Nmr in drug discovery

Key Points

  • NMR has become a valuable screening tool for analysing the binding of ligands to protein targets. Furthermore, NMR can provide structural information on protein–ligand interactions to aid in the optimization of weak-binding hits into high-affinity leads.

  • Methods for detecting binding fall into two main categories: those that monitor NMR signals from the ligand and those that monitor NMR signals from the protein.

  • Experiments that monitor the ligand exploit the large differences in the rates of rotational and translational motions of a small molecule in the free state relative to when it is bound to a macromolecules. The consequent effects on NMR properties, such as transverse and longitudinal relaxation times, are indicative of ligand binding.

  • Experiments that monitor the ligand have the advantages of requiring only small quantities of unlabelled protein, and also allowing several compounds to be studied simultaneously.

  • Experiments that monitor the protein, such as chemical-shift mapping, usually require labelled protein. However, coupled with resonance assignments, they can provide valuable information on the location of binding sites and the nature of the interactions that is not given by experiments that monitor the ligand.

  • In SAR by NMR, ligand binding is detected by chemical-shift mapping using a labelled protein target. In this way, small molecules that bind to two distinct sites on the protein are identified. Structural information on the binding modes and site positions is then used to aid the discovery of high-affinity compounds in which the two small-molecule fragments are linked.

  • SHAPES is a strategy in which ligand binding is assessed by observing signals from the ligand. Hits from a screen of a fairly small but diverse library of low-molecular weight scaffolds against an unlabelled protein target are optimized into high-affinity compounds by iterative synthetic modification and re-screening.

  • NMR-SOLVE exploits the fact that large families of proteins have adjacent binding sites, one of which is conserved throughout the family. It uses selective labelling of residues around the conserved binding site to guide the synthesis of high-affinity bi-ligand inhibitors, one part of which binds in the conserved binding site, and the other which binds in the adjacent site to give specificity.

Abstract

NMR spectroscopy has evolved into an important technique in support of structure-based drug design. Here, we survey the principles that enable NMR to provide information on the nature of molecular interactions and, on this basis, we discuss current NMR-based strategies that can identify weak-binding compounds and aid their development into potent, drug-like inhibitors for use as lead compounds in drug discovery.

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Figure 1: Chemical-shift mapping.
Figure 2: NMR properties of macromolecules and small molecules.
Figure 3: SAR by NMR.
Figure 4: SHAPES screening.
Figure 5: NMR-SOLVE.

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DATABASES

LocusLink

cytochrome P450 reductase

p38

stromelysin

FURTHER INFORMATION

NMR spectroscopy of proteins

 Protein Data Bank

Glossary

CHEMICAL SHIFT

The chemical shift of a particular nucleus is a measure of the dependence of the resonance frequency of the nucleus on its chemical environment, and is commonly indicated in parts per million (p.p.m.) relative to a reference compound.

CORRELATION SPECTROSCOPY

An experiment that correlates different spins by scalar spin–spin coupling.

ASSIGNMENT

The process of attributing a resonance in an NMR spectrum to a particular nucleus in a molecule.

POPULATION DIFFERENCE

The application of radio-frequency irradiation alters the number of magnetic nuclei in each of their possible energy states in a magnetic field.

TRIPLE-RESONANCE EXPERIMENT

An NMR experiment that correlates three different spin types — typically 1H, 15N and 13C in biological macromolecules — through scalar spin–spin couplings to obtain resonance assignments.

DIPOLE–DIPOLE INTERACTION

A through-space interaction between different nuclear spins.

CHEMICAL-SHIFT ANISOTROPY

The chemical shift of a nuclear spin in a molecule varies with the orientation of the molecule relative to the external applied field.

NUCLEAR OVERHAUSER EFFECTS (NOEs).

Changes in the intensity of NMR signals, which are caused by through-space dipole–dipole coupling. Upper distance constraints obtained from 1H–1H NOEs are used for NMR structure determination of biological macromolecules.

CRYOPROBE

Signal/noise ratios can be improved by reducing the operating temperature of some components of the NMR spectrometer.

PARAMAGNETIC CENTRE

A paramagnetic centre is characterized by the presence of localized unpaired electrons.

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Pellecchia, M., Sem, D. & Wüthrich, K. Nmr in drug discovery. Nat Rev Drug Discov 1, 211–219 (2002). https://doi.org/10.1038/nrd748

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