization of key aromatic residues leads to the restructuring of the water network that facilitates the selective termination of the secondary isobornyl cation. This work expands our mechanistic understanding of carbocation rearrangements and sets the stage for target-oriented skeletal reorganization of broadly abundant terpenes.
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Affiliation(s)
- Julian Ludwig
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Christian Curado-Carballada
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Stephan C Hammer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
- Faculty of Chemistry, Organic Chemistry and Biocatalysis, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Andreas Schneider
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Svenja Diether
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Nico Kress
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Sergi Ruiz-Barragán
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- Departament de Fisica, Universitat Politecnica de Catalunya, Rambla Sant Nebridi 22, 08222, Terrassa, Barcelona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and, Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003, Girona, Spain
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Bernhard Hauer
- Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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2
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Menendez JA, Cuyàs E, Encinar JA, Vander Steen T, Verdura S, Llop‐Hernández À, López J, Serrano‐Hervás E, Osuna S, Martin‐Castillo B, Lupu R. Fatty acid synthase (FASN) signalome: A molecular guide for precision oncology. Mol Oncol 2024; 18:479-516. [PMID: 38158755 PMCID: PMC10920094 DOI: 10.1002/1878-0261.13582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The initial excitement generated more than two decades ago by the discovery of drugs targeting fatty acid synthase (FASN)-catalyzed de novo lipogenesis for cancer therapy was short-lived. However, the advent of the first clinical-grade FASN inhibitor (TVB-2640; denifanstat), which is currently being studied in various phase II trials, and the exciting advances in understanding the FASN signalome are fueling a renewed interest in FASN-targeted strategies for the treatment and prevention of cancer. Here, we provide a detailed overview of how FASN can drive phenotypic plasticity and cell fate decisions, mitochondrial regulation of cell death, immune escape and organ-specific metastatic potential. We then present a variety of FASN-targeted therapeutic approaches that address the major challenges facing FASN therapy. These include limitations of current FASN inhibitors and the lack of precision tools to maximize the therapeutic potential of FASN inhibitors in the clinic. Rethinking the role of FASN as a signal transducer in cancer pathogenesis may provide molecularly driven strategies to optimize FASN as a long-awaited target for cancer therapeutics.
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Affiliation(s)
- Javier A. Menendez
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Jose Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC)Miguel Hernández University (UMH)ElcheSpain
| | - Travis Vander Steen
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
| | - Sara Verdura
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Àngela Llop‐Hernández
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Júlia López
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Eila Serrano‐Hervás
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
- ICREABarcelonaSpain
| | - Begoña Martin‐Castillo
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- Unit of Clinical ResearchCatalan Institute of OncologyGironaSpain
| | - Ruth Lupu
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
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3
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Casadevall G, Casadevall J, Duran C, Osuna S. The shortest path method (SPM) webserver for computational enzyme design. Protein Eng Des Sel 2024; 37:gzae005. [PMID: 38431867 DOI: 10.1093/protein/gzae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024] Open
Abstract
SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally-relevant positions of a given enzyme structure and dynamics. The server is built on top of the DynaComm.py code and enables the calculation and visualization of the SPM pathways. SPMweb is easy-to-use as it only requires three input files: the three-dimensional structure of the protein of interest, and the two matrices (distance and correlation) previously computed from a Molecular Dynamics simulation. We provide in this publication information on how to generate the files for SPM construction even for non-expert users and discuss the most relevant parameters that can be modified. The tool is extremely fast (it takes less than one minute per job), thus allowing the rapid identification of distal positions connected to the active site pocket of the enzyme. SPM applications expand from computational enzyme design, especially if combined with other tools to identify the preferred substitution at the identified position, but also to rationalizing allosteric regulation, and even cryptic pocket identification for drug discovery. The simple user interface and setup make the SPM tool accessible to the whole scientific community. SPMweb is freely available for academia at http://spmosuna.com/.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | | | - Cristina Duran
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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4
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Castelli M, Marchetti F, Osuna S, F. Oliveira AS, Mulholland AJ, Serapian SA, Colombo G. Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations. J Am Chem Soc 2024; 146:901-919. [PMID: 38116743 PMCID: PMC10785808 DOI: 10.1021/jacs.3c11396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
Protein functions are dynamically regulated by allostery, which enables conformational communication even between faraway residues, and expresses itself in many forms, akin to different "languages": allosteric control pathways predominating in an unperturbed protein are often unintuitively reshaped whenever biochemical perturbations arise (e.g., mutations). To accurately model allostery, unbiased molecular dynamics (MD) simulations require integration with a reliable method able to, e.g., detect incipient allosteric changes or likely perturbation pathways; this is because allostery can operate at longer time scales than those accessible by plain MD. Such methods are typically applied singularly, but we here argue their joint application─as a "multilingual" approach─could work significantly better. We successfully prove this through unbiased MD simulations (∼100 μs) of the widely studied, allosterically active oncotarget K-Ras4B, solvated and embedded in a phospholipid membrane, from which we decrypt allostery using four showcase "languages": Distance Fluctuation analysis and the Shortest Path Map capture allosteric hotspots at equilibrium; Anisotropic Thermal Diffusion and Dynamical Non-Equilibrium MD simulations assess perturbations upon, respectively, either superheating or hydrolyzing the GTP that oncogenically activates K-Ras4B. Chosen "languages" work synergistically, providing an articulate, mutually coherent, experimentally consistent picture of K-Ras4B allostery, whereby distinct traits emerge at equilibrium and upon GTP cleavage. At equilibrium, combined evidence confirms prominent allosteric communication from the membrane-embedded hypervariable region, through a hub comprising helix α5 and sheet β5, and up to the active site, encompassing allosteric "switches" I and II (marginally), and two proposed pockets. Upon GTP cleavage, allosteric perturbations mostly accumulate on the switches and documented interfaces.
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Affiliation(s)
- Matteo Castelli
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Filippo Marchetti
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
- INSTM, via G. Giusti 9, 50121 Florence, Italy
- E4
Computer Engineering, via Martiri delle libertà 66, 42019 Scandiano (RE), Italy
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Girona, Catalonia E-17071, Spain
- ICREA, Barcelona, Catalonia E-08010, Spain
| | - A. Sofia F. Oliveira
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Adrian J. Mulholland
- Centre for
Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Stefano A. Serapian
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department
of Chemistry, University of Pavia, viale T. Taramelli 12, 27100 Pavia, Italy
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5
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Busch MR, Drexler L, Mahato DR, Hiefinger C, Osuna S, Sterner R. Retracing the Rapid Evolution of an Herbicide-Degrading Enzyme by Protein Engineering. ACS Catal 2023; 13:15558-15571. [PMID: 38567019 PMCID: PMC7615792 DOI: 10.1021/acscatal.3c04010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The mechanisms underlying the rapid evolution of novel enzymatic activities from promiscuous side activities are poorly understood. Recently emerged enzymes catalyzing the catabolic degradation of xenobiotic substances that have been spread out into the environment during the last decades provide an exquisite opportunity to study these mechanisms. A prominent example is the herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine), which is degraded through a number of enzymatic reactions constituting the Atz pathway. Here, we analyzed the evolution of the hydroxyatrazine ethylaminohydrolase AtzB, a Zn(II)-dependent metalloenzyme that adopts the amidohydrolase fold and catalyzes the second step of the Atz pathway. We searched for promiscuous side activities of AtzB, which might point to the identity of its progenitor. These investigations revealed that AtzB has low promiscuous guanine deaminase activity. Furthermore, we found that the two closest AtzB homologues, which have not been functionally annotated up to now, are guanine deaminases with modest promiscuous hydroxyatrazine hydrolase activity. Based on sequence comparisons with the closest AtzB homologues, the guanine deaminase activity of AtzB could be increased by three orders of magnitude through the introduction of only four active site mutations. Interestingly, introducing the inverse four mutations into the AtzB homologues significantly enhanced their hydroxyatrazine hydrolase activity, and in one case is even equivalent to that of wild-type AtzB. Molecular dynamics simulations elucidated the structural and molecular basis for the mutation-induced activity changes. The example of AtzB highlights how novel enzymes with high catalytic proficiency can evolve from low promiscuous side activities by only few mutational events within a short period of time.
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Affiliation(s)
- Markus R. Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Lukas Drexler
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Dhani Ram Mahato
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Caroline Hiefinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
- ICREA, Barcelona 08010, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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6
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Casadevall G, Pierce C, Guan B, Iglesias-Fernandez J, Lim HY, Greenberg LR, Walsh ME, Shi K, Gordon W, Aihara H, Evans RL, Kazlauskas R, Osuna S. Designing Efficient Enzymes: Eight Predicted Mutations Convert a Hydroxynitrile Lyase into an Efficient Esterase. bioRxiv 2023:2023.08.23.554512. [PMID: 37662272 PMCID: PMC10473745 DOI: 10.1101/2023.08.23.554512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydroxynitrile lyase from rubber tree (HbHNL) shares 45% identical amino acid residues with the homologous esterase from tobacco, SABP2, but the two enzymes catalyze different reactions. The x-ray structures reveal a serine-histidine-aspartate catalytic triad in both enzymes along with several differing amino acid residues within the active site. Previous exchange of three amino acid residues in the active site of HbHNL with the corresponding amino acid residue in SABP2 (T11G-E79H-K236M) created variant HNL3, which showed low esterase activity toward p-nitrophenyl acetate. Further structure comparison reveals additional differences surrounding the active site. HbHNL contains an improperly positioned oxyanion hole residue and differing solvation of the catalytic aspartate. We hypothesized that correcting these structural differences would impart good esterase activity on the corresponding HbHNL variant. To predict the amino acid substitutions needed to correct the structure, we calculated shortest path maps for both HbHNL and SABP2, which reveal correlated movements of amino acids in the two enzymes. Replacing four amino acid residues (C81L-N104T-V106F-G176S) whose movements are connected to the movements of the catalytic residues yielded variant HNL7TV (stabilizing substitution H103V was also added), which showed an esterase catalytic efficiency comparable to that of SABP2. The x-ray structure of an intermediate variant, HNL6V, showed an altered solvation of the catalytic aspartate and a partially corrected oxyanion hole. This dramatic increase in catalytic efficiency demonstrates the ability of shortest path maps to predict which residues outside the active site contribute to catalytic activity.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Colin Pierce
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bo Guan
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Javier Iglesias-Fernandez
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Huey-Yee Lim
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Lauren R Greenberg
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Meghan E Walsh
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Ke Shi
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Wendy Gordon
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Hideki Aihara
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Robert L Evans
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Romas Kazlauskas
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Barcelona, Spain
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7
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Palone A, Casadevall G, Ruiz-Barragan S, Call A, Osuna S, Bietti M, Costas M. C-H Bonds as Functional Groups: Simultaneous Generation of Multiple Stereocenters by Enantioselective Hydroxylation at Unactivated Tertiary C-H Bonds. J Am Chem Soc 2023; 145:15742-15753. [PMID: 37431886 PMCID: PMC10651061 DOI: 10.1021/jacs.2c10148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 07/12/2023]
Abstract
Enantioselective C-H oxidation is a standing chemical challenge foreseen as a powerful tool to transform readily available organic molecules into precious oxygenated building blocks. Here, we describe a catalytic enantioselective hydroxylation of tertiary C-H bonds in cyclohexane scaffolds with H2O2, an evolved manganese catalyst that provides structural complementary to the substrate similarly to the lock-and-key recognition operating in enzymatic active sites. Theoretical calculations unveil that enantioselectivity is governed by the precise fitting of the substrate scaffold into the catalytic site, through a network of complementary weak non-covalent interactions. Stereoretentive C(sp3)-H hydroxylation results in a single-step generation of multiple stereogenic centers (up to 4) that can be orthogonally manipulated by conventional methods providing rapid access, from a single precursor to a variety of chiral scaffolds.
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Affiliation(s)
- Andrea Palone
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Guillem Casadevall
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Sergi Ruiz-Barragan
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Arnau Call
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Massimo Bietti
- Dipartimento
di Scienze e Tecnologie Chimiche, Università
“Tor Vergata”, Via della Ricerca Scientifica, 1, I-00133 Rome, Italy
| | - Miquel Costas
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Campus Montilivi, Girona, Catalonia E-17071, Spain
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8
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Casadevall G, Duran C, Osuna S. AlphaFold2 and Deep Learning for Elucidating Enzyme Conformational Flexibility and Its Application for Design. JACS Au 2023; 3:1554-1562. [PMID: 37388680 PMCID: PMC10302747 DOI: 10.1021/jacsau.3c00188] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
The recent success of AlphaFold2 (AF2) and other deep learning (DL) tools in accurately predicting the folded three-dimensional (3D) structure of proteins and enzymes has revolutionized the structural biology and protein design fields. The 3D structure indeed reveals key information on the arrangement of the catalytic machinery of enzymes and which structural elements gate the active site pocket. However, comprehending enzymatic activity requires a detailed knowledge of the chemical steps involved along the catalytic cycle and the exploration of the multiple thermally accessible conformations that enzymes adopt when in solution. In this Perspective, some of the recent studies showing the potential of AF2 in elucidating the conformational landscape of enzymes are provided. Selected examples of the key developments of AF2-based and DL methods for protein design are discussed, as well as a few enzyme design cases. These studies show the potential of AF2 and DL for allowing the routine computational design of efficient enzymes.
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Affiliation(s)
- Guillem Casadevall
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Cristina Duran
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Sílvia Osuna
- Institut
de Química Computacional i Catàlisi (IQCC) and Departament
de Química, Universitat de Girona, Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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9
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Schneider A, Curado C, Lystbaek TB, Osuna S, Hauer B. Harnessing the Structure and Dynamics of the Squalene-Hopene Cyclase for (-)-Ambroxide Production. Angew Chem Int Ed Engl 2023; 62:e202301607. [PMID: 36939150 DOI: 10.1002/anie.202301607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/21/2023]
Abstract
Terpene cyclases offer enormous synthetic potential, given their unique ability to forge complex hydrocarbon scaffolds from achiral precursors within a single cationic rearrangement cascade. Harnessing their synthetic power, however, proved to be challenging due to their generally low catalytic performance. In this study, we unveil the catalytic potential of the squalene-hopene cyclase (SHC) by harnessing its structure and dynamics. First, we synergistically tailored the enzyme's active site and entrance tunnel to generate a 397-fold improved (-)-ambroxide synthase. Our computational investigations explain how the introduced mutations work in concert to improve substrate acquisition, flow, and chaperoning. Kinetics, however, disclosed a terpene-induced inactivation of the membrane-bound SHC as the major turnover limitation in vivo. Merging these insights with the improved and stereoselective catalysis of the enzyme, we applied a feeding strategy to exceed 105 total turnovers. We believe that our results may bridge the gap for broader application of SHCs in synthetic chemistry.
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Affiliation(s)
| | - Christian Curado
- University of Girona: Universitat de Girona, Institut de Química, SPAIN
| | - Thomas B Lystbaek
- Universität Stuttgart Universitätsbibliothek Stuttgart: Universitat Stuttgart Universitatsbibliothek, Chemistry, GERMANY
| | - Sílvia Osuna
- University of Girona: Universitat de Girona, Institut de Química, SPAIN
| | - Bernhard Hauer
- Universitaet Stuttgart, Technische Biochemie, Allmandring 31, 70569, Stuttgart, GERMANY
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10
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Shehata M, Ünlü A, Iglesias-Fernández J, Osuna S, Sezerman OU, Timucin E. Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog. Phys Chem Chem Phys 2023; 25:2234-2247. [PMID: 36594810 DOI: 10.1039/d2cp05093e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.
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Affiliation(s)
- Mohamed Shehata
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Aişe Ünlü
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | | | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - O Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
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11
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Codony S, Entrena JM, Calvó-Tusell C, Jora B, González-Cano R, Osuna S, Corpas R, Morisseau C, Pérez B, Barniol-Xicota M, Griñán-Ferré C, Pérez C, Rodríguez-Franco MI, Martínez AL, Loza MI, Pallàs M, Verhelst SHL, Sanfeliu C, Feixas F, Hammock BD, Brea J, Cobos EJ, Vázquez S. Synthesis, In Vitro Profiling, and In Vivo Evaluation of Benzohomoadamantane-Based Ureas for Visceral Pain: A New Indication for Soluble Epoxide Hydrolase Inhibitors. J Med Chem 2022; 65:13660-13680. [PMID: 36222708 PMCID: PMC9620236 DOI: 10.1021/acs.jmedchem.2c00515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The soluble epoxide hydrolase (sEH) has been suggested as a pharmacological target for the treatment of several diseases, including pain-related disorders. Herein, we report further medicinal chemistry around new benzohomoadamantane-based sEH inhibitors (sEHI) in order to improve the drug metabolism and pharmacokinetics properties of a previous hit. After an extensive in vitro screening cascade, molecular modeling, and in vivo pharmacokinetics studies, two candidates were evaluated in vivo in a murine model of capsaicin-induced allodynia. The two compounds showed an anti-allodynic effect in a dose-dependent manner. Moreover, the most potent compound presented robust analgesic efficacy in the cyclophosphamide-induced murine model of cystitis, a well-established model of visceral pain. Overall, these results suggest painful bladder syndrome as a new possible indication for sEHI, opening a new range of applications for them in the visceral pain field.
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Affiliation(s)
- Sandra Codony
- Laboratori
de Química Farmacèutica (Unitat Associada al CSIC),
Facultat de Farmàcia i Ciències de l’Alimentació,
and Institute of Biomedicine (IBUB), Universitat
de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - José M. Entrena
- Animal
Behavior Research Unit, Scientific Instrumentation Center, Parque
Tecnológico de Ciencias de la Salud, University of Granada, Armilla, Granada 18100, Spain
| | - Carla Calvó-Tusell
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Beatrice Jora
- Laboratori
de Química Farmacèutica (Unitat Associada al CSIC),
Facultat de Farmàcia i Ciències de l’Alimentació,
and Institute of Biomedicine (IBUB), Universitat
de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Rafael González-Cano
- Department
of Pharmacology, Faculty of Medicine and Biomedical Research Center
(Neurosciences Institute), Biosanitary Research Institute ibs.GRANADA, University of Granada, Avenida de la Investigación 11, Granada 18016, Spain
| | - Sílvia Osuna
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain,Institució
Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Rubén Corpas
- Institute
of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain
| | - Christophe Morisseau
- Department
of Entomology and Nematology and Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Belén Pérez
- Department
of Pharmacology, Therapeutics and Toxicology, Institute of Neurosciences, Autonomous University of Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Marta Barniol-Xicota
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven—University of Leuven, Herestraat 49 box B901, Leuven 3000, Belgium
| | - Christian Griñán-Ferré
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av. Joan XXIII 27-31, Barcelona 08028, Spain
| | - Concepción Pérez
- Institute of Medicinal Chemistry, Spanish
National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - María Isabel Rodríguez-Franco
- Institute of Medicinal Chemistry, Spanish
National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - Antón L. Martínez
- Drug Screening
Platform/Biofarma Research Group, CIMUS Research Center, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - M. Isabel Loza
- Drug Screening
Platform/Biofarma Research Group, CIMUS Research Center, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - Mercè Pallàs
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Av. Joan XXIII 27-31, Barcelona 08028, Spain
| | - Steven H. L. Verhelst
- Laboratory
of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven—University of Leuven, Herestraat 49 box B901, Leuven 3000, Belgium,Leibniz Institute
for Analytical Sciences ISAS, AG Chemical
Proteomics, Otto-Hahn-Str.
6b, Dortmund 44227, Germany
| | - Coral Sanfeliu
- Institute
of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain
| | - Ferran Feixas
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Bruce D. Hammock
- Department
of Entomology and Nematology and Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - José Brea
- Drug Screening
Platform/Biofarma Research Group, CIMUS Research Center, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - Enrique J. Cobos
- Department
of Pharmacology, Faculty of Medicine and Biomedical Research Center
(Neurosciences Institute), Biosanitary Research Institute ibs.GRANADA, University of Granada, Avenida de la Investigación 11, Granada 18016, Spain
| | - Santiago Vázquez
- Laboratori
de Química Farmacèutica (Unitat Associada al CSIC),
Facultat de Farmàcia i Ciències de l’Alimentació,
and Institute of Biomedicine (IBUB), Universitat
de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain,. Phone: +34 934024533
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12
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Casadevall G, Duran C, Estévez‐Gay M, Osuna S. Estimating conformational heterogeneity of tryptophan synthase with a template‐based
Alphafold2
approach. Protein Sci 2022; 31:e4426. [PMID: 36173176 PMCID: PMC9601780 DOI: 10.1002/pro.4426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/29/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022]
Abstract
The three‐dimensional structure of the enzymes provides very relevant information on the arrangement of the catalytic machinery and structural elements gating the active site pocket. The recent success of the neural network Alphafold2 in predicting the folded structure of proteins from the primary sequence with high levels of accuracy has revolutionized the protein design field. However, the application of Alphafold2 for understanding and engineering function directly from the obtained single static picture is not straightforward. Indeed, understanding enzymatic function requires the exploration of the ensemble of thermally accessible conformations that enzymes adopt in solution. In the present study, we evaluate the potential of Alphafold2 in assessing the effect of the mutations on the conformational landscape of the beta subunit of tryptophan synthase (TrpB). Specifically, we develop a template‐based Alphafold2 approach for estimating the conformational heterogeneity of several TrpB enzymes, which is needed for enhanced stand‐alone activity. Our results show the potential of Alphafold2, especially if combined with molecular dynamics simulations, for elucidating the changes induced by mutation in the conformational landscapes at a rather reduced computational cost, thus revealing its plausible application in computational enzyme design.
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Affiliation(s)
- Guillem Casadevall
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Cristina Duran
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Miquel Estévez‐Gay
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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13
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Calvó-Tusell C, Maria-Solano MA, Osuna S, Feixas F. Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase. J Am Chem Soc 2022; 144:7146-7159. [PMID: 35412310 PMCID: PMC9052757 DOI: 10.1021/jacs.1c12629] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Deciphering the molecular
mechanisms of enzymatic allosteric regulation
requires the structural characterization of functional states and
also their time evolution toward the formation of the allosterically
activated ternary complex. The transient nature and usually slow millisecond
time scale interconversion between these functional states hamper
their experimental and computational characterization. Here, we combine
extensive molecular dynamics simulations, enhanced sampling techniques,
and dynamical networks to describe the allosteric activation of imidazole
glycerol phosphate synthase (IGPS) from the substrate-free form to
the active ternary complex. IGPS is a heterodimeric bienzyme complex
whose HisH subunit is responsible for hydrolyzing glutamine and delivering
ammonia for the cyclase activity in HisF. Despite significant advances
in understanding the underlying allosteric mechanism, essential molecular
details of the long-range millisecond allosteric activation of IGPS
remain hidden. Without using a priori information
of the active state, our simulations uncover how IGPS, with the allosteric
effector bound in HisF, spontaneously captures glutamine in a catalytically
inactive HisH conformation, subsequently attains a closed HisF:HisH
interface, and finally forms the oxyanion hole in HisH for efficient
glutamine hydrolysis. We show that the combined effector and substrate
binding dramatically decreases the conformational barrier associated
with oxyanion hole formation, in line with the experimentally observed
4500-fold activity increase in glutamine hydrolysis. The allosteric
activation is controlled by correlated time-evolving dynamic networks
connecting the effector and substrate binding sites. This computational
strategy tailored to describe millisecond events can be used to rationalize
the effect of mutations on the allosteric regulation and guide IGPS
engineering efforts.
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Affiliation(s)
- Carla Calvó-Tusell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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14
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Codony S, Pont C, Griñán-Ferré C, Di Pede-Mattatelli A, Calvó-Tusell C, Feixas F, Osuna S, Jarné-Ferrer J, Naldi M, Bartolini M, Loza MI, Brea J, Pérez B, Bartra C, Sanfeliu C, Juárez-Jiménez J, Morisseau C, Hammock BD, Pallàs M, Vázquez S, Muñoz-Torrero D. Discovery and In Vivo Proof of Concept of a Highly Potent Dual Inhibitor of Soluble Epoxide Hydrolase and Acetylcholinesterase for the Treatment of Alzheimer's Disease. J Med Chem 2022; 65:4909-4925. [PMID: 35271276 PMCID: PMC8958510 DOI: 10.1021/acs.jmedchem.1c02150] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With innumerable clinical failures of target-specific drug candidates for multifactorial diseases, such as Alzheimer's disease (AD), which remains inefficiently treated, the advent of multitarget drug discovery has brought a new breath of hope. Here, we disclose a class of 6-chlorotacrine (huprine)-TPPU hybrids as dual inhibitors of the enzymes soluble epoxide hydrolase (sEH) and acetylcholinesterase (AChE), a multitarget profile to provide cumulative effects against neuroinflammation and memory impairment. Computational studies confirmed the gorge-wide occupancy of both enzymes, from the main site to a secondary site, including a so far non-described AChE cryptic pocket. The lead compound displayed in vitro dual nanomolar potencies, adequate brain permeability, aqueous solubility, human microsomal stability, lack of neurotoxicity, and it rescued memory, synaptic plasticity, and neuroinflammation in an AD mouse model, after low dose chronic oral administration.
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Affiliation(s)
- Sandra Codony
- Laboratory
of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy
and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory
of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy
and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Christian Griñán-Ferré
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, and Institute of Neurosciences, University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Ania Di Pede-Mattatelli
- Department
of Pharmacy and Pharmaceutical Technology and Physical Chemistry,
Faculty of Pharmacy and Food Sciences, and Institute of Theoretical
and Computational Chemistry (IQTCUB), University
of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Carla Calvó-Tusell
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, E-17003 Girona, Spain
| | - Ferran Feixas
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, E-17003 Girona, Spain
| | - Sílvia Osuna
- CompBioLab
Group, Departament de Química and Institut de Química
Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, E-17003 Girona, Spain,Institució
Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
| | - Júlia Jarné-Ferrer
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, and Institute of Neurosciences, University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Marina Naldi
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Belmeloro, 6, I-40126 Bologna, Italy
| | - Manuela Bartolini
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Belmeloro, 6, I-40126 Bologna, Italy
| | - María Isabel Loza
- BioFarma
Research Group, Centro Singular de Investigación en Medicina
Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Av. de Barcelona s/n, E-15782 Santiago de Compostela, Spain
| | - José Brea
- BioFarma
Research Group, Centro Singular de Investigación en Medicina
Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Av. de Barcelona s/n, E-15782 Santiago de Compostela, Spain
| | - Belén Pérez
- Department
of Pharmacology, Therapeutics and Toxicology, Autonomous University of Barcelona, E-08193 Bellaterra, Spain
| | - Clara Bartra
- Institute
of Biomedical Research of Barcelona, CSIC and Institut d’Investigacions
Biomèdiques August Pi i Sunyer (IDIBAPS), Rosselló, 149, E-08036 Barcelona, Spain
| | - Coral Sanfeliu
- Institute
of Biomedical Research of Barcelona, CSIC and Institut d’Investigacions
Biomèdiques August Pi i Sunyer (IDIBAPS), Rosselló, 149, E-08036 Barcelona, Spain
| | - Jordi Juárez-Jiménez
- Department
of Pharmacy and Pharmaceutical Technology and Physical Chemistry,
Faculty of Pharmacy and Food Sciences, and Institute of Theoretical
and Computational Chemistry (IQTCUB), University
of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Christophe Morisseau
- Department
of Entomology and Nematology and Comprehensive Cancer Center, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Bruce D. Hammock
- Department
of Entomology and Nematology and Comprehensive Cancer Center, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Mercè Pallàs
- Pharmacology
Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry,
Faculty of Pharmacy and Food Sciences, and Institute of Neurosciences, University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Santiago Vázquez
- Laboratory
of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy
and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain,. Phone: (+34) 934024533
| | - Diego Muñoz-Torrero
- Laboratory
of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy
and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona (UB), Av. Joan XXIII 27-31, E-08028 Barcelona, Spain,. Phone: (+34) 934024533
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15
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Maria-Solano MA, Kinateder T, Iglesias-Fernández J, Sterner R, Osuna S. In Silico Identification and Experimental Validation of Distal Activity-Enhancing Mutations in Tryptophan Synthase. ACS Catal 2021; 11:13733-13743. [PMID: 34777912 PMCID: PMC8576815 DOI: 10.1021/acscatal.1c03950] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Allostery is a central mechanism for the regulation of multi-enzyme complexes. The mechanistic basis that drives allosteric regulation is poorly understood but harbors key information for enzyme engineering. In the present study, we focus on the tryptophan synthase complex that is composed of TrpA and TrpB subunits, which allosterically activate each other. Specifically, we develop a rational approach for identifying key amino acid residues of TrpB distal from the active site. Those residues are predicted to be crucial for shifting the inefficient conformational ensemble of the isolated TrpB to a productive ensemble through intra-subunit allosteric effects. The experimental validation of the conformationally driven TrpB design demonstrates its superior stand-alone activity in the absence of TrpA, comparable to those enhancements obtained after multiple rounds of experimental laboratory evolution. Our work evidences that the current challenge of distal active site prediction for enhanced function in computational enzyme design has become within reach.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Javier Iglesias-Fernández
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Nostrum Biodiscovery, Carrer de Baldiri Reixac, 10-12, Barcelona 08028, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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16
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Floor M, Li K, Estévez-Gay M, Agulló L, Muñoz-Torres PM, Hwang JK, Osuna S, Villà-Freixa J. SBMOpenMM: A Builder of Structure-Based Models for OpenMM. J Chem Inf Model 2021; 61:3166-3171. [PMID: 34251801 DOI: 10.1021/acs.jcim.1c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular dynamics (MD) simulations have become a standard tool to correlate the structure and function of biomolecules and significant advances have been made in the study of proteins and their complexes. A major drawback of conventional MD simulations is the difficulty and cost of obtaining converged results, especially when exploring potential energy surfaces containing considerable energy barriers. This limits the wide use of MD calculations to determine the thermodynamic properties of biomolecular processes. Indeed, this is true when considering the conformational entropy of such processes, which is ultimately critical in assessing the simulations' convergence. Alternatively, a wide range of structure-based models (SBMs) has been used in the literature to unravel the basic mechanisms of biomolecular dynamics. These models introduce simplifications that focus on the relevant aspects of the physical process under study. Because of this, SBMs incorporate the need to modify the force field definition and parameters to target specific biophysical simulations. Here we introduce SBMOpenMM, a Python library to build force fields for SBMs, that uses the OpenMM framework to create and run SBM simulations. The code is flexible and user-friendly and profits from the high customizability and performance provided by the OpenMM platform.
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Affiliation(s)
- Martin Floor
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain.,Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic-Universitat Central de Catalunya, 08500 Vic, Spain
| | - Kengjie Li
- Warshel Institute of Computational Biology, The Chinese University of Hong Kong, 518172 Shenzhen, China
| | - Miquel Estévez-Gay
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17071 Girona, Spain
| | - Luis Agulló
- Faculty of Medicine, Universitat de Vic-Universitat Central de Catalunya, 08500 Vic, Spain
| | - Pau Marc Muñoz-Torres
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain
| | - Jenn K Hwang
- Warshel Institute of Computational Biology, The Chinese University of Hong Kong, 518172 Shenzhen, China
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, 17071 Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Jordi Villà-Freixa
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain.,Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic-Universitat Central de Catalunya, 08500 Vic, Spain
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17
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Codony S, Calvó-Tusell C, Valverde E, Osuna S, Morisseau C, Loza MI, Brea J, Pérez C, Rodríguez-Franco MI, Pizarro-Delgado J, Corpas R, Griñán-Ferré C, Pallàs M, Sanfeliu C, Vázquez-Carrera M, Hammock BD, Feixas F, Vázquez S. From the Design to the In Vivo Evaluation of Benzohomoadamantane-Derived Soluble Epoxide Hydrolase Inhibitors for the Treatment of Acute Pancreatitis. J Med Chem 2021; 64:5429-5446. [PMID: 33945278 PMCID: PMC8634379 DOI: 10.1021/acs.jmedchem.0c01601] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The
pharmacological inhibition of soluble epoxide hydrolase (sEH)
is efficient for the treatment of inflammatory and pain-related diseases.
Numerous potent sEH inhibitors (sEHIs) present adamantyl or phenyl
moieties, such as the clinical candidates AR9281 or EC5026. Herein,
in a new series of sEHIs, these hydrophobic moieties have been merged
in a benzohomoadamantane scaffold. Most of the new sEHIs have excellent
inhibitory activities against sEH. Molecular dynamics simulations
suggested that the addition of an aromatic ring into the adamantane
scaffold produced conformational rearrangements in the enzyme to stabilize
the aromatic ring of the benzohomoadamantane core. A screening cascade
permitted us to select a candidate for an in vivo efficacy study in a murine model of cerulein-induced acute pancreatitis.
The administration of 22 improved the health status of
the animals and reduced pancreatic damage, demonstrating that the
benzohomoadamantane unit is a promising scaffold for the design of
novel sEHIs.
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Affiliation(s)
- Sandra Codony
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Carla Calvó-Tusell
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Elena Valverde
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Sílvia Osuna
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Christophe Morisseau
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis 95616, California, United States
| | - M Isabel Loza
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - José Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - Concepción Pérez
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - María Isabel Rodríguez-Franco
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - Javier Pizarro-Delgado
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, Madrid 28029, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, Esplugues de Llobregat 08950, Spain
| | - Rubén Corpas
- Institute of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain.,CIBER Epidemiology and Public Health (CIBERESP)-Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Christian Griñán-Ferré
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institut de Neurociències, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Mercè Pallàs
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institut de Neurociències, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Coral Sanfeliu
- Institute of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain.,CIBER Epidemiology and Public Health (CIBERESP)-Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Manuel Vázquez-Carrera
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, Madrid 28029, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, Esplugues de Llobregat 08950, Spain
| | - Bruce D Hammock
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis 95616, California, United States
| | - Ferran Feixas
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
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18
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Wessel J, Petrillo G, Estevez-Gay M, Bosch S, Seeger M, Dijkman WP, Iglesias-Fernández J, Hidalgo A, Uson I, Osuna S, Schallmey A. Insights into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2. FEBS J 2021; 288:4683-4701. [PMID: 33605544 DOI: 10.1111/febs.15777] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/07/2021] [Accepted: 02/15/2021] [Indexed: 11/30/2022]
Abstract
Halohydrin dehalogenases (HHDHs) are promising enzymes for application in biocatalysis due to their promiscuous epoxide ring-opening activity with various anionic nucleophiles. So far, seven different HHDH subtypes A to G have been reported with subtype D containing the by far largest number of enzymes. Moreover, several characterized members of subtype D have been reported to display outstanding characteristics such as high catalytic activity, broad substrate spectra or remarkable thermal stability. Yet, no structure of a D-type HHDH has been reported to date that could be used to investigate and understand those features on a molecular level. We therefore solved the crystal structure of HheD2 from gamma proteobacterium HTCC2207 at 1.6 Å resolution and used it as a starting point for targeted mutagenesis in combination with molecular dynamics (MD) simulation, in order to study the low thermal stability of HheD2 in comparison with other members of subtype D. This revealed a hydrogen bond between conserved residues Q160 and D198 to be connected with a high catalytic activity of this enzyme. Moreover, a flexible surface region containing two α-helices was identified to impact thermal stability of HheD2. Exchange of this surface region by residues of HheD3 yielded a variant with 10 °C higher melting temperature and reaction temperature optimum. Overall, our results provide important insights into the structure-function relationship of HheD2 and presumably for other D-type HHDHs. DATABASES: Structural data are available in PDB database under the accession number 7B73.
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Affiliation(s)
- Julia Wessel
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Giovanna Petrillo
- Molecular Biology Institute of Barcelona, IBMB-CSIC, Barcelona, Spain
| | - Miquel Estevez-Gay
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain
| | - Sandra Bosch
- Centro de Biología Molecular 'Severo Ochoa', UAM-CSIC, Madrid, Spain
| | - Margarita Seeger
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Willem P Dijkman
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
| | - Javier Iglesias-Fernández
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain
| | - Aurelio Hidalgo
- Centro de Biología Molecular 'Severo Ochoa', UAM-CSIC, Madrid, Spain
| | - Isabel Uson
- Molecular Biology Institute of Barcelona, IBMB-CSIC, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Spain.,ICREA, Barcelona, Spain
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Germany
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19
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Wang L, Marciello M, Estévez‐Gay M, Soto Rodriguez PED, Luengo Morato Y, Iglesias‐Fernández J, Huang X, Osuna S, Filice M, Sánchez S. Enzyme Conformation Influences the Performance of Lipase‐powered Nanomotors. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
| | - Marzia Marciello
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
| | - Miquel Estévez‐Gay
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
| | - Paul E. D. Soto Rodriguez
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
| | - Yurena Luengo Morato
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
| | - Javier Iglesias‐Fernández
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Sílvia Osuna
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Marco Filice
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
- Microscopy and Dynamic Imaging Unit Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Calle Melchor Fernandez Almagro 3 28029 Madrid Spain
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Pg. Lluís Companys 23 08010 Barcelona Spain
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20
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Wang L, Marciello M, Estévez‐Gay M, Soto Rodriguez PED, Luengo Morato Y, Iglesias‐Fernández J, Huang X, Osuna S, Filice M, Sánchez S. Enzyme Conformation Influences the Performance of Lipase‐powered Nanomotors. Angew Chem Int Ed Engl 2020; 59:21080-21087. [DOI: 10.1002/anie.202008339] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/23/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
| | - Marzia Marciello
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
| | - Miquel Estévez‐Gay
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
| | - Paul E. D. Soto Rodriguez
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
| | - Yurena Luengo Morato
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
| | - Javier Iglesias‐Fernández
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Sílvia Osuna
- Compbiolab Group Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Carrer Maria Aurelia Capmany 69 17003 Girona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Marco Filice
- Nanobiotechnology for Life Sciences Lab Department of Chemistry in Pharmaceutical Sciences Faculty of Pharmacy Universidad Complutense de Madrid (UCM) Plaza Ramón y Cajal 28040 Madrid Spain
- Microscopy and Dynamic Imaging Unit Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) Calle Melchor Fernandez Almagro 3 28029 Madrid Spain
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri i Reixac 10–12 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Pg. Lluís Companys 23 08010 Barcelona Spain
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21
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Cuetos A, Iglesias-Fernández J, Danesh-Azari HR, Zukic E, Dowle A, Osuna S, Grogan G. Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anibal Cuetos
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Hamid-Reza Danesh-Azari
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Erna Zukic
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD, York, U.K
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi, Departament de Química, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Gideon Grogan
- York Structural Biology Laboratory, Department of Chemistry, University of York, YO10 5DD York, U.K
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22
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Codony S, Pujol E, Pizarro J, Feixas F, Valverde E, Loza MI, Brea JM, Saez E, Oyarzabal J, Pineda-Lucena A, Pérez B, Pérez C, Rodríguez-Franco MI, Leiva R, Osuna S, Morisseau C, Hammock BD, Vázquez-Carrera M, Vázquez S. 2-Oxaadamant-1-yl Ureas as Soluble Epoxide Hydrolase Inhibitors: In Vivo Evaluation in a Murine Model of Acute Pancreatitis. J Med Chem 2020; 63:9237-9257. [PMID: 32787085 DOI: 10.1021/acs.jmedchem.0c00310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In vivo pharmacological inhibition of soluble epoxide hydrolase (sEH) reduces inflammatory diseases, including acute pancreatitis (AP). Adamantyl ureas are very potent sEH inhibitors, but the lipophilicity and metabolism of the adamantane group compromise their overall usefulness. Herein, we report that the replacement of a methylene unit of the adamantane group by an oxygen atom increases the solubility, permeability, and stability of three series of urea-based sEH inhibitors. Most of these oxa-analogues are nanomolar inhibitors of both the human and murine sEH. Molecular dynamics simulations rationalize the molecular basis for their activity and suggest that the presence of the oxygen atom on the adamantane scaffold results in active site rearrangements to establish a weak hydrogen bond. The 2-oxaadamantane 22, which has a good solubility, microsomal stability, and selectivity for sEH, was selected for further in vitro and in vivo studies in models of cerulein-induced AP. Both in prophylactic and treatment studies, 22 diminished the overexpression of inflammatory and endoplasmic reticulum stress markers induced by cerulein and reduced the pancreatic damage.
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Affiliation(s)
- Sandra Codony
- Laboratori de Quı́mica Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Eugènia Pujol
- Laboratori de Quı́mica Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - Javier Pizarro
- Pharmacology, Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, 28029 Madrid, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Ferran Feixas
- CompBioLab Group, Departament de Quı́mica and Institut de Quı́mica Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Elena Valverde
- Laboratori de Quı́mica Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
| | - M Isabel Loza
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - José M Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center, University of Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
| | - Elena Saez
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Antonio Pineda-Lucena
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Belén Pérez
- Department of Pharmacology, Therapeutics and Toxicology, Institute of Neurosciences, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Concepción Pérez
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - María Isabel Rodríguez-Franco
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosana Leiva
- Laboratori de Quı́mica Farmacèutica (Unitat Associada al CSIC), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Sílvia Osuna
- CompBioLab Group, Departament de Quı́mica and Institut de Quı́mica Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, 17003 Girona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Christophe Morisseau
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
| | - Bruce D Hammock
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
| | - Manuel Vázquez-Carrera
- Pharmacology, Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, 28029 Madrid, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, 08950 Esplugues de Llobregat, Spain
| | - Santiago Vázquez
- Laboratori de Quı́mica Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Quı́mica Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain
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23
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Affiliation(s)
- Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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24
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020; 59:12499-12505. [PMID: 32243054 PMCID: PMC7384163 DOI: 10.1002/anie.202003139] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/31/2020] [Indexed: 01/08/2023]
Abstract
Steroidal C7β alcohols and their respective esters have shown significant promise as neuroprotective and anti-inflammatory agents to treat chronic neuronal damage like stroke, brain trauma, and cerebral ischemia. Since C7 is spatially far away from any functional groups that could direct C-H activation, these transformations are not readily accessible using modern synthetic organic techniques. Reported here are P450-BM3 mutants that catalyze the oxidative hydroxylation of six different steroids with pronounced C7 regioselectivities and β stereoselectivities, as well as high activities. These challenging transformations were achieved by a focused mutagenesis strategy and application of a novel technology for protein library construction based on DNA assembly and USER (Uracil-Specific Excision Reagent) cloning. Upscaling reactions enabled the purification of the respective steroidal alcohols in moderate to excellent yields. The high-resolution X-ray structure and molecular dynamics simulations of the best mutant unveil the origin of regio- and stereoselectivity.
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Affiliation(s)
- Aitao Li
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Yaqin Peng
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
| | - Chenghua Gao
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Jinmei Zhu
- School of life scienceHubei UniversityState Key Laboratory of Biocatalysis and Enzyme Engineering#368 Youyi RoadWuhan430062P.R. China
| | - Harry Rickerby
- LabGeniusG.01-06 Cocoa Studios100 Drummond RdLondonSE16 4DGUK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 6917003GironaCataloniaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products ChemistryCenter for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesShanghai200032P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470MuelheimGermany
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th AvenueTianjin300308P. R. China
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25
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Semivrazhskaya O, Aroua S, Yulikov M, Romero-Rivera A, Stevenson S, Garcia-Borràs M, Osuna S, Yamakoshi Y. Regioselective Synthesis and Characterization of Tris- and Tetra-Prato Adducts of M 3N@C 80 (M = Y, Gd). J Am Chem Soc 2020; 142:12954-12965. [PMID: 32586092 DOI: 10.1021/jacs.9b13768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The tris- and tetra-adducts of M3N@Ih-C80 metallofullerenes were synthesized and characterized for the first time. The 1,3-dipolar cycloaddition (Prato reaction) of Y3N@Ih-C80 and Gd3N@Ih-C80 with an excess of N-ethylglycine and formaldehyde provided tris- and tetra-fulleropyrrolidine adducts in a regioselective manner. Purification by HPLC and analyses of the isolated peaks by NMR, MS, and vis-NIR spectra revealed that the major products were four tris- and one tetra-isomers for both Y3N@Ih-C80 and Gd3N@Ih-C80. Considering the large number of possible isomers (e.g., at least 1140 isomers for the tris-adduct), the limited number of isomers obtained indicated that the reactions proceeded with high regioselectivity. NMR analyses of the Y3N@Ih-C80 adducts found that the tris-adducts were all-[6,6]- or [6,6][6,6][5,6]-isomers and that some showed mutual isomerization or remained intact at room temperature. The tetra-adduct obtained as a major product was all-[6,6] and stable. For the structural elucidation of Gd3N@Ih-C80 tris- and tetra-adducts, density functional theory (DFT) calculations were performed to estimate the relative stabilities of tris- and tetra-adducts formed upon Prato functionalization of the most pyramidalized regions of the fullerene structure. The most stable structures corresponded to additions on the most pyramidalized (i.e., strained) bonds. Taking together the experimental vis-NIR spectra, NMR assignments, and the computed relative DFT stabilities of the potential tris- and tetra-adducts, the structures of the isolated adducts were elucidated. Electron resonance (ESR) measurements measurements of pristine, bis-, and tris-adducts of Gd3N@C80 suggested that the rotation of the endohedral metal cluster slowed upon increase of the addition numbers to C80 cage, which is favored for accommodating the Gd atoms of the relatively large Gd3N cluster inner space at the sp3 addition sites. This is presumably related to the high regioselectivity in the Prato addition reaction driven by the strain release of the Gd3N@C80 fullerene structure.
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Affiliation(s)
- Olesya Semivrazhskaya
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Safwan Aroua
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Maxim Yulikov
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland
| | - Adrian Romero-Rivera
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, Maria Aurelia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Steven Stevenson
- Department of Chemistry, Purdue University Fort Wayne, Fort Wayne, Indiana 46805, United States
| | - Marc Garcia-Borràs
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, Maria Aurelia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Sílvia Osuna
- Institut de Quı́mica Computacional i Catàlisi (IQCC) and Departament de Quı́mica, Universitat de Girona, Maria Aurelia Capmany 69, 17003 Girona, Catalonia, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Yoko Yamakoshi
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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26
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Calzadiaz-Ramirez L, Calvó-Tusell C, Stoffel GMM, Lindner SN, Osuna S, Erb TJ, Garcia-Borràs M, Bar-Even A, Acevedo-Rocha CG. In Vivo Selection for Formate Dehydrogenases with High Efficiency and Specificity toward NADP . ACS Catal 2020; 10:7512-7525. [PMID: 32733773 PMCID: PMC7384739 DOI: 10.1021/acscatal.0c01487] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/06/2020] [Indexed: 02/06/2023]
Abstract
The efficient regeneration of cofactors is vital for the establishment of biocatalytic processes. Formate is an ideal electron donor for cofactor regeneration due to its general availability, low reduction potential, and benign byproduct (CO2). However, formate dehydrogenases (FDHs) are usually specific to NAD+, such that NADPH regeneration with formate is challenging. Previous studies reported naturally occurring FDHs or engineered FDHs that accept NADP+, but these enzymes show low kinetic efficiencies and specificities. Here, we harness the power of natural selection to engineer FDH variants to simultaneously optimize three properties: kinetic efficiency with NADP+, specificity toward NADP+, and affinity toward formate. By simultaneously mutating multiple residues of FDH from Pseudomonas sp. 101, which exhibits practically no activity toward NADP+, we generate a library of >106 variants. We introduce this library into an E. coli strain that cannot produce NADPH. By selecting for growth with formate as the sole NADPH source, we isolate several enzyme variants that support efficient NADPH regeneration. We find that the kinetically superior enzyme variant, harboring five mutations, has 5-fold higher efficiency and 14-fold higher specificity in comparison to the best enzyme previously engineered, while retaining high affinity toward formate. By using molecular dynamics simulations, we reveal the contribution of each mutation to the superior kinetics of this variant. We further determine how nonadditive epistatic effects improve multiple parameters simultaneously. Our work demonstrates the capacity of in vivo selection to identify highly proficient enzyme variants carrying multiple mutations which would be almost impossible to find using conventional screening methods.
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Affiliation(s)
| | - Carla Calvó-Tusell
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Gabriele M. M. Stoffel
- Max Planck Institute of Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sílvia Osuna
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Tobias J. Erb
- Max Planck Institute of Terrestrial Microbiology, Karl-von-Frisch-Straße 10, D-35043 Marburg, Germany
- LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 16, D-35043 Marburg, Germany
| | - Marc Garcia-Borràs
- Institut de Quı́mica Computacional i Catàlisi and Departament de Quı́mica, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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27
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Li A, Acevedo‐Rocha CG, D'Amore L, Chen J, Peng Y, Garcia‐Borràs M, Gao C, Zhu J, Rickerby H, Osuna S, Zhou J, Reetz MT. Regio‐ and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003139] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Aitao Li
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | | | - Lorenzo D'Amore
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Jinfeng Chen
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Yaqin Peng
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Chenghua Gao
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Jinmei Zhu
- School of life science Hubei University State Key Laboratory of Biocatalysis and Enzyme Engineering #368 Youyi Road Wuhan 430062 P.R. China
| | - Harry Rickerby
- LabGenius G.01-06 Cocoa Studios 100 Drummond Rd London SE16 4DG UK
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry Center for Excellence in Molecular Synthesis Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Muelheim Germany
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 32 West 7th Avenue Tianjin 300308 P. R. China
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28
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Castro AC, Romero‐Rivera A, Osuna S, Houk KN, Swart M. Cover Feature: Computational NMR Spectra of
o
‐Benzyne and Stable Guests and Their Hemicarceplexes (Chem. Eur. J. 12/2020). Chemistry 2020. [DOI: 10.1002/chem.201905504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abril C. Castro
- Institut de Química Computacional i Catàlisi (IQCC)Departament de QuímicaUniversitat de Girona Campus de Montilivi 17071 Girona Spain
| | - Adrian Romero‐Rivera
- Institut de Química Computacional i Catàlisi (IQCC)Departament de QuímicaUniversitat de Girona Campus de Montilivi 17071 Girona Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC)Departament de QuímicaUniversitat de Girona Campus de Montilivi 17071 Girona Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
| | - K. N. Houk
- Department of Chemistry and BiochemistryUniversity of California Los Angeles CA 90095-1569 USA
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC)Departament de QuímicaUniversitat de Girona Campus de Montilivi 17071 Girona Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
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29
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Castro AC, Romero-Rivera A, Osuna S, Houk KN, Swart M. Computational NMR Spectra of o-Benzyne and Stable Guests and Their Hemicarceplexes. Chemistry 2020; 26:2626-2634. [PMID: 31765503 DOI: 10.1002/chem.201904756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Indexed: 12/12/2022]
Abstract
The incarceration of o-benzyne and 27 other guest molecules within hemicarcerand 1, as reported experimentally by Warmuth, and Cram and co-workers, has been studied by density functional theory (DFT). The 1 H NMR chemical shifts, rotational mobility, and conformational preference of the guests within the supramolecular cage were determined, which showed intriguing correlations of the chemical shifts with structural parameters of the host-guest system. Furthermore, based on the computed chemical shifts reassignments of some NMR signals are proposed. This affects, in particular, the putative characterization of the volatile benzyne molecule inside a hemicarcerand, for which our CCSD(T) and KT2 results indicate that the experimentally observed signals are most likely not resulting from an isolated o-benzyne within the supramolecular host. Instead, it is shown that the guest reacted with an aromatic ring of the host, and this adduct is responsible for the experimentally observed signals.
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Affiliation(s)
- Abril C Castro
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095-1569, USA
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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30
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Liutkus M, López-Andarias A, Mejías SH, López-Andarias J, Gil-Carton D, Feixas F, Osuna S, Matsuda W, Sakurai T, Seki S, Atienza C, Martín N, Cortajarena AL. Protein-directed crystalline 2D fullerene assemblies. Nanoscale 2020; 12:3614-3622. [PMID: 31912074 DOI: 10.1039/c9nr07083d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Water soluble 2D crystalline monolayers of fullerenes grow on planar assemblies of engineered consensus tetratricopeptide repeat proteins. Designed fullerene-coordinating tyrosine clamps on the protein introduce specific fullerene binding sites, which facilitate fullerene nucleation. Through reciprocal interactions between the components, the hybrid material assembles into two-dimensional 2 nm thick structures with crystalline order, that conduct photo-generated charges. Thus, the protein-fullerene hybrid material is a demonstration of the developments toward functional materials with protein-based precision control of functional elements.
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Affiliation(s)
- Mantas Liutkus
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain.
| | - Alicia López-Andarias
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Sara H Mejías
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain.
| | - Javier López-Andarias
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - David Gil-Carton
- CIC bioGUNE; Bizkaia Science and Technology Park, building 800, E-48160, Derio, Spain
| | - Ferran Feixas
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Wakana Matsuda
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Carmen Atienza
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Nazario Martín
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain. and IMDEA-Nanoscience, Campus de Cantoblanco, E-28049 Madrid, Spain
| | - Aitziber L Cortajarena
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain. and Ikerbasque, Basque Foundation for Science, Mª Díaz de Haro 3, E-48013 Bilbao, Spain
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31
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Maria-Solano MA, Iglesias-Fernández J, Osuna S. Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution. J Am Chem Soc 2019; 141:13049-13056. [DOI: 10.1021/jacs.9b03646] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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32
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Liosi K, Romero-Rivera A, Semivrazhskaya O, Caniglia CD, Garcia-Borràs M, Trapp N, Osuna S, Yamakoshi Y. Site-Selectivity of Prato Additions to C 70: Experimental and Theoretical Studies of a New Thermodynamic Product at the dd-[5,6]-Junction. Org Lett 2019; 21:5162-5166. [PMID: 31199152 DOI: 10.1021/acs.orglett.9b01756] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three Prato monoadduct isomers were synthesized and structurally characterized by 1H, 13C NMR spectra and single-crystal X-ray diffraction, and one adduct on the dd-[5,6]-bond was found as the first example of a Prato [5,6]-adduct of C70. To investigate the mechanism in the generation of this dd-[5,6]-adduct, computational studies were employed to show that it was thermodynamically obtained by sigmatropic rearrangement from the presumed initial kinetic product de-[6,6]-adduct.
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Affiliation(s)
- Korinne Liosi
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Adrian Romero-Rivera
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain
| | - Olesya Semivrazhskaya
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Caravaggio D Caniglia
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Marc Garcia-Borràs
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain
| | - Nils Trapp
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi , 17071 Girona , Catalonia , Spain.,ICREA , Pg. Lluís Companys 23 , 08010 Barcelona , Catalonia , Spain
| | - Yoko Yamakoshi
- Laboratorium für Organische Chemie , ETH Zürich , Vladimir-Prelog-Weg 3 , CH-8093 Zürich , Switzerland
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33
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Semivrazhskaya O, Romero-Rivera A, Aroua S, Troyanov SI, Garcia-Borràs M, Stevenson S, Osuna S, Yamakoshi Y. Structures of Gd 3N@C 80 Prato Bis-Adducts: Crystal Structure, Thermal Isomerization, and Computational Study. J Am Chem Soc 2019; 141:10988-10993. [PMID: 31266302 DOI: 10.1021/jacs.9b05603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The structures of two bis-ethylpyrrolidinoadducts of Gd3N@Ih-C80, obtained by regioselective 1,3-dipolar cycloadditions, were elucidated by single crystal X-ray, visible-near infrared (vis-NIR) spectra, studies on their thermal isomerization, and theoretical calculations. The structure of the minor-bis-adduct reveals a C2-symmetric carbon cage with [6,6][6,6]-addition sites and with an endohedral Gd3N cluster that is completely flattened. This is the first example of a crystal structure of Gd3N@Ih-C80 derivatives. The structure of the major-bis-adduct was inferred by the vis-NIR spectrum being corresponded to the structure of a previously reported major-bis-adduct of Y3N@Ih-C80 known to have an asymmetric [6,6][6,6]-structure. Based on experimental results showing that the minor-bis-adduct of Gd3N@Ih-C80 isomerized to the major-adduct, a possible second addition site was elucidated with support from density functional theory calculations.
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Affiliation(s)
- Olesya Semivrazhskaya
- Laboratorium für Organische Chemie, ETH Zürich , Vladimir-Prelog-Weg 3 , CH8093 Zürich , Switzerland
| | - Adrian Romero-Rivera
- CompBioLab, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi, 17071 Girona , Catalonia , Spain
| | - Safwan Aroua
- Laboratorium für Organische Chemie, ETH Zürich , Vladimir-Prelog-Weg 3 , CH8093 Zürich , Switzerland
| | - Sergey I Troyanov
- Department of Chemistry , Moscow State University , Leninskie gory, 119991 Moscow , Russia
| | - Marc Garcia-Borràs
- CompBioLab, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi, 17071 Girona , Catalonia , Spain
| | - Steven Stevenson
- Department of Chemistry , Purdue University Fort Wayne , Fort Wayne , Indiana 46805 , United States
| | - Sílvia Osuna
- CompBioLab, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química , Universitat de Girona , Campus Montilivi, 17071 Girona , Catalonia , Spain.,ICREA , Pg. Lluís Companys 23 , 08010 Barcelona , Catalonia , Spain
| | - Yoko Yamakoshi
- Laboratorium für Organische Chemie, ETH Zürich , Vladimir-Prelog-Weg 3 , CH8093 Zürich , Switzerland
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34
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Arqué X, Romero-Rivera A, Feixas F, Patiño T, Osuna S, Sánchez S. Intrinsic enzymatic properties modulate the self-propulsion of micromotors. Nat Commun 2019; 10:2826. [PMID: 31249381 PMCID: PMC6597730 DOI: 10.1038/s41467-019-10726-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022] Open
Abstract
Bio-catalytic micro- and nanomotors self-propel by the enzymatic conversion of substrates into products. Despite the advances in the field, the fundamental aspects underlying enzyme-powered self-propulsion have rarely been studied. In this work, we select four enzymes (urease, acetylcholinesterase, glucose oxidase, and aldolase) to be attached on silica microcapsules and study how their turnover number and conformational dynamics affect the self-propulsion, combining both an experimental and molecular dynamics simulations approach. Urease and acetylcholinesterase, the enzymes with higher catalytic rates, are the only enzymes capable of producing active motion. Molecular dynamics simulations reveal that urease and acetylcholinesterase display the highest degree of flexibility near the active site, which could play a role on the catalytic process. We experimentally assess this hypothesis for urease micromotors through competitive inhibition (acetohydroxamic acid) and increasing enzyme rigidity (β-mercaptoethanol). We conclude that the conformational changes are a precondition of urease catalysis, which is essential to generate self-propulsion. Self-propulsion of biocatalytic micro- and nanomotors is facilitated by enzymes converting substrates into products. Here, the authors show that intrinsic enzymatic properties such as conformational changes are crucial for the self-propulsion of silica microcapsules modified with urease.
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Affiliation(s)
- Xavier Arqué
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain
| | - Adrian Romero-Rivera
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Ferran Feixas
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain
| | - Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain.
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003, Girona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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35
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Call A, Casadevall C, Romero-Rivera A, Martin-Diaconescu V, Sommer DJ, Osuna S, Ghirlanda G, Lloret-Fillol J. Improved Electro- and Photocatalytic Water Reduction by Confined Cobalt Catalysts in Streptavidin. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04981] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Arnau Call
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Carla Casadevall
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Vlad Martin-Diaconescu
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
| | - Dayn J. Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
| | - Giovanna Ghirlanda
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Julio Lloret-Fillol
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avinguda Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluïs Companys, 23, 08010, Barcelona, Spain
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36
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Curado‐Carballada C, Feixas F, Osuna S. Molecular Dynamics Simulations on
Aspergillus niger
Monoamine Oxidase: Conformational Dynamics and Inter‐monomer Communication Essential for Its Efficient Catalysis. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christian Curado‐Carballada
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Ferran Feixas
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona, Catalonia Spain
- ICREAPg. Lluís Companys 23 08010 Barcelona Spain
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37
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Curado‐Carballada C, Feixas F, Iglesias‐Fernández J, Osuna S. Hidden Conformations in
Aspergillus niger
Monoamine Oxidase are Key for Catalytic Efficiency. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Curado‐Carballada
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Javier Iglesias‐Fernández
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC)Departament de Química Carrer Maria Aurèlia Capmany 69 17003 Girona Catalonia Spain
- ICREA Pg. Lluís Companys 23 08010 Barcelona Spain
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38
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Maria-Solano MA, Serrano-Hervás E, Romero-Rivera A, Iglesias-Fernández J, Osuna S. Role of conformational dynamics in the evolution of novel enzyme function. Chem Commun (Camb) 2018; 54:6622-6634. [PMID: 29780987 PMCID: PMC6009289 DOI: 10.1039/c8cc02426j] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/10/2018] [Indexed: 12/26/2022]
Abstract
The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Eila Serrano-Hervás
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Adrian Romero-Rivera
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Javier Iglesias-Fernández
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
| | - Sílvia Osuna
- CompBioLab Group
, Institut de Química Computacional i Catàlisi and Departament de Química
, Universitat de Girona
,
Carrer Maria Aurèlia Capmany, 69
, 17003 Girona
, Catalonia
, Spain
.
- ICREA
,
Pg. Lluís Companys 23
, 08010 Barcelona
, Spain
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39
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Serrano-Hervás E, Casadevall G, Garcia-Borràs M, Feixas F, Osuna S. Epoxide Hydrolase Conformational Heterogeneity for the Resolution of Bulky Pharmacologically Relevant Epoxide Substrates. Chemistry 2018; 24:12254-12258. [DOI: 10.1002/chem.201801068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Eila Serrano-Hervás
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Guillem Casadevall
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry; University of California, Los Angeles (UCLA); 607 Charles E. Young Drive Los Angeles CA 90095 USA
| | - Ferran Feixas
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Sílvia Osuna
- Laboratori de Bioquímica Computacional (CompBioLab); Institut de Química Computacional i Catàlisi (IQCC); Departament de Química; Universitat de Girona (UdG); Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
- ICREA; Pg. Lluís Companys 23 08010 Barcelona Spain
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40
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Javier Iglesias-Fernández
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química; Universitat de Girona; Carrer Maria Aurèlia Capmany 69 17003 Girona Spain
- ICREA; Passeig Lluís Companys, 23 08010 Barcelona Spain
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41
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Abstract
Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets, which dictate their substrate scope and selectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site, but most importantly they impact the substrate-enzyme interactions. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME and NCIplot corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants.
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Affiliation(s)
- Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Quimica, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, 17003 Girona, Spain.
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42
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Li G, Maria-Solano MA, Romero-Rivera A, Osuna S, Reetz MT. Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution. Chem Commun (Camb) 2018; 53:9454-9457. [PMID: 28795696 DOI: 10.1039/c7cc05377k] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The long-standing problem of achieving high activity of a thermophilic enzyme at low temperatures and short reaction times with little tradeoff in thermostability has been solved by directed evolution, an alcohol dehydrogenase found in hot springs serving as the catalyst in enantioselective ketone reductions.
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Affiliation(s)
- Guangyue Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Department de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 6, Girona 17003, Catalonia, Spain.
| | - Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany and Fachbereich Chemie der Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35032, Marburg, Germany.
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43
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Vidal S, Izquierdo M, Alom S, Garcia-Borràs M, Filippone S, Osuna S, Solà M, Whitby RJ, Martín N. Effect of incarcerated HF on the exohedral chemical reactivity of HF@C 60. Chem Commun (Camb) 2018; 53:10993-10996. [PMID: 28835947 DOI: 10.1039/c7cc05987f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The first chemical modification on the brand new endohedral HF@C60 is reported. In particular, the isomerization from optically pure (2S,5S)-cis-pyrrolidino[3,4:1,2][60]fullerene 2b to (2S,5R)-trans-pyrrolidino[3,4:1,2][60]fullerene 2b has been studied and compared with empty C60 (2a) and endohedral H2O@C60 (3). The comparative study shows a kinetic order for the isomerization process of H2O@C60 > HF@C60 > C60, thus confirming the effect of the incarcerated species on the zwitterionic intermediate stability.
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Affiliation(s)
- Sara Vidal
- Dep. Química Orgánica I, UCM, Avda. Complutense s/n, E-28040 Madrid, Spain.
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44
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Serrano-Hervás E, Garcia-Borràs M, Osuna S. Exploring the origins of selectivity in soluble epoxide hydrolase from Bacillus megaterium. Org Biomol Chem 2018; 15:8827-8835. [PMID: 29026902 PMCID: PMC5708342 DOI: 10.1039/c7ob01847a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Epoxide hydrolase (EH) enzymes catalyze the hydration of racemic epoxides to yield their corresponding vicinal diols. In this work, the Bacillus megaterium epoxide hydrolase (BmEH)-mediated hydrolysis of racemic styrene oxide (rac-SO) and its para-nitro styrene oxide (rac-p-NSO) derivative are computationally investigated using density functional theory (DFT).
Epoxide hydrolase (EH) enzymes catalyze the hydration of racemic epoxides to yield their corresponding vicinal diols. These enzymes present different enantio- and regioselectivity depending upon either the substrate structure or the substitution pattern of the epoxide ring. In this study, we computationally investigate the Bacillus megaterium epoxide hydrolase (BmEH)-mediated hydrolysis of racemic styrene oxide (rac-SO) and its para-nitro styrene oxide (rac-p-NSO) derivative using density functional theory (DFT) and an active site cluster model consisting of 195 and 197 atoms, respectively. Full reaction mechanisms for epoxide ring opening were evaluated considering the attack at both oxirane carbons and considering two possible orientations of the substrate at the BmEH active site. Our results indicate that for both SO and p-NSO substrates the BmEH enantio- and regioselectivity is opposite to the inherent (R)-BmEH selectivity, the attack at the benzylic position (C1) of the (S)-enantiomer being the most favoured chemical outcome.
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Affiliation(s)
- Eila Serrano-Hervás
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain.
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45
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity. ACS Catal 2017; 7:8524-8532. [PMID: 29226011 PMCID: PMC5716449 DOI: 10.1021/acscatal.7b02954] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/19/2017] [Indexed: 12/19/2022]
Abstract
![]()
Enzymes exist as
ensembles of conformations that are important
for function. Tuning these populations of conformational states through
mutation enables evolution toward additional activities. Here we computationally
evaluate the population shifts induced by distal and active site mutations
in a family of computationally designed and experimentally optimized
retro-aldolases. The conformational landscape of these enzymes was
significantly altered during evolution, as pre-existing catalytically
active conformational substates became major states in the most evolved
variants. We further demonstrate that key residues responsible for
these substate conversions can be predicted computationally. Significantly,
the identified residues coincide with those positions mutated in the
laboratory evolution experiments. This study establishes that distal
mutations that affect enzyme catalytic activity can be predicted computationally
and thus provides the enzyme (re)design field with a rational strategy
to determine promising sites for enhancing activity through mutation.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), 607 Charles E. Young Drive, Los Angeles, California 90095, United States
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
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46
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Garcia-Borràs M, Osuna S, Luis JM, Solà M. Rationalizing the relative abundances of trimetallic nitride template-based endohedral metallofullerenes from aromaticity measures. Chem Commun (Camb) 2017; 53:4140-4143. [PMID: 28352903 PMCID: PMC5436040 DOI: 10.1039/c7cc01750b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/20/2017] [Indexed: 11/25/2022]
Abstract
The synthesis of endohedral metallofullerenes (EMFs) from a carbon soot sample of an arc discharge leads to a variety of EMFs that are obtained in different relative abundances. In the present work, we show that these abundances can be predicted from aromaticity calculations. In particular, we use the normalized Additive Local Aromaticity (ALAN) index. Our results show that the most abundant Sc3N-based and Y3N-based EMFs in fullerene soot are the most aromatic. This study reinforces the idea that aromaticity plays a key role in determining the stability of EMFs.
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Affiliation(s)
- M Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA. and Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Catalonia, Spain.
| | - S Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Catalonia, Spain.
| | - J M Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Catalonia, Spain.
| | - M Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17003 Girona, Catalonia, Spain.
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47
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Romero-Rivera A, Garcia-Borràs M, Osuna S. Computational tools for the evaluation of laboratory-engineered biocatalysts. Chem Commun (Camb) 2016; 53:284-297. [PMID: 27812570 PMCID: PMC5310519 DOI: 10.1039/c6cc06055b] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.
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Affiliation(s)
- Adrian Romero-Rivera
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive, Los Angeles, California 90095, USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.
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48
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Li Y, Osuna S, Garcia-Borràs M, Qi X, Liu S, Houk KN, Lan Y. Reactivity of Single-Walled Carbon Nanotubes in the Diels-Alder Cycloaddition Reaction: Distortion-Interaction Analysis along the Reaction Pathway. Chemistry 2016; 22:12819-24. [PMID: 27465519 DOI: 10.1002/chem.201601799] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Indexed: 11/06/2022]
Abstract
Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs.
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Affiliation(s)
- Yingzi Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P. R. China
| | - Sílvia Osuna
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA
| | - Xiaotian Qi
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P. R. China
| | - Song Liu
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P. R. China
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA.
| | - Yu Lan
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P. R. China.
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Martínez JP, Garcia-Borràs M, Osuna S, Poater J, Bickelhaupt FM, Solà M. Reaction Mechanism and Regioselectivity of the Bingel-Hirsch Addition of Dimethyl Bromomalonate to La@C2v -C82. Chemistry 2016; 22:5953-62. [PMID: 26991842 DOI: 10.1002/chem.201504668] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 11/09/2022]
Abstract
We quantum chemically explore the thermodynamics and kinetics of all 65 possible mechanistic pathways of the Bingel-Hirsch addition of dimethyl bromomalonate to the endohedral metallofullerene La@C2v -C82 that result from the combination of 24 nonequivalent carbon atoms and 35 different bonds present in La@C2v -C82 by using dispersion-corrected DFT calculations. Experimentally, this reaction leads to four singly bonded derivatives and one fulleroid adduct. Of these five products, only the singly bonded derivative on C23 could be experimentally identified unambiguously. Our calculations show that La@C2v -C82 is not particularly regioselective under Bingel-Hirsch conditions. From the obtained results, however, it is possible to make a tentative assignment of the products observed experimentally. We propose that the observed fulleroid adduct results from the attack at bond 19 and that the singly bonded derivatives correspond to the C2, C19, C21, and C23 initial attacks. However, other possibilities cannot be ruled out completely.
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Affiliation(s)
- Juan Pablo Martínez
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain
| | - Jordi Poater
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boeleaan 1083, 1081 HV, Amsterdam, The Netherlands.,Departament de Química Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Catalonia, Spain
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boeleaan 1083, 1081 HV, Amsterdam, The Netherlands. .,Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Catalonia, Spain.
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50
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Garcia‐Borràs M, Cerón MR, Osuna S, Izquierdo M, Luis JM, Echegoyen L, Solà M. The Regioselectivity of Bingel–Hirsch Cycloadditions on Isolated Pentagon Rule Endohedral Metallofullerenes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona Catalonia Spain
| | - Maira R. Cerón
- Department of Chemistry University of Texas at El Paso El Paso Texas 79968 USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona Catalonia Spain
| | - Marta Izquierdo
- Department of Chemistry University of Texas at El Paso El Paso Texas 79968 USA
| | - Josep M. Luis
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona Catalonia Spain
| | - Luis Echegoyen
- Department of Chemistry University of Texas at El Paso El Paso Texas 79968 USA
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona Catalonia Spain
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