Using Theory to Reconcile Experiment: The Structural and Thermodynamic Basis of Ligand Recognition by Phenylethanolamine N-Methyltransferase (PNMT)

摘要

A fundamental challenge in computational drug design is the availability of reliable and validated experimental binding andstructural data against which theoretical calculations can be compared. In this work a combination of molecular dynamics (MD)simulations and free energy calculations has been used to analyze the structural and thermodynamic basis of ligandrecognition by phenylethanolamine N-methyltransferase (PNMT) in an attempt to resolve uncertainties in the available bindingand structural data. PNMT catalyzes the conversion of norepinephrine into epinephrine (adrenaline), and inhibitors of PNMTare of potential therapeutic importance in Alzheimer's and Parkinson's disease. Excellent agreement between the calculatedand recently revised relative binding free energies to human PNMT was obtained with the average deviation between thecalculated and the experimentally determined values being only 0.8 kJ/mol. In this case, the variation in the experimentaldata over time is much greater than the uncertainties in the theoretical estimates. The calculations have also enabled therefinement of structure-activity relationships in this system, to understand the basis of enantiomeric selectivity ofsubstitution at position three of tetrahydroisoquinoline and to identify the role of specific structural waters. Finally, thecalculations suggest that the preferred binding mode of trans-(1S,2S)-2-amino-1-tetralol is similar to that of its epimercis-(1R,2S)-2-amino-1-tetralol and that the ligand does not adopt the novel binding mode proposed in the pdb entry 2ANS. Thework demonstrates how MD simulations and free energy calculations can be used to resolve uncertainties in experimentalbinding affinities, binding modes, and other aspects related to X-ray refinement and computational drug design.