Zooming in on small-molecule ligands by magnetic resonance

Introduction

Small molecules are critical players in the chemistry of life. In the role of substrates, cofactors, solvent, inhibitors, or activators, they steer the activities of proteins and nucleic acids. For mechanistic studies, it would be desirable to single out a small ligand from a large macromolecular complex, even if their sizes lie several orders of magnitude apart, and follow its fate during chemical and structural transformations. Few experimental techniques would achieve this under native conditions.

Challenges in NMR Spectroscopy

NMR spectroscopy grants insights into molecular motions, interactions, and chemical transitions at atomic-level resolution. However, it faces challenges when observing small-molecule ligands within large complexes:

1. NMR Active Nuclei: The first prerequisite is NMR active nuclei. Unlike biomolecular NMR, where isotope labeling is routine, the site-directed introduction of desired nuclei into small molecules still requires lengthy, individual synthesis.

2. Transverse-Relaxation Optimized Experiments: These experiments have been instrumental in pushing the size limits of protein-observed NMR into the biologically relevant range of tens to hundreds of kilodaltons. Such experiments are not directly transferable to the small molecule space due to its different chemical build-up.

Proposed Solution: ZoomNMR

ZoomNMR proposes to cover this blind spot with a spectroscopic toolbox for ligand-detected NMR of large macromolecular complexes. Our approach capitalizes on late-stage isotope labeling strategies, inspired by organic chemistry, in conjunction with relaxation interference phenomena to maximize sensitivity and resolution.

Implementation and Vision

The tools will be implemented on a prototypical human enzyme and three exemplary ligand classes. We will deliver a proof-of-concept that our novel methodology can tackle diverse research problems, from fundamental mechanistic enzymology to the design of drug molecules.

Our future vision is that ligand-observed NMR of large complexes will become as straightforward and efficient as protein-observed NMR is today.