Fig. 5: Binding modes of bivalent EGFR inhibitors exhibit linker-dependent conformations within the allosteric pocket.

a The binding modes of ATP-site trisubstituted imidazole inhibitor (orange, PDB ID 6V5N) and the allosteric inhibitor DDC4002 (magenta, PDB ID 6P1D). The overlapping phenyl rings of these two compounds (bold circle) is the group at which the bivalent inhibitors are merged. b Overall protein-ligand structure of the EGFR(T790M/V948R) kinase domain in the αC-helix (αC) outward conformation in complex with 1 (yellow spheres, PDB ID 8FV3). c Active site view and binding mode of 1 (yellow) showing ATP-site binding and “outward” benzo conformation at the allosteric site (PDB ID 8FV3). d Active site view and binding mode of 2 (green) showing ATP-site binding and “inward” benzo conformation at the allosteric site 2 (PDB ID 8FV4) in complex with EGFR(T790M/V948R). e Top view overlay of 1 and 2 cocrystal structures within the allosteric pocket demonstrating the full conformational change of the benzo moiety. The angle between the benzo phenyl rings in the 2 “inward” and 1 “outward” conformation and ring-to-ring distance. The conformation of the allosteric moiety influences the positioning of L858 in (f) 1 (yellow) and (g) 2 (green). h View of allosteric pocket featuring an overlay of the C-linked bivalent 2 (green, PDB ID 8FV4) and allosteric inhibitor 8 (magenta, PDB ID 6P1D). 2D-representation of compound 1 (i) and compound 2 (j) interaction frequencies with EGFR(T790M/V948R) based on 10μs/compound MD simulations. Only interactions occurring in more than 20% of the simulation time are shown (full data is available in Supplementary Table S2, Supplementary Fig. S5). The residue and interaction color schemes are consistent for (i) and (j). Polar residues are blue, hydrophobic residues are green, negative charged residues are orange, and positive charged are purple. A green line represents π–π stacking, a red line represents the π-cations, and a purple line represents the H-bonds. A dashed line is used as an indication of side-chain interaction and a straight line of the backbone one. The interaction strength along the simulation time is shown by the percentage on the line.