Intraligand Hydrophobic Interactions Rationalize Drug Affinities for Peptidyl−Prolyl Cis−Trans Isomerase Protein

• Published in: The journal of physical chemistry. B Vol. 115; no. 19; pp. 6193 - 6201
• Main Authors: Bizzarri, Marco, Marsili, Simone, Procacci, Piero
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 19.05.2011
• Subjects: B: Biophysical Chemistry; Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Molecular Dynamics Simulation; Protein Binding; Tacrolimus - analogs & derivatives; Tacrolimus - chemistry; Tacrolimus Binding Protein 1A - chemistry; Tacrolimus Binding Protein 1A - metabolism
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp110585p

The conformational landscape of three FK506-related drugs with disparate inhibition constants is determined in bulk solution using a replica exchange simulation method with solute torsional tempering. Energetic fitness of important drug conformations with respect to the FKBP12 protein is evaluated by molecular mechanics. Results show that the experimental affinity toward peptidyl−prolyl cis−trans isomerase protein (FKBP12) of the analyzed ligands appears to be positively correlated to the observed population of specific chair structures of the drug piperidinic ring in bulk solution. This observation is rationalized on the basis that such structures, stabilized by stereospecific intramolecular hydrophobic interactions, allows the formation of a pair of protein−ligand hydrogen bonds upon binding.