| Summary: | Membrane permeability of cyclic peptides is an important factor in drug design. To investigate the membrane permeability of cyclic peptides using molecular dynamics (MD) simulations, the accurate force fields for unnatural amino acids present in the cyclic peptides are required. Therefore, we developed the CHARMM force fields of the unnatural amino acids present in cyclosporin A (CsA), a cyclic peptide used as an immune suppressor. Especially for N-methyl amino acids, which contribute to the membrane permeability of cyclic peptides, we developed a grid correction map (CMAP) of the energy surface using the φ and ψ dihedral angles in the main chain of CsA. To validate the developed force field, we performed MD simulations, including the generalized replica exchange with solute tempering method, of CsA in water and chloroform solvents. The conformations of CsA in water and chloroform sampled using the developed force field were consistent with those of the experimental results of the solution nuclear magnetic resonance spectroscopy.
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