NMR in target driven drug discovery: why not?

Abstract

No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.

Estimating the cooperativity of PROTAC-induced ternary complexes using 19F NMR displacement assay

“…NMR experiments are well established methods to detect both weak-and high-affinity binders in drug discovery campaigns. 19 Expanding the range of applications of NMR to study PROTAC-induced complexes could therefore be a beneficial addition to the PROTAC assays toolkit.…”

Estimating the cooperativity of PROTAC-induced ternary complexes using 19F NMR displacement assay

“…In this work we evaluated the application of competitive ligand-observed 19 F NMR experiments to estimate α of PROTAC induced ternary complexes (Figure 1). A highly sensitive competitive 19 F NMR assay based on spy molecule 19 (Scheme 1) was recently developed by us 20 to detect small-molecules binding to the VHL E3 ligase.…”

“…In this work we evaluated the application of competitive ligand-observed 19 F NMR experiments to estimate α of PROTAC induced ternary complexes (Figure 1). A highly sensitive competitive 19 F NMR assay based on spy molecule 19 (Scheme 1) was recently developed by us 20 to detect small-molecules binding to the VHL E3 ligase. Given the multiple examples of VHL-recruiting PROTACs that form complexes with positive (α > 1), negative (α < 1) or no (α = 1) cooperativity, we decided to explore the main advantages and limitations of an NMR-based method to investigate these systems.…”

“…All compounds shown are referred with the acronyms and numbers shown in their original citations to facilitate comparisons with reported data. 19 F NMR peak. (c) An IC50 value can be fitted from the correlation between an NMR observable (e.g.…”

“…(a) The 19 F CPMG spectra of the fluorinated spy molecule free in solution (blue sharp peak) and in the presence of protein (green broadened peak) are recorded as controls. (b) Titration of increasing concentration of a competitor causes the displacement of the spy molecule, affecting the shape and intensity of its19 F NMR peak. (c) An IC50 value can be fitted from the correlation between an NMR observable (e.g.…”