In Silico Studies of Tumor Targeted Peptide-Conjugated Natural Products for Targeting Over-Expressed Receptors in Breast Cancer Cells Using Molecular Docking, Molecular Dynamics and MMGBSA Calculations

In this work, in silico studies were carried out for the design of diterpene and polyphenol-peptide conjugates to potentially target over-expressed breast tumor cell receptors. Four point mutations were induced into the known tumor-targeting peptide sequence YHWYGYTPQN at positions 1, 2, 8 and 10, resulting in four mutated peptides. Each peptide was separately conjugated with either chlorogenate, carnosate, gallate, or rosmarinate given their known anti-tumor activities, creating dual targeting compounds. Molecular docking studies were conducted with the epidermal growth factor receptor (EGFR), to which the original peptide sequence is known to bind, as well as the estrogen receptor (ER alpha) and peroxisome proliferator-activated receptor (PPAR alpha) using both Autodock Vina and FireDock. Based on docking results, peptide conjugates and peptides were selected and subjected to molecular dynamics simulations. MMGBSA calculations were used to further probe the binding energies. ADME studies revealed that the compounds were not CYP substrates, though most were Pgp substrates. Additionally, most of the peptides and conjugates showed MDCK permeability. Our results indicated that several of the peptide conjugates enhanced binding interactions with the receptors and resulted in stable receptor-ligand complexes; Furthermore, they may successfully target ER alpha and PPAR alpha in addition to EGFR and may be further explored for synthesis and biological studies for therapeutic applications.

Automated summary

In this study, in silico studies were conducted to design diterpene and polyphenol-peptide conjugates that can potentially target over-expressed breast tumor cell receptors. The mutated peptides were created by inducing point mutations into a known tumor-targeting peptide sequence. Molecular docking studies and molecular dynamics simulations were performed to study the binding interactions and stability of the peptide conjugates with the receptors. The results showed enhanced binding interactions and stable receptor-ligand complexes, suggesting the potential therapeutic applications of these conjugates.