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. Author manuscript; available in PMC: 2024 Nov 16.
Published in final edited form as: Cell Chem Biol. 2023 Aug 30;30(11):1478–1487.e7. doi: 10.1016/j.chembiol.2023.08.002

Fig. 5. Off target explanation and validation.

Fig. 5.

a. Binding mode comparison between bafetinib and belvarafenib in complex with BRAF. The structure closest to the average structure (measured by RMSD) of bafetinib-BRAF MD simulations is displayed in brown; The co-crystal structure of belvarafenib-BRAF (PDB ID: 6XFP) is displayed in cyan. b. Comparison of binding stability scores (left) and MMPBSA binding free energies (right) of the last 150 ns of MD simulation trajectories (frame interval is 1 ns). Positive controls are displayed in green; Negative controls are displayed in red; Identified off-targets are displayed in blue. Significance levels of z-tests: ***, p <= 0.001; ****, p <= 0.0001. c. Western blot of dose-dependent CETSA of abemaciclib-CSNK2A2 and bafetinib-BRAF. The changing of blots is consistent to the LASSO score of MAPS-iTSA. d. Dose-response curve for NanoBERT in-vitro off-target validation of bafetinib-BRAF and abemaciclib-CSNK2A2. Known inhibitors are taken as positive control while their cross matching is taken as negative control. e. Dose-response curve for kinase hotpots in-vitro off-target validation of bafetinib-BRAF and abemaciclib-CSNK2A2. Relative kinase activities are obtained by normalization based on blank controls.