Navigating into the binding pockets of the HER family protein kinases: discovery of novel EGFR inhibitor as antitumor agent

Abstract

The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase–ligand interaction space in the PDB.

Pockets as structural descriptors of EGFR kinase conformations

“…This comparison was performed using a hierarchical clustering based on the root mean square deviation (RMSD) of α-carbons belonging to positions of this main pocket. Even though there are several works considering pockets related to the kinase active site, quantitative structural-derived comparisons are presented here for the first time [ 49 ]. Interestingly, our findings indicate that 53 main pocket-belonging positions hold structural conformer-specific information when compared with non-pocket positions.…”

Surmounting the resistance against EGFR inhibitors through the development of thieno[2,3-d]pyrimidine-based dual EGFR/HER2 inhibitors

“…This highlights the need to further optimize the solubilizing group balancing its hydrophilicity and the overall polarity of the compoundin order to attain optimum cellular activities. While compounds 20 and 21 showed comparable cytotoxic activities, compound 21 was selected for optimization through the second screening cycle since its aniline headgroup (3-chloro-4-(3-(trifluoromethyl)phenoxy)aniline) was previously identified through a fragment-based drug design approach as being effective against EGFR-T790M [47]. Figures S2, S3) 3.3.…”

How to train your inhibitor: Design strategies to overcome resistance to Epidermal Growth Factor Receptor inhibitors

“…The detailed structural analysis of the available crystal structures of the EGFR family, followed by a fragment-based design and an extensive docking study identified the hydrophobic group 3-chloro-4-(3-(trifluoromethyl)phenoxy)aniline as a good fit for the activity against T790M EGFR and also against HER2. [34] Compound (3) is a 6-salicyl-4-anilinoquinazoline derivative that was developed as a dual EGFR/HER2 inhibitor with IC 50 values of 0.12 M and 0.096 M, respectively. It showed 100-fold selectivity in a panel of 9 closely similar kinases.…”

“…Like Dacomitinib (32), it inhibits the T790M EGFR due to its ability to covalently modify the enzyme (Figure 25) [79]. The outstanding performance of Afatinib (34) led it to be the first irreversible EGFR inhibitor approved by the FDA in 2013 for the treatment of metastatic NSCLC with activating EGFR mutations [83].…”

“…Canertinib 35is another irreversible dual EGFR/HER2 inhibitor that is also active against mutant EGFR forms with activity comparable to Afatinib (34) [78]. Canertinib (35) has its basic tertiary amine group attached to the 7 position instead of being attached to the acrylamide group like in Afatinib (34). The basic amine attached to the acrylamide is known to act as an intramolecular catalyst for the Michael addition reaction.…”