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Soykan U, Sert Y, Yıldırım G. DFT, Molecular Docking and Drug-likeness Analysis: Acrylate molecule bearing perfluorinated pendant unit. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Gutierrez LJ, Angelina E, Gyebrovszki A, Fülöp L, Peruchena N, Baldoni HA, Penke B, Enriz RD. New small-size peptides modulators of the exosite of BACE1 obtained from a structure-based design. J Biomol Struct Dyn 2016; 35:413-426. [DOI: 10.1080/07391102.2016.1145143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Lucas J. Gutierrez
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Químicam, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Químicam, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, Corrientes 3400, Argentina
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina
| | - Andrea Gyebrovszki
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8., Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8., Hungary
| | - Nelida Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Químicam, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Av. Libertad 5470, Corrientes 3400, Argentina
| | - Héctor A. Baldoni
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
- Instituto de Matemática Aplicada San Luis (IMASL,CONICET), Italia 1556, 5700 San Luis, Argentina
| | - Botond Penke
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8., Hungary
| | - Ricardo D. Enriz
- Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL, CONICET), Ejercito de Los Andes 950, 5700 San Luis, Argentina
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
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Tosso RD, Andujar SA, Gutierrez L, Angelina E, Rodríguez R, Nogueras M, Baldoni H, Suvire FD, Cobo J, Enriz RD. Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration. J Chem Inf Model 2013; 53:2018-32. [PMID: 23834278 DOI: 10.1021/ci400178h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.
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Affiliation(s)
- Rodrigo D Tosso
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
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Chamorro ER, Sequeira AF, Zalazar MF, Peruchena NM. Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa. Bioorg Med Chem 2008; 16:8535-45. [DOI: 10.1016/j.bmc.2008.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 07/28/2008] [Accepted: 08/04/2008] [Indexed: 11/28/2022]
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Murgich J, Franco HJ, San-Blas G. Topology of Charge Density of Flucytosine and Related Molecules and Characteristics of their Bond Charge Distributions. J Phys Chem A 2006; 110:10106-15. [PMID: 16913685 DOI: 10.1021/jp061007r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular charge distribution of flucytosine (4-amino-5-fluoro-2-pyrimidone), uracil, 5-fluorouracil, and thymine was studied by means of density functional theory calculations (DFT). The resulting distributions were analyzed by means of the atoms in molecules (AIM) theory. Bonds were characterized through vectors formed with the charge density value, its Laplacian, and the bond ellipticity calculated at the bond critical point (BCP). Within each set of C=O, C-H, and N-H bonds, these vectors showed little dispersion. C-C bonds formed three different subsets, one with a significant degree of double bonding, a second corresponding to single bonds with a finite ellipticity produced by hyperconjugation, and a third one formed by a pure single bond. In N-C bonds, a decrease in bond length (an increase in double bond character) was not reflected as an increase in their ellipticity, as in all C-C bonds studied. It was also found that substitution influenced the N-C, C-O, and C-C bond ellipticity much more than density and its Laplacian at the BCP. The Laplacian of charge density pointed to the existence of both bonding and nonbonding maxima in the valence shell charge concentration of N, O, and F, while only bonding ones were found for the C atoms. The nonbonding maxima related to the sites for electrophilic attack and H bonding in O and N, while sites of nucleophilic attack were suggested by the holes in the valence shell of the C atoms of the carbonyl groups.
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Affiliation(s)
- Juan Murgich
- Centro de Química and Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Apartado 21827, Caracas 1020A, Venezuela.
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Castillo N, Boyd RJ. An Atoms in Molecules Study of the Halogen Resonance Effect. J Chem Theory Comput 2005; 2:271-80. [DOI: 10.1021/ct050238j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norberto Castillo
- Department of Chemistry, Dalhousie University, Halifax, N.S., Canada B3H 4J3
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, N.S., Canada B3H 4J3
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