Electrostatic explanation of D1228V/H/N-induced c-Met resistance and sensitivity to type I and type II kinase inhibitors in targeted gastric cancer therapy.

The c-Met D1228V/H/N mutation clinically causes acquired resistance to type I tyrosine kinase inhibitors (TKIs), while maintaining sensitivity to type II TKIs in targeted gastric cancer therapy. The mutation is located in the activation loop (A-loop) region of the c-Met kinase domain, which substitutes the negatively charged residue Asp1228 with electroneutral amino acid Val, His, or Asn, thus electrostatically destabilizing the DFG-in conformation of A-loop and inducing its transition to DFG-out state. The transition is spontaneous in a dynamics point of view and the A-loop exhibits a large intrinsic disorder during the transitional dynamics course. In DFG-in conformation, the wild-type Asp1228 is surrounded by a number of positively charged residues within its first and second shells, which can also form a hydrogen-bonding network with its vicinal residues Phe1089, Lys1110, Asp1222, and Met1229 in the first shell. Type I and type II TKIs respond oppositely to the mutation; the former shows a generic resistance to the mutation, whereas the latter is generally sensitized by the mutation. Both types of TKIs do not directly interact with the mutation. Instead, the mutation-induced conformational change in A-loop reshapes kinase active site and then influences the site interactions with inhibitor ligands, thus conferring different selectivity to the type I and type II TKIs. Graphical abstract The molecular mechanism of D1228V/H/N mutation-induced inhibitor resistance and sensitivity in c-Met kinase is investigated. The mutation electrostatically destabilizes the DFG-in conformation of kinase A-loop and induces its spontaneous transition to DFG-out state, which reshapes kinase active site and influences the site interactions with inhibitor ligands.