Molecular Insights into the Binding Specificity of Branched-Chain Amino Acids to Sestrin2: An Integrated Computational Study Using Molecular Docking, MD Simulations, and MMGBSA Analysis

Sestrin2 (SESN2) is a highly conserved stress-inducible protein that serves as a central hub for integrating cellular responses to nutrient availability, oxidative stress, and endoplasmic reticulum (ER) stress. A key function of SESN2 is its role as a direct sensor for the branched-chain amino acid (BCAA) leucine, which modulates the activity of the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of cell growth and metabolism. While the functional link between leucine and SESN2 is well-established, the precise molecular determinants that confer its high specificity for leucine over other BCAAs, such as isoleucine and valine, remain poorly understood. This study employs an integrated, multi-scale computational approach, combining molecular docking, extensive all-atom molecular dynamics (MD) simulations, and binding free energy calculations, to elucidate the structural and dynamic basis of BCAA-SESN2 recognition. Our thermodynamic analysis reveals a distinct binding affinity hierarchy (Leucine > Isoleucine > Valine), which is primarily driven by superior van der Waals interactions and shape complementarity of leucine's isobutyl side chain within the protein's hydrophobic pocket. Structural and dynamic analyses demonstrate that leucine binding induces a profound allosteric stabilization, causing a global compaction of the protein and establishing a network of long-range correlated motions. This "conformational locking" mechanism funnels the intrinsically flexible apo-protein into a singular, stable, low-energy state. These findings provide a comprehensive, atom-to-global scale model explaining SESN2's function as a specific leucine sensor. Furthermore, by contextualizing these results within the broader landscape of SESN2's mTORC1-independent functions and recent clinical trial outcomes for SESN2 modulators, this work offers a critical framework for understanding its complex role in metabolic diseases, cancer, and neurodegeneration, and provides a rationale for the design of next-generation allosteric therapeutics.