High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands

Abstract

The ability of a small molecule to bind and modify the activity of a protein target at a specific site greatly impacts the success of drugs in the pharmaceutical industry. One of the most important tools for evaluating these interactions has been high-field solution NMR because of its unique ability to examine even weak protein-drug interactions at high resolution. NMR can be used to evaluate the structural, thermodynamic and kinetic aspects of a binding reaction. The basis of NMR screening experiments is that binding causes a perturbation in the physical properties of both molecules. Unique properties of small and macromolecules allow selective detection of either the protein target or ligand, even in a mixture of compounds. This review outlines current methodologies for assessing protein-ligand interactions from the perspectives of the protein target and ligand and delineates the fundamental principles for understanding NMR approaches in drug research. Advances in instrumentation, pulse sequences, isotopic labeling strategies, and the development of competition experiments support the study of higher molecular weight protein targets, facilitate higher-throughput and expand the range of binding affinities that can be evaluated, enhancing the utility of NMR for identifying and characterizing potential therapeutics to druggable protein targets.

Correlating Structure and Function of Drug-Metabolizing Enzymes: Progress and Ongoing Challenges

“…NMR complements crystallography because it has the advantages of dealing well with ligands of moderate affinity (like many P450 substrates), with ligands that bind at a distant location from the heme iron (in contrast to binding studies based on spin-shift changes at the heme), and it provides valuable dynamic information. Straightforward analyses of changes in spectral line shape and resonance position inform understanding of such interactions (Skinner and Laurence, 2008). NMR may also have an advantage in evaluating interactions mediated by electrostatics, such as those thought to play an important Fig.…”

Magnetic resonance assays of haloperidol in human serum albumin

“…The fraction of bound of the haloperidol to HSA (p b ) was 0.89 ± 0.2. One of the novel and most important applications of high field MR in pharmaceutical sciences is its ability to examine protein-drug interactions (Skinner and Laurence, 2008). The MRS parameters of a ligand, such as chemical shifts, generally change on binding to a protein, and there is often difficulty in using 1 H MRS spectroscopy to study proteinligand binding directly because of the need to extrapolate the observed small molecules signals to obtain their values in the bound states to large protein.…”

Data quality in drug discovery: the role of analytical performance in ligand binding assays

“…Many successful applications have been reported from pharmaceutical and biotechnology companies in which NMR methods have been employed for hit identification, validation, and/or elaboration [66]. Many detailed reviews are available in the literature describing the large variety of NMR screening techniques [66][67][68][69][70][71][72][73][74] and here only a short summary is given. Specific properties of the most important methods are summarized in Table 3.…”

“…Besides its classical applications for elucidating the constitution and structure of small organic molecules and, as alternative to X-ray crystallography, the determination of the 3D structure of bio-macromolecules, it provides sensible probes for screening ligand binding to biomolecular targets like proteins and nucleic acids [66][67][68][69][70][71][72][73][74]. Many successful applications have been reported from pharmaceutical and biotechnology companies in which NMR methods have been employed for hit identification, validation, and/or elaboration [66].…”