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

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 it 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. Comparison of relaxation and exchange
matrix calculations with 1H STD NMR experimental data is
essential for the validation of 3D structures of protein–ligand
complexes. In this work, we present a new approach based on the calculation
of a reduced relaxation matrix, in combination with funnel metadynamics
MD simulations, that allows a very fast generation of experimentally
STD-NMR-validated 3D structures of low-affinity protein–ligand
complexes.