1
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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2
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Hulce KR, Jaishankar P, Lee GM, Bohn MF, Connelly EJ, Wucherer K, Ongpipattanakul C, Volk RF, Chuo SW, Arkin MR, Renslo AR, Craik CS. Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine. Cell Chem Biol 2022; 29:785-798.e19. [PMID: 35364007 PMCID: PMC9133232 DOI: 10.1016/j.chembiol.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/07/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022]
Abstract
Viruses are responsible for some of the most deadly human diseases, yet available vaccines and antivirals address only a fraction of the potential viral human pathogens. Here, we provide a methodology for managing human herpesvirus (HHV) infection by covalently inactivating the HHV maturational protease via a conserved, non-catalytic cysteine (C161). Using human cytomegalovirus protease (HCMV Pr) as a model, we screened a library of disulfides to identify molecules that tether to C161 and inhibit proteolysis, then elaborated hits into irreversible HCMV Pr inhibitors that exhibit broad-spectrum inhibition of other HHV Pr homologs. We further developed an optimized tool compound targeted toward HCMV Pr and used an integrative structural biology and biochemical approach to demonstrate inhibitor stabilization of HCMV Pr homodimerization, exploiting a conformational equilibrium to block proteolysis. Irreversible HCMV Pr inhibition disrupts HCMV infectivity in cells, providing proof of principle for targeting proteolysis via a non-catalytic cysteine to manage viral infection.
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Affiliation(s)
- Kaitlin R Hulce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Emily J Connelly
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Kristin Wucherer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Chayanid Ongpipattanakul
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Regan F Volk
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Shih-Wei Chuo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA; Small Molecule Discovery Center, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2280, USA.
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3
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Zhao H, Li W, Chu W, Bollard M, Adão R, Schuck P. Quantitative Analysis of Protein Self-Association by Sedimentation Velocity. ACTA ACUST UNITED AC 2021; 101:e109. [PMID: 32614509 DOI: 10.1002/cpps.109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Sedimentation velocity analytical ultracentrifugation is a powerful classical method to study protein self-association processes in solution based on the size-dependent macromolecular migration in the centrifugal field. This technique can elucidate the assembly scheme, measure affinities ranging from picomolar to millimolar Kd , and in favorable cases provide information on oligomer lifetimes and hydrodynamic shape. The present step-by-step protocols detail the essential steps of instrument calibration, experimental setup, and data analysis. Using a widely available commercial protein as a model system, the protocols invite replication and comparison with our results. A commentary discusses principles for modifications in the protocols that may be necessary to optimize application of sedimentation velocity analysis to other self-associating proteins. ©2020 Wiley Periodicals LLC. Basic Protocol 1: Measurement of external calibration factors Basic Protocol 2: Sedimentation velocity experiment for protein self-association Basic Protocol 3: Sedimentation coefficient distribution analysis in SEDFIT and isotherm analysis in SEDPHAT.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Wenqi Li
- National Protein Science Facility, School of Life Science, Tsinghua University, Beijing, China
| | - Wendan Chu
- National Protein Science Facility, School of Life Science, Tsinghua University, Beijing, China
| | - Mary Bollard
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Regina Adão
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
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4
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Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, Renslo AR, Craik CS. Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry 2014; 53:4648-60. [PMID: 24977643 PMCID: PMC4108181 DOI: 10.1021/bi5003234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Herpesviruses
rely on a homodimeric protease for viral capsid maturation.
A small molecule, DD2, previously shown to disrupt dimerization of
Kaposi’s sarcoma-associated herpesvirus protease (KSHV Pr)
by trapping an inactive monomeric conformation and two analogues generated
through carboxylate bioisosteric replacement (compounds 2 and 3) were shown to inhibit the associated proteases
of all three human herpesvirus (HHV) subfamilies (α, β,
and γ). Inhibition data reveal that compound 2 has
potency comparable to or better than that of DD2 against the tested
proteases. Nuclear magnetic resonance spectroscopy and a new application
of the kinetic analysis developed by Zhang and Poorman [Zhang, Z.
Y., Poorman, R. A., et al. (1991) J. Biol. Chem. 266, 15591–15594] show DD2, compound 2, and compound 3 inhibit HHV proteases by dimer disruption. All three compounds
bind the dimer interface of other HHV proteases in a manner analogous
to binding of DD2 to KSHV protease. The determination and analysis
of cocrystal structures of both analogues with the KSHV Pr monomer
verify and elaborate on the mode of binding for this chemical scaffold,
explaining a newly observed critical structure–activity relationship.
These results reveal a prototypical chemical scaffold for broad-spectrum
allosteric inhibition of human herpesvirus proteases and an approach
for the identification of small molecules that allosterically regulate
protein activity by targeting protein–protein interactions.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158-2280, United States
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5
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Le Roy A, Nury H, Wiseman B, Sarwan J, Jault JM, Ebel C. Sedimentation velocity analytical ultracentrifugation in hydrogenated and deuterated solvents for the characterization of membrane proteins. Methods Mol Biol 2013; 1033:219-251. [PMID: 23996181 DOI: 10.1007/978-1-62703-487-6_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This chapter is a step-by-step protocol for setting up, realizing, and analyzing sedimentation velocity experiments in hydrogenated and deuterated solvents, in the context of the characterization of membrane protein, in terms of homogeneity, association state, and amount of bound detergent, based on a real case study of the membrane protein BmrA solubilized in n-Dodecyl-β-D-Maltopyranoside) detergent.
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Affiliation(s)
- Aline Le Roy
- Institut de Biologie Structurale, CEA, Grenoble, France
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6
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Salvay AG, Communie G, Ebel C. Sedimentation velocity analytical ultracentrifugation for intrinsically disordered proteins. Methods Mol Biol 2012; 896:91-105. [PMID: 22821519 DOI: 10.1007/978-1-4614-3704-8_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The size of intrinsically disordered proteins (IDPs) is large compared to their molecular mass and the resulting mass-to-size ratio is unusual. The sedimentation coefficient, which can be obtained from sedimentation velocity (SV) analytical ultracentrifugation (AUC), is directly related to this ratio and can be easily interpreted in terms of frictional ratio. This chapter is a step-by-step protocol for setting up, executing and analyzing SV experiments in the context of the characterization of IDPs, based on a real case study of the partially folded C-terminal domain of Sendai virus nucleoprotein.
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Affiliation(s)
- Andrés G Salvay
- Institut de Biologie Structurale, CEA-CNRS-Université, Grenoble, France
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7
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Ebel C. Sedimentation velocity to characterize surfactants and solubilized membrane proteins. Methods 2011; 54:56-66. [DOI: 10.1016/j.ymeth.2010.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 11/18/2010] [Accepted: 11/19/2010] [Indexed: 02/07/2023] Open
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8
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Shahian T, Lee GM, Lazic A, Arnold LA, Velusamy P, Roels CM, Guy RK, Craik CS. Inhibition of a viral enzyme by a small-molecule dimer disruptor. Nat Chem Biol 2009; 5:640-6. [PMID: 19633659 PMCID: PMC2752665 DOI: 10.1038/nchembio.192] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/18/2009] [Indexed: 11/03/2022]
Abstract
Small molecule dimer disruptors that inhibit an essential dimeric protease of human Kaposi’s sarcoma-associated herpesvirus (KSHV) were identified by screening an α-helical mimetic library. Subsequently, a second generation of low micromolar inhibitors with improved potency and solubility was synthesized. Complementary methods including size exclusion chromatography and 1H-13C HSQC titration using selectively labeled 13C-Met samples revealed that monomeric protease is enriched in the presence of inhibitor. 1H-15N-HSQC titration studies mapped the inhibitor binding-site to the dimer interface, and mutagenesis studies targeting this region were consistent with a mechanism where inhibitor binding prevents dimerization through the conformational selection of a dynamic intermediate. These results validate the interface of herpesvirus proteases and other similar oligomeric interactions as suitable targets for the development of small molecule inhibitors.
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Affiliation(s)
- Tina Shahian
- Graduate Group in Biochemistry and Molecular Biology, University of California, San Francisco, California, USA
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9
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Larrat S, Morand P, Bas A, Vigne S, Crance JM, Boyer V, Nicod S, Grossi L, Buisson M, Burmeister WP, Seigneurin JM, Germi R. Inhibition of Epstein–Barr virus replication by small interfering RNA targeting the Epstein–Barr virus protease gene. Antivir Ther 2009. [DOI: 10.1177/135965350901400508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background The Epstein–Barr virus (EBV) protease (PR), coded by the BVRF2 gene, is essential for the maturation of the viral capsid and viral DNA packaging during the late stage of the EBV lytic cycle. Like the other herpesvirus serine PRs, EBV PR could be a target for the inhibition of EBV replication. To date, no data have been reported on the inhibition of EBV PR messenger RNA (mRNA) by small interfering RNA (siRNA). Methods In this study, siRNAs targeting EBV PR were delivered to the epithelial 293 cell line stably transfected with the complete B95-8 EBV episome. EBV DNA and PR mRNA were quantified by real-time PCR in cells and supernatant, protein expression was assessed by immunoblotting, and production of EBV infectious particles in the culture medium was measured by Raji cell superinfection. Results The EBV PR mRNA within the cells was reduced by 73%, the PR protein by 35% and the amount of virus in the cell supernatant was drastically decreased by 86% or 95%, depending on the method. Conclusions The strong effect of the siRNA targeting EBV PR on EBV replication attests to the crucial role played by EBV PR in the production of infectious particles and suggests that targeting this enzyme can be a new strategy against EBV-associated diseases where virus replication occurs.
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Affiliation(s)
- Sylvie Larrat
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Patrice Morand
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Ariane Bas
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Solenne Vigne
- Unité de Virologie, Centre de Recherches du Service de Santé des Armées, Grenoble, France
| | - Jean-Marc Crance
- Unité de Virologie, Centre de Recherches du Service de Santé des Armées, Grenoble, France
| | - Véronique Boyer
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
| | - Sandrine Nicod
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Laurence Grossi
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
| | - Marlyse Buisson
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Wim P Burmeister
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
| | - Jean-Marie Seigneurin
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
| | - Raphaële Germi
- UMI 3265, UJF-EMBL-CNRS, Unit of Virus Host Cell Interactions, Grenoble, France
- Département de Virologie, Centre Hospitalier Universitaire, Grenoble, France
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10
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Brown PH, Balbo A, Schuck P. Characterizing protein-protein interactions by sedimentation velocity analytical ultracentrifugation. CURRENT PROTOCOLS IN IMMUNOLOGY 2008; Chapter 18:18.15.1-18.15.39. [PMID: 18491296 DOI: 10.1002/0471142735.im1815s81] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This unit introduces the basic principles and practice of sedimentation velocity analytical ultracentrifugation for the study of reversible protein interactions, such as the characterization of self-association, heterogeneous association, multi-protein complexes, binding stoichiometry, and the determination of association constants. The analytical tools described include sedimentation coefficient and molar mass distributions, multi-signal sedimentation coefficient distributions, Gilbert-Jenkins theory, different forms of isotherms, and global Lamm equation modeling. Concepts for the experimental design are discussed, and a detailed step-by-step protocol guiding the reader through the experiment and the data analysis is available as an Internet resource.
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Affiliation(s)
| | - Andrea Balbo
- National Institutes of Health, Bethesda, Maryland
| | - Peter Schuck
- National Institutes of Health, Bethesda, Maryland
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11
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Lazic A, Goetz DH, Nomura AM, Marnett AB, Craik CS. Substrate modulation of enzyme activity in the herpesvirus protease family. J Mol Biol 2007; 373:913-23. [PMID: 17870089 PMCID: PMC2078331 DOI: 10.1016/j.jmb.2007.07.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 07/21/2007] [Accepted: 07/26/2007] [Indexed: 11/23/2022]
Abstract
The herpesvirus proteases are an example in which allosteric regulation of an enzyme activity is achieved through the formation of quaternary structure. Here, we report a 1.7 A resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex with a hexapeptide transition state analogue that stabilizes the dimeric state of the enzyme. Extended substrate binding sites are induced upon peptide binding. In particular, 104 A2 of surface are buried in the newly formed S4 pocket when tyrosine binds at this site. The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface. Concomitant with the structural changes, an increase in catalytic efficiency of the enzyme results upon extended substrate binding. A nearly 20-fold increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect. This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to modulate both the structure and activity of the enzyme.
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Affiliation(s)
- Ana Lazic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, USA
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12
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Buisson M, Rivail L, Hernandez JF, Jamin M, Martinez J, Ruigrok RWH, Burmeister WP. Kinetics, inhibition and oligomerization of Epstein-Barr virus protease. FEBS Lett 2006; 580:6570-8. [PMID: 17118362 DOI: 10.1016/j.febslet.2006.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 11/06/2006] [Indexed: 01/28/2023]
Abstract
Epstein-Barr virus (EBV) is an omnipresent human virus causing infectious mononucleosis and EBV associated cancers. Its protease is a possible target for antiviral therapy. We studied its dimerization and enzyme kinetics with two enzyme assays based either on the release of paranitroaniline or 7-amino-4-methylcoumarin from labeled pentapeptide (Ac-KLVQA) substrates. The protease is in a monomer-dimer equilibrium where only dimers are active. In absence of citrate the K(d) is 20 microM and drops to 0.2 microM in presence of 0.5M citrate. Citrate increases additionally the activity of the catalytic sites. The inhibitory constants of different substrate derived peptides and alpha-keto-amide based inhibitors, which have at best a K(i) of 4 microM, have also been evaluated.
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Affiliation(s)
- Marlyse Buisson
- Institut de Virologie Moléculaire et Structurale, FRE 2854 CNRS-UJF, BP181, 38042 Grenoble Cedex 9, France
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13
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Marnett AB, Nomura AM, Shimba N, Ortiz de Montellano PR, Craik CS. Communication between the active sites and dimer interface of a herpesvirus protease revealed by a transition-state inhibitor. Proc Natl Acad Sci U S A 2004; 101:6870-5. [PMID: 15118083 PMCID: PMC406434 DOI: 10.1073/pnas.0401613101] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Indexed: 11/18/2022] Open
Abstract
Structurally diverse organophosphonate inhibitors targeting the active site of the enzyme were used to investigate the relationship of the active site and the dimer interface of wild-type protease in solution. Positional scanning synthetic combinatorial libraries revealed Kaposi's sarcoma-associated herpesvirus protease to be highly specific, even at sites distal to the peptide bond undergoing hydrolysis. Specificity results were used to synthesize a hexapeptide diphenylphosphonate inhibitor of Kaposi's sarcoma-associated herpesvirus protease. The transition state analog inhibitors covalently phosphonylate the active site serine, freezing the enzyme structure during catalysis. An NMR-based assay was developed to monitor the native monomer-dimer equilibrium in solution and was used to demonstrate the effect of protease inhibition on the quaternary structure of the enzyme. NMR, circular dichroism, and size exclusion chromatography analysis showed that active site inhibition strongly regulates the binding affinity of the monomer-dimer equilibrium at the spatially separate dimer interface of the protease, shifting the equilibrium to the dimeric form of the enzyme. Furthermore, inhibitor studies revealed that the catalytic cycles of the spatially separate active sites are independent. These results (i) provide direct evidence that peptide bond hydrolysis is integrally linked to the quaternary structure of the enzyme, (ii) establish a molecular mechanism of protease activation and stabilization during catalysis, and (iii) highlight potential implications of substoichiometric inhibition of the viral protease in developing herpesviral therapeutics.
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Affiliation(s)
- Alan B Marnett
- Program in Chemistry and Chemical Biology, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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14
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Schuck P. On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation. Anal Biochem 2003; 320:104-24. [PMID: 12895474 DOI: 10.1016/s0003-2697(03)00289-6] [Citation(s) in RCA: 501] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Analytical ultracentrifugation is one of the classical techniques for the study of protein interactions and protein self-association. Recent instrumental and computational developments have significantly enhanced this methodology. In this paper, new tools for the analysis of protein self-association by sedimentation velocity are developed, their statistical properties are examined, and considerations for optimal experimental design are discussed. A traditional strategy is the analysis of the isotherm of weight-average sedimentation coefficients s(w) as a function of protein concentration. From theoretical considerations, it is shown that integration of any differential sedimentation coefficient distribution c(s), ls-g(*)(s), or g(s(*)) can give a thermodynamically well-defined isotherm, as long as it provides a good model for the sedimentation profiles. To test this condition for the g(s(*)) distribution, a back-transform into the original data space is proposed. Deconvoluting diffusion in the sedimentation coefficient distribution c(s) can be advantageous to identify species that do not participate in the association. Because of the large number of scans that can be analyzed in the c(s) approach, its s(w) values are very precise and allow extension of the isotherm to very low concentrations. For all differential sedimentation coefficients, corrections are derived for the slowing of the sedimentation boundaries caused by radial dilution. As an alternative to the interpretation of the isotherm of the weight-average s value, direct global modeling of several sedimentation experiments with Lamm equation solutions was studied. For this purpose, a new software SEDPHAT is introduced, allowing the global analysis of several sedimentation velocity and equilibrium experiments. In this approach, information from the shape of the sedimentation profiles is exploited, which permits the identification of the association scheme and requires fewer experiments to precisely characterize the association. Further, under suitable conditions, fractions of incompetent material that are not part of the reversible equilibrium can be detected.
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Affiliation(s)
- Peter Schuck
- Protein Biophysics Resource, Division of Bioengineering and Physical Science, ORS, OD, National Institutes of Health, Bethesda, MD 20892, USA.
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Buisson M, Hernandez JF, Lascoux D, Schoehn G, Forest E, Arlaud G, Seigneurin JM, Ruigrok RWH, Burmeister WP. The crystal structure of the Epstein-Barr virus protease shows rearrangement of the processed C terminus. J Mol Biol 2002; 324:89-103. [PMID: 12421561 DOI: 10.1016/s0022-2836(02)01040-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Epstein-Barr virus (EBV) belongs to the gamma-herpesvirinae subfamily of the Herpesviridae. The protease domain of the assemblin protein of herpesviruses forms a monomer-dimer equilibrium in solution. The protease domain of EBV was expressed in Escherichia coli and its structure was solved by X-ray crystallography to 2.3A resolution after inhibition with diisopropyl-fluorophosphate (DFP). The overall structure confirms the conservation of the homodimer and its structure throughout the alpha, beta, and gamma-herpesvirinae. The substrate recognition could be modelled using information from the DFP binding, from a crystal contact, suggesting that the substrate forms an antiparallel beta-strand extending strand beta5, and from the comparison with the structure of a peptidomimetic inhibitor bound to cytomegalovirus protease. The long insert between beta-strands 1 and 2, which was disordered in the KSHV protease structure, was found to be ordered in the EBV protease and shows the same conformation as observed for proteases in the alpha and beta-herpesvirus families. In contrast to previous structures, the long loop located between beta-strands 5 and 6 is partially ordered, probably due to DFP inhibition and a crystal contact. It also contributes to substrate recognition. The protease shows a specific recognition of its own C terminus in a binding pocket involving residue Phe210 of the other monomer interacting across the dimer interface. This suggests conformational changes of the protease domain after its release from the assemblin precursor followed by burial of the new C terminus and a possible effect onto the monomer-dimer equilibrium. The importance of the processed C terminus was confirmed using a mutant protease carrying a C-terminal extension and a mutated release site, which shows different solution properties and a strongly reduced enzymatic activity.
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Affiliation(s)
- Marlyse Buisson
- Laboratoire de Virologie, Hôpital Michallon, BP 217, 38043 Grenoble Cedex 9, France
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Pray TR, Reiling KK, Demirjian BG, Craik CS. Conformational change coupling the dimerization and activation of KSHV protease. Biochemistry 2002; 41:1474-82. [PMID: 11814340 DOI: 10.1021/bi011753g] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of herpesviral protease activation upon dimerization was studied using two independent spectroscopic assays augmented by directed mutagenesis. Spectroscopic changes, attributable to dimer interface conformational plasticity, were observed upon dimerization of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr). KSHV Pr's dissociation constant of 585 +/- 135 nM at 37 degrees C was measured by a concentration-dependent, 100-fold increase in specific activity to a value of 0.275 +/- 0.023 microM product min(-1) (microM enzyme)(-1). A 4 nm blue-shifted fluorescence emission spectrum and a 25% increase in ellipticity at 222 nm were detected by circular dichroism upon dimer association. This suggested enhanced hydrophobic packing within the dimer interface and/or core, as well as altered secondary structures. To better understand the structure-activity relationship between the monomer and the dimer, KSHV Pr molecules were engineered to remain monomeric via substitution of two separate residues within the dimer interface, L196 and M197. These mutants were proteolytically inactive while exhibiting the spectroscopic signature and thermal stability of wild type, dissociated monomers (T(M) = 75 degrees C). KSHV Pr conformational changes were found to be relevant in vivo, as the autoproteolytic inactivation of KSHV Pr at its dimer disruption site [Pray et al. (1999) J. Mol. Biol. 289, 197-203] was detected in viral particles from KSHV-infected cells. This characterization of structural plasticity suggests that the structure of the KSHV Pr monomer is stable and significantly different from its structure in the dimer. This structural uniqueness should be considered in the development of compounds targeting the dimer interface of KSHV Pr monomers.
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Affiliation(s)
- Todd R Pray
- Graduate Group in Biophysics, Department of Pharmaceutical Chemistry and of Biochemistry and Biophysics, The University of California, San Francisco, California 94143, USA
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