Exploring Multi-Subsite Binding Pockets in Proteins:DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B

Monaco, Serena, Walpole, Samuel, Doukani, Hassan, Nepravishta, Ridvan, Martínez-Bailén, Macarena, Carmona, Ana T., Ramos-Soriano, Javier, Bergström, Maria, Robina, Inmaculada and Angulo, Jesus (2020) Exploring Multi-Subsite Binding Pockets in Proteins:DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B. Chemistry - A European Journal, 26 (44). pp. 10024-10034. ISSN 0947-6539

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Abstract

Ligand-based NMR techniques to study protein–ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.

Item Type: Article
Additional Information: Special Issue: Young Chemists 2020 © 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Uncontrolled Keywords: deep-std nmr,cholera toxin inhibitors,ligand-based nmr spectroscopy,multi-subsite binding pockets,protein–ligand interactions,catalysis,organic chemistry ,/dk/atira/pure/subjectarea/asjc/1500/1503
Faculty \ School: Faculty of Science > School of Pharmacy
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 04 Jun 2020 00:07
Last Modified: 27 Sep 2020 00:13
URI: https://ueaeprints.uea.ac.uk/id/eprint/75466
DOI: 10.1002/chem.202001723

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