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Published in 2015

PubMedCentral: PMC4517520

Molecular docking study Molecular docking of designed compounds ( A-1 – B-10 ) into the three-dimensional X-ray structure of human wild-type EGFR and T790M/L858R EGFR with inactive conformatio... s (PDB code: 3W33 and 3W2R, respectively) was carried out using the Discovery Studio (version 3.5) as implemented through the graphical user interface DS-CDOCKER protocol.

For these 20 new molecules, we evaluated their performance by molecular docking study based on the wild-type EGFR protein (PDB code: 3W33) and the dual T790M/L858R mutant protein (PDB code: 3W2R).

( B ) The binding mode of A-10 in the active pocket of EGFR protein (PDB code: 3W2R, T790M/L858R) predicted by Glide docking standard precision (sp).

( C ) The binding mode of A-10 in the active pocket of EGFR protein (PDB code: 3W2R, T790M/L858R) predicted by Glide docking extra precision (xp).

As seen in Figure 5C , considering the values of 1–6 , which contained seven detailed fragments extracted from seven unique protein kinase crystal complexes (Table S1, 1-6-1 : 3W2O; 1-6-2 : 3W2P; 1-6-3 : 3W2R; 1-6-4 : 3W32; 1-6-5 : 3W33; 1-6-6 : 3POZ; 1-6-7 : 3RCD), we employed the fragments in the back pockets of 3W32 and 3W2R as the other part of new templates (A series and B series).

Table 2 General information about the mutations of the 42 HER family protein kinase domain PDB ID a TKI-sensitive TKI-resistant Protein conformation G719S LREA L858R T790M DFG-motif αC position (Å) b EGFR  4LQM − L––– + − DFG-in 7.690  4LRM − − − − DFG-in 8.028  4LL0 − − + + DFG-in 9.460  4LI5 − − − − DFG-in 8.266  4JQ7 − − − − DFG-in 8.843  4JQ8 − − − − DFG-in 8.071  4JR3 − − − DFG-in 7.903  4JRV − L––– − − DFG-in 7.929  3W32 − − − − DFG-out 12.717  3W33 − − − − DFG-out 12.846  3W2O − − + + DFG-in 8.065  3W2P − − + + DFG-in 8.109  3W2Q − − + + DFG-in 8.394  3W2R − − + + DFG-out 12.056  4I22 − LRKA + + DFG-out 12.384  4I23 − L––A − − DFG-in 7.750  4I24 − L––A − + DFG-out 12.399  4HJO − − − − DFG-out 12.327  4G5J − K––– − − DFG-in 7.807  4G5P − − − + DFG-in 8.786  3UG2 − –––– − + DFG-in 8.308  3POZ − LA–– − − DFG-out 12.430  3LZB − − − − DFG-out 11.673  3IKA − − − + DFG-in 9.314  2RGP − LR–K − − DFG-out 12.098  3BEL − − − − DFG-out 12.033  2JIU − − − + DFG-in 8.868  2JIV − − − + DFG-out-like 12.634  2ITO + − − − DFG-in 7.446  2ITP + − − − DFG-in 7.673  2ITT − − + − DFG-in 7.682  2ITY − − − − DFG-in 7.481  2ITZ − − + − DFG-in 7.717  2J6M − − − − DFG-in 7.647  2J5E − − − − DFG-in 7.394  2J5F − − − − DFG-in 7.642  1XKK − LREK − − DFG-out 11.967  1M17 − − − − DFG-in 8.037 HER2  3RCD − LR–– − − DFG-out 10.997 HER3  4OTW − IEDK L858V − DFG-out 13.635 HER4  2R4B − LN–– − − DFG-out 11.299  3BBT − LK–– − − DFG-out 12.537 Notes: a All the HER protein kinase crystal complexes collected from the PDB (up to 05/28/2014); b The distance between the αC carbon atoms of D xDFG.81 and E αC.24 .

Publication Year: 2015