Selected Publication:

SHR Neuro Cancer Cardio Lipid Metab Microb

Platzer, G; Ptaszek, AL; Böttcher, J; Fuchs, JE; Geist, L; Braun, D; McConnell, DB; Konrat, R; Sánchez-Murcia, PA; Mayer, M.
Ligand ¹ H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution.
Chemphyschem. 2024; 25(1):e202300636 Doi: 10.1002/cphc.202300636
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Leading authors Med Uni Graz

Ptaszek Aleksandra

Sánchez Murcia Pedro Alejandro

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Abstract:

The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with limited information on protein flexibility. An experimentally verified structural model of the binding interface in the native solution-state would support medicinal chemists in their molecular design decisions. Here we demonstrate that protein-bound ligand ¹ H NMR chemical shifts are highly sensitive and accurate probes for the immediate chemical environment of protein-ligand interfaces. By comparing the experimental ligand ¹ H chemical shift values with those computed from the X-ray structure using quantum mechanics methodology, we identify significant disagreements for parts of the ligand between the two experimental techniques. We show that quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) ensembles can be used to refine initial X-ray co-crystal structures resulting in a better agreement with experimental ¹ H ligand chemical shift values. Overall, our findings highlight the usefulness of ligand ¹ H NMR chemical shift information in combination with a QM/MM MD workflow for generating protein-ligand ensembles that accurately reproduce solution structural data.

Find related publications in this database (using NLM MeSH Indexing)

Molecular Docking Simulation - administration & dosage

Ligands - administration & dosage

Magnetic Resonance Spectroscopy - methods

Proteins - chemistry

Magnetic Resonance Imaging - administration & dosage

Find related publications in this database (Keywords)

chemical shift

computational chemistry

drug design

NMR spectroscopy

non-covalent interactions

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