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The Active Site of a Prototypical “Rigid” Drug Target is Marked by Extensive Conformational Dynamics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Singh H, Das CK, Vasa SK, Grohe K, Schäfer LV, Linser R. The Active Site of a Prototypical "Rigid" Drug Target is Marked by Extensive Conformational Dynamics. Angew Chem Int Ed Engl 2020; 59:22916-22921. [PMID: 32965765 PMCID: PMC7756556 DOI: 10.1002/anie.202009348] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/16/2020] [Indexed: 12/23/2022]
Abstract
Drug discovery, in particular optimization of candidates using medicinal chemistry, is generally guided by structural biology. However, for optimizing binding kinetics, relevant for efficacy and off-target effects, information on protein motion is important. Herein, we demonstrate for the prototypical textbook example of an allegedly "rigid protein" that substantial active-site dynamics have generally remained unrecognized, despite thousands of medicinal-chemistry studies on this model over decades. Comparing cryogenic X-ray structures, solid-state NMR on micro-crystalline protein at room temperature, and solution NMR structure and dynamics, supported by MD simulations, we show that under physiologically relevant conditions the pocket is in fact shaped by pronounced open/close conformational-exchange dynamics. The study, which is of general significance for pharmacological research, evinces a generic pitfall in drug discovery routines.
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Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Chandan K Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Suresh K Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Kristof Grohe
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.,Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
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Wiegand T, Schledorn M, Malär AA, Cadalbert R, Däpp A, Terradot L, Meier BH, Böckmann A. Nucleotide Binding Modes in a Motor Protein Revealed by 31 P- and 1 H-Detected MAS Solid-State NMR Spectroscopy. Chembiochem 2020; 21:324-330. [PMID: 31310428 PMCID: PMC7318265 DOI: 10.1002/cbic.201900439] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 12/16/2022]
Abstract
Protein-nucleic acid interactions play important roles not only in energy-providing reactions, such as ATP hydrolysis, but also in reading, extending, packaging, or repairing genomes. Although they can often be analyzed in detail with X-ray crystallography, complementary methods are needed to visualize them in complexes, which are not crystalline. Here, we show how solid-state NMR spectroscopy can detect and classify protein-nucleic interactions through site-specific 1 H- and 31 P-detected spectroscopic methods. The sensitivity of 1 H chemical-shift values on noncovalent interactions involved in these molecular recognition processes is exploited allowing us to probe directly the chemical bonding state, an information, which is not directly accessible from an X-ray structure. We show that these methods can characterize interactions in easy-to-prepare sediments of the 708 kDa dodecameric DnaB helicase in complex with ADP:AlF4- :DNA, and this despite the very challenging size of the complex.
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Affiliation(s)
- Thomas Wiegand
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Maarten Schledorn
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander A. Malär
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Riccardo Cadalbert
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Alexander Däpp
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Laurent Terradot
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 1-5/108093ZürichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex EcofectUMR 5086 CNRS/Université de Lyon7 Passage du vercors69367LyonFrance
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