1
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Díaz-Casado L, Villacampa A, Corzana F, Jiménez-Barbero J, Gómez AM, Santana AG, Asensio JL. Illuminating a Solvent-Dependent Hierarchy for Aromatic CH/π Complexes with Dynamic Covalent Glyco-Balances. JACS Au 2024; 4:476-490. [PMID: 38425929 PMCID: PMC10900200 DOI: 10.1021/jacsau.3c00592] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 03/02/2024]
Abstract
CH/π interactions are prevalent among aromatic complexes and represent invaluable tools for stabilizing well-defined molecular architectures. Their energy contributions are exceptionally sensitive to various structural and environmental factors, resulting in a context-dependent nature that has led to conflicting findings in the scientific literature. Consequently, a universally accepted hierarchy for aromatic CH/π interactions has remained elusive. Herein, we present a comprehensive experimental investigation of aromatic CH/π complexes, employing a novel approach that involves isotopically labeled glyco-balances generated in situ. This innovative strategy not only allows us to uncover thermodynamic insights but also delves into the often less-accessible domain of kinetic information. Our analyses have yielded more than 180 new free energy values while considering key factors such as solvent properties, the interaction geometry, and the presence and nature of accompanying counterions. Remarkably, the obtained results challenge conventional wisdom regarding the stability order of common aromatic complexes. While it was believed that cationic CH/π interactions held the highest strength, followed by polarized CH/π, nonpolarized CH/π, and finally anionic CH/π interactions, our study reveals that this hierarchy can be subverted depending on the environment. Indeed, the performance of polarized CH/π interactions can match or even outcompete that of cationic CH/π interactions making them a more reliable stabilization strategy across the entire spectrum of solvent polarity. Overall, our results provide valuable guidelines for the selection of optimal interacting partners in every chemical environment, allowing the design of tailored aromatic complexes with applications in supramolecular chemistry, organocatalysis, and/or material sciences.
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Affiliation(s)
- Laura Díaz-Casado
- Departamento
de Química Bio-Orgánica, Instituto de Química
Orgánica General (IQOG-CSIC), Consejo
Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Alejandro Villacampa
- Departamento
de Química Bio-Orgánica, Instituto de Química
Orgánica General (IQOG-CSIC), Consejo
Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Jesús Jiménez-Barbero
- Basque
Researchand Technology Alliance (BRTA), CIC bioGUNE, 48170 Derio, Spain
- Basque
Foundation for Science, Ikerbasque, 48009 Bilbao, Spain
- Centro
de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Ana M. Gómez
- Departamento
de Química Bio-Orgánica, Instituto de Química
Orgánica General (IQOG-CSIC), Consejo
Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Andrés G. Santana
- Department
of Chemistry of Natural Products and Bioactive Synthetics, Instituto de Productos Naturales y Agrobiología
(IPNA-CSIC), San Cristóbal
de La Laguna, Santa Cruz de Tenerife 38206, Spain
| | - Juan Luis Asensio
- Departamento
de Química Bio-Orgánica, Instituto de Química
Orgánica General (IQOG-CSIC), Consejo
Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
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2
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Díaz-Casado L, Santana AG, Gómez-Pinto I, Villacampa A, Corzana F, Jiménez-Barbero J, González C, Asensio JL. Binding-driven reactivity attenuation enables NMR identification of selective drug candidates for nucleic acid targets. Commun Chem 2022; 5:137. [PMID: 36697799 PMCID: PMC9814457 DOI: 10.1038/s42004-022-00755-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 01/28/2023] Open
Abstract
NMR methods, and in particular ligand-based approaches, are among the most robust and reliable alternatives for binding detection and consequently, they have become highly popular in the context of hit identification and drug discovery. However, when dealing with DNA/RNA targets, these techniques face limitations that have precluded widespread application in medicinal chemistry. In order to expand the arsenal of spectroscopic tools for binding detection and to overcome the existing difficulties, herein we explore the scope and limitations of a strategy that makes use of a binding indicator previously unexploited by NMR: the perturbation of the ligand reactivity caused by complex formation. The obtained results indicate that ligand reactivity can be utilised to reveal association processes and identify the best binders within mixtures of significant complexity, providing a conceptually different reactivity-based alternative within NMR screening methods.
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Affiliation(s)
- Laura Díaz-Casado
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G. Santana
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Irene Gómez-Pinto
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Alejandro Villacampa
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Francisco Corzana
- grid.119021.a0000 0001 2174 6969Dept. Química and Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26005 La Rioja, Spain
| | - Jesús Jiménez-Barbero
- grid.420175.50000 0004 0639 2420Center for Cooperative Research in Biosciences (CIC-bioGUNE). Derio, 48160 Bizkaia, Spain
| | - Carlos González
- grid.429036.a0000 0001 0805 7691Instituto de Química-Física Rocasolano (IQFR-CSIC), Madrid, 28006 Spain
| | - Juan Luis Asensio
- grid.419121.e0000 0004 1761 1887Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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3
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Santana AG, Robinson K, Vickers C, Deen MC, Chen H, Zhou S, Dai B, Fuller M, Boraston AB, Vocadlo DJ, Clarke LA, Withers SG. Pharmacological Chaperones for GCase that Switch Conformation with pH Enhance Enzyme Levels in Gaucher Animal Models. Angew Chem Int Ed Engl 2022; 61:e202207974. [DOI: 10.1002/anie.202207974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Andrés G. Santana
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Kyle Robinson
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Chelsea Vickers
- Dept. of Biochemistry and Microbiology University of Victoria Victoria BC, V8W 3P6 Canada
| | - Matthew C. Deen
- Dept. of Chemistry and Dept. of Mol. Biology and Biochemistry Simon Fraser University Burnaby BC, V5A 1S6 Canada
| | - Hong‐Ming Chen
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
| | - Stephen Zhou
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Ben Dai
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Maria Fuller
- Genetics and Molecular Pathology SA Pathology at Women's and Children's Hospital N. Adelaide South Australia 5006 Australia
| | - Alisdair B. Boraston
- Dept. of Biochemistry and Microbiology University of Victoria Victoria BC, V8W 3P6 Canada
| | - David J. Vocadlo
- Dept. of Chemistry and Dept. of Mol. Biology and Biochemistry Simon Fraser University Burnaby BC, V5A 1S6 Canada
| | - Lorne A. Clarke
- Dept. of Medical Genetics University of British Columbia Women's Hospital & Health Centre Vancouver BC, V6H 3N1 Canada
| | - Stephen G. Withers
- Dept. of Chemistry University of British Columbia Vancouver BC, V6T 1Z1 Canada
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4
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Méndez-Líter JA, Pozo-Rodríguez A, Madruga E, Rubert M, Santana AG, de Eugenio LI, Sánchez C, Martínez A, Prieto A, Martínez MJ. Glycosylation of Epigallocatechin Gallate by Engineered Glycoside Hydrolases from Talaromyces amestolkiae: Potential Antiproliferative and Neuroprotective Effect of These Molecules. Antioxidants (Basel) 2022; 11:antiox11071325. [PMID: 35883816 PMCID: PMC9312355 DOI: 10.3390/antiox11071325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 06/30/2022] [Indexed: 02/04/2023] Open
Abstract
Glycoside hydrolases (GHs) are enzymes that hydrolyze glycosidic bonds, but some of them can also catalyze the synthesis of glycosides by transglycosylation. However, the yields of this reaction are generally low since the glycosides formed end up being hydrolyzed by these same enzymes. For this reason, mutagenic variants with null or drastically reduced hydrolytic activity have been developed, thus enhancing their synthetic ability. Two mutagenic variants, a glycosynthase engineered from a β-glucosidase (BGL-1-E521G) and a thioglycoligase from a β-xylosidase (BxTW1-E495A), both from the ascomycete Talaromyces amestolkiae, were used to synthesize three novel epigallocatechin gallate (EGCG) glycosides. EGCG is a phenolic compound from green tea known for its antioxidant effects and therapeutic benefits, whose glycosylation could increase its bioavailability and improve its bioactive properties. The glycosynthase BGL-1-E521G produced a β-glucoside and a β-sophoroside of EGCG, while the thioglycoligase BxTW1-E495A formed the β-xyloside of EGCG. Glycosylation occurred in the 5″ and 4″ positions of EGCG, respectively. In this work, the reaction conditions for glycosides’ production were optimized, achieving around 90% conversion of EGCG with BGL-1-E521G and 60% with BxTW1-E495A. The glycosylation of EGCG caused a slight loss of its antioxidant capacity but notably increased its solubility (between 23 and 44 times) and, in the case of glucoside, also improved its thermal stability. All three glycosides showed better antiproliferative properties on breast adenocarcinoma cell line MDA-MB-231 than EGCG, and the glucosylated and sophorylated derivatives induced higher neuroprotection, increasing the viability of SH-S5Y5 neurons exposed to okadaic acid.
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Affiliation(s)
- Juan A. Méndez-Líter
- Centro de Investigaciones Biológicas Margarita Salas, Department of Microbial and Plant Biotechnology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (A.P.-R.); (L.I.d.E.); (A.P.)
| | - Ana Pozo-Rodríguez
- Centro de Investigaciones Biológicas Margarita Salas, Department of Microbial and Plant Biotechnology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (A.P.-R.); (L.I.d.E.); (A.P.)
| | - Enrique Madruga
- Centro de Investigaciones Biológicas Margarita Salas, Department of Structural and Chemical Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.M.); (A.M.)
| | - María Rubert
- Department of Biochemistry and Molecular Biology, School of Biology, Instituto de Investigación Hospital 12 de Octubre, Universidad Complutense de Madrid, C/de José Antonio Nováis 12, 28040 Madrid, Spain; (M.R.); (C.S.)
| | - Andrés G. Santana
- Department of Bioorganic Chemistry, Instituto de Química Orgánica General, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, 28006 Madrid, Spain;
| | - Laura I. de Eugenio
- Centro de Investigaciones Biológicas Margarita Salas, Department of Microbial and Plant Biotechnology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (A.P.-R.); (L.I.d.E.); (A.P.)
| | - Cristina Sánchez
- Department of Biochemistry and Molecular Biology, School of Biology, Instituto de Investigación Hospital 12 de Octubre, Universidad Complutense de Madrid, C/de José Antonio Nováis 12, 28040 Madrid, Spain; (M.R.); (C.S.)
| | - Ana Martínez
- Centro de Investigaciones Biológicas Margarita Salas, Department of Structural and Chemical Biology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.M.); (A.M.)
| | - Alicia Prieto
- Centro de Investigaciones Biológicas Margarita Salas, Department of Microbial and Plant Biotechnology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (A.P.-R.); (L.I.d.E.); (A.P.)
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, Department of Microbial and Plant Biotechnology, Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (J.A.M.-L.); (A.P.-R.); (L.I.d.E.); (A.P.)
- Correspondence:
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5
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Santana AG, Herrera AJ, González CC. Intramolecular Metal-Free C(sp 3)-H Activation Enables a Selective Mono O-Debenzylation of Fully Protected Aminosugars. J Org Chem 2021; 86:16736-16752. [PMID: 34807601 DOI: 10.1021/acs.joc.1c01977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbamate-bearing benzylated aminosugars undergo an I2/I(III)-promoted intramolecular hydrogen atom transfer (IHAT) followed by a nucleophilic attack to provide polycyclic structures. Thus, suitably positioned benzyl ethers are surgically oxidized into the corresponding mixed N/O-benzylidene acetals, which can be conveniently deprotected under mild acidic conditions to grant access to selectively O-deprotected aminosugars amenable for further derivatization. The scope of this strategy has been proven with a series of furanosic and pyranosic scaffolds. Preliminary mechanistic studies, including Hammett LFER and KIE analyses, support a reaction pathway with nucleophilic cyclization as the rate-determining step.
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Affiliation(s)
- Andrés G Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Antonio J Herrera
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Concepción C González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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6
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Scherer M, Santana AG, Robinson K, Zhou S, Overkleeft HS, Clarke L, Withers SG. Lipid-mimicking phosphorus-based glycosidase inactivators as pharmacological chaperones for the treatment of Gaucher's disease. Chem Sci 2021; 12:13909-13913. [PMID: 34760177 PMCID: PMC8549773 DOI: 10.1039/d1sc03831a] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/17/2021] [Indexed: 01/09/2023] Open
Abstract
Gaucher's disease, the most prevalent lysosomal storage disorder, is caused by missense mutation of the GBA gene, ultimately resulting in deficient GCase activity, hence the excessive build-up of cellular glucosylceramide. Among different therapeutic strategies, pharmacological chaperoning of mutant GCase represents an attractive approach that relies on small organic molecules acting as protein stabilizers. Herein, we expand upon a new class of transient GCase inactivators based on a reactive 2-deoxy-2-fluoro-β-d-glucoside tethered to an array of lipid-mimicking phosphorus-based aglycones, which not only improve the selectivity and inactivation efficiency, but also the stability of these compounds in aqueous media. This hypothesis was further validated with kinetic and cellular studies confirming restoration of catalytic activity in Gaucher cells after treatment with these pharmacological chaperones.
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Affiliation(s)
- Manuel Scherer
- Dept. of Chemistry. University of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - Andrés G Santana
- Dept. of Chemistry. University of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - Kyle Robinson
- Dept. of Chemistry. University of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - Steven Zhou
- Dept. of Medical Genetics. University of British Columbia Vancouver British Columbia V6H 3N1 Canada
| | | | - Lorne Clarke
- Dept. of Medical Genetics. University of British Columbia Vancouver British Columbia V6H 3N1 Canada
| | - Stephen G Withers
- Dept. of Chemistry. University of British Columbia Vancouver British Columbia V6T 1Z1 Canada
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7
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Díaz-Casado L, Serrano-Chacón I, Montalvillo-Jiménez L, Corzana F, Bastida A, Santana AG, González C, Asensio JL. De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot. Chemistry 2021; 27:6106. [PMID: 33615580 DOI: 10.1002/chem.202100456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Invited for the cover of this issue are Andrés G. Santana, Carlos González, Juan Luis Asensio and co-workers at Instituto de Química Orgánica General, Instituto de Química-Física Rocasolano and Universidad de La Rioja. The image depicts drug selectivity using a metaphor of an arrow hitting a target. Read the full text of the article at 10.1002/chem.202005026.
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Affiliation(s)
- Laura Díaz-Casado
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Israel Serrano-Chacón
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Laura Montalvillo-Jiménez
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Madre de Dios, 53., 26006, Logroño, Spain
| | - Agatha Bastida
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
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8
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Santana AG, Montalvillo‐Jiménez L, Díaz‐Casado L, Mann E, Jiménez‐Barbero J, Gómez AM, Asensio JL. Cover Feature: Single‐Step Glycosylations with
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C‐Labelled Sulfoxide Donors: A Low‐Temperature NMR Cartography of the Distinguishing Mechanistic Intermediates (Chem. Eur. J. 6/2021). Chemistry 2021. [DOI: 10.1002/chem.202004805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrés G. Santana
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Laura Montalvillo‐Jiménez
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Laura Díaz‐Casado
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Enrique Mann
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Jesús Jiménez‐Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) 48160 Derio Spain
- Basque Foundation for Science 48013 Bilbao Spain
| | - Ana M. Gómez
- Oligosaccharide and Glycosystems group Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
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9
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Díaz-Casado L, Serrano-Chacón I, Montalvillo-Jiménez L, Corzana F, Bastida A, Santana AG, González C, Asensio JL. De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot. Chemistry 2021; 27:6204-6212. [PMID: 33368678 DOI: 10.1002/chem.202005026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex-duplex junctions, while presenting a poorer affinity for G-quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex-duplex junctions, including the one observed in the HIV-1 LTR-III sequence. The structure of the complex between a quadruplex-duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex-duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G-tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G-quadruplex-forming regions of the genome.
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Affiliation(s)
- Laura Díaz-Casado
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Israel Serrano-Chacón
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Laura Montalvillo-Jiménez
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Madre de Dios, 53., 26006, Logroño, Spain
| | - Agatha Bastida
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
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10
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Santana AG, Montalvillo‐Jiménez L, Díaz‐Casado L, Mann E, Jiménez‐Barbero J, Gómez AM, Asensio JL. Single‐Step Glycosylations with
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C‐Labelled Sulfoxide Donors: A Low‐Temperature NMR Cartography of the Distinguishing Mechanistic Intermediates. Chemistry 2020; 27:2030-2042. [DOI: 10.1002/chem.202003850] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/18/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Andrés G. Santana
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Laura Montalvillo‐Jiménez
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Laura Díaz‐Casado
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Enrique Mann
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Jesús Jiménez‐Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) 48160 Derio Spain
- Basque Foundation for Science 48013 Bilbao Spain
| | - Ana M. Gómez
- Oligosaccharide and Glycosystems group Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group, Dpt. Bio-Organic Chemistry Instituto de Química Orgánica General (IQOG-CSIC) Juan de la Cierva 3. 28006 Madrid Spain
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11
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Santana AG, González CC. Tandem Radical Fragmentation/Cyclization of Guanidinylated Monosaccharides Grants Access to Medium-Sized Polyhydroxylated Heterocycles. Org Lett 2020; 22:8492-8495. [PMID: 33074675 DOI: 10.1021/acs.orglett.0c03091] [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] [Indexed: 12/20/2022]
Abstract
The fragmentation of anomeric alkoxyl radicals (ARF) and the subsequent cyclization promoted by hypervalent iodine provide an excellent method for the synthesis of guanidino-sugars. The methodology described herein is one of the few existing general methodologies for the formation of medium-sized exo- and endoguanidine-containing heterocycles presenting a high degree of oxygenation in their structure.
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Affiliation(s)
- Andrés G Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Concepción C González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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12
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Nieto-Domínguez M, Fernández de Toro B, de Eugenio LI, Santana AG, Bejarano-Muñoz L, Armstrong Z, Méndez-Líter JA, Asensio JL, Prieto A, Withers SG, Cañada FJ, Martínez MJ. Thioglycoligase derived from fungal GH3 β-xylosidase is a multi-glycoligase with broad acceptor tolerance. Nat Commun 2020; 11:4864. [PMID: 32978392 PMCID: PMC7519651 DOI: 10.1038/s41467-020-18667-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022] Open
Abstract
The synthesis of customized glycoconjugates constitutes a major goal for biocatalysis. To this end, engineered glycosidases have received great attention and, among them, thioglycoligases have proved useful to connect carbohydrates to non-sugar acceptors. However, hitherto the scope of these biocatalysts was considered limited to strong nucleophilic acceptors. Based on the particularities of the GH3 glycosidase family active site, we hypothesized that converting a suitable member into a thioglycoligase could boost the acceptor range. Herein we show the engineering of an acidophilic fungal β-xylosidase into a thioglycoligase with broad acceptor promiscuity. The mutant enzyme displays the ability to form O-, N-, S- and Se- glycosides together with sugar esters and phosphoesters with conversion yields from moderate to high. Analyses also indicate that the pKa of the target compound was the main factor to determine its suitability as glycosylation acceptor. These results expand on the glycoconjugate portfolio attainable through biocatalysis.
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Affiliation(s)
- Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Beatriz Fernández de Toro
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Lara Bejarano-Muñoz
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Zach Armstrong
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Juan Antonio Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular recognition group, Instituto de Química Orgánica General (CSIC), C/Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Stephen G Withers
- Department of Chemistry, Centre for High-Throughput Biology, University of British Columbia, Vancouver, Canada
| | - Francisco Javier Cañada
- NMR and Molecular Recognition Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C/Ramiro de Maeztu 9, 28040, Madrid, Spain.
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13
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Santana AG, Montalvillo-Jiménez L, Díaz-Casado L, Corzana F, Merino P, Cañada FJ, Jiménez-Osés G, Jiménez-Barbero J, Gómez AM, Asensio JL. Dissecting the Essential Role of Anomeric β-Triflates in Glycosylation Reactions. J Am Chem Soc 2020; 142:12501-12514. [DOI: 10.1021/jacs.0c05525] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | | | | | - Francisco Corzana
- Departamento Quı́mica and Centro de Investigación en Sı́ntesis Quı́mica, Universidad de La Rioja, 26006 Rioja, Spain
| | - Pedro Merino
- Instituto de Biocomputación y Fı́sica de Sistemas Complejos (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Spain
- Ikerbasque Basque Foundation for Science, 48013 Bilbao, Basque
| | - Ana M. Gómez
- Instituto de Quı́mica Orgánica (IQOG-CSIC), 28006 Madrid, Spain
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14
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Tegl G, Hanson J, Chen H, Kwan DH, Santana AG, Withers SG. Berichtigung: Facile Formation of β‐thioGlcNAc Linkages to Thiol‐Containing Sugars, Peptides, and Proteins using a Mutant GH20 Hexosaminidase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001582] [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] [Indexed: 11/07/2022]
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15
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Tegl G, Hanson J, Chen H, Kwan DH, Santana AG, Withers SG. Corrigendum: Facile Formation of β‐thioGlcNAc Linkages to Thiol‐Containing Sugars, Peptides, and Proteins using a Mutant GH20 Hexosaminidase. Angew Chem Int Ed Engl 2020; 59:8752. [DOI: 10.1002/anie.202001582] [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] [Indexed: 11/06/2022]
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16
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Montalvillo-Jiménez L, Santana AG, Corzana F, Jiménez-Osés G, Jiménez-Barbero J, Gómez AM, Asensio JL. Impact of Aromatic Stacking on Glycoside Reactivity: Balancing CH/π and Cation/π Interactions for the Stabilization of Glycosyl-Oxocarbenium Ions. J Am Chem Soc 2019; 141:13372-13384. [PMID: 31390207 DOI: 10.1021/jacs.9b03285] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Carbohydrate/aromatic stacking represents a recurring key motif for the molecular recognition of glycosides, either by protein binding domains, enzymes, or synthetic receptors. Interestingly, it has been proposed that aromatic residues might also assist in the formation/cleavage of glycosidic bonds by stabilizing positively charged oxocarbenium-like intermediates/transition states through cation/π interactions. While the significance of aromatic stacking on glycoside recognition is well stablished, its impact on the reactivity of glycosyl donors is yet to be explored. Herein, we report the first experimental study on this relevant topic. Our strategy is based on the design, synthesis, and reactivity evaluation of a large number of model systems, comprising a wide range of glycosidic donor/aromatic complexes. Different stacking geometries and dynamic features, anomeric leaving groups, sugar configurations, and reaction conditions have been explicitly considered. The obtained results underline the opposing influence exerted by van der Waals and Coulombic forces on the reactivity of the carbohydrate/aromatic complex: depending on the outcome of this balance, aromatic platforms can indeed exert a variety of effects, stretching from reaction inhibition all the way to rate enhancements. Although aromatic/glycosyl cation contacts are highly dynamic, the conclusions of our study suggest that aromatic assistance to glycosylation processes must indeed be feasible, with far reaching implications for enzyme engineering and organocatalysis.
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Affiliation(s)
| | - Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Francisco Corzana
- Departamento Quı́mica and Centro de Investigación en Sı́ntesis Quı́mica , Universidad de La Rioja , 26006 Logroño , Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain
| | - Jesús Jiménez-Barbero
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , 48160 Derio , Spain.,Basque Foundation for Science, Ikerbasque , 48013 Bilbo , Spain
| | - Ana M Gómez
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain
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17
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Zárate SG, Bastida A, Santana AG, Revuelta J. Synthesis of Ring II/III Fragment of Kanamycin: A New Minimum Structural Motif for Aminoglycoside Recognition. Antibiotics (Basel) 2019; 8:antibiotics8030109. [PMID: 31382490 PMCID: PMC6783941 DOI: 10.3390/antibiotics8030109] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 11/30/2022] Open
Abstract
A novel protocol has been established to prepare the kanamycin ring II/III fragment, which has been validated as a minimum structural motif for the development of new aminoglycosides on the basis of its bactericidal activity even against resistant strains. Furthermore, its ability to act as a AAC-(6′) and APH-(3′) binder, and as a poor substrate for the ravenous ANT-(4′), makes it an excellent candidate for the design of inhibitors of these aminoglycoside modifying enzymes.
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Affiliation(s)
- Sandra G Zárate
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
- Facultad de Tecnología, Carrera de Ingeniería Química, Universidad Mayor, Real y Pontificia de San Francisco Xavier de Chuquisaca, Regimiento Campos 180, Casilla 60-B Sucre, Bolivia
| | - Agatha Bastida
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Andrés G Santana
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Julia Revuelta
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
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18
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André-Joyaux E, Santana AG, González CC. Synthesis of Chiral Polyhydroxylated Benzimidazoles by a Tandem Radical Fragmentation/Cyclization Reaction: A Straight Avenue to Fused Aromatic-Carbohydrate Hybrids. J Org Chem 2019; 84:506-515. [PMID: 30589268 DOI: 10.1021/acs.joc.8b01988] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of benzimidazole-fused iminosugars through a tandem β-fragmentation-intramolecular cyclization reaction is described. The use of the benzimidazole ring as the internal nucleophile and the use of phenyliodosophthalate (PhI(Phth)), a new metal-free and low toxic hypervalent iodine reagent, are the most remarkable novelties of this synthetic strategy. With this approach, we have demonstrated the usefulness of the fragmentation of anomeric alkoxyl radicals promoted by the PhI(Phth)/I2 system for the preparation of new compounds with potential interest for both medicinal and synthetic chemists.
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Affiliation(s)
- Emy André-Joyaux
- Instituto de Productos Naturales y Agrobiología del C.S.I.C. , Avenida Astrofísico Francisco Sánchez 3 , 38206 La Laguna , Tenerife , Spain
| | - Andrés G Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C. , Avenida Astrofísico Francisco Sánchez 3 , 38206 La Laguna , Tenerife , Spain
| | - Concepción C González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C. , Avenida Astrofísico Francisco Sánchez 3 , 38206 La Laguna , Tenerife , Spain
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19
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Tegl G, Hanson J, Chen H, Kwan DH, Santana AG, Withers SG. Facile Formation of β-thioGlcNAc Linkages to Thiol-Containing Sugars, Peptides, and Proteins using a Mutant GH20 Hexosaminidase. Angew Chem Int Ed Engl 2019; 58:1632-1637. [PMID: 30549167 PMCID: PMC6637381 DOI: 10.1002/anie.201809928] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/17/2018] [Indexed: 01/11/2023]
Abstract
Thioglycosides are hydrolase‐resistant mimics of O‐linked glycosides that can serve as valuable probes for studying the role of glycosides in biological processes. The development of an efficient, enzyme‐mediated synthesis of thioglycosides, including S‐GlcNAcylated proteins, is reported, using a thioglycoligase derived from a GH20 hexosaminidase from Streptomyces plicatus in which the catalytic acid/base glutamate has been mutated to an alanine (SpHex E314A). This robust, easily‐prepared, engineered enzyme uses GlcNAc and GalNAc donors and couples them to a remarkably diverse set of thiol acceptors. Thioglycoligation using 3‐, 4‐, and 6‐thiosugar acceptors from a variety of sugar families produces S‐linked disaccharides in nearly quantitative yields. The set of possible thiol acceptors also includes cysteine‐containing peptides and proteins, rendering this mutant enzyme a promising catalyst for the production of thio analogues of biologically important GlcNAcylated peptides and proteins.
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Affiliation(s)
- Gregor Tegl
- Department of ChemistryUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z1Canada
| | - John Hanson
- Department of ChemistryUniversity of Puget SoundTacomaWA98416USA
| | - Hong‐Ming Chen
- Department of ChemistryUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z1Canada
| | - David H Kwan
- Department of ChemistryUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z1Canada
| | - Andrés G. Santana
- Department of ChemistryUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z1Canada
| | - Stephen G. Withers
- Department of ChemistryUniversity of British ColumbiaVancouverBritish ColumbiaV6T 1Z1Canada
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20
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Tegl G, Hanson J, Chen H, Kwan DH, Santana AG, Withers SG. Facile Formation of β‐thioGlcNAc Linkages to Thiol‐Containing Sugars, Peptides, and Proteins using a Mutant GH20 Hexosaminidase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201809928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Gregor Tegl
- Department of ChemistryUniversity of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - John Hanson
- Department of ChemistryUniversity of Puget Sound Tacoma WA 98416 USA
| | - Hong‐Ming Chen
- Department of ChemistryUniversity of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - David H Kwan
- Department of ChemistryUniversity of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - Andrés G. Santana
- Department of ChemistryUniversity of British Columbia Vancouver British Columbia V6T 1Z1 Canada
| | - Stephen G. Withers
- Department of ChemistryUniversity of British Columbia Vancouver British Columbia V6T 1Z1 Canada
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21
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Zárate SG, Claure MLDLC, Benito-Arenas R, Revuelta J, Santana AG, Bastida A. Overcoming Aminoglycoside Enzymatic Resistance: Design of Novel Antibiotics and Inhibitors. Molecules 2018; 23:molecules23020284. [PMID: 29385736 PMCID: PMC6017855 DOI: 10.3390/molecules23020284] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/12/2018] [Accepted: 01/26/2018] [Indexed: 11/17/2022] Open
Abstract
Resistance to aminoglycoside antibiotics has had a profound impact on clinical practice. Despite their powerful bactericidal activity, aminoglycosides were one of the first groups of antibiotics to meet the challenge of resistance. The most prevalent source of clinically relevant resistance against these therapeutics is conferred by the enzymatic modification of the antibiotic. Therefore, a deeper knowledge of the aminoglycoside-modifying enzymes and their interactions with the antibiotics and solvent is of paramount importance in order to facilitate the design of more effective and potent inhibitors and/or novel semisynthetic aminoglycosides that are not susceptible to modifying enzymes.
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Affiliation(s)
- Sandra G. Zárate
- Facultad de Tecnología-Carrera de Ingeniería Química, Universidad Mayor Real y Pontificia de San Francisco Xavier de Chuquisaca, Regimiento Campos 180, Casilla 60-B, Sucre, Bolivia;
| | - M. Luisa De la Cruz Claure
- Facultad de Ciencias Químico Farmacéuticas y Bioquímicas, Universidad Mayor Real y Pontificia de San Francisco Xavier de Chuquisaca, Dalence 51, Casilla 497, Sucre, Bolivia;
| | - Raúl Benito-Arenas
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
| | - Julia Revuelta
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
| | - Andrés G. Santana
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
- Correspondence: (A.G.S.); (A.B.); Tel: +34-915-612-800 (A.B.)
| | - Agatha Bastida
- Departmento de Química Bio-Orgánica, Instituto de Química Orgánica General (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (R.B.-A.); (J.R.)
- Correspondence: (A.G.S.); (A.B.); Tel: +34-915-612-800 (A.B.)
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22
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Jiménez-Moreno E, Montalvillo-Jiménez L, Santana AG, Gómez AM, Jiménez-Osés G, Corzana F, Bastida A, Jiménez-Barbero J, Cañada FJ, Gómez-Pinto I, González C, Asensio JL. Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders. J Am Chem Soc 2016; 138:6463-74. [DOI: 10.1021/jacs.6b00328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ester Jiménez-Moreno
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Andrés G. Santana
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
- Institute of Biocomputation and Physics of Complex Systems
(BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Bizkaia, Spain
- Basque Foundation for Science, Ikerbasque, 48013 Bilbao, Bizkaia, Spain
| | | | - Irene Gómez-Pinto
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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23
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Santana AG, Zárate SG, Asensio JL, Revuelta J, Bastida A. Selective modification of the 3''-amino group of kanamycin prevents significant loss of activity in resistant bacterial strains. Org Biomol Chem 2016; 14:516-525. [PMID: 26501183 DOI: 10.1039/c5ob01599e] [Citation(s) in RCA: 6] [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
Aminoglycosides are highly potent, wide-spectrum bactericidals. N-1 modification of aminoglycosides has thus far been the best approach to regain bactericidal efficiency of this class of antibiotics against resistant bacterial strains. In the present study we have evaluated the effect that both, the number of modifications and their distribution on the aminoglycoside amino groups (N-1, N-3, N-6' and N-3''), have on the antibiotic activity. The modification of N-3'' in the antibiotic kanamycin A is the key towards the design of new aminoglycoside antibiotics. This derivative maintains the antibiotic activity against aminoglycoside acetyl-transferase- and nucleotidyl-transferase-expressing strains, which are two of the most prevalent modifying enzymes found in aminoglycoside resistant bacteria.
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Affiliation(s)
- Andrés G Santana
- CSIC, Department of Bioorganic Chemistry, c/Juan de la Cierva, 3, 28006-Madrid, Spain.
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24
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Jiménez-Moreno E, Jiménez-Osés G, Gómez AM, Santana AG, Corzana F, Bastida A, Jiménez-Barbero J, Asensio JL. A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes. Chem Sci 2015; 6:6076-6085. [PMID: 28717448 PMCID: PMC5504637 DOI: 10.1039/c5sc02108a] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/29/2015] [Indexed: 12/01/2022] Open
Abstract
CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.
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Affiliation(s)
- Ester Jiménez-Moreno
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Gonzalo Jiménez-Osés
- Dept. Química and Centro de Investigación en Síntesis Química , Universidad de La Rioja , Logroño , Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI) , University of Zaragoza , BIFI-IQFR (CSIC) , Zaragoza , Spain
| | - Ana M Gómez
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Francisco Corzana
- Dept. Química and Centro de Investigación en Síntesis Química , Universidad de La Rioja , Logroño , Spain
| | - Agatha Bastida
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
| | - Jesus Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC) , Madrid , Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE) , Derio-Bizkaia , Spain
- Basque Foundation for Science , Ikerbasque , Bilbao , Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC) , Juan de la Cierva 3 , 28006 Madrid , Spain . ; ; Tel: +34 915622900
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Santana AG, Paz NR, Francisco CG, Suárez E, González CC. Synthesis of Branched Iminosugars through a Hypervalent Iodine(III)-Mediated Radical-Polar Crossover Reaction. J Org Chem 2013; 78:7527-43. [DOI: 10.1021/jo401041s] [Citation(s) in RCA: 15] [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: 01/07/2023]
Affiliation(s)
- Andrés G. Santana
- Instituto de Productos Naturales y Agrobiología del CSIC, Avenida Astrofísico Francisco Sánchez 3, 38206 La
Laguna, Tenerife, Spain
| | - Nieves R. Paz
- Instituto de Productos Naturales y Agrobiología del CSIC, Avenida Astrofísico Francisco Sánchez 3, 38206 La
Laguna, Tenerife, Spain
| | - Cosme G. Francisco
- Instituto de Productos Naturales y Agrobiología del CSIC, Avenida Astrofísico Francisco Sánchez 3, 38206 La
Laguna, Tenerife, Spain
| | - Ernesto Suárez
- Instituto de Productos Naturales y Agrobiología del CSIC, Avenida Astrofísico Francisco Sánchez 3, 38206 La
Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avenida Astrofísico Francisco Sánchez 3, 38206 La
Laguna, Tenerife, Spain
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Santana AG, Jiménez-Moreno E, Gómez AM, Corzana F, González C, Jiménez-Oses G, Jiménez-Barbero J, Asensio JL. A dynamic combinatorial approach for the analysis of weak carbohydrate/aromatic complexes: dissecting facial selectivity in CH/π stacking interactions. J Am Chem Soc 2013; 135:3347-50. [PMID: 23418701 DOI: 10.1021/ja3120218] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A dynamical combinatorial approach for the study of weak carbohydrate/aromatic interactions is presented. This methodology has been employed to dissect the subtle structure-stability relationships that govern facial selectivity in these supramolecular complexes.
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Affiliation(s)
- Andrés G Santana
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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Jiménez-Moreno E, Gómez-Pinto I, Corzana F, Santana AG, Revuelta J, Bastida A, Jiménez-Barbero J, González C, Asensio JL. Chemical Interrogation of Drug/RNA Complexes: From Chemical Reactivity to Drug Design. Angew Chem Int Ed Engl 2013; 52:3148-51. [DOI: 10.1002/anie.201209434] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Indexed: 11/08/2022]
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Jiménez-Moreno E, Gómez-Pinto I, Corzana F, Santana AG, Revuelta J, Bastida A, Jiménez-Barbero J, González C, Asensio JL. Chemical Interrogation of Drug/RNA Complexes: From Chemical Reactivity to Drug Design. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Paz NR, Santana AG, Francisco CG, Suárez E, González CC. Synthesis of Tetrazole-Fused Glycosides by a Tandem Fragmentation–Cyclization Reaction. Org Lett 2012; 14:3388-91. [DOI: 10.1021/ol3013638] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nieves R. Paz
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Andrés G. Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Cosme G. Francisco
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Ernesto Suárez
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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Matesanz R, Diaz JF, Corzana F, Santana AG, Bastida A, Asensio JL. Multiple keys for a single lock: the unusual structural plasticity of the nucleotidyltransferase (4')/kanamycin complex. Chemistry 2012; 18:2875-89. [PMID: 22298309 DOI: 10.1002/chem.201101888] [Citation(s) in RCA: 10] [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] [Received: 06/20/2011] [Revised: 12/05/2011] [Indexed: 11/09/2022]
Abstract
The most common mode of bacterial resistance to aminoglycoside antibiotics is the enzyme-catalysed chemical modification of the drug. Over the last two decades, significant efforts in medicinal chemistry have been focused on the design of non- inactivable antibiotics. Unfortunately, this strategy has met with limited success on account of the remarkably wide substrate specificity of aminoglycoside-modifying enzymes. To understand the mechanisms behind substrate promiscuity, we have performed a comprehensive experimental and theoretical analysis of the molecular-recognition processes that lead to antibiotic inactivation by Staphylococcus aureus nucleotidyltransferase 4'(ANT(4')), a clinically relevant protein. According to our results, the ability of this enzyme to inactivate structurally diverse polycationic molecules relies on three specific features of the catalytic region. First, the dominant role of electrostatics in aminoglycoside recognition, in combination with the significant extension of the enzyme anionic regions, confers to the protein/antibiotic complex a highly dynamic character. The motion deduced for the bound antibiotic seem to be essential for the enzyme action and probably provide a mechanism to explore alternative drug inactivation modes. Second, the nucleotide recognition is exclusively mediated by the inorganic fragment. In fact, even inorganic triphosphate can be employed as a substrate. Third, ANT(4') seems to be equipped with a duplicated basic catalyst that is able to promote drug inactivation through different reactive geometries. This particular combination of features explains the enzyme versatility and renders the design of non-inactivable derivatives a challenging task.
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Affiliation(s)
- Ruth Matesanz
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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Santana AG, Francisco CG, Suárez E, González CC. Synthesis of Guanidines From Azides: A General and Straightforward Methodology In Carbohydrate Chemistry. J Org Chem 2010; 75:5371-4. [DOI: 10.1021/jo100876r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [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)
- Andrés G. Santana
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Cosme G. Francisco
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Ernesto Suárez
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del C.S.I.C., Avenida Astrofísico Francisco Sánchez, 3, 38206 La Laguna Tenerife, Spain
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de Souza CP, Borges CC, Santana AG, Andrade ZA. Comparative histopathology of Biomphalaria glabrata, B. tenagophila and B. straminea with variable degrees of resistance to Schistosoma mansoni miracidia. Mem Inst Oswaldo Cruz 1997; 92:517-22. [PMID: 9361747 DOI: 10.1590/s0074-02761997000400014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [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: 02/05/2023] Open
Abstract
A comparative histopathological study of three snails species--Biomphalaria glabrata, B. tenagophila and B. straminea--which had been infected with Schistosoma mansoni miracidia revealed similar qualitative features; consisting of areas of sporocyst proliferation and differentiation associated with reactive host reaction, at the time they were actively eliminating great number of cercariae. However, in specimens that were exposed to miracidia but failed to eliminate cercariae later on, different histopathological pictures were observed in different snail species. While B. glabrata exhibited frequent focal (granulomatous) proliferation of amebocytes in several organs, B. tenagophila and B. straminea only rarely showed such reactive changes, suggesting that the mechanism of resistance to miracidial infection probably follows different pathways in the snail species studied.
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Affiliation(s)
- C P de Souza
- Laboratório de Malacologia, Centro de Pesquisas René Rachou-FIOCRUZ, Belo Horizonte, MG, Brasil
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Abstract
In 18-week-old nulliparous rabbit does, ovulation was induced with 50 IU of pure urinary luteinizing hormone (LH; LH group), or 50 IU of human chorionic gonadotrophin (HCG; HCG group), in order to determine the effect of these treatments on 17 beta-oestradiol and progesterone concentrations, and on oocyte and embryo quality. Luteinizing follicles, recovered oocytes, progesterone concentration and grade 5 embryos were significantly reduced when pure urinary LH was used. Statistically significant correlations were found: (i) between oestradiol concentration and number of degenerated oocytes in both groups (positive); (ii) between oestradiol concentration and grade 1 and 2 embryos (negative), and grade 5 embryos (positive) in the HCG group; (iii) between progesterone concentration and metaphase II oocytes (negative), and between progesterone and grade 5 embryos (positive), in the HCG group; and (iv) between progesterone and oestradiol concentrations (negative) in the LH group. It seems that the oestradiol to progesterone ratio improves during the early luteal phase when ovulation is induced with LH, and that oestradiol and progesterone concentrations could play a role in determining oocyte and embryo quality.
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Affiliation(s)
- I Molina
- Unidad de Reproducción Humana, Hospital Universitario La Fe, Valencia, Spain
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