Nida Nur Adiyan, Abdulkadir Levent, Şerife Pınar Yalçın, Mehmet Sönmez
{"title":"5-苯甲酰-6-苯基嘧啶-4- 1 -2-硫酮化合物的合成、晶体结构及电化学性能其与DNA相互作用的伏安法、分光光度法和分子对接研究","authors":"Nida Nur Adiyan, Abdulkadir Levent, Şerife Pınar Yalçın, Mehmet Sönmez","doi":"10.1007/s11164-025-05694-2","DOIUrl":null,"url":null,"abstract":"<div><p>A novel heterocyclic compound, 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione (PT), was synthesized for the first time via the cyclocondensation reaction of dibenzoyl acetic acid-N-carboxymethylamide with thiourea. The structure of the compound was characterized using elemental analysis, FT-IR, NMR, X-ray crystallography, and API-ES mass spectrometry. Electrochemical behavior of PT was investigated by cyclic voltammetry on a glassy carbon electrode in an anhydrous medium (0.1 M TBAP), revealing an irreversible cathodic peak at − 0.83 V, indicative of irreversible redox behavior and surface interaction. The interaction between PT and DNA was explored using voltammetric, spectrophotometric, and molecular docking techniques. Differential pulse voltammetry demonstrated a concentration-dependent decrease in the guanine oxidation signal, with a calculated binding free energy of − 6.5 kcal/mol. Spectrophotometric studies further supported the occurrence of a stable PT–DNA complex. Molecular docking revealed a strong binding affinity (− 8.12 kcal/mol), suggesting minor groove and electrostatic interaction modes. The consistency among electrochemical, spectroscopic, and computational findings indicates that PT forms a thermodynamically favorable and specific interaction with DNA. These results provide a foundation for future research on the therapeutic potential of PT and related pyrimidine thione derivatives.</p><h3>Graphical abstract</h3>\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":753,"journal":{"name":"Research on Chemical Intermediates","volume":"51 11","pages":"6593 - 6611"},"PeriodicalIF":3.5000,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Synthesis, crystal structure, and electrochemical properties of 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione compound; voltammetric, spectrophotometric, and molecular docking studies of its interaction with DNA\",\"authors\":\"Nida Nur Adiyan, Abdulkadir Levent, Şerife Pınar Yalçın, Mehmet Sönmez\",\"doi\":\"10.1007/s11164-025-05694-2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>A novel heterocyclic compound, 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione (PT), was synthesized for the first time via the cyclocondensation reaction of dibenzoyl acetic acid-N-carboxymethylamide with thiourea. The structure of the compound was characterized using elemental analysis, FT-IR, NMR, X-ray crystallography, and API-ES mass spectrometry. Electrochemical behavior of PT was investigated by cyclic voltammetry on a glassy carbon electrode in an anhydrous medium (0.1 M TBAP), revealing an irreversible cathodic peak at − 0.83 V, indicative of irreversible redox behavior and surface interaction. The interaction between PT and DNA was explored using voltammetric, spectrophotometric, and molecular docking techniques. Differential pulse voltammetry demonstrated a concentration-dependent decrease in the guanine oxidation signal, with a calculated binding free energy of − 6.5 kcal/mol. Spectrophotometric studies further supported the occurrence of a stable PT–DNA complex. Molecular docking revealed a strong binding affinity (− 8.12 kcal/mol), suggesting minor groove and electrostatic interaction modes. The consistency among electrochemical, spectroscopic, and computational findings indicates that PT forms a thermodynamically favorable and specific interaction with DNA. These results provide a foundation for future research on the therapeutic potential of PT and related pyrimidine thione derivatives.</p><h3>Graphical abstract</h3>\\n<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>\",\"PeriodicalId\":753,\"journal\":{\"name\":\"Research on Chemical Intermediates\",\"volume\":\"51 11\",\"pages\":\"6593 - 6611\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2025-07-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Research on Chemical Intermediates\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s11164-025-05694-2\",\"RegionNum\":3,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Research on Chemical Intermediates","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s11164-025-05694-2","RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Synthesis, crystal structure, and electrochemical properties of 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione compound; voltammetric, spectrophotometric, and molecular docking studies of its interaction with DNA
A novel heterocyclic compound, 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione (PT), was synthesized for the first time via the cyclocondensation reaction of dibenzoyl acetic acid-N-carboxymethylamide with thiourea. The structure of the compound was characterized using elemental analysis, FT-IR, NMR, X-ray crystallography, and API-ES mass spectrometry. Electrochemical behavior of PT was investigated by cyclic voltammetry on a glassy carbon electrode in an anhydrous medium (0.1 M TBAP), revealing an irreversible cathodic peak at − 0.83 V, indicative of irreversible redox behavior and surface interaction. The interaction between PT and DNA was explored using voltammetric, spectrophotometric, and molecular docking techniques. Differential pulse voltammetry demonstrated a concentration-dependent decrease in the guanine oxidation signal, with a calculated binding free energy of − 6.5 kcal/mol. Spectrophotometric studies further supported the occurrence of a stable PT–DNA complex. Molecular docking revealed a strong binding affinity (− 8.12 kcal/mol), suggesting minor groove and electrostatic interaction modes. The consistency among electrochemical, spectroscopic, and computational findings indicates that PT forms a thermodynamically favorable and specific interaction with DNA. These results provide a foundation for future research on the therapeutic potential of PT and related pyrimidine thione derivatives.
期刊介绍：
Research on Chemical Intermediates publishes current research articles and concise dynamic reviews on the properties, structures and reactivities of intermediate species in all the various domains of chemistry.
The journal also contains articles in related disciplines such as spectroscopy, molecular biology and biochemistry, atmospheric and environmental sciences, catalysis, photochemistry and photophysics. In addition, special issues dedicated to specific topics in the field are regularly published.
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