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Jamieson AM. Host resilience to emerging coronaviruses. Future Virol 2016; 11:529-534. [PMID: 32201496 PMCID: PMC7079962 DOI: 10.2217/fvl-2016-0060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022]
Abstract
Recently, two coronaviruses, severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, have emerged to cause unusually severe respiratory disease in humans. Currently, there is a lack of effective antiviral treatment options or vaccine available. Given the severity of these outbreaks, and the possibility of additional zoonotic coronaviruses emerging in the near future, the exploration of different treatment strategies is necessary. Disease resilience is the ability of a given host to tolerate an infection, and to return to a state of health. This review focuses on exploring various host resilience mechanisms that could be exploited for treatment of severe acute respiratory syndrome coronavirus, Middle East respiratory syndrome coronavirus and other respiratory viruses that cause acute lung injury and acute respiratory distress syndrome.
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Affiliation(s)
- Amanda M Jamieson
- Department of Microbiology and Immunology, Brown University, Providence, RI, USA
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52
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Lei J, Hilgenfeld R. Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin. Virol Sin 2016; 31:288-99. [PMID: 27245450 PMCID: PMC7090527 DOI: 10.1007/s12250-016-3742-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
The papain-like protease (PL(pro)) of Middle-East respiratory syndrome coronavirus (MERS-CoV) has proteolytic, deubiquitinating, and deISGylating activities. The latter two are involved in the suppression of the antiviral innate immune response of the host cell. To contribute to an understanding of this process, we present here the X-ray crystal structure of a complex between MERS-CoV PL(pro) and human ubiquitin (Ub) that is devoid of any covalent linkage between the two proteins. Five regions of the PL(pro) bind to two areas of the Ub. The C-terminal five residues of Ub, RLRGG, are similar to the P5-P1 residues of the polyprotein substrates of the PL(pro) and are responsible for the major part of the interaction between the two macromolecules. Through sitedirected mutagenesis, we demonstrate that conserved Asp165 and non-conserved Asp164 are important for the catalytic activities of MERS-CoV PL(pro). The enzyme appears not to be optimized for catalytic efficiency; thus, replacement of Phe269 by Tyr leads to increased peptidolytic and deubiquitinating activities. Ubiquitin binding by MERS-CoV PL(pro) involves remarkable differences compared to the corresponding complex with SARS-CoV PL(pro). The structure and the mutational study help understand common and unique features of the deubiquitinating activity of MERS-CoV PL(pro).
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), University of Lübeck, 23562, Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23562, Lübeck, Germany.
- German Center for Infection Research (DZIF), University of Lübeck, 23562, Lübeck, Germany.
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Hu X, Compton JR, Leary DH, Olson MA, Lee MS, Cheung J, Ye W, Ferrer M, Southall N, Jadhav A, Morazzani EM, Glass PJ, Marugan J, Legler PM. Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease. Biochemistry 2016; 55:3007-19. [PMID: 27030368 DOI: 10.1021/acs.biochem.5b00992] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.-) is essential for viral replication and is involved in the cytopathic effects (CPE) of the virus. The VEEV nsP2 protease is a member of MEROPS Clan CN and characteristically contains a papain-like protease linked to an S-adenosyl-l-methionine-dependent RNA methyltransferase (SAM MTase) domain. The protease contains an alternative active site motif, (475)NVCWAK(480), which differs from papain's (CGS(25)CWAFS), and the enzyme lacks a transition state-stabilizing residue homologous to Gln-19 in papain. To understand the roles of conserved residues in catalysis, we determined the structure of the free enzyme and the first structure of an inhibitor-bound alphaviral protease. The peptide-like E64d inhibitor was found to bind beneath a β-hairpin at the interface of the SAM MTase and protease domains. His-546 adopted a conformation that differed from that found in the free enzyme; one or both of the conformers may assist in leaving group departure of either the amine or Cys thiolate during the catalytic cycle. Interestingly, E64c (200 μM), the carboxylic acid form of the E64d ester, did not inhibit the nsP2 protease. To identify key residues involved in substrate binding, a number of mutants were analyzed. Mutation of the motif residue, N475A, led to a 24-fold reduction in kcat/Km, and the conformation of this residue did not change after inhibition. N475 forms a hydrogen bond with R662 in the SAM MTase domain, and the R662A and R662K mutations both led to 16-fold decreases in kcat/Km. N475 forms the base of the P1 binding site and likely orients the substrate for nucleophilic attack or plays a role in product release. An Asn homologous to N475 is similarly found in coronaviral papain-like proteases (PLpro) of the Severe Acute Respiratory Syndrome (SARS) virus and Middle East Respiratory Syndrome (MERS) virus. Mutation of another motif residue, K480A, led to a 9-fold decrease in kcat and kcat/Km. K480 likely enhances the nucleophilicity of the Cys. Consistent with our substrate-bound models, the SAM MTase domain K706A mutation increased Km 4.5-fold to 500 μM. Within the β-hairpin, the N545A mutation slightly but not significantly increased kcat and Km. The structures and identified active site residues may facilitate the discovery of protease inhibitors with antiviral activity.
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Affiliation(s)
- Xin Hu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | | | - Dagmar H Leary
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
| | - Mark A Olson
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Michael S Lee
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Jonah Cheung
- New York Structural Biology Center , New York, New York 10027, United States
| | - Wenjuan Ye
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Mark Ferrer
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Noel Southall
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Elaine M Morazzani
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Pamela J Glass
- United States Army Medical Research Institute of Infectious Diseases , Frederick, Maryland 21702, United States
| | - Juan Marugan
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences , Rockville, Maryland 20850, United States
| | - Patricia M Legler
- Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory , Washington, D.C. 20375, United States
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Jadav SS, Ganta NM, Kumar A, Dan N, Mohanty NP. The updates on Middle East Respiratory Syndrome coronavirus (MERS-CoV) epidemiology, pathogenesis, viral genome and currently available drugs. ACTA ACUST UNITED AC 2016. [DOI: 10.14805/jphchem.2016.art47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Middle East Respiratory Syndrome (MERS) is caused by the novel coronavirus belongs to the family Betacoronaviridae was first identified in Saudi Arabia during 2012. The first epidemic outbreak of the MERS-CoV has been started reporting in the South Korea and other Asian Countries. The disease was transmitted to humans to humans from the Middle East to other countries through travelling history. The MERS-CoV is responsible for the lower acute and severe respiratory disorder causes the shortness of breath along with fever and cough. The treatment for the disease is purely symptomatic and vaccination is not existed. In the present work we are tried to compile the epidemiology, pathogenesis, viral genome and currently available drugs. At the last the promising approaches for the drug design and development process has been presented.
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Shehata MM, Gomaa MR, Ali MA, Kayali G. Middle East respiratory syndrome coronavirus: a comprehensive review. Front Med 2016; 10:120-36. [PMID: 26791756 PMCID: PMC7089261 DOI: 10.1007/s11684-016-0430-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/18/2015] [Indexed: 01/07/2023]
Abstract
The Middle East respiratory syndrome coronavirus was first identified in 2012 and has since then remained uncontrolled. Cases have been mostly reported in the Middle East, however travel-associated cases and outbreaks have also occurred. Nosocomial and zoonotic transmission of the virus appear to be the most important routes. The infection is severe and highly fatal thus necessitating rapid and efficacious interventions. Here, we performed a comprehensive review of published literature and summarized the epidemiology of the virus. In addition, we summarized the virological aspects of the infection and reviewed the animal models used as well as vaccination and antiviral tested against it.
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Affiliation(s)
- Mahmoud M Shehata
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Mokhtar R Gomaa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Mohamed A Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Ghazi Kayali
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Abstract
This review examines the small molecules described over the past decade as inhibitors of any of the approximately 100 human deubiquitinating enzymes (DUBs). Structures from patent publications as well as from the primary literature are included. Inhibitors of two viral DUBs are also described since these proteases share structural similarity with one of the human DUB sub-families. The structure, function and disease associations of certain DUBs are presented. The evolution of the screening assays used to identify and characterise new inhibitors is discussed. Several emerging trends in the series are highlighted and the ‘drug-likeness’ of the various inhibitors is analysed. Large pharmaceutical company collaborations have drawn attention to this field, and these recent advances are discussed in the context of the wider range of therapeutically important DUB targets.
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Affiliation(s)
- Mark Kemp
- MISSION Therapeutics, Babraham Research Campus, Cambridge, United Kingdom
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57
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Cho CC, Lin MH, Chuang CY, Hsu CH. Macro Domain from Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Is an Efficient ADP-ribose Binding Module: CRYSTAL STRUCTURE AND BIOCHEMICAL STUDIES. J Biol Chem 2016; 291:4894-902. [PMID: 26740631 PMCID: PMC4777827 DOI: 10.1074/jbc.m115.700542] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Indexed: 01/12/2023] Open
Abstract
The newly emerging Middle East respiratory syndrome coronavirus (MERS-CoV)
encodes the conserved macro domain within non-structural protein 3. However, the
precise biochemical function and structure of the macro domain is unclear. Using
differential scanning fluorimetry and isothermal titration calorimetry, we
characterized the MERS-CoV macro domain as a more efficient adenosine
diphosphate (ADP)-ribose binding module than macro domains from other CoVs.
Furthermore, the crystal structure of the MERS-CoV macro domain was determined
at 1.43-Å resolution in complex with ADP-ribose. Comparison of macro
domains from MERS-CoV and other human CoVs revealed structural differences in
the α1 helix alters how the conserved Asp-20 interacts with ADP-ribose and
may explain the efficient binding of the MERS-CoV macro domain to ADP-ribose.
This study provides structural and biophysical bases to further evaluate the
role of the MERS-CoV macro domain in the host response via ADP-ribose binding
but also as a potential target for drug design.
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Affiliation(s)
- Chao-Cheng Cho
- From the Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617
| | - Meng-Hsuan Lin
- From the Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617
| | - Chien-Ying Chuang
- the Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, and the Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- From the Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, the Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, and the Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
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58
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Chen Y, Savinov SN, Mielech AM, Cao T, Baker SC, Mesecar AD. X-ray Structural and Functional Studies of the Three Tandemly Linked Domains of Non-structural Protein 3 (nsp3) from Murine Hepatitis Virus Reveal Conserved Functions. J Biol Chem 2015; 290:25293-306. [PMID: 26296883 PMCID: PMC4646180 DOI: 10.1074/jbc.m115.662130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/06/2022] Open
Abstract
Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional studies on MHV and its nsp3 domain, the structure of only one domain in nsp3, the small ubiquitin-like domain 1 (Ubl1), has been determined. We report here the x-ray structure of three tandemly linked domains of MHV nsp3, including the papain-like protease 2 (PLP2) catalytic domain, the ubiquitin-like domain 2 (Ubl2), and a third domain that we call the DPUP (domain preceding Ubl2 and PLP2) domain. DPUP has close structural similarity to the severe acute respiratory syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to the severe acute respiratory syndrome coronavirus. The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating isopeptidase activities in addition to proteolytic activity. A computationally derived model of MHV PLP2 bound to ubiquitin was generated, and the potential interactions between ubiquitin and PLP2 were probed by site-directed mutagenesis. These studies extend substantially our structural knowledge of MHV nsp3, providing a platform for further investigation of the role of nsp3 domains in MHV viral replication.
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Affiliation(s)
| | | | - Anna M Mielech
- the Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153
| | - Thu Cao
- From the Department of Biological Sciences
| | - Susan C Baker
- the Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University of Chicago, Maywood, Illinois 60153
| | - Andrew D Mesecar
- From the Department of Biological Sciences, the Center for Cancer Research, and the Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 and
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59
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Lee H, Lei H, Santarsiero BD, Gatuz JL, Cao S, Rice AJ, Patel K, Szypulinski MZ, Ojeda I, Ghosh AK, Johnson ME. Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV. ACS Chem Biol 2015; 10:1456-65. [PMID: 25746232 PMCID: PMC4845099 DOI: 10.1021/cb500917m] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Middle East Respiratory Syndrome coronavirus (MERS-CoV) papain-like protease (PLpro) blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it has been proven to play a crucial role in SARS-CoV PLpro inhibitor binding. Four SARS-CoV PLpro lead inhibitors were tested against MERS-CoV PLpro, none of which were effective against MERS-CoV PLpro. Structure and sequence alignments revealed that two residues, Y269 and Q270, responsible for inhibitor binding to SARS-CoV PLpro, were replaced by T274 and A275 in MERS-CoV PLpro, making critical binding interactions difficult to form for similar types of inhibitors. High-throughput screening (HTS) of 25 000 compounds against both PLpro enzymes identified a small fragment-like noncovalent dual inhibitor. Mode of inhibition studies by enzyme kinetics and competition surface plasmon resonance (SPR) analyses suggested that this compound acts as a competitive inhibitor with an IC50 of 6 μM against MERS-CoV PLpro, indicating that it binds to the active site, whereas it acts as an allosteric inhibitor against SARS-CoV PLpro with an IC50 of 11 μM. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpro may differ from that of SARS-CoV PLpro. In addition, inhibitory activity of this compound was selective for SARS-CoV and MERS-CoV PLpro enzymes over two human homologues, the ubiquitin C-terminal hydrolases 1 and 3 (hUCH-L1 and hUCH-L3).
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Affiliation(s)
- Hyun Lee
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Hao Lei
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Bernard D. Santarsiero
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Joseph L. Gatuz
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Shuyi Cao
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Amy J. Rice
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Kavankumar Patel
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | - Michael Z. Szypulinski
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
| | | | - Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 900 S. Ashland, Chicago, Illinois 60607, United States
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Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev 2015; 28:465-522. [PMID: 25810418 DOI: 10.1128/cmr.00102-14] [Citation(s) in RCA: 599] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The source of the severe acute respiratory syndrome (SARS) epidemic was traced to wildlife market civets and ultimately to bats. Subsequent hunting for novel coronaviruses (CoVs) led to the discovery of two additional human and over 40 animal CoVs, including the prototype lineage C betacoronaviruses, Tylonycteris bat CoV HKU4 and Pipistrellus bat CoV HKU5; these are phylogenetically closely related to the Middle East respiratory syndrome (MERS) CoV, which has affected more than 1,000 patients with over 35% fatality since its emergence in 2012. All primary cases of MERS are epidemiologically linked to the Middle East. Some of these patients had contacted camels which shed virus and/or had positive serology. Most secondary cases are related to health care-associated clusters. The disease is especially severe in elderly men with comorbidities. Clinical severity may be related to MERS-CoV's ability to infect a broad range of cells with DPP4 expression, evade the host innate immune response, and induce cytokine dysregulation. Reverse transcription-PCR on respiratory and/or extrapulmonary specimens rapidly establishes diagnosis. Supportive treatment with extracorporeal membrane oxygenation and dialysis is often required in patients with organ failure. Antivirals with potent in vitro activities include neutralizing monoclonal antibodies, antiviral peptides, interferons, mycophenolic acid, and lopinavir. They should be evaluated in suitable animal models before clinical trials. Developing an effective camel MERS-CoV vaccine and implementing appropriate infection control measures may control the continuing epidemic.
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Murine coronavirus ubiquitin-like domain is important for papain-like protease stability and viral pathogenesis. J Virol 2015; 89:4907-17. [PMID: 25694594 DOI: 10.1128/jvi.00338-15] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Ubiquitin-like domains (Ubls) now are recognized as common elements adjacent to viral and cellular proteases; however, their function is unclear. Structural studies of the papain-like protease (PLP) domains of coronaviruses (CoVs) revealed an adjacent Ubl domain in severe acute respiratory syndrome CoV, Middle East respiratory syndrome CoV, and the murine CoV, mouse hepatitis virus (MHV). Here, we tested the effect of altering the Ubl adjacent to PLP2 of MHV on enzyme activity, viral replication, and pathogenesis. Using deletion and substitution approaches, we identified sites within the Ubl domain, residues 785 to 787 of nonstructural protein 3, which negatively affect protease activity, and valine residues 785 and 787, which negatively affect deubiquitinating activity. Using reverse genetics, we engineered Ubl mutant viruses and found that AM2 (V787S) and AM3 (V785S) viruses replicate efficiently at 37°C but generate smaller plaques than wild-type (WT) virus, and AM2 is defective for replication at higher temperatures. To evaluate the effect of the mutation on protease activity, we purified WT and Ubl mutant PLP2 and found that the proteases exhibit similar specific activities at 25°C. However, the thermal stability of the Ubl mutant PLP2 was significantly reduced at 30°C, thereby reducing the total enzymatic activity. To determine if the destabilizing mutation affects viral pathogenesis, we infected C57BL/6 mice with WT or AM2 virus and found that the mutant virus is highly attenuated, yet it replicates sufficiently to elicit protective immunity. These studies revealed that modulating the Ubl domain adjacent to the PLP reduces protease stability and viral pathogenesis, revealing a novel approach to coronavirus attenuation. IMPORTANCE Introducing mutations into a protein or virus can have either direct or indirect effects on function. We asked if changes in the Ubl domain, a conserved domain adjacent to the coronavirus papain-like protease, altered the viral protease activity or affected viral replication or pathogenesis. Our studies using purified wild-type and Ubl mutant proteases revealed that mutations in the viral Ubl domain destabilize and inactivate the adjacent viral protease. Furthermore, we show that a CoV encoding the mutant Ubl domain is unable to replicate at high temperature or cause lethal disease in mice. Our results identify the coronavirus Ubl domain as a novel modulator of viral protease stability and reveal manipulating the Ubl domain as a new approach for attenuating coronavirus replication and pathogenesis.
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62
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Kong L, Shaw N, Yan L, Lou Z, Rao Z. Structural view and substrate specificity of papain-like protease from avian infectious bronchitis virus. J Biol Chem 2015; 290:7160-8. [PMID: 25609249 PMCID: PMC4358136 DOI: 10.1074/jbc.m114.628636] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Papain-like protease (PLpro) of coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses. Avian infectious bronchitis virus (IBV), the causative agent of bronchitis in chicken that results in huge economic losses every year in the poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade Lys48- and Lys63-linked polyubiquitin chains to monoubiquitin but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15-Å resolution. The overall structure is reminiscent of the structure of severe acute respiratory syndrome CoV PLpro. However, unlike the severe acute respiratory syndrome CoV PLpro that lacks blocking loop (BL) 1 of deubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys101, His264, and Asp275 is regulated by the flexible BL2. A model of ubiquitin-bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 subsites as well as residues interacting with the β-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-7-amino-4-methylcoumarin and LRGG-7-amino-4-methylcoumarin with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.
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Affiliation(s)
- Lingying Kong
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Neil Shaw
- College of Life Sciences, Nankai University, Tianjin 300071, China, and National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Lingming Yan
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhiyong Lou
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zihe Rao
- From the Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China, College of Life Sciences, Nankai University, Tianjin 300071, China, and National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
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63
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Báez-Santos YM, St John SE, Mesecar AD. The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antiviral Res 2014; 115:21-38. [PMID: 25554382 PMCID: PMC5896749 DOI: 10.1016/j.antiviral.2014.12.015] [Citation(s) in RCA: 573] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/17/2014] [Accepted: 12/19/2014] [Indexed: 02/06/2023]
Abstract
HTS and structure-based design produced naphthalene-based lead compounds with inhibition of SARS-CoV PLpro in the nM range. These naphthalene-based lead compounds have antiviral potency against SARS-CoV in cell culture. SARS-CoV PLpro naphthalene-based inhibitors are non-toxic and highly selective for SARS-CoV PLpro. Designed SARS-CoV PLpro inhibitors act through a non-covalent, competitive mechanism of inhibition. Lessons from design of SARS-CoV PLpro inhibitors have profound implications for other USPs implicated in disease processes.
Over 10 years have passed since the deadly human coronavirus that causes severe acute respiratory syndrome (SARS-CoV) emerged from the Guangdong Province of China. Despite the fact that the SARS-CoV pandemic infected over 8500 individuals, claimed over 800 lives and cost billions of dollars in economic loss worldwide, there still are no clinically approved antiviral drugs, vaccines or monoclonal antibody therapies to treat SARS-CoV infections. The recent emergence of the deadly human coronavirus that causes Middle East respiratory syndrome (MERS-CoV) is a sobering reminder that new and deadly coronaviruses can emerge at any time with the potential to become pandemics. Therefore, the continued development of therapeutic and prophylactic countermeasures to potentially deadly coronaviruses is warranted. The coronaviral proteases, papain-like protease (PLpro) and 3C-like protease (3CLpro), are attractive antiviral drug targets because they are essential for coronaviral replication. Although the primary function of PLpro and 3CLpro are to process the viral polyprotein in a coordinated manner, PLpro has the additional function of stripping ubiquitin and ISG15 from host-cell proteins to aid coronaviruses in their evasion of the host innate immune responses. Therefore, targeting PLpro with antiviral drugs may have an advantage in not only inhibiting viral replication but also inhibiting the dysregulation of signaling cascades in infected cells that may lead to cell death in surrounding, uninfected cells. This review provides an up-to-date discussion on the SARS-CoV papain-like protease including a brief overview of the SARS-CoV genome and replication followed by a more in-depth discussion on the structure and catalytic mechanism of SARS-CoV PLpro, the multiple cellular functions of SARS-CoV PLpro, the inhibition of SARS-CoV PLpro by small molecule inhibitors, and the prospect of inhibiting papain-like protease from other coronaviruses. This paper forms part of a series of invited articles in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.”
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Affiliation(s)
- Yahira M Báez-Santos
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Sarah E St John
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Andrew D Mesecar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Department of Chemistry, Purdue University, West Lafayette, IN, USA; Center for Drug Discovery, Purdue University, West Lafayette, IN, USA; Center for Cancer Research, Purdue University, West Lafayette, IN, USA.
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64
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Cheng KW, Cheng SC, Chen WY, Lin MH, Chuang SJ, Cheng IH, Sun CY, Chou CY. Thiopurine analogs and mycophenolic acid synergistically inhibit the papain-like protease of Middle East respiratory syndrome coronavirus. Antiviral Res 2014; 115:9-16. [PMID: 25542975 PMCID: PMC7113672 DOI: 10.1016/j.antiviral.2014.12.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 01/08/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a new highly pathogenic human coronaviruses that emerged in Jeddah and Saudi Arabia and has quickly spread to other countries in Middle East, Europe and North Africa since 2012. Up to 17 December 2014, it has infected at least 938 people with a fatality rate of about 36% globally. This has resulted in an urgent need to identify antiviral drugs that are active against MERS-CoV. The papain-like protease (PL(pro)) of MERS-CoV represents an important antiviral target as it is not only essential for viral maturation, but also antagonizes interferon stimulation of the host via its deubiquitination activity. Here, we report the discovery that two SARS-CoV PL(pro) inhibitors, 6-mercaptopurine (6MP) and 6-thioguanine (6TG), as well as the immunosuppressive drug mycophenolic acid, are able to inhibit MERS-CoV PL(pro). Their inhibition mechanisms and mutually binding synergistic effect were also investigated. Our results identify for the first time three inhibitors targeting MERS-CoV PL(pro) and these can now be used as lead compounds for further antiviral drug development.
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Affiliation(s)
- Kai-Wen Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Shu-Chun Cheng
- Department of Nephrology, Chang-Gung Memorial Hospital, Keelung 204, Taiwan
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Min-Han Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Shang-Ju Chuang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - I-Hsin Cheng
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Chiao-Yin Sun
- Department of Nephrology, Chang-Gung Memorial Hospital, Keelung 204, Taiwan.
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
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Bailey-Elkin BA, Knaap RCM, Johnson GG, Dalebout TJ, Ninaber DK, van Kasteren PB, Bredenbeek PJ, Snijder EJ, Kikkert M, Mark BL. Crystal structure of the Middle East respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression. J Biol Chem 2014; 289:34667-82. [PMID: 25320088 PMCID: PMC4263872 DOI: 10.1074/jbc.m114.609644] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerging human
pathogen that was first isolated in 2012. MERS-CoV replication depends in part
on a virus-encoded papain-like protease (PLpro) that cleaves the
viral replicase polyproteins at three sites releasing non-structural protein 1
(nsp1), nsp2, and nsp3. In addition to this replicative function, MERS-CoV
PLpro was recently shown to be a deubiquitinating enzyme (DUB)
and to possess deISGylating activity, as previously reported for other
coronaviral PLpro domains, including that of severe acute respiratory
syndrome coronavirus. These activities have been suggested to suppress host
antiviral responses during infection. To understand the molecular basis for
ubiquitin (Ub) recognition and deconjugation by MERS-CoV PLpro, we
determined its crystal structure in complex with Ub. Guided by this structure,
mutations were introduced into PLpro to specifically disrupt Ub
binding without affecting viral polyprotein cleavage, as determined using an in
trans nsp3↓4 cleavage assay. Having developed a
strategy to selectively disable PLpro DUB activity, we were able to
specifically examine the effects of this activity on the innate immune response.
Whereas the wild-type PLpro domain was found to suppress
IFN-β promoter activation, PLpro variants specifically
lacking DUB activity were no longer able to do so. These findings directly
implicate the DUB function of PLpro, and not its proteolytic activity
per se, in the inhibition of IFN-β promoter
activity. The ability to decouple the DUB activity of PLpro from its
role in viral polyprotein processing now provides an approach to further dissect
the role(s) of PLpro as a viral DUB during MERS-CoV infection.
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Affiliation(s)
- Ben A Bailey-Elkin
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Robert C M Knaap
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Garrett G Johnson
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Tim J Dalebout
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dennis K Ninaber
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Puck B van Kasteren
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Peter J Bredenbeek
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eric J Snijder
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Marjolein Kikkert
- the Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian L Mark
- From the Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
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66
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Catalytic function and substrate specificity of the papain-like protease domain of nsp3 from the Middle East respiratory syndrome coronavirus. J Virol 2014; 88:12511-27. [PMID: 25142582 DOI: 10.1128/jvi.01294-14] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The papain-like protease (PLpro) domain from the deadly Middle East respiratory syndrome coronavirus (MERS-CoV) was overexpressed and purified. MERS-CoV PLpro constructs with and without the putative ubiquitin-like (UBL) domain at the N terminus were found to possess protease, deubiquitinating, deISGylating, and interferon antagonism activities in transfected HEK293T cells. The quaternary structure and substrate preferences of MERS-CoV PLpro were determined and compared to those of severe acute respiratory syndrome coronavirus (SARS-CoV) PLpro, revealing prominent differences between these closely related enzymes. Steady-state kinetic analyses of purified MERS-CoV and SARS-CoV PLpros uncovered significant differences in their rates of hydrolysis of 5-aminomethyl coumarin (AMC) from C-terminally labeled peptide, ubiquitin, and ISG15 substrates, as well as in their rates of isopeptide bond cleavage of K48- and K63-linked polyubiquitin chains. MERS-CoV PLpro was found to have 8-fold and 3,500-fold higher catalytic efficiencies for hydrolysis of ISG15-AMC than for hydrolysis of the Ub-AMC and Z-RLRGG-AMC substrates, respectively. A similar trend was observed for SARS-CoV PLpro, although it was much more efficient than MERS-CoV PLpro toward ISG15-AMC and peptide-AMC substrates. MERS-CoV PLpro was found to process K48- and K63-linked polyubiquitin chains at similar rates and with similar debranching patterns, producing monoubiquitin species. However, SARS-CoV PLpro much preferred K48-linked polyubiquitin chains to K63-linked chains, and it rapidly produced di-ubiquitin molecules from K48-linked chains. Finally, potent inhibitors of SARS-CoV PLpro were found to have no effect on MERS-CoV PLpro. A homology model of the MERS-CoV PLpro structure was generated and compared to the X-ray structure of SARS-CoV PLpro to provide plausible explanations for differences in substrate and inhibitor recognition. IMPORTANCE Unlocking the secrets of how coronavirus (CoV) papain-like proteases (PLpros) perform their multifunctional roles during viral replication entails a complete mechanistic understanding of their substrate recognition and enzymatic activities. We show that the PLpro domains from the MERS and SARS coronaviruses can recognize and process the same substrates, but with different catalytic efficiencies. The differences in substrate recognition between these closely related PLpros suggest that neither enzyme can be used as a generalized model to explain the kinetic behavior of all CoV PLpros. As a consequence, decoding the mechanisms of PLpro-mediated antagonism of the host innate immune response and the development of anti-CoV PLpro enzyme inhibitors will be a challenging undertaking. The results from this study provide valuable information for understanding how MERS-CoV PLpro-mediated antagonism of the host innate immune response is orchestrated, as well as insight into the design of inhibitors against MERS-CoV PLpro.
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Hilgenfeld R. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 2014; 281:4085-96. [PMID: 25039866 PMCID: PMC7163996 DOI: 10.1111/febs.12936] [Citation(s) in RCA: 437] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023]
Abstract
This review focuses on the important contributions that macromolecular crystallography has made over the past 12 years to elucidating structures and mechanisms of the essential proteases of coronaviruses, the main protease (M(pro) ) and the papain-like protease (PL(pro) ). The role of X-ray crystallography in structure-assisted drug discovery against these targets is discussed. Aspects dealt with in this review include the emergence of the SARS coronavirus in 2002-2003 and of the MERS coronavirus 10 years later and the origins of these viruses. The crystal structure of the free SARS coronavirus M(pro) and its dependence on pH is discussed, as are efforts to design inhibitors on the basis of these structures. The mechanism of maturation of the enzyme from the viral polyprotein is still a matter of debate. The crystal structure of the SARS coronavirus PL(pro) and its complex with ubiquitin is also discussed, as is its orthologue from MERS coronavirus. Efforts at predictive structure-based inhibitor development for bat coronavirus M(pro) s to increase the preparedness against zoonotic transmission to man are described as well. The paper closes with a brief discussion of structure-based discovery of antivirals in an academic setting.
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Affiliation(s)
- Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, and German Center for Infection Research, University of Lübeck, Germany
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