Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D)

• Published in: Scientific reports 2016-11, Vol.6 (1), p.36595-36595, Article 36595
• Main Authors: He, Song-Bing, Ben Hu, Kuang, Zheng-Kun, Wang, Dong, Kong, De-Xin
• Format: Article
• Language: English
• Subjects: 631/154/309/630; 639/638/630; Adenosine; Adenosine receptors; Conformation; Diabetes mellitus; Humanities and Social Sciences; Humans; Ligands; Models, Molecular; Movement disorders; multidisciplinary; Neurodegenerative diseases; Pain; Parkinson's disease; Predictions; Protein Binding; Receptors, Purinergic P1 - metabolism; Regression analysis; Science; Stroke; Support Vector Machine
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep36595

Adenosine receptors (ARs) are potential therapeutic targets for Parkinson’s disease, diabetes, pain, stroke and cancers. Prediction of subtype selectivity is therefore important from both therapeutic and mechanistic perspectives. In this paper, we introduced a shape similarity profile as molecular descriptor, namely three-dimensional biologically relevant spectrum (BRS-3D), for AR selectivity prediction. Pairwise regression and discrimination models were built with the support vector machine methods. The average determination coefficient ( r 2 ) of the regression models was 0.664 (for test sets). The 2B-3 (A 2B vs A 3 ) model performed best with q 2  = 0.769 for training sets (10-fold cross-validation), and r 2  = 0.766, RMSE  = 0.828 for test sets. The models’ robustness and stability were validated with 100 times resampling and 500 times Y-randomization. We compared the performance of BRS-3D with 3D descriptors calculated by MOE. BRS-3D performed as good as, or better than, MOE 3D descriptors. The performances of the discrimination models were also encouraging, with average accuracy (ACC) 0.912 and MCC 0.792 (test set). The 2A-3 (A 2A vs A 3 ) selectivity discrimination model ( ACC  = 0.882 and MCC  = 0.715 for test set) outperformed an earlier reported one ( ACC  = 0.784). These results demonstrated that, through multiple conformation encoding, BRS-3D can be used as an effective molecular descriptor for AR subtype selectivity prediction.