Design and investigation of novel iridoid-based peptide conjugates for targeting EGFR and its mutants L858R and T790M/L858R/C797S: an in silico study.

Abstract

In this work, we designed novel peptide conjugates with plant-based iridoid and lichen-derived depside derivatives to target the wild-type EGFR (WT) and its mutants, L858R and T790M/L858R/C797S triple mutant. These mutations are often expressed in multiple cancers, particularly lung cancer. Specifically, the iridoids included 7-deoxyloganetic acid (7-DGA) and loganic acid (LG), while the depside derivative was sekikaic acid (SK). These compounds are known for their innate anticancer properties and were conjugated with two separate peptide sequences KLPGWSG (K) and YSIPKSS (Y). These sequences have been shown to target EGFR in previous phage display library screening, although the mechanism is unknown. Thus, we created the di-conjugates for dual targeting and investigated their interactions of the di-conjugates and that of the neat peptides with the kinase domain of EGFR (WT) and the two mutants using molecular docking, molecular dynamics (MD) simulations, and MM-GBSA analysis. Docking studies revealed that the (7-DGA)₂-K showed the highest binding affinity at - 9.3 kcal/mol with the L858R mutant, while (LG)₂-Y displayed the highest binding affinity at - 9.0 kcal/mol for the triple mutant receptor. Our results indicated that several of the conjugates interacted with crucial residues of the kinase domain, including ASP855 and THR854 (activation loop), MET793 and PRO794 (hinge region), ARG841 (catalytic loop), and LYS728 and LEU718 of the glycine-rich P-loop. Interestingly, strong hydrophobic interactions were also observed with the C-terminal tail residues, such as PHE997 and ALA1000 as well as with ARG999 for the YSIPKSS peptide and most of the conjugates. The hydroxyl group of the cyclopentane ring and the oxygen of the pyran ring of the (7-DGA)₂-peptide conjugates contributed to binding particularly in the hinge region, while the peptide components formed an extended structure that bound well into the C-lobe. The (SK)₂-Y di-conjugate and KLPGWSG peptide formed hydrogen bonds with the SER797 residue of the triple mutant. Overall, our results show that the (7-DGA)₂-K, di-conjugate, the (7-DGA)₂-Y di-conjugate, and the neat YSIPKSS demonstrated strong and stable binding with the L858R mutant and the highly resistant triple mutant EGFR, respectively. The novel designed conjugates demonstrate potential for further optimization for laboratory studies aimed at developing new therapeutics for targeting specific EGFR mutant expressing cells.