1
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Milanesi F, Burrini N, Corti G, Roelens S, Francesconi O. A Macrocyclic Tweezers-Shaped Receptor for the Biomimetic Recognition of the Gal(α1-3)Gal Disaccharide of the α-Gal Antigen. Chemistry 2024; 30:e202401771. [PMID: 38818641 DOI: 10.1002/chem.202401771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]
Abstract
The Gal(α1-3)Gal is the terminal disaccharide unit of the α-Gal epitope [Gal(α1-3)Gal(β1-4)GlcNAc], an exogenous antigenic determinant with several clinical implications, found in all non-primate mammals and in several dangerous pathogens, including certain protozoa and mycobacteria. Its absence in humans makes the α-Gal epitope an interesting target for several infectious diseases. Here we present the development of a macrocyclic tweezers-shaped receptor, resulting from the combination of the structural features of two predecessors belonging to the family of diaminocarbazole receptors, which exhibits binding properties in the low millimolar range toward the Gal(α1-3)Gal disaccharide of the α-Gal antigen.
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Affiliation(s)
- Francesco Milanesi
- Department of Chemistry "Ugo Schiff", DICUS, Università degli Studi di Firenze, Campus Sesto, 50019 Sesto Fiorentino, Firenze, Italy
| | - Nastassja Burrini
- Department of Chemistry "Ugo Schiff", DICUS, Università degli Studi di Firenze, Campus Sesto, 50019 Sesto Fiorentino, Firenze, Italy
| | - Giona Corti
- Department of Chemistry "Ugo Schiff", DICUS, Università degli Studi di Firenze, Campus Sesto, 50019 Sesto Fiorentino, Firenze, Italy
| | - Stefano Roelens
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Department of Chemistry "Ugo Schiff", DICUS, Campus Sesto, 50019 Sesto Fiorentino, Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff", DICUS, Università degli Studi di Firenze, Campus Sesto, 50019 Sesto Fiorentino, Firenze, Italy
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2
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Milanesi F, Roelens S, Francesconi O. Towards Biomimetic Recognition of Glycans by Synthetic Receptors. Chempluschem 2024; 89:e202300598. [PMID: 37942862 DOI: 10.1002/cplu.202300598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
Carbohydrates are abundant in Nature, where they are mostly assembled within glycans as free polysaccharides or conjugated to a variety of biological molecules such as proteins and lipids. Glycans exert several functions, including protein folding, stability, solubility, resistance to proteolysis, intracellular traffic, antigenicity, and recognition by carbohydrate-binding proteins. Interestingly, misregulation of their biosynthesis that leads to changes in glycan structures is frequently recognized as a mark of a disease state. Because of glycan ubiquity, carbohydrate binding agents (CBAs) targeting glycans can lead to a deeper understanding of their function and to the development of new diagnostic and prognostic strategies. Synthetic receptors selectively recognizing specific carbohydrates of biological interest have been developed over the past three decades. In addition to the success obtained in the effective recognition of monosaccharides, synthetic receptors recognizing more complex guests have also been developed, including di- and oligosaccharide fragments of glycans, shedding light on the structural and functional requirements necessary for an effective receptor. In this review, the most relevant achievements in molecular recognition of glycans and their fragments will be summarized, highlighting potentials and future perspectives of glycan-targeting synthetic receptors.
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Affiliation(s)
- Francesco Milanesi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Stefano Roelens
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff", DICUS and INSTM, Università degli Studi di Firenze, Campus Sesto, 50019, Sesto Fiorentino, Firenze, Italy
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3
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Francesconi O, Ienco A, Papi F, Dolce M, Catastini A, Nativi C, Roelens S. A Sulfonated Tweezer-Shaped Receptor Selectively Recognizes Caffeine in Water. J Org Chem 2022; 87:2662-2667. [PMID: 35107278 PMCID: PMC8902752 DOI: 10.1021/acs.joc.1c02620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
selective recognition of caffeine in water among structurally
related xanthines and purine or pyrimidine bases was achieved by a
simple tweezer-shaped receptor featuring sulfonate hydrosolubilizing
groups. The remarkable affinity for caffeine, among the highest reported
thus far in the literature and larger than that shown by adenosine
receptors of all subtypes, stems from a synergistic combination of
hydrogen bonding, CH−π, and π-stacking interactions.
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Affiliation(s)
- Oscar Francesconi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
| | - Andrea Ienco
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche (CNR), Via Madonna del Piano, I-50019 Firenze, Italy
| | - Francesco Papi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
| | - Marta Dolce
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
| | - Andrea Catastini
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
| | - Cristina Nativi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
| | - Stefano Roelens
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, Polo Scientifico e Tecnologico, University of Florence, I-50019 Firenze, Italy
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4
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Thakur K, Shlain MA, Marianski M, Braunschweig AB. Regiochemical Effects on the Carbohydrate Binding and Selectivity of Flexible Synthetic Carbohydrate Receptors with Indole and Quinoline Heterocyclic Groups. European J Org Chem 2021; 2021:5262-5274. [PMID: 35694139 PMCID: PMC9186342 DOI: 10.1002/ejoc.202100763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 08/07/2023]
Abstract
Synthetic carbohydrate receptors (SCRs) that bind cell-surface carbohydrates could be used for disease detection, drug-delivery, and therapeutics, or for the site-selective modification of complex carbohydrates but their potential has not been realized because of remaining challenges associated with binding affinity and substrate selectivity. We have reported recently a series of flexible SCRs based upon a biaryl core with four pendant heterocyclic groups that bind glycans selectively through noncovalent interactions. Here we continue to explore the role of heterocycles on substrate selectivity by expanding our library to include a series of indole and quinoline heterocycles that vary in their regiochemistry of attachment to the biaryl core. The binding of these SCRs to a series of biologically-relevant carbohydrates was studied by 1H NMR titrations in CD2Cl2 and density-functional theory calculations. We find SCR030, SCR034 and SCR037 are selective, SCR031, SCR032, and SCR039 are strong binders, and SCR033, SCR035, SCR036, and SCR038 are promiscuous and bind weakly. Computational analysis reveals the importance of C-H⋯π and H-bonding interactions in defining the binding properties of these new receptors. By combining these data with those obtained from our previous studies on this class of flexible SCRs, we develop a series of design rules that account for the binding of all SCRs of this class and anticipate the binding of future, not-yet imagined tetrapodal SCRs.
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Affiliation(s)
- Khushabu Thakur
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Milan A Shlain
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
| | - Mateusz Marianski
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
| | - Adam B Braunschweig
- Nanoscience Initiative, Advanced Science Research Center at The Graduate Center of the City University of New York 85 St Nicholas Terrace, New York, NY 10031 (USA)
- Department of Chemistry and Biochemistry, Hunter College 695 Park Ave, New York, NY 10065 (USA)
- The PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
- The PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 5 Ave, New York, NY 10016 (USA)
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5
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Francesconi O, Milanesi F, Nativi C, Roelens S. Molecular Recognition of Disaccharides in Water: Preorganized Macrocyclic or Adaptive Acyclic? Chemistry 2021; 27:10456-10460. [PMID: 33945180 PMCID: PMC8361761 DOI: 10.1002/chem.202101238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 12/02/2022]
Abstract
When facing the dilemma of following a preorganized or adaptive design approach in conceiving the architecture of new biomimetic receptors for carbohydrates, shape-persistent macrocyclic structures were most often chosen to achieve effective recognition of neutral saccharides in water. In contrast, acyclic architectures have seldom been explored, even though potentially simpler and more easily accessible. In this work, comparison of the binding properties of two structurally related diaminocarbazolic receptors, featuring a macrocyclic and an acyclic tweezer-shaped architecture, highlighted the advantages provided by the acyclic receptor in terms of selectivity in the recognition of 1,4-disaccharides of biological interest. Selective recognition of GlcNAc2 , the core fragment of N-glycans exposed on the surface of enveloped viruses, stands as an emblematic example. NMR spectroscopic data and molecular modeling calculations were used to ascertain the differences in binding mode and to shed light on the origin of recognition efficacy and selectivity.
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Affiliation(s)
- Oscar Francesconi
- Department of Chemistry “Ugo Schiff” and INSTMUniversity of FlorencePolo Scientifico e Tecnologico50019Sesto Fiorentino, FirenzeItaly
| | - Francesco Milanesi
- Department of Chemistry “Ugo Schiff” and INSTMUniversity of FlorencePolo Scientifico e Tecnologico50019Sesto Fiorentino, FirenzeItaly
- Magnetic Resonance Center CERMVia L. Sacconi 650019Sesto Fiorentino, FirenzeItaly
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff” and INSTMUniversity of FlorencePolo Scientifico e Tecnologico50019Sesto Fiorentino, FirenzeItaly
| | - Stefano Roelens
- Department of Chemistry “Ugo Schiff” and INSTMUniversity of FlorencePolo Scientifico e Tecnologico50019Sesto Fiorentino, FirenzeItaly
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6
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Bravo MF, Lema MA, Marianski M, Braunschweig AB. Flexible Synthetic Carbohydrate Receptors as Inhibitors of Viral Attachment. Biochemistry 2020; 60:999-1018. [PMID: 33094998 DOI: 10.1021/acs.biochem.0c00732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Carbohydrate-receptor interactions are often involved in the docking of viruses to host cells, and this docking is a necessary step in the virus life cycle that precedes infection and, ultimately, replication. Despite the conserved structures of the glycans involved in docking, they are still considered "undruggable", meaning these glycans are beyond the scope of conventional pharmacological strategies. Recent advances in the development of synthetic carbohydrate receptors (SCRs), small molecules that bind carbohydrates, could bring carbohydrate-receptor interactions within the purview of druggable targets. Here we discuss the role of carbohydrate-receptor interactions in viral infection, the evolution of SCRs, and recent results demonstrating their ability to prevent viral infections in vitro. Common SCR design strategies based on boronic ester formation, metal chelation, and noncovalent interactions are discussed. The benefits of incorporating the idiosyncrasies of natural glycan-binding proteins-including flexibility, cooperativity, and multivalency-into SCR design to achieve nonglucosidic specificity are shown. These studies into SCR design and binding could lead to new strategies for mitigating the grave threat to human health posed by enveloped viruses, which are heavily glycosylated viroids that are the cause of some of the most pressing and untreatable diseases, including HIV, Dengue, Zika, influenza, and SARS-CoV-2.
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Affiliation(s)
- M Fernando Bravo
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Manuel A Lema
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, New York 10031, United States
| | - Mateusz Marianski
- Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,The PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Adam B Braunschweig
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York 10031, United States.,Department of Chemistry and Biochemistry, Hunter College, New York, New York 10065, United States.,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States.,The PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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7
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Bravo MF, Palanichamy K, Shlain MA, Schiro F, Naeem Y, Marianski M, Braunschweig AB. Synthesis and Binding of Mannose‐Specific Synthetic Carbohydrate Receptors. Chemistry 2020; 26:11782-11795. [DOI: 10.1002/chem.202000481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/15/2020] [Indexed: 12/16/2022]
Affiliation(s)
- M. Fernando Bravo
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The PhD Program in Chemistry The Graduate Center of the, City University of New York 365 5th Ave New York NY 10016 USA
| | - Kalanidhi Palanichamy
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Milan A. Shlain
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Frank Schiro
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Yasir Naeem
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Mateusz Marianski
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The PhD Program in Chemistry The Graduate Center of the, City University of New York 365 5th Ave New York NY 10016 USA
- The PhD Program in Biochemistry The Graduate Center of the, City University of New York 365 5th Ave New York NY 10016 USA
| | - Adam B. Braunschweig
- Advanced Science Research Center at the Graduate Center City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The PhD Program in Chemistry The Graduate Center of the, City University of New York 365 5th Ave New York NY 10016 USA
- The PhD Program in Biochemistry The Graduate Center of the, City University of New York 365 5th Ave New York NY 10016 USA
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8
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Francesconi O, Roelens S. Biomimetic Carbohydrate‐Binding Agents (CBAs): Binding Affinities and Biological Activities. Chembiochem 2019; 20:1329-1346. [DOI: 10.1002/cbic.201800742] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Oscar Francesconi
- Department of Chemistry and INSTMUniversity of Florence Polo Scientifico e Tecnologico 50019 Sesto Fiorentino, Firenze Italy
| | - Stefano Roelens
- Department of Chemistry and INSTMUniversity of Florence Polo Scientifico e Tecnologico 50019 Sesto Fiorentino, Firenze Italy
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9
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Palanichamy K, Bravo MF, Shlain MA, Schiro F, Naeem Y, Marianski M, Braunschweig AB. Binding Studies on a Library of Induced‐Fit Synthetic Carbohydrate Receptors with Mannoside Selectivity. Chemistry 2018; 24:13971-13982. [DOI: 10.1002/chem.201803317] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Kalanidhi Palanichamy
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - M. Fernando Bravo
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA
| | - Milan A. Shlain
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Frank Schiro
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Yasir Naeem
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
| | - Mateusz Marianski
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA
| | - Adam B. Braunschweig
- Nanoscience Initiative Advanced Science Research Center at, The Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA
- Department of Chemistry and Biochemistry Hunter College 695 Park Ave New York NY 10065 USA
- The Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA
- The Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA
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10
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Long A, Perraud O, Albalat M, Robert V, Dutasta JP, Martinez A. Helical Chirality Induces a Substrate-Selectivity Switch in Carbohydrates Recognitions. J Org Chem 2018; 83:6301-6306. [DOI: 10.1021/acs.joc.8b00276] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Augustin Long
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille F-13397, France
| | - Olivier Perraud
- Laboratoire de Chimie, CNRS, École Normale Supérieure de Lyon, UCBL 46, Allée d’Italie, Lyon F-69364, France
| | - Muriel Albalat
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille F-13397, France
| | - Vincent Robert
- Laboratoire de Chimie Quantique Institut de Chimie, UMR CNRS 7177, Université de Strasbourg, 4, rue Blaise Pascal, Strasbourg F-67070, France
| | - Jean-Pierre Dutasta
- Laboratoire de Chimie, CNRS, École Normale Supérieure de Lyon, UCBL 46, Allée d’Italie, Lyon F-69364, France
| | - Alexandre Martinez
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille F-13397, France
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11
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Francesconi O, Martinucci M, Badii L, Nativi C, Roelens S. A Biomimetic Synthetic Receptor Selectively Recognising Fucose in Water. Chemistry 2018; 24:6828-6836. [DOI: 10.1002/chem.201800390] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Oscar Francesconi
- Department of Chemistry and INSTM; University of Florence, Polo Scientifico e Tecnologico; 50019 Sesto Fiorentino Firenze Italy
| | - Marco Martinucci
- Department of Chemistry and INSTM; University of Florence, Polo Scientifico e Tecnologico; 50019 Sesto Fiorentino Firenze Italy
| | - Lorenzo Badii
- Department of Chemistry and INSTM; University of Florence, Polo Scientifico e Tecnologico; 50019 Sesto Fiorentino Firenze Italy
| | - Cristina Nativi
- Department of Chemistry and INSTM; University of Florence, Polo Scientifico e Tecnologico; 50019 Sesto Fiorentino Firenze Italy
| | - Stefano Roelens
- Department of Chemistry and INSTM; University of Florence, Polo Scientifico e Tecnologico; 50019 Sesto Fiorentino Firenze Italy
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12
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Ohishi Y, Abe H, Inouye M. Native Mannose‐Dominant Extraction by Pyridine–Phenol Alternating Oligomers Having an Extremely Efficient Repeating Motif of Hydrogen‐Bonding Acceptors and Donors. Chemistry 2015; 21:16504-11. [DOI: 10.1002/chem.201503149] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Yuki Ohishi
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
| | - Hajime Abe
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama 930‐0194 (Japan)
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13
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Francesconi O, Nativi C, Gabrielli G, De Simone I, Noppen S, Balzarini J, Liekens S, Roelens S. Antiviral Activity of Synthetic Aminopyrrolic Carbohydrate Binding Agents: Targeting the Glycans of Viral gp120 to Inhibit HIV Entry. Chemistry 2015; 21:10089-93. [DOI: 10.1002/chem.201501030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 01/18/2023]
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14
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Francesconi O, Gentili M, Nativi C, Ardá A, Cañada FJ, Jiménez-Barbero J, Roelens S. Systematic Dissection of an Aminopyrrolic Cage Receptor for β-Glucopyranosides Reveals the Essentials for Effective Recognition. Chemistry 2014; 20:6081-91. [DOI: 10.1002/chem.201400365] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Indexed: 12/17/2022]
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15
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Abstract
Lectins are proteins of non-immune origin that bind specific carbohydrates without chemical modification. Coupled with the emerging biological and pathological significance of carbohydrates, lectins have become extensively used as research tools in glycobiology. However, lectin-based drug development has been impeded by high manufacturing costs, low chemical stability, and the potential risk of initiating an unfavorable immune response. As alternatives to lectins, non-protein small molecules having carbohydrate-binding properties (lectin mimics) are currently attracting a great deal of attention because of their ease of preparation and chemical modification. Lectin mimics of synthetic origin are divided roughly into two groups, boronic acid-dependent and boronic acid-independent lectin mimics. This article outlines their representative architectures and carbohydrate-binding properties, and discusses their therapeutic potential by reviewing recent attempts to develop antiviral and antimicrobial agents using their architectures. We also focus on the naturally occurring lectin mimics, pradimicins and benanomicins. They are the only class of non-protein natural products having a C-type lectin-like ability to recognize d-mannopyranosides in the presence of Ca2 + ions. Their molecular basis of carbohydrate recognition and therapeutic potential are also discussed.
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Affiliation(s)
- Yu Nakagawa
- Synthetic Cellular Chemistry Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
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16
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Rieth S, Miner MR, Chang CM, Hurlocker B, Braunschweig AB. Saccharide receptor achieves concentration dependent mannoside selectivity through two distinct cooperative binding pathways. Chem Sci 2013. [DOI: 10.1039/c2sc20873c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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17
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Francesconi O, Gentili M, Roelens S. Synthetic Tripodal Receptors for Carbohydrates. Pyrrole, a Hydrogen Bonding Partner for Saccharidic Hydroxyls. J Org Chem 2012; 77:7548-54. [DOI: 10.1021/jo301341c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Oscar Francesconi
- Dipartimento
di Chimica and ‡Istituto di Metodologie Chimiche (IMC), Consiglio Nazionale delle
Ricerche (CNR), Dipartimento di Chimica, Università di Firenze, I-50019 Sesto Fiorentino,
Firenze, Italy
| | - Matteo Gentili
- Dipartimento
di Chimica and ‡Istituto di Metodologie Chimiche (IMC), Consiglio Nazionale delle
Ricerche (CNR), Dipartimento di Chimica, Università di Firenze, I-50019 Sesto Fiorentino,
Firenze, Italy
| | - Stefano Roelens
- Dipartimento
di Chimica and ‡Istituto di Metodologie Chimiche (IMC), Consiglio Nazionale delle
Ricerche (CNR), Dipartimento di Chimica, Università di Firenze, I-50019 Sesto Fiorentino,
Firenze, Italy
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18
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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19
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Gavette JV, Lara J, Berryman OB, Zakharov LN, Haley MM, Johnson DW. Lithium cation enhances anion binding in a tripodal phosphine oxide-based ditopic receptor. Chem Commun (Camb) 2011; 47:7653-5. [PMID: 21655566 PMCID: PMC3344749 DOI: 10.1039/c1cc12475g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A tripodal ditopic receptor presents H-bond donors and a phosphine oxide to potential guests. In the idealized binding conformation, an endohedral P=O functionality provides enhanced halide binding in the presence of lithium with the greatest ΔΔG° observed for bromide, while minimal changes in K(a) are observed in the presence of sodium.
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Affiliation(s)
- Jesse V. Gavette
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
| | - Juven Lara
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
| | - Orion B. Berryman
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
| | - Lev N. Zakharov
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
| | - Michael M. Haley
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
| | - Darren W. Johnson
- Department of Chemistry and the Materials Science Institute, University of Oregon, Eugene, OR 97403-1253, USA
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20
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Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 633] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
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21
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Abe H, Chida Y, Kurokawa H, Inouye M. Selective binding of D2h-symmetrical, acetylene-linked pyridine/pyridone macrocycles to maltoside. J Org Chem 2011; 76:3366-71. [PMID: 21410290 DOI: 10.1021/jo2003055] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A macrocyclic host molecule having pyridine-pyridone-pyridine modules for saccharide recognition was prepared by Cu(II)-mediated oxidative homocoupling of a tandem diethynyl precursor. In CH(2)Cl(2), the host molecule associated with dodecyl β-maltoside much more strongly (K(a) = 1.4 × 10(6) M(-1)) than with octyl monohexosides (K(a) = ca. 2 × 10(3) to 1 × 10(4) M(-1)), accompanied with induced CDs. An all-pyridine macrocyclic host was also studied, and its binding strength with saccharides was weaker than that for the pyridine-pyridone-pyridine host.
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Affiliation(s)
- Hajime Abe
- Graduate School of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan.
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22
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Ardá A, Cañada FJ, Nativi C, Francesconi O, Gabrielli G, Ienco A, Jiménez-Barbero J, Roelens S. Chiral Diaminopyrrolic Receptors for Selective Recognition of Mannosides, Part 2: A 3D View of the Recognition Modes by X-ray, NMR Spectroscopy, and Molecular Modeling. Chemistry 2011; 17:4821-9. [DOI: 10.1002/chem.201002872] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 11/29/2011] [Indexed: 11/12/2022]
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23
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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24
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Fernández-Trillo F, Fernandez-Megia E, Riguera R. Evaluation of Amino Acids as Chiral Ligands for the Enantiodifferentiation of Carbohydrates by TOCSY NMR. J Org Chem 2010; 75:3878-81. [DOI: 10.1021/jo1004263] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francisco Fernández-Trillo
- Departamento de Quimica Organica, Facultad de Quimica and Unidad de RMN de Biomoleculas Asociada al CSIC, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Departamento de Quimica Organica, Facultad de Quimica and Unidad de RMN de Biomoleculas Asociada al CSIC, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ricardo Riguera
- Departamento de Quimica Organica, Facultad de Quimica and Unidad de RMN de Biomoleculas Asociada al CSIC, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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