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Investigating the binding affinity, molecular dynamics, and ADMET properties of 2,3-dihydrobenzofuran derivatives as an inhibitor of fungi, bacteria, and virus protein
Beni-Suef University Journal of Basic and Applied Sciences Pub Date : 2021-06-02 , DOI: 10.1186/s43088-021-00117-8
Ashutosh Nath , Ajoy Kumer , Fahmida Zaben , Md. Wahab Khan

2,3-Dihydrobenzofurans (DHB) have proposed as advantages structures, and used as chemical entresol to design small compound libraries. The present study illustrates to explore 2,3-dihydrobenzofurans(DHB) in comparison to selected some derivatives drugs by using molecular docking and molecular dynamics, as well as ADMET studies. The online database “Molinspiration online server” was used to detect the physicochemical pharmacokinetics and drug likeness score of DHB drugs. For estimation of molecular docking, six pathogens, such as r (PDB id: 1kum), Candida albicans (3dra), Escherichia coli (6og7), Salmonella typhi (4k6l), Influenza (1ru7), and Hepatitis C (4tyd), were chosen due to close biological studies. From Molinspiration online server has showed that DHB did not violate the “Lipinski five rule” as drugs, leading compound for molecular docking exhibited the potential interaction to the active residue. The binding affinity of DHB2 (−7.00 kcal/mol) against 3dra was higher than DHB8 (−6.40 kcal/mol) and DHB (5.70 kcal/mol) for compounds. The results of molecular docking show that the compounds mentioned in this study are not equally effective against pathogens, such as fungi, viruses, and bacteria. However, DHB2, DHB3, and DHB 8 compounds can work against almost given pathogens which results are derived from auto dock vina in terms of binding affinity around 6.00 kcal/mol, and Fire Dock has values from about 38.0 to 42.0 kcal/mol. To explore the dynamic nature of the interaction, 50 ns molecular dynamics (MD) simulation was performed on the selected protein-DHB complexes. Thus, DHB 8 has greater potential to interact for further for fungi. Finding from this study can play an effective role as a drug in any biological system. This study as well recommends to researchers to synthesize these DHBs for evaluation of its biological activity.

中文翻译:

研究 2,3-二氢苯并呋喃衍生物作为真菌、细菌和病毒蛋白抑制剂的结合亲和力、分子动力学和 ADMET 特性

2,3-二氢苯并呋喃 (DHB) 已被提出作为优势结构,并用作化学间醇来设计小型化合物库。本研究说明通过使用分子对接和分子动力学以及 ADMET 研究来探索 2,3-二氢苯并呋喃 (DHB) 与选定的一些衍生物药物的比较。在线数据库“Molinspiration在线服务器”用于检测DHB药物的理化药代动力学和药物相似性评分。对于分子对接的估计,六种病原体,如 r (PDB id: 1kum)、白色念珠菌 (3dra)、大肠杆菌 (6og7)、伤寒沙门氏菌 (4k6l)、流感 (1ru7) 和丙型肝炎 (4tyd),由于密切的生物学研究而被选中。来自 Molinspiration 在线服务器的显示,DHB 作为毒品并没有违反“Lipinski 五项规则”,分子对接的先导化合物表现出与活性残基的潜在相互作用。DHB2 (-7.00 kcal/mol) 对 3dra 的结合亲和力高于 DHB8 (-6.40 kcal/mol) 和 DHB (5.70 kcal/mol)。分子对接的结果表明,本研究中提到的化合物对真菌、病毒和细菌等病原体的作用并不相同。然而,DHB2、DHB3 和 DHB 8 化合物可以对抗几乎给定的病原体,这些病原体源自 Auto Dock vina,结合亲和力约为 6.00 kcal/mol,Fire Dock 的值约为 38.0 至 42.0 kcal/mol。为了探索相互作用的动态特性,对选定的蛋白质-DHB 复合物进行了 50 ns 分子动力学 (MD) 模拟。因此,DHB 8 具有更大的潜力与真菌进一步相互作用。这项研究的发现可以在任何生物系统中作为药物发挥有效作用。本研究还建议研究人员合成这些 DHBs 以评估其生物活性。
更新日期:2021-06-02
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