PI by NMR: Probing CH-π Interactions in Protein-Ligand Complexes by NMR Spectroscopy

Abstract

While CH-π interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH-π interactions in drug-protein complexes. Herein, we present a fast and reliable methodology called PI (π interactions) by NMR, which can differentiate the strength of protein-ligand CH-π interactions in solution. By combining selective amino-acid side-chain labeling with ¹ H-¹³ C NMR, we are able to identify specific protein protons of side-chains engaged in CH-π interactions with aromatic ring systems of a ligand, based solely on ¹ H chemical-shift values of the interacting protein aromatic ring protons. The information encoded in the chemical shifts induced by such interactions serves as a proxy for the strength of each individual CH-π interaction. PI by NMR changes the paradigm by which chemists can optimize the potency of drug candidates: direct determination of individual π interactions rather than averaged measures of all interactions.

Keywords: CH-π interactions; NMR spectroscopy; medicinal chemistry; protein-ligand interactions; structure-based drug design.