Determination of Ligand-Binding Affinity (<i>K</i><sub>d</sub>) Using Transverse Relaxation Rate (<i>R</i><sub>2</sub>) in the Ligand-Observed <sup>1</sup>H NMR Experiment and Applications to Fragment-Based Drug Discovery
Manjuan Liu, Amin Mirza, Craig McAndrew, Arjun Thapaliya, Olivier A. Pierrat, Mark Stubbs, Tamas Hahner, N. Chessum, Paolo Innocenti, John Caldwell, Matthew D. Cheeseman, Benjamin R. Bellenie, Rob L. M. van Montfort, Gary Newton, Rosemary Burke, Ian Collins, Swen Hoelder
Abstract
High Resolution Image Download MS PowerPoint Slide High hit rates from initial ligand-observed NMR screening can make it challenging to prioritize which hits to follow up, especially in cases where there are no available crystal structures of these hits bound to the target proteins or other strategies to provide affinity ranking. Here, we report a reproducible, accurate, and versatile quantitative ligand-observed NMR assay, which can determine K d values of fragments in the affinity range of low μM to low mM using transverse relaxation rate R 2 as the observable parameter. In this study, we examined the theory and proposed a mathematical formulation to obtain K d values using non-linear regression analysis. We designed an assay format with automated sample preparation and simplified data analysis. Using tool compounds, we explored the assay reproducibility, accuracy, and detection limits. Finally, we used this assay to triage fragment hits, yielded from fragment screening against the CRBN/DDB1 complex.