Structural Insight and Development of EGFR Tyrosine Kinase Inhibitors

Abstract

Lung cancer has a high prevalence, with a growing number of new cases and mortality every year. Furthermore, the survival rate of patients with non-small-cell lung carcinoma (NSCLC) is still quite low in the majority of cases. Despite the use of conventional therapy such as tyrosine kinase inhibitor for Epidermal Growth Factor Receptor (EGFR), which is highly expressed in most NSCLC cases, there was still no substantial improvement in patient survival. This is due to the drug's ineffectiveness and high rate of resistance among individuals with mutant EGFR. Therefore, the development of new inhibitors is urgently needed. Understanding the EGFR structure, including its kinase domain and other parts of the protein, and its activation mechanism can accelerate the discovery of novel compounds targeting this protein. This study described the structure of the extracellular, transmembrane, and intracellular domains of EGFR. This was carried out along with identifying the binding pose of commercially available inhibitors in the ATP-binding and allosteric sites, thereby clarifying the research gaps that can be filled. The binding mechanism of inhibitors that have been used clinically was also explained, thereby aiding the structure-based development of new drugs.

Keywords: EGFR; activation; binding; inhibitor; kinase.

Figure 1

HER/ErbB signaling (created by BioRender.com on 14 October 2021). Green and purple spheres indicate the EGFR-activating ligands.

Figure 2

Schematic diagrams of EGFR domains. (a) Domain structure of human EGFR and exons encoding it (created by BioRender.com on 14 October 2021), (b) EGFR phosphorylation sites [18]. Blue spheres indicate the molecules present outside the cell, and red spheres indicate the EGFR-activating ligand.

Figure 3

Three-dimensional visualization of EGFR extracellular domain in complex with EGF (yellow) (PDB ID: 1IVO). Subdomains are marked in colors: L1, blue; CR1, green; L2, orange; part of CR2, grey. The three sites interacting with EGF are marked in red circles.

Figure 4

Conformations of active and inactive EGFR classified by Zhao et al. (2019) [62]. The crystal structures 1M17 [42] and 3IKA [63] represent class-1 and class-2 of the active conformations, while 1XKK [64], 3GOP [30], 2RF9 [65], and 5HG5 [66] represent class-3, class-4, class-5, and class-6 of the inactive conformations, respectively.

Figure 5

ATP and allosteric binding site of EGFR TK domain. (a) Allosteric binding site is marked by blue spheres, while ATP-binding site is marked by red spheres. (b) The close visualization of the allosteric inhibitor EAI001 and AMP-PNP in the binding pocket. EAI001 binds to the allosteric site close to αC-helix. The visualizations are made using the crystal structure with PDB code 5D41 [100] by Chimera 1.15 (accessed on 13 August 2021).

Figure 6

Timeline in the development of EGFR TKIs during the last two decades. Green boxes above the line indicates the drugs approved by FDA, while the black boxes below the lines indicates the phase I clinical trial of the TKIs.

Figure 7

Chemical structure of EGFR TKI (first to fourth generations).