Roles of Water Molecules in STING Activation: A Computational Perspective

The cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway is crucial in the innate immune response, particularly in cancer immunotherapy. Despite promising preclinical results, 5,6-dimethylxanthenone-4-acetic acid (DMXAA) showed limited efficacy in human clinical trials due to species-specific differences in STING activation. This study investigates these differences by analyzing the binding dynamics and affinities of various STING-ligand complexes using molecular dynamics (MD) simulations and binding free energy calculations. We confirmed that specific point mutations, notably G230I and S162A/Q266I, significantly improve DMXAA’s binding affinity to human STING (hSTING), replicating the behavior observed in mouse STING (mSTING). Explicit solvent MD simulations revealed the essential role of water molecules in the binding site. Bridge water molecules, forming hydrogen bonds between the ligand and the protein, were significant in stabilizing the cyclic GMP-AMP (cGAMP) system, influencing local dielectric constants. Additionally, for DMXAA systems, we found that the mutations lowered the interaction energies required for ligand binding by reducing the number of water molecules and localizing them to specific locations within the binding site. These findings deepen our understanding of STING-DMXAA interactions and highlight potential pharmacological modifications required to enhance STING-targeted therapies. Integrating structural biology, computational simulations, and thermodynamic analyses offers a robust framework for advancing STING-based therapeutic development.