Targeting the RARα-Gankyrin-PI3K axis with retinoid analogs to modulate autophagy in breast cancer cells: Computational insights and experimental validation

Pijush Kanti Khanra; Thirukumaran Kandasamy; Siddhartha Sankar Ghosh

doi:10.1016/j.compbiolchem.2025.108575

Targeting the RARα-Gankyrin-PI3K axis with retinoid analogs to modulate autophagy in breast cancer cells: Computational insights and experimental validation

Comput Biol Chem. 2025 Jun 26:119:108575. doi: 10.1016/j.compbiolchem.2025.108575. Online ahead of print.

Authors

Pijush Kanti Khanra¹, Thirukumaran Kandasamy¹, Siddhartha Sankar Ghosh²

Affiliations

¹ Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 39, Guwahati, Assam, India.
² Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 39, Guwahati, Assam, India; Centre for Nanotechnology, Indian Institute of Technology Guwahati, 39, Guwahati, Assam, India. Electronic address: sghosh@iitg.ac.in.

PMID: 40582253
DOI: 10.1016/j.compbiolchem.2025.108575

Abstract

This study explores the therapeutic potential of Retinoid analogs to overcome this resistance by modulating autophagy and lysosomal activity in breast cancer. Comprehensive bioinformatics analyses such as gene correlation, mutation, co-expression, and functional network analysis revealed a strong correlation between RARα, NRF2, Gankyrin, p110α, and p110β, alongside the PI3K/Akt/mTOR axis in regulating autophagy. Given its upstream role, RARα was identified as the primary target, with NRF2, Gankyrin, p110α, and p110β serving as co-target macromolecules to influence downstream autophagy pathways. Molecular docking analyses identified six RAR agonists-CD437, BMS961, CD437-¹³C₆, Adapalene, Adapalene-d₃, and CD1530-as promising candidates, all exhibiting high-profile binding affinities with all 5 target proteins RARα (< -10 kcal/mol), NRF2 (< -7.6 kcal/mol), Gankyrin (< -7.4 kcal/mol), p110α (< -8.9 kcal/mol), and p110β (< -8.6 kcal/mol). Among all, Adapalene (a synthetic Retinoid analog) was selected as a potent multi-target drug based on average docking score. Further, molecular dynamics simulation studies demonstrated enhanced protein stability with notable binding free energies of -82.712 kJ/mol (Gankyrin) and -25.526 kJ/mol (p110α). Subsequent in vitro validation using MCF7 and MDA-MB-468 breast cancer cell lines corroborated the computational findings. Adapalene markedly inhibited autophagy by downregulating the proteomic conversion of the core autophagy marker LC3B-I/LC3B-II, with reductions of up to 2.99-fold in MCF7 and 1.11-fold in MDA-MB-468 cell lines. In addition, it suppressed lysosomal activity by 2.73-fold in MCF7 and 2.52-fold in MDA-MB-468, as demonstrated by lysotracker assays. These findings underscore the potential of Adapalene as a multi-targeted modulator of RARα-PI3K signaling, effectively disrupting autophagy and cancer cell survival mechanisms in luminal and triple-negative breast cancer cells.

Keywords: Adapalene; Autophagy regulation; Cancer cell survival; Lysosomal activity; MD Simulation; RAR agonists.