Zia Qamar, Rehman Md Tabish, Hashmi Md Amiruddin, Siddiqui Sahabjada, Bin Dukhyil Abdulaziz, Ahmed Mohammad Z, Jamal Azfar, Banawas Saeed, Almalki Sami G, Owais Mohammad, Aldhafeeri Hamad Qasem, Ibrahim Ibrahim M, Alturaiki Wael, AlAjmi Mohamed F, Alsieni Mohammed, Alqurashi Yaser E
Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia.
Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia.
Front Neurosci. 2022 Jul 25;16:915122. doi: 10.3389/fnins.2022.915122. eCollection 2022.
Alzheimer's disease (AD) is a neurodegenerative disease and the most prevalent form of dementia. The generation of oxygen free radicals and oxidative damage is believed to be involved in the pathogenesis of AD. It has been suggested that date palm, a plant rich in phenolic compounds and flavonoids, can provide an alternative treatment to fight memory loss and cognitive dysfunction due to its potent antioxidant activity. Thus, we studied the effect of flavonoids present in date palm on Aβ amyloid formation using molecular docking and molecular dynamics simulation. AutoDock. Myricetin was used as a positive control drug. The flavonoids Diosmetin, Luteolin, and Rutin were found to be potent inhibitors of aggregation (docking energies ≤ -8.05 kcal mol) targeting Aβ fibrils (both 2LMO and 6TI5), simultaneously. Further screening by physicochemical properties and drug-likeness analysis suggested that all flavonoids except Rutin followed Lipinski's rule of five. Rutin was, thus, taken as a negative control (due to its violation of Lipinski's rule) to compare its dynamics with Diosmetin. Diosmetin exhibited the highest positive scores for drug likeness. Since Luteolin exhibited moderate drug-likeness and better absorption properties, it was also included in molecular dynamics simulation. Molecular dynamics of shortlisted compounds (Rutin, Diosmetin, and Luteolin) were performed for 200 ns, and the results were analyzed by monitoring root mean square deviations (RMSD), root mean square fluctuation (RMSF) analysis, the radius of gyration (Rg), and solvent accessible surface area (SASA). The results proved the formation of a stable protein-compound complex. Based on binding energies and non-bonded interactions, Rutin and Luteolin emerged as better lead molecules than Diosmetin. However, high MW (610.5), lowest absorption rate (16.04%), and more than one violation of Lipinski's rule make Rutin a less likely candidate as an anti-amyloidogenic agent. Moreover, among non-violators of Lipinski's rule, Diosmetin exhibited a greater absorption rate than Luteolin as well as the highest positive scores for drug-likeness. Thus, we can conclude that Diosmetin and Luteolin may serve as a scaffold for the design of better inhibitors with higher affinities toward the target proteins. However, these results warrant and validation before practical use.
阿尔茨海默病(AD)是一种神经退行性疾病,也是最常见的痴呆形式。氧自由基的产生和氧化损伤被认为与AD的发病机制有关。有人提出,海枣富含酚类化合物和黄酮类化合物,由于其强大的抗氧化活性,可为对抗记忆力丧失和认知功能障碍提供一种替代治疗方法。因此,我们使用分子对接和分子动力学模拟研究了海枣中存在的黄酮类化合物对Aβ淀粉样蛋白形成的影响。使用了AutoDock。杨梅素用作阳性对照药物。发现黄酮类化合物香叶木素、木犀草素和芦丁是针对Aβ原纤维(2LMO和6TI5)的聚集的有效抑制剂(对接能量≤-8.05 kcal/mol)。通过物理化学性质和类药性分析进一步筛选表明,除芦丁外的所有黄酮类化合物均符合Lipinski的五规则。因此,芦丁被用作阴性对照(由于其违反了Lipinski规则),以将其动力学与香叶木素进行比较。香叶木素在类药性方面表现出最高的正分数。由于木犀草素表现出中等的类药性和更好的吸收特性,它也被纳入分子动力学模拟。对入围化合物(芦丁、香叶木素和木犀草素)进行了200 ns的分子动力学模拟,并通过监测均方根偏差(RMSD)、均方根波动(RMSF)分析、回转半径(Rg)和溶剂可及表面积(SASA)对结果进行了分析。结果证明形成了稳定的蛋白质-化合物复合物。基于结合能和非键相互作用,芦丁和木犀草素比香叶木素更适合作为先导分子。然而,高分子量(610.5)、最低吸收率(16.04%)以及多次违反Lipinski规则使得芦丁作为抗淀粉样蛋白生成剂的可能性较小。此外,在未违反Lipinski规则的化合物中,香叶木素的吸收率高于木犀草素,并且在类药性方面表现出最高的正分数。因此,我们可以得出结论,香叶木素和木犀草素可作为设计对靶蛋白具有更高亲和力的更好抑制剂的支架。然而,这些结果在实际应用前需要进一步验证。
Front Neurosci. 2022-7-25
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