Abstract View

Objectives:

This study investigates the structural stability and binding behavior of Compound 3c as the ligand component of the ATX-101 radioligand therapy platform in complex with the protein target 5O5T using molecular dynamics (MD) simulations. The objective is to evaluate dynamic stability, conformational flexibility, and intermolecular interactions under physiological conditions to support structure-guided optimization of radioligand design.

Methods:

A 100 ns all-atom molecular dynamics simulation of the 5O5T–Compound 3c complex was performed using GROMACS (v2025.3) with the CHARMM36m force field and CGenFF ligand parameters. The system was solvated using the TIP4P-Ew water model, neutralized, and maintained at 300 K and 1 bar using a Nosé–Hoover thermostat and Parrinello–Rahman barostat. Trajectory analyses included root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bonding. Triplicate simulations were performed to ensure reproducibility.

Results:

The protein backbone RMSD stabilized within 0.22–0.30 nm after an initial equilibration phase (~10–15 ns), indicating attainment of a stable conformational state. Ligand RMSD remained within 0.30–0.35 nm, reflecting controlled repositioning within the binding pocket without dissociation. RMSF analysis showed limited residue flexibility (0.08–0.15 nm for most residues), with localized fluctuations up to 0.25 nm in loop and terminal regions. The radius of gyration remained stable between 2.44 and 2.46 nm, confirming sustained global compactness of the protein structure. SASA values fluctuated narrowly between 95 and 120 nm², indicating preserved tertiary structure and stable hydration behavior. Persistent hydrogen bonding and hydrophobic interactions were observed throughout the simulation, supporting stable ligand engagement within the binding pocket.

Conclusions:

The 5O5T–Compound 3c complex, representing the ligand component of the ATX-101 radioligand therapy platform, demonstrates strong structural stability and consistent binding behavior over 100 ns molecular dynamics simulations. The combined RMSD, RMSF, Rg, and SASA profiles indicate a robust and stable ligand–protein interaction network. These findings support Compound 3c as a structurally stable radioligand scaffold and provide quantitative computational evidence to guide further optimization of ATX-101 and future experimental validation.

Acknowledgments:

The authors acknowledge computational resources and support from the Ayutara research team

References:

1. Molecular dynamics simulation methodologies (GROMACS)
2. CHARMM36m force field literature
3. Radioligand therapy computational modeling studies