Assessing the Performance of GOLD, Glide and MM-GBSA on a Dataset of Hydrazide-hydrazone-based Tuberculostatics

对接(动物) 相关系数 生物信息学 化学 皮尔逊积矩相关系数 成对比较 虚拟筛选 马修斯相关系数 计算机科学 分子动力学 计算生物学 计算化学 人工智能 机器学习 数学 生物化学 统计 医学 护理部 生物 支持向量机 基因
作者
Emilio Mateev,Maya Georgieva,Alexander Zlatkov
出处
期刊:Letters in Drug Design & Discovery [Bentham Science]
卷期号:20 (10): 1557-1568 被引量:1
标识
DOI:10.2174/1570180819666220512115015
摘要

Background: Tuberculosis is considered a global health problem; hence, the screening and synthesis of novel tuberculostatic drugs are a necessity. Molecular docking could drastically reduce the time of hit identification; however, initial validation is required to reduce the false-positive results. Objective: Assessment of several searching and scoring algorithms for a custom dataset of hydrazidehydrazone- based tuberculostatics was conducted to obtain a reliable docking protocol for future virtual screening. Methods: Modification in the scoring functions, size of the grid space, and presence of active waters of a GOLD 5.3 docking protocol was conducted. Subsequently, side-chain flexibility and ensemble docking were carried out to assess the role of protein flexibility in the correlation coefficient. In addition, docking simulations with Glide and free binding energy calculations with MM-GBSA were implemented. The Pearson correlation coefficient between the experimental and the acquired in silico data was calculated after each work step. The major interactions between the top-scored ligands and the active site of 2X22 were visualized applying Discovery Studio. Results: An optimized GOLD 5.3 docking protocol led to a drastically enhanced Pearson correlation coefficient of the training set, from 0.461 to 0.823, as well as an excellent pairwise correlation coefficient in the test set - 0,8405. Interestingly, the Glide docking scores and the free binding energy calculations with MM-GBSA did not achieve reliable results. During the visualization of the top-ranked compounds, it was observed that Lys165 played a major role in the formation of stable complexes. Conclusion: It could be concluded that the performance of the optimized GOLD 5.3 docking protocol demonstrated significantly higher reliability against the hydrazide-hydrazone dataset when compared to Glide docking simulations and MM-GBSA free binding energy calculations. The results could be utilized for future virtual screenings.

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