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Chernikova EY, Ruleva AY, Tsvetkov VB, Fedorov YV, Novikov VV, Aliyeu TM, Pavlov AA, Shepel NE, Fedorova OA. Cucurbit[7]uril-driven modulation of ligand-DNA interactions by ternary assembly. Org Biomol Chem 2020; 18:755-766. [PMID: 31912862 DOI: 10.1039/c9ob02543j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of small organic molecules with a predictable and desirable DNA-binding mechanism is a topical research task for biomedicine application. Herein, we demonstrate an attractive supramolecular strategy for controlling the non-covalent ligand-DNA interaction by binding with cucurbituril as a synthetic receptor. With a combination of UV/vis, CD and NMR experiments, we demonstrate that the bis-styryl dye with two suitable binding sites can involve double stranded DNA and cucurbituril in the formation of the supramolecular triad. The ternary assembly is formed as a result of the interaction of macrocyclic cucurbituril with one pyridinium fragment of the bis-styryl dye, while the second pyridinium fragment of the dye is effectively associated with DNA backbones, which leads to a change in the ligand-DNA binding mode from aggregation to a minor groove. This exciting outcome was supported by molecular docking studies that help to understand the molecular orientation of the supramolecular triad and elucidate the destruction of dye aggregates caused by cucurbituril. These studies provide valuable information on the mechanisms of DNA binding to small molecules and recognition processes in bioorganic supramolecular assemblies constructed from multiple non-covalent interactions.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Anna Y Ruleva
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Vladimir B Tsvetkov
- Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow, 119146 Russia and Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia and Polyelectrolytes and Biomedical Polymers Laboratory, A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow, 119991, Russia
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Valentin V Novikov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Tseimur M Aliyeu
- Center for Molecule Composition Studies, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Alexander A Pavlov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Nikolay E Shepel
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
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Blázquez-Sánchez MT, Marcelo F, Fernández-Alonso MDC, del Villar-Guerra R, Samadi A, Cañada FJ, Jiménez-Barbero J, Vicent C. D- andL-Mannose-Containingglyco-Oligoamides Show Distinct Recognition Properties When Interacting with DNA. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Blázquez-Sánchez MT, Marcelo F, Fernández-Alonso MC, Poveda A, Jiménez-Barbero J, Vicent C. Cooperative hydrogen bonding in glyco-oligoamides: DNA minor groove binders in aqueous media. Chemistry 2014; 20:17640-52. [PMID: 25359390 DOI: 10.1002/chem.201403911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 12/26/2022]
Abstract
A strategy to create cooperative hydrogen-bonding centers by using strong and directional intramolecular hydrogen-bonding motifs that can survive in aqueous media is presented. In particular, glyco-oligoamides, a family of DNA minor groove binders, with cooperative and non-cooperative hydrogen-bonding donor centers in the carbohydrate residues have been designed, synthesized, and studied by means of NMR spectroscopy and molecular modeling methods. Indeed, two different sugar moieties, namely, β-D-Man-Py-γ-Py-Ind (1; Ind=indole, Man=mannose, Py=pyrrole) and β-D-Tal-Py-γ-Py-Ind (2; Tal=talose), were chosen according to our design. These sugar molecules should present one- or two-directional intramolecular hydrogen bonds. The challenge has been to study the conformation of the glyco-oligoamides at low temperature in physiological media by detecting the exchangeable protons (amide NH and OH resonances) by means of NMR spectroscopic analysis. In addition, two more glyco-oligoamides with non-cooperative hydrogen-bonding centers, that is, β-D-Glc-Py-γ-Py-Ind (3; Glc=glucose), β-D-Gal-Py-γ-Py-Ind (4; Gal=galactose), and the model compounds β-D-Man-Py-NHAc (5) and β-D-Tal-Py-NHAc (6) were synthesized and studied for comparison. We have demonstrated the existence of directional intramolecular hydrogen bonds in 1 and 2 in aqueous media. The unexpected differences in terms of stabilization of the intramolecular hydrogen bonds in 1 and 2 relative to 5 and 6 promoted us to evaluate the influence of CH-π interactions on the establishment of intramolecular hydrogen bonds by using computational methods. Initial binding studies of 1 and 2 with calf-thymus DNA and poly(dA-dT)2 by NMR spectroscopic analysis and molecular dynamics simulations were also carried out. Both new sugar-oligoamides are bound in the minor groove of DNA, thus keeping a stable hairpin structure, as in the free state, in which both intramolecular hydrogen-bonding and CH-π interactions are present.
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Taladriz-Sender A, Vicent C. Synthesis of cationic glyco-oligoamide for DNA–carbohydrate interaction studies. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.814776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Andrea Taladriz-Sender
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Cristina Vicent
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
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Karidi K, Ypsilantis K, Papakyriakou A, Garoufis A. Synthesis and characterization of ruthenium(II)-oligopyridine-peptide conjugates. Interactions of the diasteromeres Δ- and Λ-[Ru(bpy)2(4-COY-4'-Mebpy)]Cl2 (Y=Gly-Lys(1)-Lys(2)CONH2, Lys(1)-Gly-Lys(2)CONH2, Lys(1)-Lys(2)-GlyCONH2) with the oligonucleotide d(5'-CGCGAATTCGCG-3')2. J Inorg Biochem 2013; 127:13-23. [PMID: 23838117 DOI: 10.1016/j.jinorgbio.2013.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/16/2013] [Accepted: 06/17/2013] [Indexed: 01/12/2023]
Abstract
Diastereomeric complexes of the general formulae Λ- and Δ-[Ru(bpy)2(4-COY-4'-Mebpy)]Cl2 where bpy=2,2'-bipyridine and Y=Gly-Lys(1)-Lys(2)CONH2, Lys(1)-Gly-Lys(2)CONH2, Lys(1)-Lys(2)-GlyCONH2, were synthesized and characterized. The ability of these compounds to bind to the oligonucleotide duplex d(5'-CGCGAATTCGCG-3') was studied with NMR techniques. Complex Λ-2, Λ-[Ru(bpy)2(4-COLys(1)-Gly-Lys(2)CONH2),4'-Mebpy)]Cl2 (Mebpy=methyl-2,2'-bipyridine), interacts non-specifically causing changes for both complex and oligonucleotide (1)H NMR signals. Both Λ-1, Λ-[Ru(bpy)2(4-COGly-Lys(1)-Lys(2)CONH2),4'-Mebpy)]Cl2 and Λ-3, Λ-[Ru(bpy)2(4-COLys(1)-Lys(2)-GlyCONH2),4'-Mebpy)]Cl2, were bound to the oligonucleotide through both lysine aliphatic chains, indicating that the side chains of the sequential lysines create a kind of "clamp" to connect the complex with the oligonucleotide. Complex Δ-1, Δ-[Ru(bpy)2(4-COGly-Lys(1)-Lys(2)CONH2),4'-Mebpy)]Cl2, interacts with the oligonucleotide duplex with both lysine side chains in a manner similar to Λ-1. Δ-2, Δ-[Ru(bpy)2(4-COLys(1)-Gly-Lys(2)CONH2),4'-Mebpy)]Cl2, interacts with the oligonucleotide with the bipyridine ligands. In addition, the formation of a hydrogen bond between the Gly-NH and the carbonyl groups of the oligonucleotide bases was detected. A completely different binding mode was observed for Δ-3 Δ-[Ru(bpy)2(4-COLys(1)-Lys(2)-GlyCONH2),4'-Mebpy)]Cl2, which at a ratio of 1:1 ([Ru]/[nucleotide]) opens the oligonucleotide strands. In addition, participation of all three peptidic NH of Δ-3 in hydrogen bonds was observed.
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Affiliation(s)
- Konstantina Karidi
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina 45110, Greece
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Badı́a C, Souard F, Vicent C. Sugar–Oligoamides: Synthesis of DNA Minor Groove Binders. J Org Chem 2012; 77:10870-81. [DOI: 10.1021/jo302238u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Concepción Badı́a
- Departamento de Sı́ntesis,
Estructura y Propiedades de los Compuestos Orgánicos, Instituto de Quı́mica Orgánica General,
CSIC, c/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Florence Souard
- Departamento de Sı́ntesis,
Estructura y Propiedades de los Compuestos Orgánicos, Instituto de Quı́mica Orgánica General,
CSIC, c/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Cristina Vicent
- Departamento de Sı́ntesis,
Estructura y Propiedades de los Compuestos Orgánicos, Instituto de Quı́mica Orgánica General,
CSIC, c/Juan de la Cierva 3, 28006 Madrid, Spain
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Pace CJ, Kim D, Gao J. Experimental evaluation of CH-π interactions in a protein core. Chemistry 2012; 18:5832-6. [PMID: 22473937 DOI: 10.1002/chem.201200334] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Indexed: 11/08/2022]
Abstract
CH-π stacks up! Using the protein α(2) D as a model system, we estimate that a CH-π contact between cyclohexylalanine (Cha) and phenylalanine (F) contributes approximately -0.7 kcal mol(-1) to the protein stability. The stacking F-Cha pairs are sequestered in the core of the protein, where water interference does not exist (see figure). Therefore, the observed energetic gain should represent the inherent magnitude and upper limit of the CH-π interactions.
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Affiliation(s)
- Christopher J Pace
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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STD-NMR: application to transient interactions between biomolecules—a quantitative approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1357-69. [DOI: 10.1007/s00249-011-0749-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 09/06/2011] [Indexed: 02/02/2023]
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