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Naves LFN, Borges NM, Custodio JMF, Vaz WF, Bastos RM, Cunha S, Napolitano HB. Structural insights into the biological activity of a thioxopyrimidine derivative. J Mol Model 2021; 27:73. [PMID: 33547505 DOI: 10.1007/s00894-021-04700-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/27/2021] [Indexed: 11/28/2022]
Abstract
Bacterial resistance to the main widespread antibiotics, such as those based on quinolones, is a concern of the scientific community, leading to the search for new classes of molecules that can be used as an alternative. Here, we investigate the crystalline and chemical characteristics of a thioxopyrimide to understand its demonstrated biological activity and to identify which portion of the molecule can be used as a framework to develop new antibiotics. For this purpose, structural studies of ethyl 4-methyl-2-phenyl-6-thioxo-1,6-dihydro-5-pyrimidinecarboxylate were carried out aided by Hirshfeld surface analysis, as well as theoretical calculations on frontier molecular orbitals, molecular electrostatic potential, and conformational stability, in addition to docking studies targeting topoisomerase IV. The docking results show a reasonable accommodation of the molecule at the topoisomerase IV binding site and interact mainly by hydrogen bonds between the thioxopyrimidine portion with Glu198, Thr292, and Gly225, aided by hydrophobic interactions involving the rest of the molecule. These results suggest a relationship between the antibacterial activity shown mainly with the 4-thioxopyrimidine portion, leading to the investigation of new compounds that use this scaffold.
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Affiliation(s)
- Luiz F N Naves
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Nadia M Borges
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Jean M F Custodio
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil. .,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46665, USA.
| | - Wesley F Vaz
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
| | - Rodrigo M Bastos
- Instituto de Química, Universidade Federal da Bahia, Campus de Ondina, Salvador, BA, 40170-115, Brazil
| | - Silvio Cunha
- Instituto de Química, Universidade Federal da Bahia, Campus de Ondina, Salvador, BA, 40170-115, Brazil
| | - Hamilton B Napolitano
- Grupo de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, Anápolis, GO, 75001-970, Brazil
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Hussain A, Khan MU, Ibrahim M, Khalid M, Ali A, Hussain S, Saleem M, Ahmad N, Muhammad S, Al-Sehemi AG, Sultan A. Structural parameters, electronic, linear and nonlinear optical exploration of thiopyrimidine derivatives: A comparison between DFT/TDDFT and experimental study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127183] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Stolarczyk M, Bryndal I, Matera-Witkiewicz A, Lis T, Królewska-Golińska K, Cieślak M, Kaźmierczak-Barańska J, Cieplik J. Synthesis, crystal structure and cytotoxic activity of novel 5-methyl-4-thiopyrimidine derivatives. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:1138-1145. [PMID: 30284980 DOI: 10.1107/s2053229618012706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/07/2018] [Indexed: 11/10/2022]
Abstract
This article presents the synthesis of three new 4-thiopyrimidine derivatives obtained from ethyl 4-methyl-2-phenyl-6-sulfanylpyrimidine-5-carboxylate as the starting material, namely, ethyl 4-[(4-chlorobenzyl)sulfanyl]-6-methyl-2-phenylpyrimidine-5-carboxylate, C21H19ClN2O2S, (2), {4-[(4-chlorobenzyl)sulfanyl]-6-methyl-2-phenylpyrimidin-5-yl}methanol, C19H17ClN2OS, (3), and 4-[(4-chlorobenzyl)sulfanyl]-5,6-dimethyl-2-phenylpyrimidine, C19H17ClN2S, (4), which vary in the substituent at the 5-position of the pyrimidine ring. The compounds were characterized by 1H NMR, 13C NMR, IR and mass spectroscopies, and also elemental analysis. The molecular structures were further studied by single-crystal X-ray diffraction. Compound (2) crystallizes in the space group P-1 with one molecule in the asymmetric unit, whereas compounds (3) and (4) crystallize in the space group P21/c with two and one molecule, respectively, in their asymmetric units. The conformation of each molecule is best defined by the dihedral angles formed between the pyrimidine ring and the planes of the two aryl substituents attached at the 2- and 4-positions. The only structural difference between the three compounds is the substituent at the 5-position of the pyrimidine ring, but they present significantly different features in the hydrogen-bond interactions. Compound (2) displays a one-dimensional chain formed by hydrogen bonds and the chains are further extended into a two-dimensional network. Molecules of (3) and (4) generate one-dimensional chains formed through intermolecular interactions. The study examines the cytotoxicity of compounds (3) and (4) against Human umbilical vein endothelial cells (HUVEC) and HeLa, K562 and CFPAC cancer cell lines. The presence of the hydroxymethyl and methyl groups in (3) and (4), respectively, offers an interesting new insight into the structures and behaviour of these derivatives. Compound (4) was found to be nontoxic against CFPAC and HUVEC; however, it shows weak activity against the HeLa and K563 cell lines. The presence of a hydroxy group in (3) significantly increases its cytotoxicity towards both, i.e. the cancer (HeLa, K562 and CFPAC) and normal (HUVEC) cell lines.
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Affiliation(s)
- Marcin Stolarczyk
- Department of Organic Chemistry, Faculty of Pharmacy with Division of Laboratory Diagnostics, Wroclaw Medical University, Borowska 211A, 50-556 Wrocław, Poland
| | - Iwona Bryndal
- Department of Bioorganic Chemistry, Institute of Chemistry and Food Technology, Faculty of Engineering and Economics, Wroclaw University of Economics, Komandorska 118/120, 53-345 Wrocław, Poland
| | - Agnieszka Matera-Witkiewicz
- Screening Laboratory of Biological Activity Test and Collection of Biological Material, Faculty of Pharmacy with Division of Laboratory Diagnostics, Wroclaw Medical University, Borowska 211A, 50-556 Wrocław, Poland
| | - Tadeusz Lis
- Faculty of Chemistry, University of Wroclaw, Joliot-Curie Street 14, 50-383 Wrocław, Poland
| | - Karolina Królewska-Golińska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Marcin Cieślak
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Julia Kaźmierczak-Barańska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Jerzy Cieplik
- Department of Drugs Technology, Faculty of Pharmacy with Division of Laboratory Diagnostics, Wroclaw Medical University, Borowska 211A, 50-556 Wrocław, Poland
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Kalaiarasi N, Manivarman S. Structural, vibrational (FTIR and FT-Raman), NMR, UV–vis spectral analysis, and DFT study of 2-(6-oxo-2-thioxotetrahydropyrimidin-4(1H)-ylidene) hydrazine carboxamide. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vibrational and spectral characterizations of 2-(6-oxo-2-thioxo tetrahydro pyrimidin-4(1h)-ylidene) hydrazine carboxamide (OTHHPYHC) were experimentally presented for the ground state using FTIR and FT-Raman and theoretically presented by density functional theory (DFT) using B3LYP correlation function with the basis set 6-31G(d,p). The geometrical parameters, energies, and wavenumbers have been obtained. The fundamental assignments were performed on the basis of total energy distribution. The first order hyperpolarizability (β0) and relative properties (β, α0, and Δα) were calculated using B3LYP/6-31G(d, p) method. Solidity of the molecule due to hyperconjugative interactions and charge delocalization has been analysed using natural bond orbital (NBO) analysis. The charge distribution and electron transfer from bonding to antibonding orbitals and electron density in the σ* and π* antibonding orbitals confirms interaction within the molecule. In addition to this, Mulliken population and HOMO–LUMO analysis have been used to support the information of structural properties.
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Affiliation(s)
- N. Kalaiarasi
- Post Graduate and Research Department of Chemistry, Government Arts College, C. Mutlur, Chidambaram, Tamil Nadu, India
- Post Graduate and Research Department of Chemistry, Government Arts College, C. Mutlur, Chidambaram, Tamil Nadu, India
| | - S. Manivarman
- Post Graduate and Research Department of Chemistry, Government Arts College, C. Mutlur, Chidambaram, Tamil Nadu, India
- Post Graduate and Research Department of Chemistry, Government Arts College, C. Mutlur, Chidambaram, Tamil Nadu, India
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