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 1H‐13C 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 1H 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.

Inverse PI by NMR: Analysis of Ligand 1H-Chemical Shifts in the Protein-Bound State

“…We have previously confirmed experimental vs calculated CSPs based on the crystal structure coordinates using the classical Pople formalism for CH protein -π ligand interactions. 11 In the case of the six NSD3 CH ligand -π protein interaction CSPs observed, there is agreement between calculated and experimental results for CH donor positions 3, 11 and 12, while positions 2, 6 and 10 have an additional upfield chemical shift of around -1 ppm beyond what would be expected from aromatic ringcurrent anisotropy effects only. A similar behavior, although not explicitly discussed, is evident for the binding of GPI-1046 to the peptidyl-prolyl cis-trans isomerase FKBP12.…”

“…10 We previously presented the PI by NMR methodology which can quantify the strength of CH-π interactions in protein-ligand complexes. 11 The approach relies on the pronounced shielding effect exerted by aromatic ring-systems on interacting protons.…”

Noncovalent CH–π and π–π Interactions in Phosphoramidite Palladium(II) Complexes with Strong Conformational Preference

“…Among such interactions, those involving aromatic rings (notably π–π and CH–π) have been studied in great detail using physical organic chemistry approaches, including molecular balances, thermodynamic double‐mutant cycles, evaluation of solvent effects, and computational methods [9–14] . Recently, such interactions were also analyzed in protein–ligand complexes by NMR [15] . However, the systematic application of these concepts in transition metal catalysis is still rare, [16, 17] and a suitable, realistic model that can aid in assessment and quantification of the interactions is sought.…”

A Volumetric Analysis of the 1H NMR Chemical Shielding in Supramolecular Systems

“…The 1 H CS isosurfaces may have practical implications for studies of host–guest systems, in particular, if the structural information is inferred from changes in measured 1 H chemical shift data. The most recent examples involve details of the molecular recognition by C–H…π interactions [ 36 ], and of binding modes inside relatively small (of “yoctoliter” volume) capsules [ 37 ]. In such investigations, a possibility should be considered that fairly different position(s) of the ligand might be compatible with an experimental value of the complexation shift.…”

“…. π interactions [36], and of binding modes inside relatively small (of "yoctoliter" volume) capsules [37]. In such investigations, a possibility should be considered that fairly different position(s) of the ligand might be compatible with an experimental value of the complexation shift.…”