Fig. 4: Allosteric site and drug screening strategy. | Nature Communications

Fig. 4: Allosteric site and drug screening strategy.

From: Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR

Fig. 4

a, b Allosteric site identified by a combination of FTMap and the LIME interpreter of RHML for two representative conformations (Conf1 (a) and Conf2 (b)). The predicted allosteric sites are shown as surface and important residues identified by the LIME interpreter are highlighted in blue. c Virtual screening workflow employed in the work and structures of four hit compounds screened. The binding energies between the receptor and the four ligands screened are highlighted in red, which is derived from the MM/GBSA calculations based on the last 10-ns trajectories of 120-ns short cMD simulations. d Binding modes of the four hit compounds with β2AR. Ligands are represented by stick (ZINC5042, salmon; ZINC252008995, cyan; ZINC4213962, wheat; ZINC11681534, skyblue). The receptor is represented  as cartoon (yellow for Conf1 and green for Conf2). The polar interactions are shown as black dashed lines.

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