Free Energy Calculations of Sparsomycin Analogs Binding to the Ribosome with Molecular Dynamics Simulations

Abstract

The accurate calculation of absolute binding free energy is one of the holy grails of computer-aided drug design. The emerging successes reported in computing the binding free energy of small ligands to proteins using molecular dynamics (MD) simulations indicated that such physics-based approaches hold the promise of expediting the rational drug discovery process. Among numerous receptor-ligand systems, ribosome-antibiotic binding provides an important paradigm for studying the molecular recognition of RNAs by small molecules. The interactions of the 50S bacteria ribosomal subunit with antibiotic sparsomycin and its derivatives have been studied through the calculation of the binding free energy and the characterization of conformational dynamics. The standard binding free energies of the complexes were calculated using free energy perturbation (FEP) method. Restraining potentials affecting the orientational, translational and conformational freedom of the ligand and receptor were applied and then removed during the simulations to enhance the sampling and the convergence. The loss of ligand conformational entropy upon binding was estimated with Umbrella Sampling method by calculating the Potential of Mean Force as a function of the RMSD relative to the reference conformation of the ligand. Due to the large size of the ribosome, the Generalized Solvent Boundary Potential method was used to reduce the computational cost of MD/FEP calculations. For a deeply buried binding pocket in the ribosome, the fluctuation of solvent occupancy during the alchemical free energy calculation was also characterized by combining the MD with Grand Canonical Monte Carlo simulation. This computational study further revealed the mechanism of ribosome-antibiotics interactions and shed light on the design of ribosomal drugs. With the above stated developments, the evaluation of the binding free energies has become computationally more appealing for large systems.