Abstract 3708: Targeting the ATG101 And ULK1 complex in pancreatic ductal adenocarcinoma: computational approach

Abstract Introduction: Pancreatic Ductal Adenocarcinoma (PDAC) is an aggressive malignancy with poor prognosis (five-year survival rate around 13%). PDAC progression mainly depends on autophagy signaling for cell homeostasis. The current study holds significant importance in this context as it aims to identify the interaction between ULK2 and ATG101 and evaluate hydroxychloroquine's effect on the ULK2 and ATG101 complex. Methods: The proteins ULK2 (Q9QY01, MOUSE) and ATG101 (Q9D8Z6, MOUSE) were retrieved from the UniProtKB database. The domain region of the protein structures was carefully trimmed using BIOVIA Discovery Studio 4.5 Visualizer, and the interacting residues were identified with precision using HawkDock. The ULK2-ATG101 complex was then imported into DimPlot to recognize and display the presence of intermolecular hydrogen bonds. To validate the complex structure, we employed the Desmond Program, Molecular Dynamic (MD) Simulations, Principal Component Analysis (PCA), Root Mean Square Deviation (RMSD), and Root Mean Square Fluctuation (RMSF). To confirm the functional activity of the interaction, we conducted an in vitro pulldown assay. All samples were lysed with RIPA buffer, and the lysate (500 µg) was added to 30 µL of agarose beads and anti-ULK2. The samples were resolved on the SDS page and transferred to the PVDF membrane. The membrane was probed with ATG101, and the intensity of protein bands was quantified using the Image J program. Unpaired t-tests were conducted to acknowledge the difference between treated and untreated samples. Results: The formation of hydrogen bonds between these complexes are Arg19 vs. Glu146 and Glu150; Gln67 vs. Ser160; Arg4 vs. Thr63. Among the top 10 scoring ATG101-ULK2 PPI complex models, the highest binding energy was found at -48.13 kcal/mol. The RSMD graph displayed a stable trajectory, following 80 ns of simulation time using RMSD values ∼3.1A to ∼3.7A, depicting stabilization during 100 ns for the PPI complex. The pulldown assay results indicated hydroxychloroquine reduced the interaction between the ATG101 and ULK2, suggesting a potential impact on PDAC treatment. Discussion/Conclusion: Results suggested that the interaction of ATG101-ULK1 was strong, and hydroxychloroquine reduced this interaction. Site-directed mutagenesis is essential to understanding the molecular interaction (ATG101-ULK2) and the role of residues in PDAC. Citation Format: Raasil R. Basha, Vaishnavi Kuppala, Ganji Purnachandra Nagaraju. Targeting the ATG101 And ULK1 complex in pancreatic ductal adenocarcinoma: computational approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3708.