Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis

• DOI: 10.1021/acs.joc.8b02811
• Publication Date: 2019-01-03T19:48:08Z
• Authors: Kathleen A. Farley; Ye Che; Armando Navarro-V...; Chris Limberakis; Dennis Anderson; Jiangli Yan; Michael Shapiro; Veerabahu Shanmug...; Roberto R. Gil
• Keywords: Protein Conformation; Hydrogen Bonding; Molecular Dynamics Simulation; Peptides, Cyclic; 01 natural sciences; Density Functional Theory; 0104 chemical sciences

Cyclic peptides have long tantalized drug designers with their potential ability to combine the best attributes of antibodies and small molecules. An ideal cyclic peptide drug candidate would be able to recognize a protein surface like an antibody while achieving the oral bioavailability of a small molecule. It has been hypothesized that such cyclic peptides balance permeability and solubility using their solvent-dependent conformational flexibility. Herein we report a conformational deconvolution NMR methodology that combines residual dipolar couplings, J-couplings, and intramolecular hydrogen bond analysis along with conformational analysis using molecular dynamics simulations and density functional theory calculations for studying cyclic peptide conformations in both low-dielectric solvent (chloroform) and high-dielectric solvent (DMSO) to experimentally study the solvent-dependent conformational change hypothesis. Taken together, the combined experimental and computational approaches can illuminate conformational ensembles of cyclic peptides in solution and help identify design opportunities for better permeability.