Coarse Master Equation-Based Analysis of N-Methylation and Temperature Effects on the Dynamics of Cyclic Peptides

Cyclosporin A (CsA) is a cyclic peptide widely used as an important immunosuppressant drug to prevent organ rejection following transplants. It is eleven residues in length, cyclized head-to-tail and is multiply N-methylated and largely hydrophobic, which makes it an excellent template for drug design. This study elucidates the important effects of N-methylation and temperature on the conformational dynamics, and specifically in altering the intramolecular hydrogen bond geometries of N-methylated cyclic peptides, such as CsA. We have run several normal and high-temperature molecular dynamics (MD) simulations of CsA and of a de-methylated variant (dCsA) whereby all backbone N-methyl groups have been removed. We have found that the numerous N-methyl sites introduce a large degree of conformational specificity to CsA by modulating the formation of intramolecular hydrogen bonds. Geometric measures such as cross-sectional distances, solvent accessible surface area (SASA), and intramolecular hydrogen bonding are used to explore and compare the conformational ensemble of CsA and dCsA. We use data-driven methods to cluster the conformational states, providing an increasingly automatic method of state identification. Representative structures are analyzed further using a coarse master equation-based kinetic analysis method. This formalism can be used for a systematic comparison of the conformational dynamics of cyclic peptides in MD simulations in explicit water, under various conditions, quantifying the mechanisms and effects of N-methylation and the T-dependence.