1
|
Viviano-Posadas AO, Romero-Mendoza U, Bazany-Rodríguez IJ, Velázquez-Castillo RV, Martínez-Otero D, Bautista-Renedo JM, González-Rivas N, Galindo-Murillo R, Salomón-Flores MK, Dorazco-González A. Efficient fluorescent recognition of ATP/GTP by a water-soluble bisquinolinium pyridine-2,6-dicarboxamide compound. Crystal structures, spectroscopic studies and interaction mode with DNA. RSC Adv 2022; 12:27826-27838. [PMID: 36320280 PMCID: PMC9520314 DOI: 10.1039/d2ra05040d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 11/04/2023] Open
Abstract
The new dicationic pyridine-2,6-dicarboxamide-based compound 1 bearing two N-alkylquinolinium units was synthesized, structurally determined by single-crystal X-ray diffraction, and studied in-depth as a fluorescent receptor for nucleotides and inorganic phosphorylated anions in pure water. The addition of nucleotides to 1 at pH = 7.0 quenches its blue emission with a selective affinity towards adenosine 5'-triphosphate (ATP) and guanosine 5'-tripohosphate (GTP) over other nucleotides such CTP, UTP, ADP, AMP, dicarboxylates and inorganic anions. On the basis of the spectroscopic tools (1H, 31P NMR, UV-vis, fluorescence), MS measurements and DFT calculations, receptor 1 binds ATP with high affinity (log K = 5.04) through the simultaneous formation of strong hydrogen bonds and π-π interactions between the adenosine fragment and quinolinium ring with binding energy calculated in 8.7 kcal mol-1. High affinity for ATP/GTP is attributed to the high acidity of amides and preorganized rigid structure of 1. Receptor 1 is an order of magnitude more selective for ATP than GTP. An efficient photoinduced electron transfer quenching mechanism with simultaneous receptor-ATP complexation in both the excited and ground states is proposed. Additionally, multiple spectroscopic studies and molecular dynamics simulations showed that 1 can intercalate into DNA base pairs.
Collapse
Affiliation(s)
- Alejandro O Viviano-Posadas
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Ulises Romero-Mendoza
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Iván J Bazany-Rodríguez
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Rocío V Velázquez-Castillo
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Diego Martínez-Otero
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Joanatan M Bautista-Renedo
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Nelly González-Rivas
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM km 14.5 Carrera Toluca-Atlacomulco, Campus UAEMex "El Rosedal" San Cayetano-Toluca Toluca de Lerdo 50200 Estado de México Mexico
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah 2000 East 30 South Skaggs 306 Salt Lake City 84112 Utah USA
| | - María K Salomón-Flores
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| | - Alejandro Dorazco-González
- Institute of Chemistry, National Autonomous University of Mexico Circuito Exterior, Ciudad Universitaria México, D.F., 04510 Mexico +52-55-56224514
| |
Collapse
|
2
|
Agafontsev AM, Ravi A, Shumilova TA, Oshchepkov AS, Kataev EA. Molecular Receptors for Recognition and Sensing of Nucleotides. Chemistry 2018; 25:2684-2694. [PMID: 30289184 DOI: 10.1002/chem.201802978] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/05/2018] [Indexed: 12/15/2022]
Abstract
Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.
Collapse
Affiliation(s)
- Aleksandr M Agafontsev
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany.,N. N. Vorozhtsov Institute of Organic Chemistry SB RAS, 9 Lavrentiev Avenue, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova St. 1, 630090, Novosibirsk, Russia
| | - Anil Ravi
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Tatiana A Shumilova
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| | - Aleksandr S Oshchepkov
- Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklay St. 6, Moscow, 117198, Russia
| | - Evgeny A Kataev
- Institute of Chemistry, Technische Universität Chemnitz, 09107, Chemnitz, Germany
| |
Collapse
|
3
|
Rivera-Márquez KI, Godoy-Alcántar C, Claudio-Catalán MÁ, Medrano F. Adenine nucleotide recognition by spiramycin and some of its aromatic derivatives. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0654-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Fuentes-Martínez JP, Gutiérrez-Rodríguez D, García ER, Rivera-Márquez KI, Medrano F, Torres-Ángeles O, Castillo-Vargas E, Montaño BED, Godoy-Alcántar C. Streptomycin Hydrazone Derivatives: Synthesis and Molecular Recognition in Aqueous Solution. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400901012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Five hydrazone derivatives of streptomycin were synthetized (D0h, D1ph, D2bt, D3dctf, D4ag) and characterized by IR, 1H and 13C NMR spectroscopy, mass spectrometry and elemental analysis. Protonation constants were determined by potentiometry for all derivatives. D1ph and D2bt derivatives were investigated as receptors of dicarboxylates and adenine nucleotides in aqueous solution by potentiometric and 1H NMR titrations. D1ph and D2bt derivatives have the highest affinity with AMP and ATP, respectively, which shows that electrostatic forces are not always the dominant factor in binding of streptomycin derivatives with nucleotides, but the conformational fit between them. Calculated structures at the DFT level of the D1ph derivative bonded with either AMP or ADP showed that the complexes are stabilized by the formation of multiple interactions with the receptors. The antibiotic activity of the derivatives was explored and compared with native streptomycin.
Collapse
Affiliation(s)
- Juan P. Fuentes-Martínez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Diana Gutiérrez-Rodríguez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Edgar Rogel García
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Karla I. Rivera-Márquez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Felipe Medrano
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Oscar Torres-Ángeles
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Evelin Castillo-Vargas
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Blanca E. Duque Montaño
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| | - Carolina Godoy-Alcántar
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Morelos, México
| |
Collapse
|
5
|
Schneider HJ, Agrawal P, Yatsimirsky AK. Supramolecular complexations of natural products. Chem Soc Rev 2014; 42:6777-800. [PMID: 23703643 DOI: 10.1039/c3cs60069f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Complexations of natural products with synthetic receptors as well as the use of natural products as host compounds are reviewed, with an emphasis on possible practical uses or on biomedical significance. Applications such as separation, sensing, enzyme monitoring, and protection of natural drugs are first outlined. We then discuss examples of complexes with all important classes of natural compounds, such as amino acids, peptides, nucleosides/nucleotides, carbohydrates, catecholamines, flavonoids, terpenoids/steroids, alkaloids, antibiotics and toxins.
Collapse
Affiliation(s)
- Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, D 66041 Saarbrücken, Germany.
| | | | | |
Collapse
|
6
|
Dorazco-González A, Alamo MF, Godoy-Alcántar C, Höpfl H, Yatsimirsky AK. Fluorescent anion sensing by bisquinolinium pyridine-2,6-dicarboxamide receptors in water. RSC Adv 2014. [DOI: 10.1039/c3ra44363a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
7
|
|
8
|
Godoy-Alcántar C, Yatsimirsky AK. Biological Small Molecules as Receptors. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc065] [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: 11/06/2022]
|
9
|
|
10
|
Gutiérrez-Moreno NJ, Medrano F, Yatsimirsky AK. Schiff base formation and recognition of amino sugars, aminoglycosides and biological polyamines by 2-formyl phenylboronic acid in aqueous solution. Org Biomol Chem 2012; 10:6960-72. [DOI: 10.1039/c2ob26290h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
11
|
Fuentes-Martínez Y, Godoy-Alcántar C, Medrano F, Dikiy A, Yatsimirsky AK. Protonation of kanamycin A: detailing of thermodynamics and protonation sites assignment. Bioorg Chem 2010; 38:173-80. [PMID: 20457465 DOI: 10.1016/j.bioorg.2010.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/15/2010] [Accepted: 04/19/2010] [Indexed: 10/19/2022]
Abstract
Protonation of an aminoglycoside antibiotic kanamycin A sulfate was studied by potentiometric titrations at variable ionic strength, sulfate concentration and temperature. From these results the association constants of differently protonated forms of kanamycin A with sulfate and enthalpy changes for protonation of each amino group were determined. The protonation of all amino groups of kanamycin A is exothermic, but the protonation enthalpy does not correlate with basicity as in a case of simple polyamines. The sites of stepwise protonation of kanamycin A have been assigned by analysis of (1)H-(13)C-HSQC spectra at variable pH in D(2)O. Plots of chemical shifts for each H and C atom of kanamycin A vs. pH were fitted to the theoretical equation relating them to pK(a) values of ionogenic groups and it was observed that changes in chemical shifts of all atoms in ring C were controlled by ionization of a single amino group with pK(a) 7.98, in ring B by ionization of two amino groups with pK(a) 6.61 and 8.54, but in ring A all atoms felt ionization of one group with pK(a) 9.19 and some atoms felt ionization of a second group with pK(a) 6.51, which therefore should belong to amino group at C3 in ring B positioned closer to the ring A while higher pK(a) 8.54 can be assigned to the group at C1. This resolves the previously existed uncertainty in assignment of protonation sites in rings B and C.
Collapse
Affiliation(s)
- Yanet Fuentes-Martínez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, C.P. 62209 Cuernavaca, Mexico
| | | | | | | | | |
Collapse
|