What question did this study set out to answer?

This research aims to understand how Excavatolide B interacts with the human STING receptor to inform therapeutic strategies for inflammation-related cancers.

March 1, 2026Open Access

Computational Analysis of Excavatolide B–Human STING Interactions Implicates a Cys148–Adjacent Corridor with Within-Cavity Sub-Pose Diversity

Key Points

This research aims to understand how Excavatolide B interacts with the human STING receptor to inform therapeutic strategies for inflammation-related cancers.
Utilized AlphaFold3 for receptor modeling of human STING.
Performed diffusion-based docking to explore ligand-receptor interactions.
Conducted explicit-solvent molecular dynamics simulations on multiple replicas.
Assessed geometric consistency of critical pocket-residue interactions.
Evaluated competitive docking of cGAMP in conditioned receptor snapshots.
Excavatolide B engages the STING receptor through non-covalent mechanisms.
The analysis revealed a corridor near Cys148 with diverse binding poses.
Competitive docking showed less favorable interactions of cGAMP in ExcB-conditioned states.
Structural insights provide a basis for targeted mutagenesis and further SAR studies.

Abstract

Chronic, dysregulated inflammation contributes to colitis-associated colorectal cancer (CRC), and the cGAS–STING pathway represents a central but therapeutically challenging node because both insufficient and excessive STING activity can be pathogenic. Here, we integrate AlphaFold3 (AF3) receptor modeling, diffusion-based docking, and explicit-solvent molecular dynamics (MD) simulations to characterize how the marine briarane diterpenoid excavatolide B (ExcB) engages the human STING (hSTING) cyclic dinucleotide (CDN)-binding cleft. The structural integrity of the AF3 hSTING model was validated through both intrinsic confidence scores (pLDDT, PAE) and comparative benchmarking against experimental CTD structures (PDB: 4EF5, 6A05). Notably, the local geometries of key pocket-defining residues—including His157, Tyr167, and Thr263—remained consistent with established crystallographic data. Across three independent 100 ns MD replicas, ExcB exhibits a consistent spatial progression from an entrance-proximal pose at the solvent-accessible rim of the cleft (Site-2) to a more embedded, non-canonical corridor on the Cys148-adjacent side (Site-2′). Distance and contact analyses support a predominantly non-covalent within-cleft mechanism and do not indicate a persistent approach to the literature-reported covalent regime near Cys91. Residue-level profiling over the stabilized sampling window defines a reproducible corridor “contact signature” and reveals within-cavity sub-pose diversity rather than a single rigid bound pose. Mechanistically, competitive docking of the native agonist cGAMP to ExcB-conditioned receptor snapshots yields consistently less favorable docking outcomes in ExcB-conditioned conformations than docking to the native/open receptor; retaining ExcB coordinates does not further penalize cGAMP, supporting a receptor-reshaping (conformational conditioning) component rather than persistent static steric clash. Our findings characterize ExcB as a non-covalent modulator targeting a cryptic pocket within the STING CDN-binding cleft, establishing a structural basis for targeted mutagenesis and structure-activity relationship (SAR) studies.

Computational Analysis of Excavatolide B–Human STING Interactions Implicates a Cys148–Adjacent Corridor with Within-Cavity Sub-Pose Diversity

Key Points

Abstract

Cite This Study