Structure-Based Design and Characterization of Cyclosenegalin Derivatives as Novel Breast Cancer Therapeutics

Triple-negative breast cancer (TNBC), which lacks ER, PR, and HER۲ expression, remains challenging to treat due to the absence of targeted therapeutic options and frequent chemoresistance. Cyclosenegalin A, a cyclic heptapeptide, offers a compact β-turn scaffold amenable to selective receptor engagement but displays only moderate native activity. In this study, computational modeling, chemical synthesis, and cell-based evaluation were integrated to develop cyclosenegalin-derived peptides as anticancer candidates. A ۲۹-member analog panel was sketched in ChemDraw, converted to ۳D in Chem۳D, and subjected to geometry and frequency optimization using Gaussian (DFT B۳LYP/۳-۲۱G) to afford electronically stable conformers. Molecular docking with AutoDock Vina against ERα (PDB: ۳ERT), PR (۲OVH), EGFR kinase (۲ITY), and the IκBα/NF-κB complex (۱NFI) identified two multi-target leads, A۱۴ and A۲۱, which exhibited consistently lower predicted binding free energies and extensive hydrogen-bond and hydrophobic contact networks at key pocket residues. Both peptides were synthesized via Fmoc-based solid-phase assembly, macrocyclized under dilute conditions, purified by RP-HPLC to >۹۵% purity, and structurally confirmed by ESI-MS (calcd/obs: A۱۴, ۷۵۷.۸۹ Da / [M+H]⁺ ۷۶۱–۷۶۲; A۲۱, ۷۶۲.۸۷ Da / [M+H]⁺ ۷۶۲). Antiproliferative activity evaluated using the MTT assay against luminal T-۴۷D and TNBC MDA-MB-۲۳۱ cells showed that A۲۱ was the most potent analog, with IC₅₀ values of ۳۸۷.۹۹ ± ۱۰.۲ µg/mL (T-۴۷D) and ۱۴۳.۱۵ ± ۶.۴ µg/mL (MDA-MB-۲۳۱), outperforming A۱۴ (۷۱۰.۲۸ ± ۱۲.۴ µg/mL and ۲۲۰.۰۵ ± ۸.۶ µg/mL, respectively). Both peptides demonstrated preferential cytotoxicity toward the TNBC subtype, with A۲۱ offering a favorable balance of potency and subtype selectivity. Collectively, these findings validate a docking-led design pipeline for cyclosenegalin-based cyclic peptides and identify A۲۱ as a tractable lead for further optimization, mechanistic studies focused on EGFR/NF-κB pathway modulation, and future in vivo investigations.

کلیدواژه ها:

Cyclosenegalin A ، Solid-phase peptide synthesis ، Molecular docking ، MTT assay ، Antiproliferative activity