Geometrical Features of Epidermal Growth Factor Receptor-Related Dimers Reveal the Mechanisms of Drug Resistance in Lung Cancer Patients

Epidermal growth factor receptor (EGFR) plays an important role in lung cell proliferation. Dimerization of EGFR family members and other receptor tyrosine kinases (RTKs) act as a vital controller for lung cell life cycle signals. Mutations in the kinase domain of EGFR may disorder the signaling networks and lead to cancer. Drug resistance occurs in several generations of EGFR drugs due to genetic mutations, and there is a very less understanding about the mechanism of EGFR-mutated drug resistance. In this work, we investigate the mechanism of wild type EGFR protein and its drug-sensitive and drug-resistant mutations. We performed molecular dynamics (MD) simulation for the 10-ns EGFR-drug mutant complex and investigated the structures' geometrical properties. With features extracted by alpha shape modeling, different geometrical properties, such as matching rates of atom solid angles at interaction sites and centroid distances between interfacial atoms, were calculated to characterize the binding intensity. Wilcoxon rank sum test was applied to reveal the differences between mutations based on extracted properties. We have developed a framework that explains the drug resistance mechanism based on geometrical properties and binding free energy. Results revealed that drug-sensitive mutants have tighter interactions with corresponding RTK in the complex for all protein-drug systems, while drug-resistant mutants are bound looser. The extracted geometrical properties of the drug mutant complex help understand the drug response mechanism at atomic level.