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Zrilić SS, Živković JM, Zarić SD. Hydrogen bonds of a water molecule in the second coordination sphere of amino acid metal complexes: Influence of amino acid coordination. J Inorg Biochem 2023; 242:112151. [PMID: 36857976 DOI: 10.1016/j.jinorgbio.2023.112151] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023]
Abstract
The hydrogen bonds of free and coordinated amino acids with water molecule were studied by analyzing data in the crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The CSD data indicate bifurcated NH/O hydrogen bonds and O1/HO hydrogen bonds of coordinated oxygen. The O/HO hydrogen bonds of free zwitterions and non-coordinated carbonyl oxygen (O2/HO) in metal complexes form primarily linear, non-bifurcated hydrogen bonds. Calculated M06L-GD3/def2-TZVPP interaction energies for free zwitterions (glycine, cysteine, phenylalanine and, serine) and water molecule are in the range from -5.1 to -9.6 kcal/mol for NH/O and from -6.9 to -7.6 kcal/mol for O/HO interactions. Coordinated amino acids in neutral octahedral cobalt(III) complexes have NH/O interaction energies ca. -7.4 kcal/mol, independent of the amino acid. The singly and doubly charged complexes have stronger NH/O interactions; the strongest has energy of -16.9 kcal/mol. In the case of O1/HO hydrogen bond, the interaction energy decreases upon coordination; interactions are quite weak for neutral complexes (-2.2 to -2.6 kcal/mol). For O2/HO hydrogen bonds, all amino acids except serine show slightly stronger interaction in singly negative complexes (-6.3 to -8.0 kcal/mol), while interactions are weaker for neutral complexes (-2.8 to -4.4 kcal/mol), comparing to zwitterions.
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Affiliation(s)
- Sonja S Zrilić
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Jelena M Živković
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia.
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Xu X, Bošnjaković-Pavlović N, Čolović MB, Krstić DZ, Vasić VM, Gillet JM, Wu P, Wei Y, Spasojević-de Biré A. A combined crystallographic analysis and ab initio calculations to interpret the reactivity of functionalized hexavanadates and their inhibitor potency toward Na(+)/K(+)-ATPase. J Inorg Biochem 2016; 161:27-36. [PMID: 27235271 DOI: 10.1016/j.jinorgbio.2016.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/16/2016] [Accepted: 04/25/2016] [Indexed: 02/02/2023]
Abstract
In vitro influence of five synthesized functionalized hexavanadates (V6) on commercial porcine cerebral cortex Na(+)/K(+)-ATPase activity has been studied. Dose dependent Na(+)/K(+)-ATPase inhibition was obtained for all investigated compounds. Calculated half maximal inhibitory concentration IC50 values, in mol/L, for Na(+)/K(+)-ATPase were 7.6×10(-5), 1.8×10(-5), 2.9×10(-5), 5.5×10(-5) for functionalized hexavanadates (V6) with tetrabutylammonium (TBA) [V6-CH3][TBA]2, [V6-NO2][TBA]2, [V6-OH][TBA]2 and [V6-C3][TBA]2 respectively. [V6-OH][Na]2 inhibited Na(+)/K(+)-ATPase activity up to 30% at maximal investigated concentration 1×10(-3)mol/L. This reactivity has been interpreted using a study of the non-covalent interactions of functionalized hexavanadate hybrids through Cambridge Structural Database (CSD) analysis. Bibliographic searching has led to 18 different structures and 99 contacts. We have observed that C-H⋯O contacts consolidate the structures. We have also performed density functional theory (DFT) calculations and have determined electrostatic potential values at the molecular surface on a series of functionalized V6. These results enlightened their chemical reactivity and their potential biological applications such as the inhibition of the ATPase.
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Affiliation(s)
- Xiao Xu
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
| | | | - Mirjana B Čolović
- Department of Physical Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, P.O.Box 522, Belgrade, Serbia
| | - Danijela Z Krstić
- University School of Medicine, Institute of Medical Chemistry, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia
| | - Vesna M Vasić
- Department of Physical Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, P.O.Box 522, Belgrade, Serbia
| | - Jean-Michel Gillet
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
| | - Pingfan Wu
- Institute of POM-based Materials, The Synergistic Innovation Center of Catalysis Materials of Hubei Province, Hubei University of Technology, 430086 Wuhan, Hubei Province, P. R. China
| | - Yongge Wei
- Department of Chemistry, Tsinghua University, 100084 Beijing, P.R. China
| | - Anne Spasojević-de Biré
- Université Paris Saclay, CentraleSupélec, Campus de Châtenay, Grande Voie des Vignes, 92295 Châtenay-Malabry, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Grande Voie des Vignes, 92295 Châtenay-Malabry, France
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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Sousa SF, Pinto GRP, Ribeiro AJM, Coimbra JTS, Fernandes PA, Ramos MJ. Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. J Comput Chem 2013; 34:2079-90. [PMID: 23798313 DOI: 10.1002/jcc.23349] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 12/26/2022]
Abstract
In this study, a set of 50 transition-metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In addition, 14 different basis sets were considered, including four commonly used Pople's all-electron basis sets; four basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden; and six triple-ζ basis sets. The results illustrate the performance of different methodological alternatives for the treatment of geometrical properties in relevant copper complexes, pointing out Double-Hybrid (DH) and Long-range Correction (LC) Generalized Gradient Approximation (GGA) methods as better descriptors of the geometry of the evaluated systems. These however, are associated with a computational cost several times higher than some of the other methods employed, such as the M06 functional, which has also demonstrated a comparable performance. Regarding the basis sets, 6-31+G(d) and 6-31+G(d,p) were the best performing approaches. In addition, the results show that the use of effective-core potentials has a limited impact, in terms of the accuracy in the determination of metal-ligand bond-lengths and angles in our dataset of copper complexes. Hence, these could become a good alternative for the geometrical description of these systems, particularly CEP-121G and SDD basis sets, if one is considering larger copper complexes where the computational cost could be an issue.
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Affiliation(s)
- Sérgio F Sousa
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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