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Secker C, Fackeldey K, Weber M, Ray S, Gorgulla C, Schütte C. Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists. J Cheminform 2023; 15:85. [PMID: 37726792 PMCID: PMC10510211 DOI: 10.1186/s13321-023-00746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023] Open
Abstract
Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the [Formula: see text]-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported [Formula: see text]-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale.
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Affiliation(s)
- Christopher Secker
- Zuse Institute Berlin, Berlin, Germany.
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | - Konstantin Fackeldey
- Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | | | | | - Christoph Gorgulla
- Zuse Institute Berlin, Berlin, Germany
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christof Schütte
- Zuse Institute Berlin, Berlin, Germany
- Mathematics Institute, Freie Universität Berlin, Berlin, Germany
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2
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Gisdon FJ, Feiler CG, Kempf O, Foerster JM, Haiss J, Blankenfeldt W, Ullmann GM, Bombarda E. Structural and Biophysical Analysis of the Phytochelatin-Synthase-Like Enzyme from Nostoc sp. Shows That Its Protease Activity is Sensitive to the Redox State of the Substrate. ACS Chem Biol 2022; 17:883-897. [PMID: 35377603 DOI: 10.1021/acschembio.1c00941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phytochelatins (PCs) are nonribosomal thiol-rich oligopeptides synthetized from glutathione (GSH) in a γ-glutamylcysteinyl transpeptidation reaction catalyzed by PC synthases (PCSs). Ubiquitous in plant and present in some invertebrates, PCSs are involved in metal detoxification and homeostasis. The PCS-like enzyme from the cyanobacterium Nostoc sp. (NsPCS) is considered to be an evolutionary precursor enzyme of genuine PCSs because it shows sufficient sequence similarity for homology to the catalytic domain of the eukaryotic PCSs and shares the peptidase activity consisting in the deglycination of GSH. In this work, we investigate the catalytic mechanism of NsPCS by combining structural, spectroscopic, thermodynamic, and theoretical techniques. We report several crystal structures of NsPCS capturing different states of the catalyzed chemical reaction: (i) the structure of the wild-type enzyme (wt-NsPCS); (ii) the high-resolution structure of the γ-glutamyl-cysteine acyl-enzyme intermediate (acyl-NsPCS); and (iii) the structure of an inactive variant of NsPCS, with the catalytic cysteine mutated into serine (C70S-NsPCS). We characterize NsPCS as a relatively slow enzyme whose activity is sensitive to the redox state of the substrate. Namely, NsPCS is active with reduced glutathione (GSH), but is inhibited by oxidized glutathione (GSSG) because the cleavage product is not released from the enzyme. Our biophysical analysis led us to suggest that the biological function of NsPCS is being a part of a redox sensing system. In addition, we propose a mechanism how PCS-like enzymes may have evolved toward genuine PCS enzymes.
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Affiliation(s)
- Florian J. Gisdon
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Christian G. Feiler
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Oxana Kempf
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Johannes M. Foerster
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Jonathan Haiss
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - G. Matthias Ullmann
- Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
| | - Elisa Bombarda
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95440 Bayreuth, Germany
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3
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Akram M, Bock J, Dietl A, Barends TR. Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation. ACS OMEGA 2021; 6:21457-21464. [PMID: 34471748 PMCID: PMC8388095 DOI: 10.1021/acsomega.1c02275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.
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4
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. Enhancing the population of the encounter complex affects protein complex formation efficiency. FEBS J 2021; 289:535-548. [PMID: 34403572 PMCID: PMC9293183 DOI: 10.1111/febs.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022]
Abstract
Optimal charge distribution is considered to be important for efficient formation of protein complexes. Electrostatic interactions guide encounter complex formation that precedes the formation of an active protein complex. However, disturbing the optimized distribution by introduction of extra charged patches on cytochrome c peroxidase does not lead to a reduction in productive encounters with its partner cytochrome c. To test whether a complex with a high population of encounter complex is more easily affected by suboptimal charge distribution, the interactions of cytochrome c mutant R13A with wild‐type cytochrome c peroxidase and a variant with an additional negative patch were studied. The complex of the peroxidase and cytochrome c R13A was reported to have an encounter state population of 80%, compared to 30% for the wild‐type cytochrome c. NMR analysis confirms the dynamic nature of the interaction and demonstrates that the mutant cytochrome c samples the introduced negative patch. Kinetic experiments show that productive complex formation is fivefold to sevenfold slower at moderate and high ionic strength values for cytochrome c R13A but the association rate is not affected by the additional negative patch on cytochrome c peroxidase, showing that the total charge on the protein surface can compensate for less optimal charge distribution. At low ionic strength (44 mm), the association with the mutant cytochrome c reaches the same high rates as found for wild‐type cytochrome c, approaching the diffusion limit.
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Di Savino A, Foerster JM, Ullmann GM, Ubbink M. The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed. Biochemistry 2021; 60:747-755. [PMID: 33646750 PMCID: PMC8041253 DOI: 10.1021/acs.biochem.1c00021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
Protein complex formation
depends strongly on electrostatic interactions.
The distribution of charges on the surface of redox proteins is often
optimized by evolution to guide recognition and binding. To test the
degree to which the electrostatic interactions between cytochrome c peroxidase (CcP) and cytochrome c (Cc)
are optimized, we produced five CcP variants, each with a different
charge distribution on the surface. Monte Carlo simulations show that
the addition of negative charges attracts Cc to the new patches, and
the neutralization of the charges in the regular, stereospecific binding
site for Cc abolishes the electrostatic interactions in that region
entirely. For CcP variants with the charges in the regular binding
site intact, additional negative patches slightly enhance productive
complex formation, despite disrupting the optimized charge distribution.
Removal of the charges in the regular binding site results in a dramatic
decrease in the complex formation rate, even in the presence of highly
negative patches elsewhere on the surface. We conclude that additional
charge patches can result in either productive or futile encounter
complexes, depending on whether negative residues are located also
in the regular binding site.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447 Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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6
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020; 59:23239-23243. [PMID: 32827196 PMCID: PMC7756542 DOI: 10.1002/anie.202010006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Electrostatic interactions can strongly increase the efficiency of protein complex formation. The charge distribution in redox proteins is often optimized to steer a redox partner to the electron transfer active binding site. To test whether the optimized distribution is more important than the strength of the electrostatic interactions, an additional negative patch was introduced on the surface of cytochrome c peroxidase, away from the stereospecific binding site, and its effect on the encounter complex as well as the rate of complex formation was determined. Monte Carlo simulations and paramagnetic relaxation enhancement NMR experiments indicate that the partner, cytochrome c, interacts with the new patch. Unexpectedly, the rate of the active complex formation was not reduced, but rather slightly increased. The findings support the idea that for efficient protein complex formation the strength of the electrostatic interaction is more critical than an optimized charge distribution.
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Affiliation(s)
- Antonella Di Savino
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Johannes M Foerster
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Thijmen La Haye
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands.,Present address: University of Delft, TNW Applied Sciences, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anneloes Blok
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - Monika Timmer
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
| | - G Matthias Ullmann
- University of Bayreuth, Computational Biochemistry, Universitätsstraße 30, NW I, 95447, Bayreuth, Germany
| | - Marcellus Ubbink
- Leiden University, Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, Netherlands
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7
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Di Savino A, Foerster JM, La Haye T, Blok A, Timmer M, Ullmann GM, Ubbink M. Efficient Encounter Complex Formation and Electron Transfer to Cytochrome
c
Peroxidase with an Additional, Distant Electrostatic Binding Site. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Antonella Di Savino
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Johannes M. Foerster
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Thijmen La Haye
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
- Present address: University of Delft TNW Applied Sciences Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Anneloes Blok
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - Monika Timmer
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
| | - G. Matthias Ullmann
- University of Bayreuth Computational Biochemistry Universitätsstraße 30, NW I 95447 Bayreuth Germany
| | - Marcellus Ubbink
- Leiden University Institute of Chemistry Einsteinweg 55 2333 CC Leiden Netherlands
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