VALIDATION OF A MOLECULAR DOCKING WORKFLOW AS A FIRST STEP FOR RTB INHIBITOR DISCOVERY

Ricin, a toxin found in the seeds of Ricinus communis (castor bean), is a type II ribosome-inactivating protein. Due to its high toxicity, availability, ease of production, and lack of antidotes, ricin poses a threat as a bioterrorism agent and source of accidental exposure, particularly among workers handling castor bean seeds. Ricin consists of two chains linked by a disulfide bridge: the catalytic A chain (RTA) and the lectin B chain (RTB), which exhibit N-glycosidase and carbohydrate-binding activities, respectively. While RTA inhibits protein synthesis, RTB mediates cellular uptake through carbohydrate recognition, making it a therapeutic target. Considering the time and cost limitations of conventional drug discovery, molecular modeling provides a strategy for identifying RTB inhibitors. This study aimed to validate a molecular docking protocol through redocking of the crystallographic ligand into the RTB lectin subunit, ensuring that the parameters can be applied in subsequent computational analyses. Validation is essential because accurate reproduction of the ligand’s experimental orientation and conformation increases confidence in predicting receptor-ligand interactions. An RMSD value below 2 Å and conservation of key intermolecular interactions, especially hydrogen bonds, were adopted as validation criteria. Therefore, the 3D structure of RTB complexed with beta-D-galactopyranose-(1-4)-beta-D-glucopyranose was retrieved from the Protein Data Bank (PDB ID: 2AAI). The receptor and ligand were prepared separately using AutoDockTools v.1.5.7. Docking was performed with AutoDock Vina v.1.1.2 using a 30 Å grid centered at x = −2.686, y = 34.065, z = 54.353, exhaustiveness 32, and 30 output poses. RMSD values were calculated using OpenBabel v.2.4.1, while intermolecular interactions were analyzed with Discovery Studio Visualizer v.2025. The best docking pose showed an RMSD of 0.94 Å and a binding score of −4.597 kcal/mol, preserving the main hydrogen bonds with Asp234, Arg236, Ala237, His251 and Asn255 observed in the crystal structure. These results validate the protocol and support its application in subsequent virtual screening, pharmacokinetic and toxicological prediction, molecular dynamics simulations, and MM-GBSA binding free energy calculations.
This study was financed in part by the Coordination for the Improvement of Higher Education Personnel – Brazil (CAPES) – Finance Code 001 and by the Army Biology Institute (IBEx).