Peptide-Based Drug Design

NMR of Peptides 99
Fig. 7. Schematic representation of chemical shift changes. The scheme in the box
represents the binding event observed. The unfilled shape represents a labeled substance,
and three of its residues are in contact with a binding partner (grey). The solid line circles
represent cross peaks in a HSQC spectrum of the unbound labeled compound. The F2
domain displays the 1 H chemical shift, the F1 domain either 13 Cor 15 N chemical shift.
The chemical shifts of the three positions in contact with the binding partner change
upon binding, as indicated by the arrows and the new cross peaks shown in dotted
lines.
4.3. Chemical Shift–Based Methods
A change from the free state to the bound state results in changes in
the chemical environment of nuclei involved in binding interfaces, causing
changes of their respective chemical shifts. This effect is commonly used to
detect binding of molecules to their receptors, and 1H/ 15Nor 1H/ 13CHSQC experiments are particularly useful for these studies. A schematic representation
of the changes in an HSQC spectrum on binding is given in Fig. 7.
Residues proximal to the binding interface are affected, while those more distant
are not.
For the 1H/ 15N experiment, uniformly labeled substance is obtainable at a
reasonable cost, but uniform 13C labeled proteins are more expensive. However,
in some cases selective labeling of the methyl groups in valine, leucine, or
isoleucine residues of a protein proves sufficient for screening purposes (59).
The employment of HSQC experiments to detect binding is especially well
exemplified in the technique termed SAR by NMR (33).
4.4. NOE-Based Experiments
NOEs are a particularly powerful NMR tool, and several NOE-based methods
are applied in drug design. It should be noted NOEs are dependent on correlation