HOMOLOGY MODELING, DOCKING, VIRTUAL SCREENING AND MOLECULAR DINAMIC STUDY OF EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR) WITH RESISTANCE MUTATIONS OF L858R/T790M/L718Q TO ALLOSTERIC INHIBITOR ACTIVITY

• Main Author: Syah Fitra Ramadhan, Dwi
• Format: Theses
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/36941
• Institution: Institut Teknologi Bandung

The third generation of TKIs-EGFR (Tirosin Kinese Inhibitors-Epidermal Growth Factor Receptor) underwent 2 resistance mutations that are C797S and L718Q. EGFR-C797S has been overcome with allosteric inhibitor i.e. EAI001. However, its activity on the EGFR-L718Q mutation is still unknown. The aim of present study was to determine the activity of allosteric inhibitor against resistance mutations L858R/T790M/L718Q, and to screen compounds that have better activity against EGFR resistance mutations. Three types of mutant protein were constructed using expasy SWISS-MODEL server, namely mutant A (L858R/T790M/L718Q) as a target, and mutant B (L858R/T790M) and mutant C (T790M/L718Q) as controls. EGFR with PDB-ID of 5D41 was used as the template to build the mutant structure. The proteins were then evaluated, refined, and minimized. The EAI001 ligand as native ligand was docked against protein template and mutant proteins. Data set of compounds from NCI Open Chemical Repository integrated in http://pharmit.csb.pitt.edu/ were screened based on pharmacophore and molecular docking. Molecular Dynamics is done using GROMACS software for 50 ns (nano second) Simulation. The complexes of molecular dynamics simulation results are analyzed based on the RMSD, RMSF, and occupancy values of hydrogen bonds formed. Three mutant proteins were successfully constructed. Docking of EAI001 ligand into protein template showed its binding energy of –11.33 kJ/mol, while its binding energy to mutant A, mutant B, and mutant C, are –5.84, –8.14, –4.99 kJ/mol, respectively. Virtual screening using the model_4 with Aro- Hyd-Acc&ML-Don-Acc&ML2-Acc&ML3 features and drug-like criteria, to 144,104 compounds resulted in 1,628 hits. The compounds were then screened by docking protocol into the template protein, and 14 compounds showed have better activity than EAI001 ligand. When those compounds were docked into mutant A protein, compound NSC3 showed highest activity. Four complexes were simulated for 50 ns and analyzed. NSC3 compounds showed good stability based on the RMSD value, RMSF, and hydrogen bond occupancy compared to natural ligands, both in the protein template and in Mutan_A. Thus, the results showed that EGFR allosteric inhibitor EAI001 has poor activity to the resistance mutations with L718Q mutant, and NSC3 has shown a potential chance as new inhibitor candidate to inhibit both T790M and L718Q resistance mutations, via the allosteric site of EGFR.