Navigating the Molecular Realm: Cutting-Edge NMR Techniques for Drug Design and Revealing Secrets of Protein (Thermo)-Dynamics

Navigating the Molecular Realm: Cutting-Edge NMR Techniques for Drug Design and Revealing Secrets of Protein (Thermo)-Dynamics

Julien Orts

University of Vienna, Department of Pharmaceutical Sciences, Austria

X-ray crystallography molecular replacement (MR) is a highly versatile tool for the detailed characterization of lead compound and binding modes in the pharmaceutical industry. MR is one of the most successful approaches in structural biology. MR stands out as one of the most successful approaches in structural biology.

I will present our work on establishing a similar MR approach in NMR spectroscopy, known as NMR² (NMR Molecular Replacement). NMR² is an MR-like method in NMR that aims to determine the structures of ligand binding pockets at atomic resolution. The NMR² approach employs a high-throughput structure calculation protocol instead of a docking-scoring simulation. It is characterized by its speed, requiring only a few days of measuring time, and it circumvents the time-consuming steps of sequential assignment for the protein.

During the presentation, we will showcase multiple applications of NMR², encompassing various ligand topologies, ranging from peptidomimetics to small molecules that bind strongly or weakly to protein receptors. Additionally, we will discuss how NMR² can effectively utilize partially labeled proteins through methyl-specific isotope labeling. Lastly, we will present our latest methodology development aimed at further advancing this technique. Our findings demonstrate that NMR² holds the potential to open a fast and robust avenue for determining the binding pocket structure of ligand-protein complexes at atomic resolution.

The physical chemistry frame for studying intra- and inter-molecular interactions is thermodynamics. The extent to which two molecules interact is dictated by the Gibbs energy change (ΔG) of the interactions, which is composed of enthalpic (ΔH) and entropic (ΔS) terms.

X-ray crystallographic and NMR structures provide a detailed description of the static interactions associated with enthalpic contributions. However, up to now, the entropic components remain difficult to address experimentally.

I will present our strategy using NMR to study protein thermodynamics. It is anticipated that quantitative thermodynamic measurements within molecules and molecular complexes will open a new avenue in the fundamental understanding of how atomistic mechanism create a function.