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Fingerprint‐based computational models of 5‐lipo‐oxygenase activating protein inhibitors: Activity prediction and structure clustering
Author(s) -
Tu Guiping,
Qin Zijian,
Huo Donghui,
Zhang Shengde,
Yan Aixia
Publication year - 2020
Publication title -
chemical biology and drug design
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.59
H-Index - 77
eISSN - 1747-0285
pISSN - 1747-0277
DOI - 10.1111/cbdd.13657
Subject(s) - cluster analysis , fingerprint (computing) , test set , chemistry , virtual screening , computational biology , computer science , artificial intelligence , bioinformatics , stereochemistry , biology , pharmacophore
Abstract Inflammatory diseases can be treated by inhibiting 5‐lipo‐oxygenase activating protein (FLAP). In this study, a data set containing 2,112 FLAP inhibitors was collected. A total of 25 classification models were built by five machine learning algorithms with five different types of fingerprints. The best model, which was built by support vector machine algorithm with ECFP_4 fingerprint had an accuracy and a Matthews correlation coefficient of 0.862 and 0.722 on the test set, respectively. The predicted results were further evaluated by the application domain d STD‐PRO (a distance between one compound to models). Each compound had a d STD‐PRO value, which was calculated by the predicted probabilities obtained from all 25 models. The application domain results suggested that the reliability of predicted results depended mainly on the compounds themselves rather than algorithms or fingerprints. A group of customized 10‐bit fingerprint was manually defined for clustering the molecular structures of 2,112 FLAP inhibitors into eight subsets by K‐Means. According to the clustering results, most of inhibitors in two subsets (subsets 2 and 4) were highly active inhibitors. We found that aryl oxadiazole/oxazole alkanes, biaryl amino‐heteroarenes, two aromatic rings (often N‐containing) linked by a cyclobutene group, and 1,2,4‐triazole group were typical fragments in highly active inhibitors.