151
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Schuetz DA, Seidel T, Garon A, Martini R, Körbel M, Ecker GF, Langer T. GRAIL: GRids of phArmacophore Interaction fieLds. J Chem Theory Comput 2018; 14:4958-4970. [DOI: 10.1021/acs.jctc.8b00495] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Doris A. Schuetz
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, A-1070 Vienna, Austria
| | - Thomas Seidel
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Arthur Garon
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Riccardo Martini
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, A-1070 Vienna, Austria
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Markus Körbel
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Thierry Langer
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, A-1070 Vienna, Austria
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
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152
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Güldenhaupt J, Amaral M, Kötting C, Schartner J, Musil D, Frech M, Gerwert K. Zeitaufgelöst und markerfrei gemessene ligandeninduzierte Konformationsänderungen von HSP90 - hin zu einem Konformationsaktivitätsscreening für die Wirkstoffentwicklung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Marta Amaral
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
- Derzeitige Adresse: Sanofi-Aventis (Deutschland) GmbH; Biologics Research/ Protein Therapeutics; Frankfurt am Main Deutschland
| | - Carsten Kötting
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Jonas Schartner
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
| | - Djordje Musil
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
| | - Matthias Frech
- Molecular Interactions and Biophysics; Merck KGaA; Frankfurter Straße 250 64293 Darmstadt Deutschland
| | - Klaus Gerwert
- Lehrstuhl für Biophysik; Ruhr-Universität Bochum; 44780 Bochum Deutschland
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153
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Lu H, Iuliano JN, Tonge PJ. Structure-kinetic relationships that control the residence time of drug-target complexes: insights from molecular structure and dynamics. Curr Opin Chem Biol 2018; 44:101-109. [PMID: 29986213 DOI: 10.1016/j.cbpa.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/04/2018] [Indexed: 12/15/2022]
Abstract
Time-dependent target occupancy is a function of both the thermodynamics and kinetics of drug-target interactions. However, while the optimization of thermodynamic affinity through approaches such as structure-based drug design is now relatively straight forward, less is understood about the molecular interactions that control the kinetics of drug complex formation and breakdown since this depends on both the ground and transition state energies on the binding reaction coordinate. In this opinion we highlight several recent examples that shed light on current approaches that are elucidating the factors that control the life-time of the drug-target complex.
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Affiliation(s)
- Hao Lu
- EMD Serono Research & Development Institute, Inc., Billerica, Massachusetts, USA
| | - James N Iuliano
- Department of Chemistry, Institute for Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - Peter J Tonge
- Department of Chemistry, Institute for Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA; Department of Radiology, Stony Brook University School of Medicine, Stony Brook, New York, USA
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154
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Komarov IV, Afonin S, Babii O, Schober T, Ulrich AS. Efficiently Photocontrollable or Not? Biological Activity of Photoisomerizable Diarylethenes. Chemistry 2018; 24:11245-11254. [PMID: 29633378 DOI: 10.1002/chem.201801205] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 12/14/2022]
Abstract
Diarylethene derivatives, the biological activity of which can be reversibly changed by irradiation with light of different wavelengths, have shown promise as scientific tools and as candidates for photocontrollable drugs. However, examples demonstrating efficient photocontrol of their biological activity are still relatively rare. This concept article discusses the possible reasons for this situation and presents a critical analysis of existing data and hypotheses in this field, in order to extract the design principles enabling the construction of efficient photocontrollable diarylethene-based molecules. Papers addressing biologically relevant interactions between diarylethenes and biomolecules are analyzed; however, in most published cases, the efficiency of photocontrol in living systems remains to be demonstrated. We hope that this article will encourage further discussion of design principles, primarily among pharmacologists, synthetic and medicinal chemists.
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Affiliation(s)
- Igor V Komarov
- Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601, Kyiv, Ukraine.,Lumobiotics GmbH, Auer Str. 2, 76227, Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany
| | - Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany
| | - Tim Schober
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, POB 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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155
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Güldenhaupt J, Amaral M, Kötting C, Schartner J, Musil D, Frech M, Gerwert K. Ligand-Induced Conformational Changes in HSP90 Monitored Time Resolved and Label Free-Towards a Conformational Activity Screening for Drug Discovery. Angew Chem Int Ed Engl 2018; 57:9955-9960. [PMID: 29772085 PMCID: PMC6099472 DOI: 10.1002/anie.201802603] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 11/25/2022]
Abstract
Investigation of protein–ligand interactions is crucial during early drug‐discovery processes. ATR‐FTIR spectroscopy can detect label‐free protein–ligand interactions with high spatiotemporal resolution. Here we immobilized, as an example, the heat shock protein HSP90 on an ATR crystal. This protein is an important molecular target for drugs against several diseases including cancer. With our novel approach we investigated a ligand‐induced secondary structural change. Two specific binding modes of 19 drug‐like compounds were analyzed. Different binding modes can lead to different efficacy and specificity of different drugs. In addition, the kobs values of ligand dissociation were obtained. The results were validated by X‐ray crystallography for the structural change and by SPR experiments for the dissociation kinetics, but our method yields all data in a single and simple experiment.
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Affiliation(s)
- Jörn Güldenhaupt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Marta Amaral
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.,Current address: Sanofi-Aventis (Deutschland) GmbH, Biologics Research/Protein Therapeutics, Frankfurt am Main, Germany
| | - Carsten Kötting
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Jonas Schartner
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Djordje Musil
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Matthias Frech
- Molecular Interactions and Biophysics, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Klaus Gerwert
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany
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156
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157
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Kokh DB, Amaral M, Bomke J, Grädler U, Musil D, Buchstaller HP, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC. Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:3859-3869. [PMID: 29768913 DOI: 10.1021/acs.jctc.8b00230] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly challenging to predict computationally and, therefore, is usually not considered in the early stages of drug design. Here, we present an efficient computational method, τ-random acceleration molecular dynamics (τRAMD), for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanisms. We assessed τRAMD on a data set of 70 diverse drug-like ligands of the N-terminal domain of HSP90α, a pharmaceutically important target with a highly flexible binding site, obtaining computed relative residence times with an accuracy of about 2.3τ for 78% of the compounds and less than 2.0τ within congeneric series. Analysis of dissociation trajectories reveals features that affect ligand unbinding rates, including transient polar interactions and steric hindrance. These results suggest that τRAMD will be widely applicable as a computationally efficient aid to improving drug residence times during lead optimization.
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Affiliation(s)
- Daria B Kokh
- Molecular and Cellular Modeling Group , Heidelberg Institute for Theoretical Studies , Heidelberg 69118 , Germany
| | - Marta Amaral
- Molecular Interactions and Biophysics , Merck KGaA , Darmstadt 64293 , Germany.,Instituto de Biologia Experimental e Tecnológica, Oeiras 2780-157 , Portugal
| | - Joerg Bomke
- Molecular Pharmacology , Merck KGaA , Darmstadt 64293 , Germany
| | - Ulrich Grädler
- Molecular Interactions and Biophysics , Merck KGaA , Darmstadt 64293 , Germany
| | - Djordje Musil
- Molecular Interactions and Biophysics , Merck KGaA , Darmstadt 64293 , Germany
| | | | - Matthias K Dreyer
- R&D Integrated Drug Discovery , Sanofi-Aventis Deutschland GmbH , Frankfurt am Main 65926 , Germany
| | - Matthias Frech
- Molecular Interactions and Biophysics , Merck KGaA , Darmstadt 64293 , Germany
| | - Maryse Lowinski
- Integrated Drug Discovery , Sanofi R&D , Vitry-sur-Seine F-94403 , France
| | - Francois Vallee
- Integrated Drug Discovery , Sanofi R&D , Vitry-sur-Seine F-94403 , France
| | - Marc Bianciotto
- Integrated Drug Discovery , Sanofi R&D , Vitry-sur-Seine F-94403 , France
| | - Alexey Rak
- Integrated Drug Discovery , Sanofi R&D , Vitry-sur-Seine F-94403 , France
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group , Heidelberg Institute for Theoretical Studies , Heidelberg 69118 , Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance , Heidelberg University , Heidelberg 69120 , Germany.,Interdisciplinary Center for Scientific Computing (IWR) , Heidelberg University , Heidelberg 69120 , Germany
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158
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Rydzewski J, Jakubowski R, Nowak W, Grubmüller H. Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways. J Chem Theory Comput 2018; 14:2843-2851. [PMID: 29715428 DOI: 10.1021/acs.jctc.8b00173] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 μs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.
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Affiliation(s)
- J Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - R Jakubowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland.,Centre of New Technologies, University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland
| | - W Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - H Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany
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159
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Schuetz DA, Richter L, Amaral M, Grandits M, Grädler U, Musil D, Buchstaller HP, Eggenweiler HM, Frech M, Ecker GF. Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors. J Med Chem 2018; 61:4397-4411. [DOI: 10.1021/acs.jmedchem.8b00080] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Doris A. Schuetz
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Marta Amaral
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Melanie Grandits
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
| | - Ulrich Grädler
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Djordje Musil
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | | | | | - Matthias Frech
- Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, UZA 2, Althanstrasse 14, 1090 Vienna, Austria
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160
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Chen J, Wang J, Lai F, Wang W, Pang L, Zhu W. Dynamics revelation of conformational changes and binding modes of heat shock protein 90 induced by inhibitor associations. RSC Adv 2018; 8:25456-25467. [PMID: 35539786 PMCID: PMC9082529 DOI: 10.1039/c8ra05042b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/10/2018] [Indexed: 11/21/2022] Open
Abstract
Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment. The current work integrates molecular dynamics (MD) simulations, calculations of binding free energy, and principal component (PC) analysis with scanning of inhibitor–residue interaction to probe the binding modes of inhibitors YK9, YKJ and YKI to Hsp90 and identify the hot spot of the inhibitor–Hsp90 binding. The results suggest that the introductions of two groups G1 and G2 into YKJ and YKI strengthen the binding ability of YKJ and YKI to Hsp90 compared to YK9. PC analysis based MD trajectories prove that inhibitor bindings exert significant effects on the conformational changes, internal dynamics and motion modes of Hsp90, especially for the helix α2 and the loops L1 and L2. The calculations of residue-based free energy decomposition and scanning of the inhibitor–Hsp90 interaction suggest that six residues L107, G108, F138, Y139, W162 and F170 construct the common hot spot of the inhibitor–residue interactions. Moreover the substitutions of the groups G1 and G2 in YKJ and YKI lead to two additional hydrogen bonding interactions and multiple hydrophobic interactions for bindings of YKJ and YKI to Hsp90. This work is also expected to contribute theoretical hints for the design of potent inhibitors toward Hsp90. Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment.![]()
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Affiliation(s)
- Jianzhong Chen
- School of Science
- Shandong Jiaotong University
- Jinan
- China
- Drug Discovery and Design Center
| | - Jinan Wang
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Fengbo Lai
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Wei Wang
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Laixue Pang
- School of Science
- Shandong Jiaotong University
- Jinan
- China
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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