Fig. 6: Structural basis for linker-dependent strong binding of the C-linked bivalent inhibitor 2.
Variations in crystallographic B-factors of the bound ligands (a) 1 and (b) 2 in complex with EGFR. The blue-to-red gradient is averaged to the overall average B-factors are 36 Å2 for 1 (PDB ID 8FV3) and 44 Å2 for 2 (PDB ID 8FV4). c) WaterMap simulation of the unbound EGFR(T790M/V948R) binding pocket for compounds 1 and 2, highlighting unfavorable hydration sites (yellow spheres for 1 and green spheres for 2) and their relative location to bound 1 and 2. Color-coded ΔG values reflect the compound associated with each water molecule (See Supplementary Fig. S11 for complete analysis). Conformational analysis of compound (d) 1 and (e) 2 (MacroModel). The potential energy values highlight that 2 adopts a conformation that is over 3-fold more energetically favorable in the binding site compared to 1 in the binding site. Relative potential energy indicates the energy difference to the lowest energy conformation in the predicted set and highlights a closer alignment to the ideal conformation for 2 compared to 1. The root-mean-square deviation (RMSD) was used to justify the ligand conformation closest to the crystal structure. Ligands are displayed with ball and stick representations using yellow and green colors for carbon-atoms of 1 and 2, respectively. Chemical structures of (f) 1 and (g) 2 denoting linker rotatable bonds and their torsion angles from MD simulations (see Supplementary Fig. S12 for complete analysis).
