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Torres F, Walser R, Kaderli J, Rossi E, Bobby R, Packer MJ, Sarda S, Walker G, Hitchin JR, Milbradt AG, Orts J. NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24. J Med Chem 2022; 65:5565-5574. [PMID: 35357834 PMCID: PMC9017284 DOI: 10.1021/acs.jmedchem.1c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR2) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints, bypassing the laborious process of obtaining sequence-specific resonance assignments for the protein target. We apply this method to two therapeutic targets, the bromodomain of TRIM24 and the second bromodomain of BRD4. We show that the NMR2 methodology can guide SBDD by rationalizing the observed SAR. We also demonstrate that new types of restraints and selective methyl labeling have the potential to dramatically reduce "time to structure" and extend the method to targets beyond the reach of traditional NMR structure elucidation.
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Affiliation(s)
- Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Reto Walser
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Emanuele Rossi
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Romel Bobby
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Martin J Packer
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Sunil Sarda
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Graeme Walker
- Drug Discovery Unit, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - James R Hitchin
- Drug Discovery Unit, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Department of Pharmaceutical Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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Orts J, Riek R. Protein-ligand structure determination with the NMR molecular replacement tool, NMR 2. JOURNAL OF BIOMOLECULAR NMR 2020; 74:633-642. [PMID: 32621003 DOI: 10.1007/s10858-020-00324-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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Torres F, Ghosh D, Strotz D, Chi CN, Davis B, Orts J. Protein-fragment complex structures derived by NMR molecular replacement. RSC Med Chem 2020; 11:591-596. [PMID: 33479661 PMCID: PMC7649837 DOI: 10.1039/d0md00068j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/23/2020] [Indexed: 01/16/2023] Open
Abstract
Recently we have established an NMR molecular replacement method, which is capable of solving the structure of the interaction site of protein-ligand complexes in a fully automated manner. While the method was successfully applied for ligands with strong and weak binding affinities, including small molecules and peptides, its applicability on ligand fragments remains to be shown. Structures of fragment-protein complexes are more challenging for the method since fragments contain only few protons. Here we show a successful application of the NMR molecular replacement method in solving structures of complexes between three derivatives of a ligand fragment and the protein receptor PIN1. We anticipate that this approach will find a broad application in fragment-based lead discovery.
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Affiliation(s)
- Felix Torres
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Dean Strotz
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Celestine N Chi
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
| | - Ben Davis
- Vernalis , Granta Park , Cambridge , UK
| | - Julien Orts
- Laboratory of Physical Chemistry , ETH , Swiss Federal Institute of Technology , HCI F217, Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland .
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