1
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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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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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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Sikdar A, Gupta R, Boura E. Reviewing Antiviral Research Against Viruses Causing Human Diseases - A Structure Guided Approach. Curr Mol Pharmacol 2021; 15:306-337. [PMID: 34348638 DOI: 10.2174/1874467214666210804152836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 11/22/2022]
Abstract
The littlest of all the pathogens, viruses have continuously been the foremost strange microorganisms to consider. Viral Infections can cause extreme sicknesses as archived by the HIV/AIDS widespread or the later Ebola or Zika episodes. Apprehensive framework distortions are too regularly watched results of numerous viral contaminations. Besides, numerous infections are oncoviruses, which can trigger different sorts of cancer. Nearly every year a modern infection species rises debilitating the world populace with an annihilating episode. Subsequently, the need of creating antivirals to combat such rising infections. In any case, from the innovation of to begin with antiviral medicate Idoxuridine in 1962 to the revelation of Baloxavir marboxil (Xofluza) that was FDA-approved in 2018, the hone of creating antivirals has changed significantly. In this article, different auxiliary science strategies have been described that can be referral for therapeutics innovation.
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Affiliation(s)
- Arunima Sikdar
- Department of Hematology and Oncology, School of Medicine, The University of Tennessee Health Science Center, 920 Madison Ave, P.O.Box-38103, Memphis, Tennessee. United States
| | - Rupali Gupta
- Department of Neurology, Duke University Medical Center, Durham, North Carolina. United States
| | - Evzen Boura
- Department of Molecular Biology and Biochemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, P.O. Box:16000, Prague. Czech Republic
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5
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Tsurumi S, Watanabe T, Iwaisako Y, Suzuki Y, Nakano T, Fujimuro M. Kaposi's sarcoma-associated herpesvirus ORF17 plays a key role in capsid maturation. Virology 2021; 558:76-85. [PMID: 33735753 DOI: 10.1016/j.virol.2021.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus is a human rhadinovirus of the gammaherpesvirus sub-family. Although herpesviruses are well-studied models of capsid formation and its processes, those of KSHV remain unknown. KSHV ORF17 encoding the viral protease precursor (ORF17-prePR) is thought to contribute to capsid formation; however, functional information is largely unknown. Here, we evaluated the role of ORF17 during capsid formation by generating ORF17-deficient and ORF17 protease-dead KSHV. Both mutants showed a decrease in viral production but not DNA replication. ORF17 R-mut, with a point-mutation at the restriction or release site (R-site) by which ORF17-prePR can be functionally cleaved into a protease (ORF17-PR) and an assembly region (ORF17-pAP/-AP), failed to play a role in viral production. Furthermore, wild type KSHV produced a mature capsid, whereas ORF17-deficient and protease-dead KSHV produced a B-capsid, (i.e., a closed body possessing a circular inner structure). Therefore, ORF17 and its protease function are essential for appropriate capsid maturation.
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Affiliation(s)
- Sayaka Tsurumi
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan
| | - Tadashi Watanabe
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan; Department of Virology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Nakagami, Okinawa, 903-0215, Japan
| | - Yuki Iwaisako
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan.
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6
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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Juárez-Jiménez J, Gupta AA, Karunanithy G, Mey ASJS, Georgiou C, Ioannidis H, De Simone A, Barlow PN, Hulme AN, Walkinshaw MD, Baldwin AJ, Michel J. Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A. Chem Sci 2020; 11:2670-2680. [PMID: 34084326 PMCID: PMC8157532 DOI: 10.1039/c9sc04696h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins need to interconvert between many conformations in order to function, many of which are formed transiently, and sparsely populated. Particularly when the lifetimes of these states approach the millisecond timescale, identifying the relevant structures and the mechanism by which they interconvert remains a tremendous challenge. Here we introduce a novel combination of accelerated MD (aMD) simulations and Markov state modelling (MSM) to explore these 'excited' conformational states. Applying this to the highly dynamic protein CypA, a protein involved in immune response and associated with HIV infection, we identify five principally populated conformational states and the atomistic mechanism by which they interconvert. A rational design strategy predicted that the mutant D66A should stabilise the minor conformations and substantially alter the dynamics, whereas the similar mutant H70A should leave the landscape broadly unchanged. These predictions are confirmed using CPMG and R1ρ solution state NMR measurements. By efficiently exploring functionally relevant, but sparsely populated conformations with millisecond lifetimes in silico, our aMD/MSM method has tremendous promise for the design of dynamic protein free energy landscapes for both protein engineering and drug discovery.
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Affiliation(s)
- Jordi Juárez-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Arun A Gupta
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Gogulan Karunanithy
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Antonia S J S Mey
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Charis Georgiou
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Harris Ioannidis
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alessio De Simone
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Paul N Barlow
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Alison N Hulme
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
| | - Malcolm D Walkinshaw
- School of Biological Sciences Michael Swann Building, Max Born Crescent Edinburgh EH9 3BF UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road Edinburgh EH9 3FJ UK
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8
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Tang A, Caballero AR, Marquart ME, Bierdeman MA, O'Callaghan RJ. Mechanism of Pseudomonas aeruginosa Small Protease (PASP), a Corneal Virulence Factor. Invest Ophthalmol Vis Sci 2019; 59:5993-6002. [PMID: 30572344 PMCID: PMC6306078 DOI: 10.1167/iovs.18-25834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Pseudomonas aeruginosa is the leading cause of contact lens-associated bacterial keratitis. Secreted bacterial proteases have a key role in keratitis, including the P. aeruginosa small protease (PASP), a proven corneal virulence factor. We investigated the mechanism of PASP and its importance to corneal toxicity. Methods PASP, a serine protease, was tested for activity on various substrates. The catalytic triad of PASP was sought by bioinformatic analysis and site-directed mutagenesis. All mutant constructs were expressed in a P. aeruginosa PASP-deficient strain; the resulting proteins were purified using ion-exchange, gel filtration, or affinity chromatography; and the proteolytic activity was assessed by gelatin zymography and a fluorometric assay. The purified PASP proteins with single amino acid changes were injected into rabbit corneas to determine their pathological effects. Results PASP substrates were cleaved at arginine or lysine residues. Alanine substitution of PASP residues Asp-29, His-34, or Ser-47 eliminated protease activity, whereas PASP with substitution for Ser-59 (control) retained activity. Computer modeling and Western blot analysis indicated that formation of a catalytic triad required dimer formation, and zymography demonstrated the protease activity of the homodimer, but not the monomer. PASP with the Ser-47 mutation, but not with the control mutation, lacked corneal toxicity, indicating the importance of protease activity. Conclusions PASP is a secreted serine protease that can cleave proteins at arginine or lysine residues and PASP activity requires dimer or larger aggregates to create a functional active site. Most importantly, proteolytic PASP molecules demonstrated highly significant toxicity for the rabbit cornea.
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Affiliation(s)
- Aihua Tang
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Armando R Caballero
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Mary E Marquart
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Michael A Bierdeman
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Richard J O'Callaghan
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
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9
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Yuan F, Gao ZQ, Majerciak V, Bai L, Hu ML, Lin XX, Zheng ZM, Dong YH, Lan K. The crystal structure of KSHV ORF57 reveals dimeric active sites important for protein stability and function. PLoS Pathog 2018; 14:e1007232. [PMID: 30096191 PMCID: PMC6105031 DOI: 10.1371/journal.ppat.1007232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/22/2018] [Accepted: 07/19/2018] [Indexed: 11/19/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a γ-herpesvirus closely associated with Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman disease. Open reading frame 57 (ORF57), a viral early protein of KSHV promotes splicing, stability and translation of viral mRNA and is essential for viral lytic replication. Previous studies demonstrated that dimerization of ORF57 stabilizes the protein, which is critical for its function. However, the detailed structural basis of dimerization was not elucidated. In this study, we report the crystal structures of the C-terminal domain (CTD) of ORF57 (ORF57-CTD) in both dimer at 3.5 Å and monomer at 3.0 Å. Both structures reveal that ORF57-CTD binds a single zinc ion through the consensus zinc-binding motif at the bottom of each monomer. In addition, the N-terminal residues 167-222 of ORF57-CTD protrudes a long "arm" and holds the globular domains of the neighboring monomer, while the C-terminal residues 445-454 are locked into the globular domain in cis and the globular domains interact in trans. In vitro crosslinking and nuclear translocation assays showed that either deletion of the "arm" region or substitution of key residues at the globular interface led to severe dimer dissociation. Introduction of point mutation into the zinc-binding motif also led to sharp degradation of KSHV ORF57 and other herpesvirus homologues. These data indicate that the "arm" region, the residues at the globular interface and the zinc-binding motif are all equally important in ORF57 protein dimerization and stability. Consistently, KSHV recombinant virus with the disrupted zinc-binding motif by point mutation exhibited a significant reduction in the RNA level of ORF57 downstream genes ORF59 and K8.1 and infectious virus production. Taken together, this study illustrates the first structure of KSHV ORF57-CTD and provides new insights into the understanding of ORF57 protein dimerization and stability, which would shed light on the potential design of novel therapeutics against KSHV infection and related diseases.
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Affiliation(s)
- Fei Yuan
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan, P. R. China
| | - Zeng-Qiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
| | - Lei Bai
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan, P. R. China
| | - Meng-Lu Hu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Xi Lin
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan, P. R. China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- * E-mail: (ZMZ); (YHD); (KL)
| | - Yu-Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (ZMZ); (YHD); (KL)
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan, P. R. China
- * E-mail: (ZMZ); (YHD); (KL)
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10
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Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS. Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. J Am Chem Soc 2017; 139:11650-11653. [PMID: 28759216 PMCID: PMC6089631 DOI: 10.1021/jacs.7b04030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic X-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room-temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.
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Affiliation(s)
- Timothy M. Acker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jonathan E. Gable
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Markus-Frederik Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Michael C. Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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11
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Zühlsdorf M, Hinrichs W. Assemblins as maturational proteases in herpesviruses. J Gen Virol 2017; 98:1969-1984. [PMID: 28758622 DOI: 10.1099/jgv.0.000872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During assembly of herpesvirus capsids, a protein scaffold self-assembles to ring-like structures forming the scaffold of the spherical procapsids. Proteolytic activity of the herpesvirus maturational protease causes structural changes that result in angularization of the capsids. In those mature icosahedral capsids, the packaging of viral DNA into the capsids can take place. The strictly regulated protease is called assemblin. It is inactive in its monomeric state and activated by dimerization. The structures of the dimeric forms of several assemblins from all herpesvirus subfamilies have been elucidated in the last two decades. They revealed a unique serine-protease fold with a catalytic triad consisting of a serine and two histidines. Inhibitors that disturb dimerization by binding to the dimerization area were found recently. Additionally, the structure of the monomeric form of assemblin from pseudorabies virus and some monomer-like structures of Kaposi's sarcoma-associated herpesvirus assemblin were solved. These findings are the proof-of-principle for the development of new anti-herpesvirus drugs. Therefore, the most important information on this fascinating and unique class of proteases is summarized here.
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Affiliation(s)
- Martin Zühlsdorf
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489 Greifswald, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489 Greifswald, Germany
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12
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Skoreński M, Grzywa R, Sieńczyk M. Why should we target viral serine proteases when developing antiviral agents? Future Virol 2016. [DOI: 10.2217/fvl-2016-0106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marcin Skoreński
- Faculty of Chemistry, Division of Medicinal Chemistry & Microbiology, Wroclaw University of Science & Technology, Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland
| | - Renata Grzywa
- Faculty of Chemistry, Division of Medicinal Chemistry & Microbiology, Wroclaw University of Science & Technology, Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland
| | - Marcin Sieńczyk
- Faculty of Chemistry, Division of Medicinal Chemistry & Microbiology, Wroclaw University of Science & Technology, Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland
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13
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Topalis D, Gillemot S, Snoeck R, Andrei G. Distribution and effects of amino acid changes in drug-resistant α and β herpesviruses DNA polymerase. Nucleic Acids Res 2016; 44:9530-9554. [PMID: 27694307 PMCID: PMC5175367 DOI: 10.1093/nar/gkw875] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/13/2016] [Accepted: 09/21/2016] [Indexed: 12/15/2022] Open
Abstract
Emergence of drug-resistance to all FDA-approved antiherpesvirus agents is an increasing concern in immunocompromised patients. Herpesvirus DNA polymerase (DNApol) is currently the target of nucleos(t)ide analogue-based therapy. Mutations in DNApol that confer resistance arose in immunocompromised patients infected with herpes simplex virus 1 (HSV-1) and human cytomegalovirus (HCMV), and to lesser extent in herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV) and human herpesvirus 6 (HHV-6). In this review, we present distinct drug-resistant mutational profiles of herpesvirus DNApol. The impact of specific DNApol amino acid changes on drug-resistance is discussed. The pattern of genetic variability related to drug-resistance differs among the herpesviruses. Two mutational profiles appeared: one favoring amino acid changes in the Palm and Finger domains of DNApol (in α-herpesviruses HSV-1, HSV-2 and VZV), and another with mutations preferentially in the 3′-5′ exonuclease domain (in β-herpesvirus HCMV and HHV-6). The mutational profile was also related to the class of compound to which drug-resistance emerged.
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Affiliation(s)
- D Topalis
- Rega Institute for Medical Research, Department Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - S Gillemot
- Rega Institute for Medical Research, Department Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - R Snoeck
- Rega Institute for Medical Research, Department Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - G Andrei
- Rega Institute for Medical Research, Department Microbiology and Immunology, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
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14
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Kaposi's sarcoma-associated herpesvirus: the role of lytic replication in targeted therapy. Curr Opin Infect Dis 2016; 28:611-24. [PMID: 26524334 DOI: 10.1097/qco.0000000000000213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW To discuss the role of Kaposi's sarcoma-associated herpesvirus (KSHV) lytic replication in viral-associated diseases and assess the progress on targeting KSHV lytic replication as a strategy to prevent KSHV-related malignancies. RECENT FINDINGS New inhibitors of viral lytic replication are being developed as well as novel modalities are being investigated to target cellular processes that the virus hijacks during its life cycle. Research has also focused on reactivating viral lytic replication in latently infected tumour cells (lytic induction therapy) to promote death of tumour cells. SUMMARY KSHV is linked to three malignancies: Kaposi sarcoma, primary effusion lymphoma, and multicentric Castleman disease. Despite significant progress in understanding KSHV pathobiology, no therapeutic guidelines for the management of KSHV-related diseases exist, and current treatments are suboptimal and associated with toxicity. Antiherpesvirus drugs have shown inconsistent results in KSHV-associated malignancies that harbour the virus in a latent state. However, lytic replication plays a crucial role in the process of tumorigenesis. Therefore, not only antiviral agents directed against the virus replicative cycle but also agents that target cellular processes that are activated by the virus are being investigated. Antivirals may also be used in combination with inducers of the viral lytic stage.
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15
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Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
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Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
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16
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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17
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Gable JE, Lee GM, Acker TM, Hulce KR, Gonzalez ER, Schweigler P, Melkko S, Farady CJ, Craik CS. Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem 2016; 11:862-9. [PMID: 26822284 DOI: 10.1002/cmdc.201500526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Indexed: 11/11/2022]
Abstract
Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Biophysics Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Timothy M Acker
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Kaitlin R Hulce
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.,Chemistry and Chemical Biology Graduate Group, University of California, San Francisco, CA, 94158-2280, USA
| | - Eric R Gonzalez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA
| | - Patrick Schweigler
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Samu Melkko
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Christopher J Farady
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, 4002, Basel, Switzerland
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158-2280, USA.
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18
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Long C, Guo W, Zhou H, Wang J, Wang H, Sun X. Triptolide decreases expression of latency-associated nuclear antigen 1 and reduces viral titers in Kaposi's sarcoma-associated and herpesvirus-related primary effusion lymphoma cells. Int J Oncol 2016; 48:1519-30. [PMID: 26821279 DOI: 10.3892/ijo.2016.3353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/11/2016] [Indexed: 11/06/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) can establish a life-long persistence in the host after primary infection and is associated with certain malignancies, which are resistant to conventional chemotherapeutic agents with a poor prognosis. Latency-associated nuclear antigen 1 (LANA1) encoded by KSHV is essential for segregation, replication and maintenance of viral genome. In addition, LANA1 upregulates the transcriptional activity of signal transducer and activator of transcription 3 (STAT3), which plays an important role in promoting survival of KSHV-associated primary effusion lymphoma (PEL) cells. Furthermore, LANA1 mediates transcriptional modulation of KSHV and host genome in host cells. In the present study, the antitumor effect of triptolide was assessed. CCK-8 assays were performed to demonstrate that the proliferations of PEL cells were efficiently inhibited by triptolide in a dose- and time-dependent manner. Flow cytometric results indicated that triptolide induced cell cycle arrest and apoptosis. Western blot results suggested that triptolide downregulated LANA1 expression and reduced half-life of LANA1 in the KSHV-infected malignant cells. Viral titer experiments indicated that triptolide treatment impaired the number of viral DNA copies and the production of virions in BCBL-1 cells. Triptolide also suppressed STAT3 activity and inhibited secretion of IL-6 in PEL cells. In a mouse xenograft model of primary effusion lymphoma by BCBL-1 cells, triptolide treatment significantly inhibited ascites formation and diffused organ infiltration. These results indicate that triptolide impairs the expression of LANA1 and shows antitumor activity against PEL in vitro and in vivo. Triptolide may be a potential agent for treatment of PEL.
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Affiliation(s)
- Cong Long
- Department of Pathogen Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wei Guo
- Department of Pathology and Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Heng Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Jingchao Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Huan Wang
- Department of Pathogen Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiaoping Sun
- Department of Pathogen Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P.R. China
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19
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Wilson AJ. Helix mimetics: Recent developments. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:33-40. [DOI: 10.1016/j.pbiomolbio.2015.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
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20
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Zühlsdorf M, Werten S, Klupp BG, Palm GJ, Mettenleiter TC, Hinrichs W. Dimerization-Induced Allosteric Changes of the Oxyanion-Hole Loop Activate the Pseudorabies Virus Assemblin pUL26N, a Herpesvirus Serine Protease. PLoS Pathog 2015; 11:e1005045. [PMID: 26161660 PMCID: PMC4498786 DOI: 10.1371/journal.ppat.1005045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/24/2015] [Indexed: 01/01/2023] Open
Abstract
Herpesviruses encode a characteristic serine protease with a unique fold and an active site that comprises the unusual triad Ser-His-His. The protease is essential for viral replication and as such constitutes a promising drug target. In solution, a dynamic equilibrium exists between an inactive monomeric and an active dimeric form of the enzyme, which is believed to play a key regulatory role in the orchestration of proteolysis and capsid assembly. Currently available crystal structures of herpesvirus proteases correspond either to the dimeric state or to complexes with peptide mimetics that alter the dimerization interface. In contrast, the structure of the native monomeric state has remained elusive. Here, we present the three-dimensional structures of native monomeric, active dimeric, and diisopropyl fluorophosphate-inhibited dimeric protease derived from pseudorabies virus, an alphaherpesvirus of swine. These structures, solved by X-ray crystallography to respective resolutions of 2.05, 2.10 and 2.03 Å, allow a direct comparison of the main conformational states of the protease. In the dimeric form, a functional oxyanion hole is formed by a loop of 10 amino-acid residues encompassing two consecutive arginine residues (Arg136 and Arg137); both are strictly conserved throughout the herpesviruses. In the monomeric form, the top of the loop is shifted by approximately 11 Å, resulting in a complete disruption of the oxyanion hole and loss of activity. The dimerization-induced allosteric changes described here form the physical basis for the concentration-dependent activation of the protease, which is essential for proper virus replication. Small-angle X-ray scattering experiments confirmed a concentration-dependent equilibrium of monomeric and dimeric protease in solution. Herpesviruses encode a unique serine protease, which is essential for herpesvirus capsid maturation and is therefore an interesting target for drug development. In solution, this protease exists in an equilibrium of an inactive monomeric and an active dimeric form. All currently available crystal structures of herpesvirus proteases represent complexes, particularly dimers. Here we show the first three-dimensional structure of the native monomeric form in addition to the native and the chemically inactivated dimeric form of the protease derived from the porcine herpesvirus pseudorabies virus. Comparison of the monomeric and dimeric form allows predictions on the structural changes that occur during dimerization and shed light onto the process of protease activation. These new crystal structures provide a rational base to develop drugs preventing dimerization and therefore impeding herpesvirus capsid maturation. Furthermore, it is likely that this mechanism is conserved throughout the herpesviruses.
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Affiliation(s)
- Martin Zühlsdorf
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastiaan Werten
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Barbara G. Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Gottfried J. Palm
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Thomas C. Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
- * E-mail:
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21
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Gable J, Acker TM, Craik CS. Current and potential treatments for ubiquitous but neglected herpesvirus infections. Chem Rev 2014; 114:11382-412. [PMID: 25275644 PMCID: PMC4254030 DOI: 10.1021/cr500255e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan
E. Gable
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
- Graduate
Group in Biophysics, University of California,
San Francisco, 600 16th
Street, San Francisco, California 94158-2280, United States
| | - Timothy M. Acker
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
| | - Charles S. Craik
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
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22
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Coen N, Duraffour S, Snoeck R, Andrei G. KSHV targeted therapy: an update on inhibitors of viral lytic replication. Viruses 2014; 6:4731-59. [PMID: 25421895 PMCID: PMC4246246 DOI: 10.3390/v6114731] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/07/2014] [Accepted: 11/17/2014] [Indexed: 01/01/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. Since the discovery of KSHV 20 years ago, there is still no standard treatment and the management of virus-associated malignancies remains toxic and incompletely efficacious. As the majority of tumor cells are latently infected with KSHV, currently marketed antivirals that target the virus lytic cycle have shown inconsistent results in clinic. Nevertheless, lytic replication plays a major role in disease progression and virus dissemination. Case reports and retrospective studies have pointed out the benefit of antiviral therapy in the treatment and prevention of KSHV-associated diseases. As a consequence, potent and selective antivirals are needed. This review focuses on the anti-KSHV activity, mode of action and current status of antiviral drugs targeting KSHV lytic cycle. Among these drugs, different subclasses of viral DNA polymerase inhibitors and compounds that do not target the viral DNA polymerase are being discussed. We also cover molecules that target cellular kinases, as well as the potential of new drug targets and animal models for antiviral testing.
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Affiliation(s)
- Natacha Coen
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Sophie Duraffour
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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23
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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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24
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Skoreński M, Sieńczyk M. Anti-herpesvirus agents: a patent and literature review (2003 to present). Expert Opin Ther Pat 2014; 24:925-41. [PMID: 25010889 DOI: 10.1517/13543776.2014.927442] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION The standard therapy used to treat herpesvirus infections is based on the application of DNA polymerase inhibitors such as ganciclovir or aciclovir. Unfortunately, all of these compounds exhibit relatively high toxicity and the mutation of herpesviruses results in the appearance of new drug-resistant strains. Consequently, there is a great need for the development of new, effective and safe anti-herpesvirus agents that employ different patterns of therapeutic action at various stages of the virus life cycle. AREAS COVERED Patents and patent applications concerning the development of anti-herpesvirus agents displaying different mechanisms of action that have been published since 2003 are reviewed. In addition, major discoveries in this field that have been published in academic papers have also been included. EXPERT OPINION Among all the anti-herpesvirus agents described in this article, the inhibitors of viral serine protease seem to present one of the most effective/promising therapeutics. Unfortunately, the practical application of these antiviral agents has not yet been proven in any clinical trials. Nevertheless, the dynamic and extensive work on this subject gives hope that a new class of anti-herpesvirus agents aimed at the enzymatic activity of herpesvirus serine protease may be developed.
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Affiliation(s)
- Marcin Skoreński
- Wroclaw University of Technology, Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw , Poland +48 71 320 24 39 ; +48 71 320 24 27 ;
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25
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Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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Duran-Frigola M, Mosca R, Aloy P. Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development. ACTA ACUST UNITED AC 2013; 20:674-84. [DOI: 10.1016/j.chembiol.2013.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 03/05/2013] [Indexed: 01/12/2023]
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27
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Lee GM, Balouch E, Goetz DH, Lazic A, McKerrow JH, Craik CS. Mapping inhibitor binding modes on an active cysteine protease via nuclear magnetic resonance spectroscopy. Biochemistry 2012. [PMID: 23181936 DOI: 10.1021/bi301305k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cruzain is a member of the papain/cathepsin L family of cysteine proteases, and the major cysteine protease of the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We report an autoinduction methodology that provides soluble cruzain in high yields (>30 mg/L in minimal medium). These increased yields provide sufficient quantities of active enzyme for use in nuclear magnetic resonance (NMR)-based ligand mapping. Using circular dichroism and NMR spectroscopy, we also examined the solution-state structural dynamics of the enzyme in complex with a covalently bound vinyl sulfone inhibitor (K777). We report the backbone amide and side chain carbon chemical shift assignments of cruzain in complex with K777. These resonance assignments were used to identify and map residues located in the substrate binding pocket, including the catalytic Cys25 and His162. Selective [(15)N]Cys, [(15)N]His, and [(13)C]Met labeling was performed to quickly assess cruzain-ligand interactions for a set of eight low-molecular weight compounds exhibiting micromolar binding or inhibition. Chemical shift perturbation mapping verified that six of the eight compounds bind to cruzain at the active site. Three different binding modes were delineated for the compounds, namely, covalent, noncovalent, and noninteracting. These results provide examples of how NMR spectroscopy can be used to screen compounds for fast evaluation of enzyme-inhibitor interactions to facilitate lead compound identification and subsequent structural studies.
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Affiliation(s)
- Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280, USA
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28
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Nussinov R, Tsai CJ, Csermely P. Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol Sci 2011; 32:686-93. [PMID: 21925743 PMCID: PMC7380718 DOI: 10.1016/j.tips.2011.08.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/16/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
Abstract
Allosteric drugs are increasingly used because they produce fewer side effects. Allosteric signal propagation does not stop at the 'end' of a protein, but may be dynamically transmitted across the cell. We propose here that the concept of allosteric drugs can be broadened to 'allo-network drugs' - whose effects can propagate either within a protein, or across several proteins, to enhance or inhibit specific interactions along a pathway. We posit that current allosteric drugs are a special case of allo-network drugs, and suggest that allo-network drugs can achieve specific, limited changes at the systems level, and in this way can achieve fewer side effects and lower toxicity. Finally, we propose steps and methods to identify allo-network drug targets and sites that outline a new paradigm in systems-based drug design.
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Affiliation(s)
- Ruth Nussinov
- Center for Cancer Research Nanobiology Program, Science Applications International Corporation-Frederick, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
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