Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

Abstract

Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such compounds. We present an enhanced sampling-one step perturbation method (ES-OS) to tackle this problem in a highly efficient way. A single molecular dynamics simulation of a judiciously chosen reference state (using two sets of soft-core interactions) is sufficient to determine conformational distributions of chemically similar compounds and the free energy differences between them. The ES-OS method is applied to a set of five biologically relevant 8-substituted GTP analogs having high energy barriers between the anti and the syn conformations of the base with respect to the ribose part. The reliability of ES-OS is verified by comparing the results to Hamiltonian replica exchange simulations of GTP and 8-Br-GTP and the experimentally determined 3J(C4,H1') coupling constant for GMP in water. Additional simulations in vacuum and octanol allow us to calculate differences in the solvation free energies and in lipophilicities (log P). Free energy contributions from individual conformational regions are also calculated, and their relationship with the overall free energy is derived leading to a set of multiconformational free energy formulas. These relationships are of general applicability and can be used in free energy calculations for a more diverse set of compounds.