Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy

Abstract

Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but is challenging due to the low-affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor-ligand interactions enabling binding detection and structural characterization. However, the use of the STD NMR technique together with full relaxation matrix calculations for the validation of 3D structures of protein-ligand complexes remains a major milestone in the field. In this work, we present a new approach based on a reduced relaxation matrix that allows very fast 3D structure evaluation of lowaffinity protein-ligand complexes by STD NMR data and molecular dynamics simulations.