Synthesis, structure, DFT study and molecular docking inspection of spirobi[hexahydropyrimidine]-diones derivative

IF 3.8 Q2 CHEMISTRY, PHYSICAL Chemical Physics Impact Pub Date : 2024-08-23 DOI:10.1016/j.chphi.2024.100716

Malahat Kurbanova , Suraj N. Mali , Fidan Gurbanova , Haya Yasin , Shailesh S. Gurav , Chin-Hung Lai

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Abstract

It has been established that three-component condensation of benzaldehyde, acetone and urea catalyzed H₂SO₄ leads to the formation of spirobi[hexahidropyrimidine]-dione derivatives. The structure of the synthesized compound has been proved by X-ray method. The results of the quantum theory of atom-in-molecule and noncovalent interaction index analysis showed no intramolecular hydrogen bonds in the molecule studied. However, it contains four NH bonds and two CO groups. Based on the result of the DFT-NBO analysis, it was the lone pairs of oxygen on the CO group which are forming strong orbital interactions with the antibonding orbital of the CN single bond. The molecular docking was performed to investigate potential binding interactions of the compound with four target proteins including 5I4T (HIV-1), 5R7Z, 6M71 and 6VYB (SARS-Cov-2). Additionally, in-silico drug-likeness and ADME studies suggested oral activity (violations ≤ 1) of scaffold and predicted to be actively effluxed by P-gp (PGP+).

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螺双[六氢嘧啶]二酮衍生物的合成、结构、DFT 研究和分子对接检验

研究证实，在 H2SO4 催化下，苯甲醛、丙酮和尿素的三组分缩合可生成螺双[六氢嘧啶]二酮衍生物。合成化合物的结构已通过 X 射线方法得到证实。原子分子内量子理论和非共价相互作用指数分析的结果表明，所研究的分子中没有分子内氢键。不过，它含有四个 NH 键和两个 CO 基团。根据 DFT-NBO 分析结果，是 CO 基团上的氧孤对作用与 CN 单键的反键轨道形成了强烈的轨道相互作用。通过分子对接研究了该化合物与四种目标蛋白的潜在结合相互作用，包括 5I4T（HIV-1）、5R7Z、6M71 和 6VYB（SARS-Cov-2）。此外，室内药物相似性和 ADME 研究表明，该支架具有口服活性（违规行为 ≤ 1），并预测可通过 P-gp (PGP+) 积极外流。

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