Computational Prediction of Resistance Induced Alanine-Mutation in ATP Site of Epidermal Growth Factor Receptor

Abstract

Epidermal growth factor receptor (EGFR) resistance to tyrosine kinase inhibitors can cause low survival rates in mutation-positive non-small cell lung cancer patients. It is necessary to predict new mutations in the development of more potent EGFR inhibitors since classical and rare mutations observed were known to affect the effectiveness of the therapy. Therefore, this research aimed to perform alanine mutagenesis scanning on ATP binding site residues without COSMIC data, followed by molecular dynamic simulations to determine their molecular interactions with ATP and erlotinib compared to wild-type complexes. Based on the result, eight mutations were found to cause changes in the binding energy of the ATP analogue to become more negative. These included G779A, Q791A, L792A, R841A, N842A, V843A, I853A, and D855A, which were predicted to enhance the affinity of ATP and reduce the binding ability of inhibitors with the same interaction site. Erlotinib showed more positive energy among G779A, Q791A, I853A, and D855A, due to their weaker binding energy than ATP. These four mutations could be anticipated in the development of the next inhibitor to overcome the incidence of resistance in lung cancer patients.

Keywords: EGFR; erlotinib; mutation; prediction; resistance.

Figure 1

Distribution of exons encoded EGFR and the mutation site of EGFR in NSCLC patients. The most common mutations in each exon are shown in bold.

Figure 2

Two-dimensional interaction of ANP in the wild-type and mutated EGFR. Interactions are colored based on the type: , hydrogen bond; , van der Waals; , metal acceptor; , pi-alkyl.

Figure 3

Two- and three-dimensional interaction of ANP in E709A and G719A EGFR. Interactions are colored based on the type: , hydrogen bond; , van der Waals; , metal acceptor; , pi-sigma; , pi-sulfur; , pi-alkyl.

Figure 4

(a) Binding pocket of ANP-Mg in EGFR based on 5D41 crystal structure; (b) Mutation position of the reference mutation (blue) and test mutation (pink) on 1M17 crystal structure.

Figure 5

Trajectories of ANP during 200 ns simulation in the binding site of E762A (a), K745A (b), I789A (c), and (d) Two-dimensional interaction of ANP to the mutated receptor: , hydrogen bond; , van der Waals; , metal acceptor; , pi-sulfur; , pi-alkyl.

Figure 5

Trajectories of ANP during 200 ns simulation in the binding site of E762A (a), K745A (b), I789A (c), and (d) Two-dimensional interaction of ANP to the mutated receptor: , hydrogen bond; , van der Waals; , metal acceptor; , pi-sulfur; , pi-alkyl.

Figure 6

Trajectories of ANP in the I853A (a) and G779A (b) binding site during simulation, and (c) 2D interaction of ANP to the I853A and G779A receptor: , hydrogen bond; , van der Waals; , metal acceptor; , pi-sigma; , pi-alkyl.

Figure 7

The position of erlotinib in ATP binding site of EGFR (left) and two-dimensional interaction of erlotinib to wildtype EGFR (right): , hydrogen bond; , van der Waals; , metal acceptor; , pi-alkyl.

Figure 8

Two-dimensional interaction of erlotinib to G779A, Q791A, I853A, and D855A (, hydrogen bond; , van der Waals; , metal acceptor; , pi-sulfur; , pi-alkyl).

Figure 8

Two-dimensional interaction of erlotinib to G779A, Q791A, I853A, and D855A (, hydrogen bond; , van der Waals; , metal acceptor; , pi-sulfur; , pi-alkyl).