1
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Ferro-Costas D, Sánchez-Murcia PA, Fernández-Ramos A. Unraveling the Catalytic Mechanism of β-Cyclodextrin in the Vitamin D Formation. J Chem Inf Model 2024; 64:3865-3873. [PMID: 38598310 DOI: 10.1021/acs.jcim.3c02049] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Previous experimental studies have shown that the isomerization reaction of previtamin D3 (PreD3) to vitamin D3 (VitD3) is accelerated 40-fold when it takes place within a β-cyclodextrin dimer, in comparison to the reaction occurring in conventional isotropic solutions. In this study, we employ quantum mechanics-based molecular dynamics (MD) simulations and statistical multistructural variational transition state theory to unveil the origin of this acceleration. We find that the conformational landscape in the PreD3 isomerization is highly dependent on whether the system is encapsulated. In isotropic media, the triene moiety of the PreD3 exhibits a rich torsional flexibility. However, when encapsulated, such a flexibility is limited to a more confined conformational space. In both scenarios, our calculated rate constants are in close agreement with experimental results and allow us to identify the PreD3 flexibility restriction as the primary catalytic factor. These findings enhance our understanding of VitD3 isomerization and underscore the significance of MD and environmental factors in biochemical modeling.
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Affiliation(s)
- David Ferro-Costas
- Departamento de Química Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Pedro A Sánchez-Murcia
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
- Institute of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Antonio Fernández-Ramos
- Departamento de Química Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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2
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Saridakis I, Riomet M, Belleza OJV, Coussanes G, Singer NK, Kastner N, Xiao Y, Smith E, Tona V, de la Torre A, Lopes EF, Sánchez-Murcia PA, González L, Sitte HH, Maulide N. PyrAtes: Modular Organic Salts with Large Stokes Shifts for Fluo-rescence Microscopy. Angew Chem Int Ed Engl 2024; 63:e202318127. [PMID: 38570814 DOI: 10.1002/anie.202318127] [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: 11/29/2023] [Indexed: 04/05/2024]
Abstract
The deployment of small-molecule fluorescent agents plays an ever-growing role in medicine and drug development. Herein, we complement the portfolio of powerful fluorophores, reporting the serendipitous discovery and development of a novel class with an imidazo[1,2-a]pyridinium triflate core, which we term PyrAtes. These fluorophores are synthesized in a single step from readily available materials (>60 examples) and display Stokes shifts as large as 240 nm, while also reaching NIR-I emissions at λmax as long as 720 nm. Computational studies allow the development of a platform for the prediction of λmax and λEm. Furthermore, we demonstrate the compatibility of these novel fluorophores with live cell imaging in HEK293 cells, suggesting PyrAtes as potent intracellular markers.
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Affiliation(s)
- Iakovos Saridakis
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Strasse 42, 1090, Vienna, Austria
| | - Margaux Riomet
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Oliver J V Belleza
- Centre of Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090, Vienna, Austria
| | - Guilhem Coussanes
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Nadja K Singer
- Institute of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Strasse 42, 1090, Vienna, Austria
| | - Nina Kastner
- Centre of Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090, Vienna, Austria
| | - Yi Xiao
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Strasse 42, 1090, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the, Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Elliot Smith
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Veronica Tona
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Aurélien de la Torre
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Eric F Lopes
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
| | - Harald H Sitte
- Centre of Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17A, 1090, Vienna, Austria
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, 19328, Amman, Jordan
- Center for Addiction Research and Science - AddRess, Medical University Vienna, Währinger Strasse 13 A, 1090, Vienna, Austria
| | - Nuno Maulide
- Institute of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the, Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
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3
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Platzer G, Ptaszek AL, Böttcher J, Fuchs JE, Geist L, Braun D, McConnell DB, Konrat R, Sánchez-Murcia PA, Mayer M. Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution. Chemphyschem 2024; 25:e202300636. [PMID: 37955910 DOI: 10.1002/cphc.202300636] [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: 09/06/2023] [Revised: 10/23/2023] [Indexed: 11/14/2023]
Abstract
The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with limited information on protein flexibility. An experimentally verified structural model of the binding interface in the native solution-state would support medicinal chemists in their molecular design decisions. Here we demonstrate that protein-bound ligand 1 H NMR chemical shifts are highly sensitive and accurate probes for the immediate chemical environment of protein-ligand interfaces. By comparing the experimental ligand 1 H chemical shift values with those computed from the X-ray structure using quantum mechanics methodology, we identify significant disagreements for parts of the ligand between the two experimental techniques. We show that quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) ensembles can be used to refine initial X-ray co-crystal structures resulting in a better agreement with experimental 1 H ligand chemical shift values. Overall, our findings highlight the usefulness of ligand 1 H NMR chemical shift information in combination with a QM/MM MD workflow for generating protein-ligand ensembles that accurately reproduce solution structural data.
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Affiliation(s)
- Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
- MAG-LAB GmbH, Karl-Farkas-Gasse 22, 1030-, Vienna, Austria
| | - Aleksandra L Ptaszek
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
- Laboratory for Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University Graz, Neue Stiftingtalstrasse 6/III, 8010-, Graz, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Daniel Braun
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, 1030-, Vienna, Austria
| | - Pedro A Sánchez-Murcia
- Laboratory for Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University Graz, Neue Stiftingtalstrasse 6/III, 8010-, Graz, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr. Boehringer Gasse 5-11, 1121-, Vienna, Austria
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4
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Bitter J, Pfeiffer M, Borg AJE, Kuhlmann K, Pavkov-Keller T, Sánchez-Murcia PA, Nidetzky B. Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation. Nat Commun 2023; 14:7123. [PMID: 37932298 PMCID: PMC10628242 DOI: 10.1038/s41467-023-42750-0] [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: 01/04/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Biological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-D-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn2+ active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in β-elimination of 3-keto C-β-D-glucosides. We show that CGE catalyzes β-elimination of 3-keto O- and C-β-D-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for β-elimination of 3-keto O-β-D-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.
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Affiliation(s)
- Johannes Bitter
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
| | - Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
| | - Annika J E Borg
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, A-8010, Graz, Austria
| | - Kirill Kuhlmann
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstraße 50/III, A-8010, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Humboldtstraße 50/III, A-8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, A-8010, Graz, Austria
- BioHealth Field of Excellence, University of Graz, Humboldtstraße 50, A-8010, Graz, Austria
| | - Pedro A Sánchez-Murcia
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingstalstraße 6/III, A-8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Krenngasse 37, A-8010, Graz, Austria.
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5
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Gubensäk N, Sagmeister T, Buhlheller C, Geronimo BD, Wagner GE, Petrowitsch L, Gräwert MA, Rotzinger M, Berger TMI, Schäfer J, Usón I, Reidl J, Sánchez-Murcia PA, Zangger K, Pavkov-Keller T. Vibrio cholerae's ToxRS bile sensing system. eLife 2023; 12:e88721. [PMID: 37768326 PMCID: PMC10624426 DOI: 10.7554/elife.88721] [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: 04/20/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
The seventh pandemic of the diarrheal cholera disease, which began in 1960, is caused by the Gram-negative bacterium Vibrio cholerae. Its environmental persistence provoking recurring sudden outbreaks is enabled by V. cholerae's rapid adaption to changing environments involving sensory proteins like ToxR and ToxS. Located at the inner membrane, ToxR and ToxS react to environmental stimuli like bile acid, thereby inducing survival strategies for example bile resistance and virulence regulation. The presented crystal structure of the sensory domains of ToxR and ToxS in combination with multiple bile acid interaction studies, reveals that a bile binding pocket of ToxS is only properly folded upon binding to ToxR. Our data proposes an interdependent functionality between ToxR transcriptional activity and ToxS sensory function. These findings support the previously suggested link between ToxRS and VtrAC-like co-component systems. Besides VtrAC, ToxRS is now the only experimentally determined structure within this recently defined superfamily, further emphasizing its significance. In-depth analysis of the ToxRS complex reveals its remarkable conservation across various Vibrio species, underlining the significance of conserved residues in the ToxS barrel and the more diverse ToxR sensory domain. Unravelling the intricate mechanisms governing ToxRS's environmental sensing capabilities, provides a promising tool for disruption of this vital interaction, ultimately inhibiting Vibrio's survival and virulence. Our findings hold far-reaching implications for all Vibrio strains that rely on the ToxRS system as a shared sensory cornerstone for adapting to their surroundings.
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Affiliation(s)
- Nina Gubensäk
- Institute of Molecular Biosciences, University of GrazGrazAustria
| | - Theo Sagmeister
- Institute of Molecular Biosciences, University of GrazGrazAustria
| | | | - Bruno Di Geronimo
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto-Loewi Research Center, Medical University of GrazGrazAustria
| | - Gabriel E Wagner
- Institute of Chemistry / Organic and Bioorganic Chemistry, Medical University of GrazGrazAustria
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of GrazGrazAustria
| | | | | | - Markus Rotzinger
- Institute of Chemistry / Organic and Bioorganic Chemistry, Medical University of GrazGrazAustria
| | | | | | - Isabel Usón
- Institute of Molecular Biology of BarcelonaBarcelonaSpain
- ICREA, Institució Catalana de Recerca i Estudis AvançatsBarcelonaSpain
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of GrazGrazAustria
- BioHealth Field of Excellence, University of GrazGrazAustria
- BioTechMed-GrazGrazAustria
| | - Pedro A Sánchez-Murcia
- Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Otto-Loewi Research Center, Medical University of GrazGrazAustria
| | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, Medical University of GrazGrazAustria
- BioHealth Field of Excellence, University of GrazGrazAustria
- BioTechMed-GrazGrazAustria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of GrazGrazAustria
- BioHealth Field of Excellence, University of GrazGrazAustria
- BioTechMed-GrazGrazAustria
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6
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Platero-Rochart D, Krivobokova T, Gastegger M, Reibnegger G, Sánchez-Murcia PA. Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. J Chem Inf Model 2023; 63:4623-4632. [PMID: 37479222 PMCID: PMC10430765 DOI: 10.1021/acs.jcim.3c00772] [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: 05/19/2023] [Indexed: 07/23/2023]
Abstract
The prediction of enzyme activity is one of the main challenges in catalysis. With computer-aided methods, it is possible to simulate the reaction mechanism at the atomic level. However, these methods are usually expensive if they are to be used on a large scale, as they are needed for protein engineering campaigns. To alleviate this situation, machine learning methods can help in the generation of predictive-decision models. Herein, we test different regression algorithms for the prediction of the reaction energy barrier of the rate-limiting step of the hydrolysis of mono-(2-hydroxyethyl)terephthalic acid by the MHETase ofIdeonella sakaiensis. As a training data set, we use steered quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation snapshots and their corresponding pulling work values. We have explored three algorithms together with three chemical representations. As an outcome, our trained models are able to predict pulling works along the steered QM/MM MD simulations with a mean absolute error below 3 kcal mol-1 and a score value above 0.90. More challenging is the prediction of the energy maximum with a single geometry. Whereas the use of the initial snapshot of the QM/MM MD trajectory as input geometry yields a very poor prediction of the reaction energy barrier, the use of an intermediate snapshot of the former trajectory brings the score value above 0.40 with a low mean absolute error (ca. 3 kcal mol-1). Altogether, we have faced in this work some initial challenges of the final goal of getting an efficient workflow for the semiautomatic prediction of enzyme-catalyzed energy barriers and catalytic efficiencies.
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Affiliation(s)
- Daniel Platero-Rochart
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Tatyana Krivobokova
- Department
of Statistics and Operations Research, University
of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Michael Gastegger
- Institute
of Software Engineering and Theoretical Computer Science, Machine
Learning Group, Technische Universität, 10587 Berlin, Germany
| | - Gilbert Reibnegger
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
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7
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de Lucio H, Revuelto A, Carriles AA, de Castro S, García-González S, García-Soriano JC, Alcón-Calderón M, Sánchez-Murcia PA, Hermoso JA, Gago F, Camarasa MJ, Jiménez-Ruiz A, Velázquez S. Identification of 1,2,3-triazolium salt-based inhibitors of Leishmania infantum trypanothione disulfide reductase with enhanced antileishmanial potency in cellulo and increased selectivity. Eur J Med Chem 2022; 244:114878. [DOI: 10.1016/j.ejmech.2022.114878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/04/2022]
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8
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Spreitzer E, Alderson TR, Bourgeois B, Eggenreich L, Habacher H, Brahmersdorfer G, Pritišanac I, Sánchez-Murcia PA, Madl T. FOXO transcription factors differ in their dynamics and intra/intermolecular interactions. Curr Res Struct Biol 2022; 4:118-133. [PMID: 35573459 PMCID: PMC9097636 DOI: 10.1016/j.crstbi.2022.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/19/2022] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Affiliation(s)
- Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - T. Reid Alderson
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Loretta Eggenreich
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Hermann Habacher
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Greta Brahmersdorfer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Iva Pritišanac
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Corresponding author. Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria.
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9
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Revuelto A, de Lucio H, García-Soriano JC, Sánchez-Murcia PA, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Efficient Dimerization Disruption of Leishmania infantum Trypanothione Reductase by Triazole-phenyl-thiazoles. J Med Chem 2021; 64:6137-6160. [PMID: 33945281 PMCID: PMC8480782 DOI: 10.1021/acs.jmedchem.1c00206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/06/2023]
Abstract
Inhibition of Leishmania infantum trypanothione disulfide reductase (LiTryR) by disruption of its homodimeric interface has proved to be an alternative and unexploited strategy in the search for novel antileishmanial agents. Proof of concept was first obtained by peptides and peptidomimetics. Building on previously reported dimerization disruptors containing an imidazole-phenyl-thiazole scaffold, we now report a new 1,2,3-triazole-based chemotype that yields noncompetitive, slow-binding inhibitors of LiTryR. Several compounds bearing (poly)aromatic substituents dramatically improve the ability to disrupt LiTryR dimerization relative to reference imidazoles. Molecular modeling studies identified an almost unexplored hydrophobic region at the interfacial domain as the putative binding site for these compounds. A subsequent structure-based design led to a symmetrical triazole analogue that displayed even more potent inhibitory activity over LiTryR and enhanced leishmanicidal activity. Remarkably, several of these novel triazole-bearing compounds were able to kill both extracellular and intracellular parasites in cell cultures.
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Affiliation(s)
- Alejandro Revuelto
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Héctor de Lucio
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | | | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Jiménez-Ruiz
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
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10
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Cardenas G, Menger MFSJ, Ramos-Berdullas N, Sánchez-Murcia PA. Deciphering the Chemical Basis of Fluorescence of a Selenium-Labeled Uracil Probe when Bound at the Bacterial Ribosomal A-Site. Chemistry 2021; 27:4927-4931. [PMID: 33368691 DOI: 10.1002/chem.202004818] [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: 11/03/2020] [Indexed: 12/23/2022]
Abstract
We unveil in this work the main factors that govern the turn-on/off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. Whereas the constraint into an "in-plane" conformation of the two rings of the fluorophore is the main driver for the observed turn-on fluorescence emission in the presence of the antibiotic paromomycin, the electrostatics of the environment plays a minor role during the emission process. Our computational strategy clearly indicates that, in the absence of paromomycin, the probe prefers conformations that show a dark S1 electronic state with participation of nπ* electronic transition contributions between the selenium atom and the π-system of the uracil moiety.
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Affiliation(s)
- Gustavo Cardenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - Maximilian F S J Menger
- Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nicolás Ramos-Berdullas
- Department of Physical Chemistry, University of Vigo, Lagoas Marcosende s/n, 36310, Vigo, Spain
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria.,Present address: Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingstalstraße 6/III, 8010, Graz, Austria
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11
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Acosta J, Pérez E, Sánchez-Murcia PA, Fillat C, Fernández-Lucas J. Molecular Basis of NDT-Mediated Activation of Nucleoside-Based Prodrugs and Application in Suicide Gene Therapy. Biomolecules 2021; 11:biom11010120. [PMID: 33477716 PMCID: PMC7831932 DOI: 10.3390/biom11010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
Herein we report the first proof for the application of type II 2′-deoxyribosyltransferase from Lactobacillus delbrueckii (LdNDT) in suicide gene therapy for cancer treatment. To this end, we first confirm the hydrolytic ability of LdNDT over the nucleoside-based prodrugs 2′-deoxy-5-fluorouridine (dFUrd), 2′-deoxy-2-fluoroadenosine (dFAdo), and 2′-deoxy-6-methylpurine riboside (d6MetPRib). Such activity was significantly increased (up to 30-fold) in the presence of an acceptor nucleobase. To shed light on the strong nucleobase dependence for enzymatic activity, different molecular dynamics simulations were carried out. Finally, as a proof of concept, we tested the LdNDT/dFAdo system in human cervical cancer (HeLa) cells. Interestingly, LdNDT/dFAdo showed a pronounced reduction in cellular viability with inhibitory concentrations in the low micromolar range. These results open up future opportunities for the clinical implementation of nucleoside 2′-deoxyribosyltransferases (NDTs) in cancer treatment.
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Affiliation(s)
- Javier Acosta
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Elena Pérez
- Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; (J.A.); (E.P.)
| | - Pedro A. Sánchez-Murcia
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
| | - Cristina Fillat
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Jesús Fernández-Lucas
- Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria;
- Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66 Barranquilla, Colombia
- Correspondence:
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12
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Avagliano D, Tkaczyk S, Sánchez-Murcia PA, González L. Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics. J Phys Chem Lett 2020; 11:10212-10218. [PMID: 33206544 PMCID: PMC7735745 DOI: 10.1021/acs.jpclett.0c03070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/11/2020] [Indexed: 05/10/2023]
Abstract
The urge to discover selective fluorescent binders to G-quadruplexes (G4s) for rapid diagnosis must be linked to understand the effect that those have on the DNA photophysics. Herein, we report on the electronic excited states of a bound merocyanine dye to c-Myc G4 using extensive multiscale quantum mechanics/molecular mechanics calculations. We find that the absorption spectra of c-Myc G4, both without and with the intercalated dye, are mainly composed of exciton states and mixed local/charge-transfer states. The presence of merocyanine hardly affects the energy range of the guanine absorption or the number of guanines excited. However, it triggers a substantial amount (16%) of detrimental pure charge-transfer states involving oxidized guanines. We identify the rigidity introduced by the probe in G4, reducing the overlap among guanines, as the one responsible for the changes in the exciton and charge-transfer states, ultimately leading to a redshift of the absorption maximum.
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Affiliation(s)
- Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Sara Tkaczyk
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Pedro A. Sánchez-Murcia
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
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13
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Ibele LM, Sánchez-Murcia PA, Mai S, Nogueira JJ, González L. Excimer Intermediates en Route to Long-Lived Charge-Transfer States in Single-Stranded Adenine DNA as Revealed by Nonadiabatic Dynamics. J Phys Chem Lett 2020; 11:7483-7488. [PMID: 32794719 PMCID: PMC7503858 DOI: 10.1021/acs.jpclett.0c02193] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/14/2020] [Indexed: 05/25/2023]
Abstract
The ultrafast time evolution of a single-stranded adenine DNA is studied using a hybrid multiscale quantum mechanics/molecular mechanics (QM/MM) scheme coupled to nonadiabatic surface hopping dynamics. As a model, we use (dA)20 where a stacked adenine tetramer is treated quantum chemically. The dynamical simulations combined with on-the-fly quantitative wave function analysis evidence the nature of the long-lived electronically excited states formed upon absorption of UV light. After a rapid decrease of the initially excited excitons, relaxation to monomer-like states and excimers occurs within 100 fs. The former monomeric states then relax into additional excimer states en route to forming stabilized charge-transfer states on a longer timescale of hundreds of femtoseconds. The different electronic-state characters is reflected on the spatial separation between the adenines: excimers and charge-transfer states show a much smaller spatial separation than the monomer-like states and the initially formed excitons.
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Affiliation(s)
- Lea M. Ibele
- Department
of Chemistry, Durham University, Durham DH1 3LE, U.K.
| | - Pedro A. Sánchez-Murcia
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Juan J. Nogueira
- Chemistry
Department, Universidad Autónoma
de Madridand IADCHEM, Institute for Advanced Research in Chemistry, Calle Francisco Tomás y Valiente
7, 28049 Madrid, Spain
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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14
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Sánchez-Murcia PA, Nogueira JJ, Plasser F, González L. Orbital-free photophysical descriptors to predict directional excitations in metal-based photosensitizers. Chem Sci 2020; 11:7685-7693. [PMID: 32864087 PMCID: PMC7425079 DOI: 10.1039/d0sc01684e] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/14/2020] [Indexed: 12/02/2022] Open
Abstract
The development of dye-sensitized solar cells, metalloenzyme photocatalysis or biological labeling heavily relies on the design of metal-based photosensitizes with directional excitations. Directionality is most often predicted by characterizing the excitations manually via canonical frontier orbitals. Although widespread, this traditional approach is, at the very least, cumbersome and subject to personal bias, as well as limited in many cases. Here, we demonstrate how two orbital-free photophysical descriptors allow an easy and straightforward quantification of the degree of directionality in electron excitations using chemical fragments. As proof of concept we scrutinize the effect of 22 chemical modifications on the archetype [Ru(bpy)3]2+ with a new descriptor coined "substituent-induced exciton localization" (SIEL), together with the concept of "excited-electron delocalization length" (EEDL n ). Applied to quantum ensembles of initially excited singlet and the relaxed triplet metal-to-ligand charge-transfer states, the SIEL descriptor allows quantifying how much and whereto the exciton is promoted, as well as anticipating the effect of single modifications, e.g. on C-4 atoms of bpy units of [Ru(bpy)3]2+. The general applicability of SIEL and EEDL n is further established by rationalizing experimental trends through quantification of the directionality of the photoexcitation. We thus demonstrate that SIEL and EEDL descriptors can be synergistically employed to design improved photosensitizers with highly directional and localized electron-transfer transitions.
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Affiliation(s)
- Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Str. 17 , 1090 Vienna , Austria . ;
| | - Juan J Nogueira
- Department of Chemistry and Institute for Advanced Research in Chemistry , Universidad Autónoma de Madrid , Madrid , 28049 , Spain
| | - Felix Plasser
- Department of Chemistry , Loughborough University , Loughborough , LE11 3TU , UK
| | - Leticia González
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Str. 17 , 1090 Vienna , Austria . ;
- Vienna Research Platform for Accelerating Photoreaction Discovery , University of Vienna , Währinger Str. 17 , 1090 Vienna , Austria
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15
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Martínez-Camarena Á, Sánchez-Murcia PA, Blasco S, González L, García-España E. Unveiling the reaction mechanism of novel copper N-alkylated tetra-azacyclophanes with outstanding superoxide dismutase activity. Chem Commun (Camb) 2020; 56:7511-7514. [PMID: 32510075 DOI: 10.1039/d0cc01926g] [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: 12/21/2022]
Abstract
Quantum chemical and multiscale calculations reveal the mechanistic pathway of two superoxide dismutase mimetic N-alkylated tetra-azacyclophane copper complexes with remarkable activity. The arrangement of the binding site afforded by the bulky alkyl substituents and the coordinated water molecule as a proton source play key roles in the reaction mechanism.
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Affiliation(s)
- Álvaro Martínez-Camarena
- ICMol, Departamento de Química Inorgánica, University of Valencia, C/Catedrático José Beltrán 2, 46980, Paterna, Spain.
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16
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Sánchez-Murcia PA, de Castro S, García-Aparicio C, Jiménez MA, Corona A, Tramontano E, Sluis-Cremer N, Menéndez-Arias L, Velázquez S, Gago F, Camarasa MJ. Peptides Mimicking the β7/β8 Loop of HIV-1 Reverse Transcriptase p51 as "Hotspot-Targeted" Dimerization Inhibitors. ACS Med Chem Lett 2020; 11:811-817. [PMID: 32435389 DOI: 10.1021/acsmedchemlett.9b00623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/24/2020] [Indexed: 02/04/2023] Open
Abstract
A conformationally constrained short peptide designed to target a protein-protein interaction hotspot in HIV-1 reverse transcriptase (RT) disrupts p66-p51 interactions and paves the way to the development of novel RT dimerization inhibitors.
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Affiliation(s)
| | - Sonia de Castro
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | | | - M. Angeles Jiménez
- Instituto de Química-Física Rocasolano (IQFR, CSIC), Serrano 119, E-28006Madrid, Spain
| | - Angela Corona
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- University of Cagliari, Department of Life and Environmental Sciences, Cittadella Universitaria di
Monserrato, 09042 Monserrato, Cagliari, Italy
| | - Nicolas Sluis-Cremer
- University of Pittsburgh School of Medicine, Division of Infectious Diseases, Pittsburgh, Pennsylvania 15261, United States
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC & Universidad Autónoma de Madrid), Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada CSIC, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
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17
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Del Arco J, Perona A, González L, Fernández-Lucas J, Gago F, Sánchez-Murcia PA. Reaction mechanism of nucleoside 2'-deoxyribosyltransferases: free-energy landscape supports an oxocarbenium ion as the reaction intermediate. Org Biomol Chem 2020; 17:7891-7899. [PMID: 31397456 DOI: 10.1039/c9ob01315f] [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: 01/17/2023]
Abstract
Insight into the catalytic mechanism of Lactobacillus leichmannii nucleoside 2'-deoxyribosyltransferase (LlNDT) has been gained by calculating a quantum mechanics-molecular mechanics (QM/MM) free-energy landscape of the reaction within the enzyme active site. Our results support an oxocarbenium species as the reaction intermediate and thus an SN1 reaction mechanism in this family of bacterial enzymes. Our mechanistic proposal is validated by comparing experimental kinetic data on the impact of the single amino acid replacements Tyr7, Glu98 and Met125 with Ala, Asp and Ala/norLeu, respectively, and accounts for the specificity shown by this enzyme on a non-natural substrate. This work broadens our understanding of enzymatic C-N bond cleavage and C-N bond formation.
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Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain
| | - Almudena Perona
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, Währinger Str. 17, A-1090 University of Vienna, Vienna, Austria.
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, European University of Madrid, Villaviciosa de Odón, Spain and Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, Barranquilla, Colombia
| | - Federico Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, Währinger Str. 17, A-1090 University of Vienna, Vienna, Austria.
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18
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Gavin DP, Reen FJ, Rocha-Martin J, Abreu-Castilla I, Woods DF, Foley AM, Sánchez-Murcia PA, Schwarz M, O'Neill P, Maguire AR, O'Gara F. Genome mining and characterisation of a novel transaminase with remote stereoselectivity. Sci Rep 2019; 9:20285. [PMID: 31889089 PMCID: PMC6937235 DOI: 10.1038/s41598-019-56612-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/21/2019] [Accepted: 11/20/2019] [Indexed: 01/27/2023] Open
Abstract
Microbial enzymes from pristine niches can potentially deliver disruptive opportunities in synthetic routes to Active Pharmaceutical Ingredients and intermediates in the Pharmaceutical Industry. Advances in green chemistry technologies and the importance of stereochemical control, further underscores the application of enzyme-based solutions in chemical synthesis. The rich tapestry of microbial diversity in the oceanic ecosystem encodes a capacity for novel biotransformations arising from the chemical complexity of this largely unexplored bioactive reservoir. Here we report a novel ω-transaminase discovered in a marine sponge Pseudovibrio sp. isolate. Remote stereoselection using a transaminase has been demonstrated for the first time using this novel protein. Application to the resolution of an intermediate in the synthesis of sertraline highlights the synthetic potential of this novel biocatalyst discovered through genomic mining. Integrated chemico-genomics revealed a unique substrate profile, while molecular modelling provided structural insights into this ‘first in class’ selectivity at a remote chiral centre.
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Affiliation(s)
- D P Gavin
- School of Chemistry; Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
| | - F J Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, T12 K8AF, Cork, Ireland
| | - J Rocha-Martin
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - I Abreu-Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - D F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - A M Foley
- School of Chemistry, School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - P A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, A-1090, Vienna, Austria
| | - M Schwarz
- School of Chemistry; Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland
| | - P O'Neill
- Pfizer Process Development Centre, Loughbeg, Cork, Ireland
| | - A R Maguire
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland. .,School of Chemistry, School of Pharmacy, Analytical and Biological Chemistry Research Facility, University College Cork, Cork, Ireland.
| | - F O'Gara
- Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland. .,BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland. .,Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia and Telethon Kids Institute, Perth, WA, 6008, Australia.
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19
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Revuelto A, Ruiz-Santaquiteria M, de Lucio H, Gamo A, Carriles AA, Gutiérrez KJ, Sánchez-Murcia PA, Hermoso JA, Gago F, Camarasa MJ, Jiménez-Ruiz A, Velázquez S. Pyrrolopyrimidine vs Imidazole-Phenyl-Thiazole Scaffolds in Nonpeptidic Dimerization Inhibitors of Leishmania infantum Trypanothione Reductase. ACS Infect Dis 2019; 5:873-891. [PMID: 30983322 DOI: 10.1021/acsinfecdis.8b00355] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 12/27/2022]
Abstract
Disruption of protein-protein interactions of essential oligomeric enzymes by small molecules represents a significant challenge. We recently reported some linear and cyclic peptides derived from an α-helical region present in the homodimeric interface of Leishmania infantum trypanothione reductase ( Li-TryR) that showed potent effects on both dimerization and redox activity of this essential enzyme. Here, we describe our first steps toward the design of nonpeptidic small-molecule Li-TryR dimerization disruptors using a proteomimetic approach. The pyrrolopyrimidine and the 5-6-5 imidazole-phenyl-thiazole α-helix-mimetic scaffolds were suitably decorated with substituents that could mimic three key residues (K, Q, and I) of the linear peptide prototype (PKIIQSVGIS-Nle-K-Nle). Extensive optimization of previously described synthetic methodologies was required. A library of 15 compounds bearing different hydrophobic alkyl and aromatic substituents was synthesized. The imidazole-phenyl-thiazole-based analogues outperformed the pyrrolopyrimidine-based derivatives in both inhibiting the enzyme and killing extracellular and intracellular parasites in cell culture. The most active imidazole-phenyl-thiazole compounds 3e and 3f inhibit Li-TryR and prevent growth of the parasites at low micromolar concentrations similar to those required by the peptide prototype. The intrinsic fluorescence of these compounds inside the parasites visually demonstrates their good permeability in comparison with previous peptide-based Li-TryR dimerization disruptors.
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Affiliation(s)
| | | | - Héctor de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Ana Gamo
- Instituto de Química Médica (IQM-CSIC), Madrid E-28006, Spain
| | - Alejandra A. Carriles
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Kilian Jesús Gutiérrez
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
| | - Pedro A. Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano” (IQFR-CSIC), Madrid E-28006, Spain
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Madrid E-28805, Spain
| | | | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá
de Henares, Madrid E-28805, Spain
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20
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Sánchez-Murcia PA, Mills A, Cortés-Cabrera Á, Gago F. Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. J Comput Aided Mol Des 2019; 33:627-644. [DOI: 10.1007/s10822-019-00208-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 01/27/2023]
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21
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Abstract
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods.
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods. It is found that the electrostatic term in the probe:DNA binding energy, modulates the binding mode, providing new guidelines for the design of spiropyran photoswitches with specific binding modes to DNA.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria.
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22
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Bravo A, de Lucio H, Sánchez-Murcia PA, Jiménez-Ruiz A, Petrone PM, Gago F, Cortés Cabrera A. Identification of NEK3 and MOK as novel targets for lithium. Chem Biol Drug Des 2019; 93:965-969. [PMID: 30667602 DOI: 10.1111/cbdd.13487] [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] [Received: 10/15/2018] [Revised: 11/23/2018] [Accepted: 01/09/2019] [Indexed: 11/28/2022]
Abstract
Lithium ion, commonly used as the carbonate salt in the treatment of bipolar disorders, has been identified as an inhibitor of several kinases, including Glycogen Synthase Kinase-3β, for almost 20 years. However, both the exact mechanism of enzymatic inhibition and its apparent specificity for certain metalloenzymes are still a matter of debate. A data-driven hypothesis is presented that accounts for the specificity profile of kinase inhibition by lithium in terms of the presence of a unique protein environment in the magnesium-binding site. This hypothesis has been validated by the discovery of two novel potential targets for lithium, namely NEK3 and MOK, which are related to neuronal function.
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Affiliation(s)
- Ana Bravo
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Spain.,Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Héctor de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Paula M Petrone
- Pharma Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Alvaro Cortés Cabrera
- Área de Farmacología, Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Alcalá de Henares, Spain.,Pharma Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland
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23
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Bernardo-García N, Sánchez-Murcia PA, Espaillat A, Martínez-Caballero S, Cava F, Hermoso JA, Gago F. Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org Biomol Chem 2019; 17:4350-4358. [DOI: 10.1039/c9ob00223e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The commonly used Tris buffer acts as a surrogate substrate and deformylates pyridoxal phosphate in a bacterial alanine racemase at subzero temperatures.
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Affiliation(s)
- Noelia Bernardo-García
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | | | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine
- Department of Molecular Biology
- Umeå Centre for Microbial Research
- Umeå University
- 90187 Umeå
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology
- Institute of Physical Chemistry “Rocasolano”
- CSIC
- 28006 Madrid
- Spain
| | - Federico Gago
- Department of Biomedical Sciences
- “Unidad Asociada IQM-CSIC”
- University of Alcalá
- Madrid
- Spain
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Maity D, Gigante A, Sánchez-Murcia PA, Sijbesma E, Li M, Bier D, Mosel S, Knauer S, Ottmann C, Schmuck C. Arginine mimetic appended peptide-based probes for fluorescence turn-on detection of 14-3-3 proteins. Org Biomol Chem 2019; 17:4359-4363. [DOI: 10.1039/c9ob00620f] [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: 12/17/2022]
Abstract
Development of fluorescence markers for the 14-3-3 adapter protein class.
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Affiliation(s)
- Debabrata Maity
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - Alba Gigante
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - Pedro A. Sánchez-Murcia
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- Währinger Str. 17 A-1090 Vienna
- Austria
| | - Eline Sijbesma
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - Mao Li
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
| | - David Bier
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
- Eindhoven University of Technology
- 5600 MB Eindhoven
- The Netherlands
| | - Stefanie Mosel
- Institute for Biology
- University of Duisburg Essen
- 45141, Essen
- Germany
| | - Shirley Knauer
- Institute for Biology
- University of Duisburg Essen
- 45141, Essen
- Germany
| | - Christian Ottmann
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
- Department of Biomedical Engineering and Institute for Complex Molecular Systems
| | - Carsten Schmuck
- Institute of Organic Chemistry
- University of Duisburg Essen
- Essen
- Germany
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25
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Avagliano D, Sánchez-Murcia PA, González L. Directional and regioselective hole injection of spiropyran photoswitches intercalated into A/T-duplex DNA. Phys Chem Chem Phys 2019; 21:17971-17977. [DOI: 10.1039/c9cp03398j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hole electron transfer of UV excited spiropyran intercalated in dsDNA is directional, asymmetric and regioselective, as shown by quantitative multiscale computations.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Pedro A. Sánchez-Murcia
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Leticia González
- Institute of Theoretical Chemistry
- Faculty of Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
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26
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Ma YT, Yang Y, Cai P, Sun DY, Sánchez-Murcia PA, Zhang XY, Jia WQ, Lei L, Guo M, Gago F, Wang H, Fang WS. A Series of Enthalpically Optimized Docetaxel Analogues Exhibiting Enhanced Antitumor Activity and Water Solubility. J Nat Prod 2018; 81:524-533. [PMID: 29359935 DOI: 10.1021/acs.jnatprod.7b00857] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A dual-purpose strategy aimed at enhancing the binding affinity for microtubules and improving the water solubility of docetaxel led to the design and synthesis of a series of C-2- and C-3'-modified analogues. Both aims were realized when the C-3' phenyl group present in docetaxel was replaced with a propargyl alcohol. The resulting compound, 3f, was able to overcome drug resistance in cultured P-gp-overexpressing tumor cells and showed greater activity than docetaxel against drug-resistant A2780/AD ovarian cancer xenografts in mice. In addition, the considerably lower hydrophobicity of 3f relative to both docetaxel and paclitaxel led to better aqueous solubility. A molecular model of tubulin-bound 3f revealed novel hydrogen-bonding interactions between the propargyl alcohol and the polar environment provided by the side chains of Ser236, Glu27, and Arg320.
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Affiliation(s)
- Yun-Tao Ma
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - Yanting Yang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education , Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University , Yantai 264005 , People's Republic of China
| | - Pei Cai
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - De-Yang Sun
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - Pedro A Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas , Unidad Asociada al Instituto de Química Médica del CSIC, Universidad de Alcalá , E-28805 Alcalá de Henares , Madrid , Spain
| | - Xiao-Ying Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - Wen-Qiang Jia
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
| | - Lei Lei
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education , Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University , Yantai 264005 , People's Republic of China
| | - Mengqi Guo
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education , Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University , Yantai 264005 , People's Republic of China
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas , Unidad Asociada al Instituto de Química Médica del CSIC, Universidad de Alcalá , E-28805 Alcalá de Henares , Madrid , Spain
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education , Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University , Yantai 264005 , People's Republic of China
| | - Wei-Shuo Fang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines , Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100050 , People's Republic of China
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Abstract
The characterization of electronic properties of metal complexes embedded in membrane environments is of paramount importance to develop efficient photosensitizers in optogenetic applications. Molecular dynamics and QM/MM simulations together with quantitative wave function analysis reveal a directional electronic redistribution of the exciton formed upon excitation of [Ru(bpy)2(bpy-C17)]2+ when going from water to a lipid bilayer, despite the fact that the media influence neither the metal-to-ligand charge-transfer character nor the excitation energy of the absorption spectra. When the photosensitizer is embedded into the DOPC lipid membrane, exciton population is mainly located in the bypyridyl sites proximal to the positively charged surface of the bilayer due to electrostatic interactions. This behavior shows that the electronic structure of metal complexes can be controlled through the binding to external species, underscoring the crucial role of the environment in directing the electronic flow upon excitation and thus helping rational tuning of optogenetic agents.
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Affiliation(s)
- Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna , Währinger Str. 17, A-1090 Vienna, Austria
| | - Juan J Nogueira
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna , Währinger Str. 17, A-1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna , Währinger Str. 17, A-1090 Vienna, Austria
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Torres-Salas P, Bernal V, López-Gallego F, Martínez-Crespo J, Sánchez-Murcia PA, Barrera V, Morales-Jiménez R, García-Sánchez A, Mañas-Fernández A, Seoane JM, Sagrera Polo M, Miranda JD, Calvo J, Huertas S, Torres JL, Alcalde-Bascones A, González-Barrera S, Gago F, Morreale A, González-Barroso MDM. Engineering Erg10 Thiolase from Saccharomyces cerevisiae as a Synthetic Toolkit for the Production of Branched-Chain Alcohols. Biochemistry 2018; 57:1338-1348. [PMID: 29360348 DOI: 10.1021/acs.biochem.7b01186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiolases catalyze the condensation of acyl-CoA thioesters through the Claisen condensation reaction. The best described enzymes usually yield linear condensation products. Using a combined computational/experimental approach, and guided by structural information, we have studied the potential of thiolases to synthesize branched compounds. We have identified a bulky residue located at the active site that blocks proper accommodation of substrates longer than acetyl-CoA. Amino acid replacements at such a position exert effects on the activity and product selectivity of the enzymes that are highly dependent on a protein scaffold. Among the set of five thiolases studied, Erg10 thiolase from Saccharomyces cerevisiae showed no acetyl-CoA/butyryl-CoA branched condensation activity, but variants at position F293 resulted the most active and selective biocatalysts for this reaction. This is the first time that a thiolase has been engineered to synthesize branched compounds. These novel enzymes enrich the toolbox of combinatorial (bio)chemistry, paving the way for manufacturing a variety of α-substituted synthons. As a proof of concept, we have engineered Clostridium's 1-butanol pathway to obtain 2-ethyl-1-butanol, an alcohol that is interesting as a branched model compound.
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Affiliation(s)
- Pamela Torres-Salas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Vicente Bernal
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Fernando López-Gallego
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain.,CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain.,ARAID Foundation , Zaragoza, Spain
| | - Javier Martínez-Crespo
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Pedro A Sánchez-Murcia
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Victor Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Rocío Morales-Jiménez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana García-Sánchez
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Aurora Mañas-Fernández
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José M Seoane
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Marta Sagrera Polo
- Centro de Investigaciones Biológicas (CSIC) , Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juande D Miranda
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Javier Calvo
- CIC biomaGUNE , Paseo de Miramón 182, 20014 San Sebastián, Spain
| | - Sonia Huertas
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - José L Torres
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Ana Alcalde-Bascones
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Sergio González-Barrera
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas and "Unidad Asociada IQM-CSIC", Universidad de Alcalá , E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Morreale
- Centro de Tecnología de Repsol, REPSOL S. A. Calle Agustín de Betancourt , s/n, 28935 Móstoles, Madrid, Spain
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Cortés Cabrera Á, Sánchez-Murcia PA, Gago F. Making sense of the past: hyperstability of ancestral thioredoxins explained by free energy simulations. Phys Chem Chem Phys 2018; 19:23239-23246. [PMID: 28825743 DOI: 10.1039/c7cp03659k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thioredoxin (Trx), a small and globular protein, is present in all kinds of organisms, from Archea to higher mammals. Throughout evolution, the Trx sequence has undergone subtle modifications to adapt to varying environmental conditions. The high degree of sequence conservation makes Trx very amenable to ancestral protein reconstruction techniques. In this work, we address the study of the structural and energetic determinants of thermostability in E. coli Trx using a dataset of mutations inspired by ancestral reconstruction. We compute, from first principles, the expected contribution of 19 different amino acid substitutions to the stability (ΔΔG) and the melting temperature (ΔTm) of the protein. We also describe the specific changes in structure and protein dynamics responsible for the stabilizing or destabilizing effects of these mutations. Our results point to local and independent changes for most of the variants. Our predictions are accurate enough to substantiate the proposal of new hypotheses regarding evolutionary relationships between mutations, as in the case of T89R, P68A and G74S or K90L and F102A, and reach beyond the initial set to suggest improved variants, such as K90I or K90Y.
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Affiliation(s)
- Álvaro Cortés Cabrera
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
| | - Pedro A Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Facultad de Medicina y Ciencias de la Salud, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain.
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de Lucio H, Gamo AM, Ruiz-Santaquiteria M, de Castro S, Sánchez-Murcia PA, Toro MA, Gutiérrez KJ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Improved proteolytic stability and potent activity against Leishmania infantum trypanothione reductase of α/β-peptide foldamers conjugated to cell-penetrating peptides. Eur J Med Chem 2017; 140:615-623. [DOI: 10.1016/j.ejmech.2017.09.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023]
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Oliva C, Sánchez-Murcia PA, Rico E, Bravo A, Menéndez M, Gago F, Jiménez-Ruiz A. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences. Nucleic Acids Res 2017; 45:9030-9045. [PMID: 28911117 PMCID: PMC5587815 DOI: 10.1093/nar/gkx629] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/28/2022] Open
Abstract
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145–180 is indeed far more active than its wild-type counterpart at pH values >7.0. In addition, we discovered that (i) LiEndoG exists as a homodimer, (ii) replacement of Ser211 in the active-site SRGH motif with the canonical aspartate from the DRGH motif of other nucleases leads to a catalytically deficient enzyme, (iii) the activity of the S211D variant can be restored upon the concomitant replacement of Ala247 with Arg and (iv) a C-terminal extension is responsible for the observed preferential cleavage of single-stranded DNA (ssDNA) and ssDNA–dsDNA junctions. Taken together, our results support the view that LiEndoG is a multidomain molecular machine whose nuclease activity can be subtly modulated or even abrogated through architectural changes brought about by environmental conditions and interaction with other binding partners.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Catalytic Domain
- Cloning, Molecular
- DNA Cleavage
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Endodeoxyribonucleases/chemistry
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Hydrogen-Ion Concentration
- Kinetics
- Leishmania infantum/chemistry
- Leishmania infantum/enzymology
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Multimerization
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Deletion
- Sequence Homology, Amino Acid
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- Cristina Oliva
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Pedro A. Sánchez-Murcia
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Eva Rico
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Ana Bravo
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), E-28006 Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas y “Unidad Asociada IQM-CSIC”, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 918 855 109; Fax: +34 918 854 585; . Correspondence may also be addressed to Federico Gago. Tel: +34 918 854 514; Fax: +34 918 854 591;
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32
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Crespo N, Sánchez-Murcia PA, Gago F, Cejudo-Sanches J, Galmes MA, Fernández-Lucas J, Mancheño JM. 2'-Deoxyribosyltransferase from Leishmania mexicana, an efficient biocatalyst for one-pot, one-step synthesis of nucleosides from poorly soluble purine bases. Appl Microbiol Biotechnol 2017; 101:7187-7200. [PMID: 28785897 DOI: 10.1007/s00253-017-8450-y] [Citation(s) in RCA: 14] [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: 05/18/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022]
Abstract
Processes catalyzed by enzymes offer numerous advantages over chemical methods although in many occasions the stability of the biocatalysts becomes a serious concern. Traditionally, synthesis of nucleosides using poorly water-soluble purine bases, such as guanine, xanthine, or hypoxanthine, requires alkaline pH and/or high temperatures in order to solubilize the substrate. In this work, we demonstrate that the 2'-deoxyribosyltransferase from Leishmania mexicana (LmPDT) exhibits an unusually high activity and stability under alkaline conditions (pH 8-10) across a broad range of temperatures (30-70 °C) and ionic strengths (0-500 mM NaCl). Conversely, analysis of the crystal structure of LmPDT together with comparisons with hexameric, bacterial homologues revealed the importance of the relationships between the oligomeric state and the active site architecture within this family of enzymes. Moreover, molecular dynamics and docking approaches provided structural insights into the substrate-binding mode. Biochemical characterization of LmPDT identifies the enzyme as a type I NDT (PDT), exhibiting excellent activity, with specific activity values 100- and 4000-fold higher than the ones reported for other PDTs. Interestingly, LmPDT remained stable during 36 h at different pH values at 40 °C. In order to explore the potential of LmPDT as an industrial biocatalyst, enzymatic production of several natural and non-natural therapeutic nucleosides, such as vidarabine (ara A), didanosine (ddI), ddG, or 2'-fluoro-2'-deoxyguanosine, was carried out using poorly water-soluble purines. Noteworthy, this is the first time that the enzymatic synthesis of 2'-fluoro-2'-deoxyguanosine, ara G, and ara H by a 2'-deoxyribosyltransferase is reported.
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Affiliation(s)
- N Crespo
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, E-28006, Madrid, Spain.,Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - P A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, 1090, Vienna, Austria.,Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, E-28871, Alcalá de Henares, Spain
| | - F Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, E-28871, Alcalá de Henares, Spain
| | - J Cejudo-Sanches
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - M A Galmes
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, European University of Madrid, E-28670, Villaviciosa de Odón, Madrid, Spain. .,Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Department of Agroindustrial Engineering, School of Environmental Sciences, Universidad de la Costa, Cra. 55 #58-66, Barranquilla, Colombia.
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute Rocasolano (CSIC), Serrano 119, E-28006, Madrid, Spain.
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Trigili C, Barasoain I, Sánchez-Murcia PA, Bargsten K, Redondo-Horcajo M, Nogales A, Gardner NM, Meyer A, Naylor GJ, Gómez-Rubio E, Gago F, Steinmetz MO, Paterson I, Prota AE, Díaz JF. Structural Determinants of the Dictyostatin Chemotype for Tubulin Binding Affinity and Antitumor Activity Against Taxane- and Epothilone-Resistant Cancer Cells. ACS Omega 2016; 1:1192-1204. [PMID: 30023505 PMCID: PMC6044705 DOI: 10.1021/acsomega.6b00317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/28/2016] [Indexed: 05/21/2023]
Abstract
A combined biochemical, structural, and cell biology characterization of dictyostatin is described, which enables an improved understanding of the structural determinants responsible for the high-affinity binding of this anticancer agent to the taxane site in microtubules (MTs). The study reveals that this macrolide is highly optimized for MT binding and that only a few of the structural modifications featured in a library of synthetic analogues resulted in small gains in binding affinity. The high efficiency of the dictyostatin chemotype in overcoming various kinds of clinically relevant resistance mechanisms highlights its potential for therapeutic development for the treatment of drug-resistant tumors. A structural explanation is advanced to account for the synergy observed between dictyostatin and taxanes on the basis of their differential effects on the MT lattice. The X-ray crystal structure of a tubulin-dictyostatin complex and additional molecular modeling have allowed the rationalization of the structure-activity relationships for a set of synthetic dictyostatin analogues, including the highly active hybrid 12 with discodermolide. Altogether, the work reported here is anticipated to facilitate the improved design and synthesis of more efficacious dictyostatin analogues and hybrids with other MT-stabilizing agents.
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Affiliation(s)
- Chiara Trigili
- Chemical
and Physical Biology, Centro de Investigaciones
Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Isabel Barasoain
- Chemical
and Physical Biology, Centro de Investigaciones
Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
- E-mail: (J.F.D.)
| | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada al IQM (CSIC), Alcalá de Henares, E-28871 Madrid, Spain
| | - Katja Bargsten
- Department
of Biology and Chemistry Laboratory of Biomolecular Research, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Mariano Redondo-Horcajo
- Chemical
and Physical Biology, Centro de Investigaciones
Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | - Aurora Nogales
- Instituto
de Estructura de la Materia, Consejo Superior
de Investigaciones Científicas IEM-CSIC, Serrano 121, E-28006 Madrid, Spain
| | - Nicola M. Gardner
- University
Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Arndt Meyer
- University
Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Guy J. Naylor
- University
Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Elena Gómez-Rubio
- Área
de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada al IQM (CSIC), Alcalá de Henares, E-28871 Madrid, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, Unidad Asociada al IQM (CSIC), Alcalá de Henares, E-28871 Madrid, Spain
| | - Michel O. Steinmetz
- Department
of Biology and Chemistry Laboratory of Biomolecular Research, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - Ian Paterson
- University
Chemical Laboratory, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Andrea E. Prota
- Department
of Biology and Chemistry Laboratory of Biomolecular Research, Paul Scherrer Institut (PSI), 5232 Villigen, Switzerland
| | - J. Fernando Díaz
- Chemical
and Physical Biology, Centro de Investigaciones
Biológicas, CSIC, Ramiro de Maeztu 9, E-28040 Madrid, Spain
- E-mail: (I.B.)
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34
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Gutiérrez-Fernández J, Saleh M, Alcorlo M, Gómez-Mejía A, Pantoja-Uceda D, Treviño MA, Voß F, Abdullah MR, Galán-Bartual S, Seinen J, Sánchez-Murcia PA, Gago F, Bruix M, Hammerschmidt S, Hermoso JA. Modular Architecture and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L (CbpL) Contributing to Pneumococcal Pathogenesis. Sci Rep 2016; 6:38094. [PMID: 27917891 PMCID: PMC5137146 DOI: 10.1038/srep38094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 05/13/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022] Open
Abstract
The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca2+-binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp_Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.
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Affiliation(s)
- Javier Gutiérrez-Fernández
- Department of Crystallography and Structural Biology, "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Malek Saleh
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - Martín Alcorlo
- Department of Crystallography and Structural Biology, "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Alejandro Gómez-Mejía
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - David Pantoja-Uceda
- Department of Biological Physical Chemistry. "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Miguel A Treviño
- Department of Biological Physical Chemistry. "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Franziska Voß
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - Mohammed R Abdullah
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - Sergio Galán-Bartual
- Department of Crystallography and Structural Biology, "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Jolien Seinen
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - Pedro A Sánchez-Murcia
- Department of Biomedical Sciences, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Marta Bruix
- Department of Biological Physical Chemistry. "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
| | - Sven Hammerschmidt
- Department Genetics of Microorganisms, Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University of Greifswald, D-17487 Greifswald, Germany
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, "Rocasolano" Institute of Physical-Chemistry, CSIC, Serrano 119, E-28006-Madrid, Spain
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35
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Sánchez-Murcia PA, Bueren-Calabuig JA, Camacho-Artacho M, Cortés-Cabrera Á, Gago F. Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase. Biochemistry 2016; 55:5854-5864. [DOI: 10.1021/acs.biochem.6b00744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Juan A. Bueren-Calabuig
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Marta Camacho-Artacho
- Structural
Biology Department, Centro Nacional de Investigaciones Oncológicas (CNIO), E-28029 Madrid, Spain
| | - Álvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
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36
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Losada A, Muñoz-Alonso MJ, García C, Sánchez-Murcia PA, Martínez-Leal JF, Domínguez JM, Lillo MP, Gago F, Galmarini CM. Translation Elongation Factor eEF1A2 is a Novel Anticancer Target for the Marine Natural Product Plitidepsin. Sci Rep 2016; 6:35100. [PMID: 27713531 PMCID: PMC5054363 DOI: 10.1038/srep35100] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [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: 04/15/2016] [Accepted: 09/22/2016] [Indexed: 12/18/2022] Open
Abstract
eEF1A2 is one of the isoforms of the alpha subunit of the eukaryotic Elongation Factor 1. It is overexpressed in human tumors and is endowed with oncogenic properties, favoring tumor cell proliferation while inhibiting apoptosis. We demonstrate that plitidepsin, an antitumor agent of marine origin that has successfully completed a phase-III clinical trial for multiple myeloma, exerts its antitumor activity by targeting eEF1A2. The drug interacts with eEF1A2 with a KD of 80 nM and a target residence time of circa 9 min. This protein was also identified as capable of binding [14C]-plitidepsin in a cell lysate from K-562 tumor cells. A molecular modelling approach was used to identify a favorable binding site for plitidepsin at the interface between domains 1 and 2 of eEF1A2 in the GTP conformation. Three tumor cell lines selected for at least 100-fold more resistance to plitidepsin than their respective parental cells showed reduced levels of eEF1A2 protein. Ectopic expression of eEF1A2 in resistant cells restored the sensitivity to plitidepsin. FLIM-phasor FRET experiments demonstrated that plitidepsin localizes in tumor cells sufficiently close to eEF1A2 as to suggest the formation of drug-protein complexes in living cells. Altogether, our results strongly suggest that eEF1A2 is the primary target of plitidepsin.
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Affiliation(s)
- Alejandro Losada
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
| | - María José Muñoz-Alonso
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
| | - Carolina García
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Madrid, Spain
| | - Pedro A Sánchez-Murcia
- Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Madrid, Spain
| | | | - Juan Manuel Domínguez
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
| | - M Pilar Lillo
- Departamento de Química Física Biológica, Instituto de Química-Física "Rocasolano" (CSIC), Madrid, Spain
| | - Federico Gago
- Departamento de Ciencias Biomédicas, Unidad Asociada al IQM-CSIC, Universidad de Alcalá, Madrid, Spain
| | - Carlos M Galmarini
- Departamento de Biología Celular y Farmacogenómica, Pharma Mar S.A., Colmenar Viejo, Madrid, Spain
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37
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Wang SR, Sánchez-Murcia PA, Gago F, Fang WS. A novel C,D-spirodioxene taxoid synthesized through an unexpected Pd-mediated ring cyclization. Org Biomol Chem 2016; 14:345-52. [PMID: 26603551 DOI: 10.1039/c5ob02131f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A novel C,D-spirodioxene taxoid (6) was prepared from paclitaxel (1a), with the key steps including an unexpected Pd-mediated ring cyclization. The anti-tubulin activity of 6 was decreased relative to that of 1a and a previously reported C,D-spirolactone taxane (5). These observations could be rationalized on the basis of molecular modeling results. To the best of our knowledge, this is the first example indicating that 1,4-dioxenes can be synthesized from a mono-allyl vicinal diol through a Wacker-type cyclization. This strategy may be applicable to the synthesis of other C,D-spiro taxoids.
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Affiliation(s)
- Shao-Rong Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China.
| | - Pedro A Sánchez-Murcia
- Área de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, E-28871 Alcalá de Henares, Unidad Asociada al Instituto de Química Médica del CSIC, E-28871 Madrid, Spain
| | - Federico Gago
- Área de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, E-28871 Alcalá de Henares, Unidad Asociada al Instituto de Química Médica del CSIC, E-28871 Madrid, Spain
| | - Wei-Shuo Fang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China.
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38
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Gherbovet O, Sánchez-Murcia PA, García Alvarez MC, Bignon J, Thoret S, Gago F, Roussi F. Synthesis and evaluation of hybrid molecules targeting the vinca domain of tubulin. Org Biomol Chem 2016; 13:3144-54. [PMID: 25634805 DOI: 10.1039/c4ob02114b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Some hybrids of vinca alkaloids and phomopsin A, linked by a glycine pattern, have been synthesized in one or two steps, by an insertion reaction and shown to inhibit microtubule assembly. These compounds have been elaborated in order to interact with both the "vinca site" and the "peptide site" of the vinca domain in tubulin. Two out of three hybrids are potent inhibitors of microtubules assembly and they present good cytotoxicity against different cell lines. Molecular modelling studies show that they could bind, within the vinca domain, in similar spatial regions as those of vinca and phomopsin thanks to the flexibility provided by the glycine linker used to elaborate these hybrids.
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Affiliation(s)
- O Gherbovet
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, UPR 2301 du CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France.
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39
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Filace F, Sánchez-Murcia PA, Sucunza D, Pérez-Redondo A, Álvarez-Buílla J, Gago F, Burgos C. Silyl Assistance in the Intramolecular Addition of Pyridyl Radicals onto Pyridines and Quinolines. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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40
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Genes CM, de Lucio H, González VM, Sánchez-Murcia PA, Rico E, Gago F, Fasel N, Jiménez-Ruiz A. A functional BH3 domain in an aquaporin from Leishmania infantum. Cell Death Discov 2016; 2:16043. [PMID: 27551533 PMCID: PMC4979448 DOI: 10.1038/cddiscovery.2016.43] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/10/2016] [Accepted: 05/15/2016] [Indexed: 02/08/2023] Open
Abstract
Despite the absence of sequences showing significant similarity to any of the members of the Bcl-2 family of proteins in protozoa, experiments carried out in yeast or trypanosomatids have demonstrated that ectopic expression of some of these members alters their response to different death stimuli. Because the BH3 domain is the smallest common signature in all the proteins of this family of apoptosis regulators and also because they are essential for molecular interactions between antagonistic members, we looked for sequences with significant similarity to the BH3 motif in the Leishmania infantum genome. Among the top scoring ones, we found the MYLALQNLGDEV amino-acid stretch at the C terminus of a previously described aquaporin, now renamed as Li-BH3AQP. This motif is highly conserved in homologous proteins from other species of the Leishmania genus. The association of Li-BH3AQP with human Bcl-XL was demonstrated by both co-immunoprecipitation and yeast two-hybrid experiments. Ectopic expression of Li-BH3AQP reduced viability of HeLa cells and this deleterious effect was abrogated by the simultaneous overexpression of Bcl-XL. Although we were not able to demonstrate a reduction in parasite viability when the protein was overexpressed in Leishmania promastigotes, a prodeath effect could be observed when the parasites overexpressing Li-BH3AQP were treated with staurosporine or antimycin A. Surprisingly, these parasites were more resistant, compared with wild-type parasites, to hypotonic stress or nutrient deprivation. The prodeath activity was abolished upon replacement of two highly conserved amino acids in this BH3 domain. Taken together, these results point to Li-BH3AQP as the first non-enzymatic protein ever described in trypanosomatids that is involved in cell death.
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Affiliation(s)
- C M Genes
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - H de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - V M González
- Laboratory of aptamers, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - P A Sánchez-Murcia
- Departamento de Ciencias Biomédicas, Universidad de Alcalá, Facultad de Medicina, Alcalá de Henares 28805, Spain
| | - E Rico
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - F Gago
- Departamento de Ciencias Biomédicas, Universidad de Alcalá, Facultad de Medicina, Alcalá de Henares 28805, Spain
| | - N Fasel
- Department of Biochemistry, University of Lausanne, 155 Chemin des Boveresses, Epalinges 1066, Switzerland
| | - A Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares 28805, Spain
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41
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Wang SR, Yang CG, Sánchez-Murcia PA, Snyder JP, Yan N, Sáez-Calvo G, Díaz JF, Gago F, Fang WS. Restoration of Microtubule Interaction and Cytotoxicity in D-seco Taxanes upon Incorporation of 20-Hydroxymethyl-4-allyloxy Groups. Org Lett 2015; 17:6098-101. [DOI: 10.1021/acs.orglett.5b03119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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)
- Shao-Rong Wang
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China
| | - Chun-Gang Yang
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China
| | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, E-28871 Alcalá de Henares, Unidad Asociada al Instituto de Química Médica del CSIC, E-28871 Madrid, Spain
| | - James P. Snyder
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Ning Yan
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China
| | - Gonzalo Sáez-Calvo
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José Fernando Díaz
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas, Universidad de Alcalá, E-28871 Alcalá de Henares, Unidad Asociada al Instituto de Química Médica del CSIC, E-28871 Madrid, Spain
| | - Wei-Shuo Fang
- State
Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 2A Nanwei Road, Beijing 100050, China
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42
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Díez-Dacal B, Sánchez-Gómez FJ, Sánchez-Murcia PA, Milackova I, Zimmerman T, Ballekova J, García-Martín E, Agúndez JAG, Gharbi S, Gago F, Stefek M, Pérez-Sala D. Molecular Interactions and Implications of Aldose Reductase Inhibition by PGA1 and Clinically Used Prostaglandins. Mol Pharmacol 2015; 89:42-52. [DOI: 10.1124/mol.115.100693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/19/2015] [Indexed: 12/20/2022] Open
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Benavente R, Esteban-Torres M, Kohring GW, Cortés-Cabrera Á, Sánchez-Murcia PA, Gago F, Acebrón I, de las Rivas B, Muñoz R, Mancheño JM. Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. ACTA ACUST UNITED AC 2015; 71:1540-54. [PMID: 26143925 DOI: 10.1107/s1399004715009281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/15/2015] [Indexed: 11/11/2022]
Abstract
Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily. It catalyses the Zn(2+)- and NAD(+)-dependent stereoselective dehydrogenation of L-galactitol 1-phosphate to D-tagatose 6-phosphate. Here, three crystal structures of GPDH from Escherichia coli are reported: that of the open state of GPDH with Zn(2+) in the catalytic site and those of the closed state in complex with the polyols Tris and glycerol, respectively. The closed state of GPDH reveals no bound cofactor, which is at variance with the conformational transition of the prototypical mammalian liver alcohol dehydrogenase. The main intersubunit-contacting interface within the GPDH homodimer presents a large internal cavity that probably facilitates the relative movement between the subunits. The substrate analogue glycerol bound within the active site partially mimics the catalytically relevant backbone of galactitol 1-phosphate. The glycerol binding mode reveals, for the first time in the polyol dehydrogenases, a pentacoordinated zinc ion in complex with a polyol and also a strong hydrogen bond between the primary hydroxyl group and the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.
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Affiliation(s)
- Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Esteban-Torres
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Gebäude A1.5, 66123 Saarbruecken, Germany
| | - Álvaro Cortés-Cabrera
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Federico Gago
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Blanca de las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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44
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Sánchez-Murcia PA, Ruiz-Santaquiteria M, Toro MA, de Lucio H, Jiménez MÁ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Comparison of hydrocarbon-and lactam-bridged cyclic peptides as dimerization inhibitors of Leishmania infantum trypanothione reductase. RSC Adv 2015. [DOI: 10.1039/c5ra06853c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Helical peptides stabilizedviaall-hydrocarbon or lactam side-chain bridging were investigated as disruptors ofLeishmania infantumtrypanothione reductase.
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Affiliation(s)
| | | | - Miguel A. Toro
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | - Héctor de Lucio
- Departamento de Biología de Sistemas
- Universidad de Alcalá
- Madrid
- Spain
| | | | - Federico Gago
- Departamento de Ciencias Biomédicas
- Unidad Asociada al CSIC
- Universidad de Alcalá
- Madrid
- Spain
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45
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Canales A, Nieto L, Rodríguez-Salarichs J, Sánchez-Murcia PA, Coderch C, Cortés-Cabrera A, Paterson I, Carlomagno T, Gago F, Andreu JM, Altmann KH, Jiménez-Barbero J, Díaz JF. Molecular recognition of epothilones by microtubules and tubulin dimers revealed by biochemical and NMR approaches. ACS Chem Biol 2014; 9:1033-43. [PMID: 24524625 DOI: 10.1021/cb400673h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The binding of epothilones to dimeric tubulin and to microtubules has been studied by means of biochemical and NMR techniques. We have determined the binding constants of epothilone A (EpoA) and B (EpoB) to dimeric tubulin, which are 4 orders of magnitude lower than those for microtubules, and we have elucidated the conformation and binding epitopes of EpoA and EpoB when bound to tubulin dimers and microtubules in solution. The determined conformation of epothilones when bound to dimeric tubulin is similar to that found by X-ray crystallographic techniques for the binding of EpoA to the Tubulin/RB3/TTL complex; it is markedly different from that reported for EpoA bound to zinc-induced sheets obtained by electron crystallography. Likewise, only the X-ray structure of EpoA bound to the Tubulin/RB3/TTL complex at the luminal site, but not the electron crystallography structure, is compatible with the results obtained by STD on the binding epitope of EpoA bound to dimeric tubulin, thus confirming that the allosteric change (structuring of the M-loop) is the biochemical mechanism of induction of tubulin assembly by epothilones. TR-NOESY signals of EpoA bound to microtubules have been obtained, supporting the interaction with a transient binding site with a fast exchange rate (pore site), consistent with the notion that epothilones access the luminal site through the pore site, as has also been observed for taxanes. Finally, the differences in the tubulin binding affinities of a series of epothilone analogues has been quantitatively explained using the newly determined binding pose and the COMBINE methodology.
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Affiliation(s)
- Angeles Canales
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Dep.
Química Orgánica I, Fac. C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n, 28040 Madrid, Spain
| | - Lidia Nieto
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Javier Rodríguez-Salarichs
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de
Estudios
Avanzados de Cuba, Carretera San Antonio
km 1 1/2, Valle Grande, La Lisa, Ciudad Habana CP 17100, Cuba
| | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Claire Coderch
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Alvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - Ian Paterson
- University
Chemical Laboratory, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Teresa Carlomagno
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas−Unidad
Asociada de I+D+i del CSIC, Universidad de Alcalá E-28871 Alcalá de Henares, Madrid, Spain
| | - José M. Andreu
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, HCI H405, Wolfgang-Pauli-Str. 10, CH-8093 Zürich, Switzerland
| | - Jesús Jiménez-Barbero
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Fernando Díaz
- Centro
de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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46
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Toro MA, Sánchez-Murcia PA, Moreno D, Ruiz-Santaquiteria M, Alzate JF, Negri A, Camarasa MJ, Gago F, Velázquez S, Jiménez-Ruiz A. Probing the dimerization interface of Leishmania infantum trypanothione reductase with site-directed mutagenesis and short peptides. Chembiochem 2013; 14:1212-7. [PMID: 23744811 DOI: 10.1002/cbic.201200744] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 11/29/2012] [Revised: 03/22/2013] [Indexed: 11/07/2022]
Abstract
Binding at the interface: We tested the inhibitory activity of a set of peptide sequences derived from an α-helix of the dimeric trypanothione reductase from Leishmania infantum. Replacement of a glutamic acid residue with a lysine promoted monomer dissociation and enzyme inhibition.
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Affiliation(s)
- Miguel A Toro
- Departamento de Biología de Sistemas, Unidad Asociada de I+D+I al CSIC, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
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47
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Cruz DC, Sánchez-Murcia PA, Jørgensen KA. Formal asymmetric enone aminohydroxylation: organocatalytic one-pot synthesis of 4,5-disubstituted oxazolidinones. Chem Commun (Camb) 2012; 48:6112-4. [DOI: 10.1039/c2cc32385k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- David Cruz Cruz
- Center for Catalysis, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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