1
|
Le NMT, So KK, Chun J, Kim DH. Expression of virus-like particles (VLPs) of foot-and-mouth disease virus (FMDV) using Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2024; 108:81. [PMID: 38194136 PMCID: PMC10776484 DOI: 10.1007/s00253-023-12902-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/19/2023] [Accepted: 09/30/2023] [Indexed: 01/10/2024]
Abstract
We engineered Saccharomyces cerevisiae to express structural proteins of foot-and-mouth disease virus (FMDV) and produce virus-like particles (VLPs). The gene, which encodes four structural capsid proteins (VP0 (VP4 and VP2), VP3, and VP1), followed by a translational "ribosomal skipping" sequence consisting of 2A and protease 3C, was codon-optimized and chemically synthesized. The cloned gene was used to transform S. cerevisiae 2805 strain. Western blot analysis revealed that the polyprotein consisting of VP0, VP3, and VP1 was processed into the discrete capsid proteins. Western blot analysis of 3C confirmed the presence of discrete 3C protein, suggesting that the 2A sequence functioned as a "ribosomal skipping" signal in the yeast for an internal re-initiation of 3C translation from a monocistronic transcript, thereby indicating polyprotein processing by the discrete 3C protease. Moreover, a band corresponding to only VP2, which was known to be non-enzymatically processed from VP0 to both VP4 and VP2 during viral assembly, further validated the assembly of processed capsid proteins into VLPs. Electron microscopy showed the presence of the characteristic icosahedral VLPs. Our results clearly demonstrate that S. cerevisiae processes the viral structural polyprotein using a viral 3C protease and the resulting viral capsid subunits are assembled into virion particles. KEY POINTS: • Ribosomal skipping by self-cleaving FMDV peptide in S. cerevisiae. • Proteolytic processing of a structural polyprotein from a monocistronic transcript. • Assembly of the processed viral capsid proteins into a virus-like particle.
Collapse
Affiliation(s)
- Ngoc My Tieu Le
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, 54896, Jeollabuk-do, Republic of Korea
| | - Kum-Kang So
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, Republic of Korea
| | - Jeesun Chun
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, Republic of Korea
| | - Dae-Hyuk Kim
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, 54896, Jeollabuk-do, Republic of Korea.
- Institute for Molecular Biology and Genetics, Department of Molecular Biology, Jeonbuk National University, Jeonju, Jeollabuk-Do, Republic of Korea.
| |
Collapse
|
2
|
Kim Y, Pool E, Kim E, Dampalla CS, Nguyen HN, Johnson DK, Lovell S, Groutas WC, Chang KO. Potent small molecule inhibitors against the 3C protease of foot-and-mouth disease virus. Microbiol Spectr 2024; 12:e0337223. [PMID: 38466127 DOI: 10.1128/spectrum.03372-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/18/2024] [Indexed: 03/12/2024] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most devastating diseases of livestock which can cause significant economic losses, especially when introduced to FMD-free countries. FMD virus (FMDV) belongs to the family Picornaviridae and is antigenically heterogeneous with seven established serotypes. The prevailing preventive and control strategies are limited to restriction of animal movement and elimination of infected or exposed animals, which can be potentially combined with vaccination. However, FMD vaccination has limitations including delayed protection and lack of cross-protection against different serotypes. Recently, antiviral drug use for FMD outbreaks has increasingly been recognized as a potential tool to augment the existing early response strategies, but limited research has been reported on potential antiviral compounds for FMDV. FMDV 3C protease (3Cpro) cleaves the viral-encoded polyprotein into mature and functional proteins during viral replication. The essential role of viral 3Cpro in viral replication and the high conservation of 3Cpro among different FMDV serotypes make it an excellent target for antiviral drug development. We have previously reported multiple series of inhibitors against picornavirus 3Cpro or 3C-like proteases (3CLpros) encoded by coronaviruses or caliciviruses. In this study, we conducted structure-activity relationship studies for our in-house focused compound library containing 3Cpro or 3CLpro inhibitors against FMDV 3Cpro using enzyme and cell-based assays. Herein, we report the discovery of aldehyde and α-ketoamide inhibitors of FMDV 3Cpro with high potency. These data inform future preclinical studies that are related to the advancement of these compounds further along the drug development pathway.IMPORTANCEFood-and-mouth disease (FMD) virus (FMDV) causes devastating disease in cloven-hoofed animals with a significant economic impact. Emergency response to FMD outbreaks to limit FMD spread is critical, and the use of antivirals may overcome the limitations of existing control measures by providing immediate protection for susceptible animals. FMDV encodes 3C protease (3Cpro), which is essential for virus replication and an attractive target for antiviral drug discovery. Here, we report a structure-activity relationship study on multiple series of protease inhibitors and identified potent inhibitors of FMDV 3Cpro. Our results suggest that these compounds have the potential for further development as FMD antivirals.
Collapse
Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Emma Pool
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Eunji Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - David K Johnson
- Computational Chemical Biology Core, The University of Kansas, Lawrence, Kansas, USA
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas, USA
| | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| |
Collapse
|
3
|
Wu J, Sun C, Guan J, Abdullah SW, Wang X, Ren M, Qiao L, Sun S, Guo H. Nuclear ribonucleoprotein RALY downregulates foot-and-mouth disease virus replication but antagonized by viral 3C protease. Microbiol Spectr 2024; 12:e0365823. [PMID: 38323828 PMCID: PMC10913732 DOI: 10.1128/spectrum.03658-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
The internal ribosome entry site (IRES) element constitutes a cis-acting RNA regulatory sequence that recruits the ribosomal initiation complex in a cap-independent manner, assisted by various RNA-binding proteins and IRES trans-acting factors. Foot-and-mouth disease virus (FMDV) contains a functional IRES element and takes advantage of this element to subvert host translation machinery. Our study identified a novel mechanism wherein RALY, a member of the heterogeneous nuclear ribonucleoproteins (hnRNP) family belonging to RNA-binding proteins, binds to the domain 3 of FMDV IRES via its RNA recognition motif residue. This interaction results in the downregulation of FMDV replication by inhibiting IRES-driven translation. Furthermore, our findings reveal that the inhibitory effect exerted by RALY on FMDV replication is not attributed to the FMDV IRES-mediated assembly of translation initiation complexes but rather to the impediment of 80S ribosome complex formation after binding with 40S ribosomes. Conversely, 3Cpro of FMDV counteracts RALY-mediated inhibition by the ubiquitin-proteasome pathway. Therefore, these results indicate that RALY, as a novel critical IRES-binding protein, inhibits FMDV replication by blocking the formation of 80S ribosome, providing a deeper understanding of how viruses recruit and manipulate host factors. IMPORTANCE The translation of FMDV genomic RNA driven by IRES element is a crucial step for virus infections. Many host proteins are hijacked to regulate FMDV IRES-dependent translation, but the regulatory mechanism remains unknown. Here, we report for the first time that cellular RALY specifically interacts with the IRES of FMDV and negatively regulates viral replication by blocking 80S ribosome assembly on FMDV IRES. Conversely, RALY-mediated inhibition is antagonized by the viral 3C protease by the ubiquitin-proteasome pathway. These results would facilitate further understanding of virus-host interactions and translational control during viral infection.
Collapse
Affiliation(s)
- Jin'en Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Chao Sun
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Junyong Guan
- Division of Livestock Infectious Diseases, State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Sahibzada Waheed Abdullah
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuefei Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Ren
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Qiao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shiqi Sun
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huichen Guo
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
- School of Animal Science, Yangtze University, Jingzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
| |
Collapse
|
4
|
Song J, Guo Y, Wang D, Quan R, Wang J, Liu J. Seneca Valley virus 3C protease cleaves OPTN (optineurin) to Impair selective autophagy and type I interferon signaling. Autophagy 2024; 20:614-628. [PMID: 37930946 PMCID: PMC10936645 DOI: 10.1080/15548627.2023.2277108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
Seneca Valley virus (SVV) causes vesicular disease in pigs, posing a threat to global pork production. OPTN (optineurin) is a macroautophagy/autophagy receptor that restricts microbial propagation by targeting specific viral or bacterial proteins for degradation. OPTN is degraded and cleaved at glutamine 513 following SVV infection via the activity of viral 3C protease (3C[pro]), resulting in N-terminal and a C-terminal OPTN fragments. Moreover, OPTN interacts with VP1 and targets VP1 for degradation to inhibit viral replication. The N-terminal cleaved OPTN sustained its interaction with VP1, whereas the degradation capacity targeting VP1 decreased. The inhibitory effect of N-terminal OPTN against SVV infection was significantly reduced, C-terminal OPTN failed to inhibit viral replication, and degradation of VP1 was blocked. The knockdown of OPTN resulted in reduced TBK1 activation and phosphorylation of IRF3, whereas overexpression of OPTN led to increased TBK1-IRF3 signaling. Additionally, the N-terminal OPTN diminished the activation of the type I IFN (interferon) pathway. These results show that SVV 3C[pro] targets OPTN because its cleavage impairs its function in selective autophagy and type I IFN production, revealing a novel model in which the virus develops diverse strategies for evading host autophagic machinery and type I IFN response for survival.Abbreviations: Co-IP: co-immunoprecipitation; GFP-green fluorescent protein; hpi: hours post-infection; HRP: horseradish peroxidase; IFN: interferon; IFNB/IFN-β: interferon beta; IRF3: interferon regulatory factor 3; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; OPTN: optineurin; PBS: phosphate-buffered saline; SVV: Seneca Valley virus; SQSTM1: sequestosome 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TCID50: 50% tissue culture infectious doses; UBAN: ubiquitin binding in TNIP/ABIN (TNFAIP3/A20 and inhibitor of NFKB/NF-kB) and IKBKG/NEMO; UBD: ubiquitin-binding domain; ZnF: zinc finger.
Collapse
Affiliation(s)
- Jiangwei Song
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yitong Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dan Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Rong Quan
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jing Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| |
Collapse
|
5
|
Dušeková E, Berta M, Sedláková D, Řeha D, Dzurillová V, Shaposhnikova A, Fadaei F, Tomková M, Minofar B, Sedlák E. Specific anion effect on properties of HRV 3C protease. Biophys Chem 2022; 287:106825. [PMID: 35597150 DOI: 10.1016/j.bpc.2022.106825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence. Stability and flexibility of the enzyme have been analyzed by CD in the far-UV region, differential scanning calorimetry and molecular dynamics simulations, respectively. We showed significant influence of the anions on the enzyme properties in accordance with the Hofmeister effect. The HRV 3C protease in the presence of kosmotropic anions, in contrast with chaotropic anions, exhibits increased stability, rigidity. Correlations of stabilization effect of anions on the enzyme with their charge density and the rate constant of the enzyme with the viscosity B-coefficients of anions suggest direct interaction of the anions with HRV 3C protease. The role of stabilization and decreased fluctuation of the polypeptide chain of HRV 3C protease on its activation in the presence of kosmotropic anions is discussed within the frame of the macromolecular rate theory.
Collapse
Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - David Řeha
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Mária Tomková
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
| |
Collapse
|
6
|
Luptak J, Mallery DL, Jahun AS, Albecka A, Clift D, Ather O, Slodkowicz G, Goodfellow I, James LC. TRIM7 Restricts Coxsackievirus and Norovirus Infection by Detecting the C-Terminal Glutamine Generated by 3C Protease Processing. Viruses 2022; 14:v14081610. [PMID: 35893676 PMCID: PMC9394474 DOI: 10.3390/v14081610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
TRIM7 catalyzes the ubiquitination of multiple substrates with unrelated biological functions. This cross-reactivity is at odds with the specificity usually displayed by enzymes, including ubiquitin ligases. Here we show that TRIM7's extreme substrate promiscuity is due to a highly unusual binding mechanism, in which the PRYSPRY domain captures any ligand with a C-terminal helix that terminates in a hydrophobic residue followed by a glutamine. Many of the non-structural proteins found in RNA viruses contain C-terminal glutamines as a result of polyprotein cleavage by 3C protease. This viral processing strategy generates novel substrates for TRIM7 and explains its ability to inhibit Coxsackie virus and norovirus replication. In addition to viral proteins, cellular proteins such as glycogenin have evolved C-termini that make them a TRIM7 substrate. The 'helix-ΦQ' degron motif recognized by TRIM7 is reminiscent of the N-end degron system and is found in ~1% of cellular proteins. These features, together with TRIM7's restricted tissue expression and lack of immune regulation, suggest that viral restriction may not be its physiological function.
Collapse
Affiliation(s)
- Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Donna L. Mallery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Aminu S. Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (A.S.J.); (I.G.)
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Osaid Ather
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | | | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (A.S.J.); (I.G.)
| | - Leo C. James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
- Correspondence:
| |
Collapse
|
7
|
Xu J, Nakanishi T, Kato T, Park E. In vivo enzymatic digestion of HRV 3C protease cleavage sites-containing proteins produced in a silkworm-baculovirus expression system. Biosci Rep 2022; 42:BSR20220739. [PMID: 35642592 PMCID: PMC9202508 DOI: 10.1042/bsr20220739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 12/30/2022] Open
Abstract
Baculovirus expression vector system (BEVS) has been recognized as a potent protein expression system in engineering valuable enzymes and vaccines. Various fusion tags facilitate protein purification, leaving the potential risk to influence the target protein's biological activity negatively. It is of great interest to consider removing the additional tags using site-specific proteases, such as human rhinoviruses (HRV) 3C protease. The current study validated the cleavage activity of 3C protease in Escherichia coli and silkworm-BEVS systems by mixing the cell or fat body lysates of 3C protein and 3C site containing target protein in vitro. Further verification has been performed in the fat body lysate from co-expression of both constructs, showing remarkable cleavage efficiency in vivo silkworm larvae. We also achieved the glutathione-S-transferase (GST) tag-cleaved product of the VP15 protein from the White spot syndrome virus after purification, suggesting that we successfully established a coinfection-based recognition-and-reaction BEVS platform for the tag-free protein engineering.
Collapse
Affiliation(s)
- Jian Xu
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
| | - Takafumi Nakanishi
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Tatsuya Kato
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Enoch Y. Park
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| |
Collapse
|
8
|
Abstract
Deformed wing virus (DWV) is the most prevalent Iflavirus that is infecting honey bees worldwide. However, the mechanisms of its infection and replication in host cells are poorly understood. In this study, we analyzed the structure and function of DWV 3C protease (3Cpro), which is necessary for the cleavage of the polyprotein to synthesize mature viral proteins. Thus, it is one of the nonstructural viral proteins essential for the replication. We found that the 3Cpros of DWV and picornaviruses share common enzymatic properties, including sensitivity to the same inhibitors, such as rupintrivir. The predicted structure of DWV 3Cpro by AlphaFold2, the predicted rupintrivir binding domain, and the protease activities of mutant proteins revealed that it has a Cys-His-Asn catalytic triad. Moreover, 3Cpros of other Iflaviruses and Dicistrovirus appear to contain Asn, Ser, Asp, or Glu as the third residue of the catalytic triad, suggesting diversity in insect RNA viruses. Both precursor 3Cpro with RNA-dependent RNA polymerase and mature 3Cpro are present in DWV-infected cells, suggesting that they may have different enzymatic properties and functions. DWV 3Cpro is the first 3Cpro characterized among insect RNA viruses, and our study uncovered both the common and unique characteristics among 3Cpros of Picornavirales. Furthermore, it would be possible to use the specific inhibitors of DWV 3Cpro to control DWV infection in honey bees in future. IMPORTANCE The number of managed honey bee (Apis mellifera) colonies has considerably declined in many developed countries in the recent years. Deformed wing virus (DWV) vectored by the mites is the major threat to honey bee colonies and health. To give insight into the mechanism of DWV replication in the host cells, we studied the structure-function relationship of 3C protease (3Cpro), which is necessary to cleave a viral polyprotein at the specific sites to produce the mature proteins. We found that the overall structure, some inhibitors, and processing of 3Cpro are shared between Picornavirales; however, there is diversity in the catalytic triad. DWV 3Cpro is the first viral protease characterized among insect RNA viruses and reveals the evolutionary history of 3Cpro among Picornavirales. Furthermore, DWV 3Cpro inhibitors identified in our study could also be applied to control DWV in honey bees in future.
Collapse
Affiliation(s)
- Xuye Yuan
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Jiangsu Province, China
| |
Collapse
|
9
|
Zhou X, Tian L, Wang J, Zheng B, Zhang W. EV71 3C protease cleaves host anti-viral factor OAS3 and enhances virus replication. Virol Sin 2022; 37:418-426. [PMID: 35504537 PMCID: PMC9243667 DOI: 10.1016/j.virs.2022.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
The global spread of enteroviruses (EVs) has become more frequent, severe and life-threatening. Intereron (IFN) I has been proved to control EVs by regulating IFN-stimulated genes (ISG) expression. 2'-5'-oligoadenylate synthetases 3 (OAS3) is an important ISG in the OAS/RNase L antiviral system. The relationship between OAS3 and EVs is still unclear. Here, we reveal that OAS3, superior to OAS1 and OAS2, significantly inhibited EV71 replication in vitro. However, EV71 utilized autologous 3C protease (3Cpro) to cleave intracellular OAS3 and enhance viral replication. Rupintrivir, a human rhinovirus 3C protease inhibitor, completely abolished the cleavage of EV71 3Cpro on OAS3. And the proteolytically deficient mutants H40G, E71A, and C147G of EV71 3Cpro also lost the ability of OAS3 cleavage. Mechanistically, the Q982-G983 motif in C-terminal of OAS3 was identified as a crucial 3Cpro cutting site. Further investigation indicated that OAS3 inhibited not only EV71 but also Coxsackievirus B3 (CVB3), Coxsackievirus A16 (CA16), Enterovirus D68 (EVD68), and Coxsackievirus A6 (CA6) subtypes. Notably, unlike other four subtypes, CA16 3Cpro could not cleave OAS3. Two key amino acids variation Ile36 and Val86 in CA16 3Cpro might result in weak and delayed virus replication of CA16 because of failure of OAS and 3AB cleavage. Our works elucidate the broad anti-EVs function of OAS3, and illuminate a novel mechanism by which EV71 use 3Cpro to escape the antiviral effect of OAS3. These findings can be an important entry point for developing novel therapeutic strategies for multiple EVs infection.
Collapse
Affiliation(s)
- Xiaolei Zhou
- Center for Infectious Diseases and Pathogen Biology, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, 130021, China
| | - Li Tian
- Center for Infectious Diseases and Pathogen Biology, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, 130021, China
| | - Jian Wang
- Center for Infectious Diseases and Pathogen Biology, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, 130021, China
| | - Baisong Zheng
- Center for Infectious Diseases and Pathogen Biology, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, 130021, China.
| | - Wenyan Zhang
- Center for Infectious Diseases and Pathogen Biology, Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Jilin, 130021, China.
| |
Collapse
|
10
|
Sasaki-Tanaka R, Nagulapalli Venkata KC, Okamoto H, Moriyama M, Kanda T. Evaluation of Potential Anti-Hepatitis A Virus 3C Protease Inhibitors Using Molecular Docking. Int J Mol Sci 2022; 23:6044. [PMID: 35682728 PMCID: PMC9181686 DOI: 10.3390/ijms23116044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Hepatitis A virus (HAV) infection is a major cause of acute hepatitis worldwide and occasionally causes acute liver failure and can lead to death in the absence of liver transplantation. Although HAV vaccination is available, the prevalence of HAV vaccination is not adequate in some countries. Additionally, the improvements in public health reduced our immunity to HAV infection. These situations motivated us to develop potentially new anti-HAV therapeutic options. We carried out the in silico screening of anti-HAV compounds targeting the 3C protease enzyme using the Schrodinger Modeling software from the antiviral library of 25,000 compounds to evaluate anti-HAV 3C protease inhibitors. Additionally, in vitro studies were introduced to examine the inhibitory effects of HAV subgenomic replicon replication and HAV HA11-1299 genotype IIIA replication in hepatoma cell lines using luciferase assays and real-time RT-PCR. In silico studies enabled us to identify five lead candidates with optimal binding interactions in the active site of the target HAV 3C protease using the Schrodinger Glide program. In vitro studies substantiated our hypothesis from in silico findings. One of our lead compounds, Z10325150, showed 47% inhibitory effects on HAV genotype IB subgenomic replicon replication and 36% inhibitory effects on HAV genotype IIIA HA11-1299 replication in human hepatoma cell lines, with no cytotoxic effects at concentrations of 100 μg/mL. The effects of the combination therapy of Z10325150 and RNA-dependent RNA polymerase inhibitor, favipiravir on HAV genotype IB HM175 subgenomic replicon replication and HAV genotype IIIA HA11-1299 replication showed 64% and 48% inhibitory effects of HAV subgenomic replicon and HAV replication, respectively. We identified the HAV 3C protease inhibitor Z10325150 through in silico screening and confirmed the HAV replication inhibitory activity in human hepatocytes. Z10325150 may offer the potential for a useful HAV inhibitor in severe hepatitis A.
Collapse
Affiliation(s)
- Reina Sasaki-Tanaka
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
| | - Kalyan C. Nagulapalli Venkata
- Department of Pharmaceutical and Administrative Sciences, Saint Louis College of Pharmacy, University of Health Sciences and Pharmacy, St. Louis, MO 63010, USA;
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan;
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
| | - Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
| |
Collapse
|
11
|
Kristensen T, Normann P, Belsham GJ. The N-terminal region (VP4) of the foot-and-mouth disease capsid precursor (P1-2A) is not required during its synthesis to allow subsequent processing by the 3C protease. Virology 2022; 570:29-34. [PMID: 35364457 DOI: 10.1016/j.virol.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/22/2022] [Indexed: 11/21/2022]
Abstract
The capsid precursor (P1-2A) of foot-and-mouth disease virus is processed by the 3C protease (3Cpro) to VP0, VP3 and VP1 plus 2A. During capsid assembly, the VP0 is cleaved to VP4 plus VP2. Single amino acid changes in a conserved motif (YCPRP) near the C-terminus of VP1 can block processing of the capsid precursor by the 3Cpro, although the cleavage sites are located hundreds of amino acids distant from this motif, presumably due to misfolding. In contrast, we show here that the absence of the VP4 sequence during the synthesis of the capsid precursor does not affect its subsequent processing. Cleavage of this truncated precursor by 3Cpro at the VP3/VP1 and VP2/VP3 junctions occurred efficiently. Thus, in contrast to the presence of the YCPRP motif in VP1, there are no critical motifs near the N-terminus of the precursor, within VP4, required for correct cleavage by 3Cpro.
Collapse
Affiliation(s)
- Thea Kristensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark
| | - Preben Normann
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870, Frederiksberg C, Denmark.
| |
Collapse
|
12
|
Li Z, Wu Y, Li H, Li W, Tan J, Qiao W. 3C protease of enterovirus 71 cleaves promyelocytic leukemia protein and impairs PML-NBs production. Virol J 2021; 18:255. [PMID: 34930370 PMCID: PMC8686290 DOI: 10.1186/s12985-021-01725-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/08/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Enterovirus 71 (EV71) usually infects infants causing hand-foot-mouth disease (HFMD), even fatal neurological disease like aseptic meningitis. Effective drug for preventing and treating EV71 infection is unavailable currently. EV71 3C mediated the cleavage of many proteins and played an important role in viral inhibiting host innate immunity. Promyelocytic leukemia (PML) protein, the primary organizer of PML nuclear bodies (PML-NBs), can be induced by interferon and is involved in antiviral activity. PML inhibits EV71 replication, and EV71 infection reduces PML expression, but the molecular mechanism is unclear. METHODS The cleavage of PMLIII and IV was confirmed by co-transfection of EV71 3C protease and PML. The detailed cleavage sites were evaluated further by constructing the Q to A mutant of PML. PML knockout cells were infected with EV71 to identify the effect of cleavage on EV71 replication. Immunofluorescence analysis to examine the interference of EV71 3C on the formation of PML-NBs. RESULTS EV71 3C directly cleaved PMLIII and IV. Furthermore, 3C cleaved PMLIV at the sites of Q430-A431 and Q444-S445 through its protease activity. Overexpression of PMLIV Q430A/Q444A variant exhibited stronger antiviral potential than the wild type. PMLIV Q430A/Q444A formed normal nuclear bodies that were not affected by 3C, suggesting that 3C may impair PML-NBs production via PMLIV cleavage and counter its antiviral activities. PML, especially PMLIV, which sequesters viral proteins in PML-NBs and inhibits viral production, is a novel target of EV71 3C cleavage. CONCLUSIONS EV71 3C cleaves PMLIV at Q430-A431 and Q444-S445. Cleavage reduces the antiviral function of PML and decomposes the formation of PML-NBs, which is conducive to virus replication.
Collapse
Affiliation(s)
- Zhuoran Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ya'ni Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hui Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Wenqian Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Juan Tan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Wentao Qiao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| |
Collapse
|
13
|
Xiao H, Li J, Yang X, Li Z, Wang Y, Rui Y, Liu B, Zhang W. Ectopic Expression of TRIM25 Restores RIG-I Expression and IFN Production Reduced by Multiple Enteroviruses 3C pro. Virol Sin 2021; 36:1363-1374. [PMID: 34170466 PMCID: PMC8226358 DOI: 10.1007/s12250-021-00410-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Enteroviruses (EVs) 3C proteins suppress type I interferon (IFN) responses mediated by retinoid acid-inducible gene I (RIG-I), while an E3 ubiquitin ligase, tripartite motif protein 25 (TRIM25)-mediated RIG-I ubiquitination is essential for RIG-I antiviral activity. Therefore, whether the effect of EVs 3C on RIG-I is associated with TRIM25 expression is worth to be further investigated. Here, we demonstrate that 3C proteins of EV71 and coxsackievirus B3 (CVB3) reduced not only RIG-I expression but also TRIM25 expression through protease cleavage activity, while overexpression of TRIM25 restored RIG-I expression and IFN-β production reduced by 3C proteins. Further investigation confirmed that the two amino acids and functional domains in TRIM25 required for RIG-I ubiquitination and TRIM25 structural conformation were essential for the recovery of RIG-I expression. Moreover, we also observed that TRIM25 could rescue RIG-I expression reduced by 3C proteins of CVA6 and EV-D68 but not CVA16. Our findings provide an insightful interpretation of 3C-mediated host innate immune suppression and support TRIM25 as an attractive target against multiple EVs infection.
Collapse
Affiliation(s)
- Huimin Xiao
- Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, China
| | - Jingliang Li
- Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, China
- Changchun Institute of Biological Products Co., Ltd, Changchun, 130012, China
| | - Xu Yang
- Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, China
| | - Zhaolong Li
- Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, China
| | - Ying Wang
- Changchun Institute of Biological Products Co., Ltd, Changchun, 130012, China
| | - Yajuan Rui
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Bin Liu
- Department of Hand Surgery, First Hospital of Jilin University, Changchun, 130021, China.
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, 130021, China.
| |
Collapse
|
14
|
Wang C, Feng H, Zhang X, Li K, Yang F, Cao W, Liu H, Gao L, Xue Z, Liu X, Zhu Z, Zheng H. Porcine Picornavirus 3C Protease Degrades PRDX6 to Impair PRDX6-mediated Antiviral Function. Virol Sin 2021; 36:948-957. [PMID: 33721217 PMCID: PMC7957437 DOI: 10.1007/s12250-021-00352-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Peroxiredoxin-6 (PRDX6) is an antioxidant enzyme with both the activities of peroxidase and phospholipase A2 (PLA2), which is involved in regulation of many cellular reactions. However, the function of PRDX6 during virus infection remains unknown. In this study, we found that the abundance of PRDX6 protein was dramatically decreased in foot-and-mouth disease virus (FMDV) infected cells. Overexpression of PRDX6 inhibited FMDV replication. In contrast, knockdown of PRDX6 expression promoted FMDV replication, suggesting an antiviral role of PRDX6. To explore whether the activity of peroxidase and PLA2 was associated with PRDX6-mediated antiviral function, a specific inhibitor of PLA2 (MJ33) and a specific inhibitor of peroxidase activity (mercaptosuccinate) were used to treat the cells before FMDV infection. The results showed that incubation of MJ33 but not mercaptosuccinate promoted FMDV replication. Meanwhile, overexpression of PRDX6 slightly enhanced type I interferon signaling. We further determined that the viral 3Cpro was responsible for degradation of PRDX6, and 3Cpro-induced reduction of PRDX6 was independent of the proteasome, lysosome, and caspase pathways. The protease activity of 3Cpro was required for induction of PRDX6 reduction. Besides, PRDX6 suppressed the replication of another porcine picornavirus Senecavirus A (SVA), and the 3Cpro of SVA induced the reduction of PRDX6 through its proteolytic activity as well. Together, our results suggested that PRDX6 plays an important antiviral role during porcine picornavirus infection, and the viral 3Cpro induces the degradation of PRDX6 to overcome PRDX6-mediated antiviral function.
Collapse
Affiliation(s)
- Congcong Wang
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Huanhuan Feng
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Xiangle Zhang
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Kangli Li
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Huisheng Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Lili Gao
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Zhaoning Xue
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
| |
Collapse
|
15
|
Abstract
Recent studies provide evidence that two chemically and mechanistically distinct signals activate the human NLRP1 inflammasome, challenging the concept that it-like other mammalian inflammasomes characterized thus far-evolved to detect and respond to a single danger-associated molecular pattern.
Collapse
Affiliation(s)
- Daniel A Bachovchin
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA; Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.
| |
Collapse
|
16
|
Abdelkader EH, Otting G. NT*-HRV3CP: An optimized construct of human rhinovirus 14 3C protease for high-yield expression and fast affinity-tag cleavage. J Biotechnol 2021; 325:145-151. [PMID: 33166527 DOI: 10.1016/j.jbiotec.2020.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/20/2022]
Abstract
The human rhinovirus 14 3C protease (HRV3C protease), in fusion with glutathione S-transferase also referred to as PreScission™ protease, is a cysteine protease of particular interest for affinity tag removal from fusion proteins due to its stringent recognition sequence specificity (LEVLFQ/GX) and superior activity at low temperature. Here we report the expression, purification and use of a fusion construct of HRV3C protease, NT*-HRV3CP, that affords high expression yield in E. coli (over 300 mg/L cell culture), facile single-step purification, high solubility (>10 mg/mL) and excellent storage properties. NT*-HRV3CP cleaves affinity tags at 4 °C in minutes, making it an attractive tool for the production of recombinant proteins for biotechnological, industrial and pharmaceutical applications.
Collapse
Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence in Innovations in Peptide and Protein Science, Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence in Innovations in Peptide and Protein Science, Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| |
Collapse
|
17
|
Robinson KS, Teo DET, Tan KS, Toh GA, Ong HH, Lim CK, Lay K, Au BV, Lew TS, Chu JJH, Chow VTK, Wang DY, Zhong FL, Reversade B. Enteroviral 3C protease activates the human NLRP1 inflammasome in airway epithelia. Science 2020; 370:eaay2002. [PMID: 33093214 DOI: 10.1126/science.aay2002] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/11/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2023]
Abstract
Immune sensor proteins are critical to the function of the human innate immune system. The full repertoire of cognate triggers for human immune sensors is not fully understood. Here, we report that human NACHT, LRR, and PYD domains-containing protein 1 (NLRP1) is activated by 3C proteases (3Cpros) of enteroviruses, such as human rhinovirus (HRV). 3Cpros directly cleave human NLRP1 at a single site between Glu130 and Gly131 This cleavage triggers N-glycine-mediated degradation of the autoinhibitory NLRP1 N-terminal fragment via the cullinZER1/ZYG11B complex, which liberates the activating C-terminal fragment. Infection of primary human airway epithelial cells by live human HRV triggers NLRP1-dependent inflammasome activation and interleukin-18 secretion. Our findings establish 3Cpros as a pathogen-derived trigger for the human NLRP1 inflammasome and suggest that NLRP1 may contribute to inflammatory diseases of the airway.
Collapse
Affiliation(s)
- Kim S Robinson
- Skin Research Institute of Singapore (SRIS), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Daniel Eng Thiam Teo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
| | - Kai Sen Tan
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
| | - Hsiao Hui Ong
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Chrissie Kaishi Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Kenneth Lay
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
| | - Bijin Veonice Au
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Tian Sheng Lew
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Justin Jang Hann Chu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Vincent Tak Kwong Chow
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
| | - Franklin L Zhong
- Skin Research Institute of Singapore (SRIS), 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore.
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, 308232, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
| | - Bruno Reversade
- Institute of Medical Biology, Agency of Science, Technological and Research, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore.
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
- Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 10 Medical Drive, 117597, Singapore
- The Medical Genetics Department, Koç University School of Medicine, 34010 Istanbul, Turkey
| |
Collapse
|
18
|
Abdullah SW, Han S, Wu J, Zhang Y, Bai M, Jin Y, Zhi X, Guan J, Sun S, Guo H. The DDX23 Negatively Regulates Translation and Replication of Foot-and-Mouth Disease Virus and Is Degraded by 3C Proteinase. Viruses 2020; 12:E1348. [PMID: 33255534 PMCID: PMC7760909 DOI: 10.3390/v12121348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
DEAD-box helicase 23 (DDX23) is a host nuclear helicase, which is a part of the spliceosomal complex and involved in pre-mRNA splicing. To investigate whether DDX23, an internal ribosomal entry sites transacting factor (ITAF) affects foot-and-mouth disease virus (FMDV) replication and translation through internal ribosome entry site (IRES)-dependent manner. For this, we utilized a pull-down assay, Western blotting, quantitative real-time PCR, confocal microscopy, overexpression and small interfering RNA knockdown, as well as the median tissue culture infective dose. Our findings showed that FMDV infection inhibited DDX23 expression and the overexpression of DDX23 reduced viral replication, however, CRISPR Cas9 knockout/small interfering RNA knockdown increased FMDV replication. FMDV IRES domain III and IV interacted with DDX23, whereas DDX23 interacted with FMDV 3C proteinase and significantly degraded. The enzymatic activity of FMDV 3C proteinase degraded DDX23, whereas FMDV degraded DDX23 via the lysosomal pathway. Additionally, IRES-driven translation was suppressed in DDX23-overexpressing cells, and was enhanced in DDX23 knocked down. Collectively, our results demonstrated that DDX23 negatively affects FMDV IRES-dependent translation, which could be a useful target for the design of antiviral drugs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Shiqi Sun
- State Key Laboratory of Veterinary Etiological Biology, O.I.E./China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (S.W.A.); (S.H.); (J.W.); (Y.Z.); (M.B.); (Y.J.); (X.Z.); (J.G.)
| | - Huichen Guo
- State Key Laboratory of Veterinary Etiological Biology, O.I.E./China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; (S.W.A.); (S.H.); (J.W.); (Y.Z.); (M.B.); (Y.J.); (X.Z.); (J.G.)
| |
Collapse
|
19
|
Abstract
Enterovirus 71 (EV71) is the main pathogen of the hand, foot, and mouth disease. It was firstly isolated from sputum specimens of infants with central nervous system diseases in California in 1969, and has been repeatedly reported in various parts of the world, especially in the Asia-Pacific region. EV71 3C protein is a 183 amino acid cysteine protease that can cleave most structural and non-structural proteins of EV71. Based on the analysis and understanding of EV71 3C protease, it is helpful to study and treat diseases caused by EV71 virus infection. The EV71 3C protease promotes virus replication by cleaving EV71 synthesis or host proteins. Moreover, EV71 3C protease inhibits the innate immune system and causes apoptosis. At present, in order to deal with the damage caused by the EV71, it is urgent to develop antiviral drugs targeting 3C protease. This review will focus on the structure, function, and mechanism of EV71 3C protease.
Collapse
Affiliation(s)
- Weihui Wen
- Department of Microbiology, School of Medicine, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Zixuan Qi
- School of Medicine, Forth Clinical College, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Jing Wang
- Department of Microbiology, School of Medicine, Nanchang University, Nanchang, Jiangxi, People's Republic of China.
| |
Collapse
|
20
|
Liu W, Yang D, Sun C, Wang H, Zhao B, Zhou G, Yu L. hnRNP K Is a Novel Internal Ribosomal Entry Site-Transacting Factor That Negatively Regulates Foot-and-Mouth Disease Virus Translation and Replication and Is Antagonized by Viral 3C Protease. J Virol 2020; 94:e00803-20. [PMID: 32581104 PMCID: PMC7431795 DOI: 10.1128/jvi.00803-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Cap-independent translation initiation on picornavirus mRNAs is mediated by an internal ribosomal entry site (IRES) in the 5' untranslated region. The regulation of internal initiation requires the interaction of IRES-transacting factors (ITAFs) with the IRES. In this study, we identified a novel ITAF, heterogeneous nuclear ribonucleoprotein K (hnRNP K), which negatively regulates foot-and-mouth disease virus (FMDV) translation and viral replication. Further investigation revealed that the KH2 and KH3 domains of hnRNP K directly bind to domains II, III, and IV of the FMDV IRES, resulting in the inhibition of IRES-mediated translation by interfering with the recognition of another positive ITAF, polypyrimidine tract-binding protein (PTB). Conversely, hnRNP K-mediated inhibition was antagonized by the viral 3C protease through the cleavage of hnRNP K at the Glu-364 residue during FMDV infection. Interestingly, the N-terminal cleavage product, hnRNP K1-364, retained partial inhibitory effects on IRES activity, whereas the C-terminal cleavage product, hnRNP K364-465, became a positive regulator of FMDV replication. Our findings expand the current understanding of virus-host interactions concerning viral recruitment and the modulation of ITAFs, providing new insights into translational control during viral infection.IMPORTANCE The translation of picornaviral genome RNA mediated by the internal ribosomal entry site (IRES) is a crucial step for virus infections. Virus-host interactions play a critical role in the regulation of IRES-dependent translation, but the regulatory mechanism remains largely unknown. In this study, we identified an ITAF, hnRNP K, that negatively regulates FMDV replication by inhibiting viral IRES-mediated translation. In addition, we describe a novel translational regulation mechanism involving the proteolytic cleavage of hnRNP K by FMDV protease 3C. The cleavage of hnRNP K yields two cleavage products with opposite functions: the cleavage product hnRNP K1-364 retains a partial inhibitory effect on IRES activity, and the cleavage product hnRNP K364-465 becomes a positive regulator of FMDV replication. Our findings shed light on the effect of a novel ITAF on the translational regulation of picornavirus and provide new insights into translational control during viral infection.
Collapse
Affiliation(s)
- Wenming Liu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Decheng Yang
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Chao Sun
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Haiwei Wang
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Bo Zhao
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Guohui Zhou
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| |
Collapse
|
21
|
Fonseca MC, Pupo-Meriño M, García-González LA, Resik S, Hung LH, Muné M, Rodríguez H, Morier L, Norder H, Sarmiento L. Molecular evolution of coxsackievirus A24v in Cuba over 23-years, 1986-2009. Sci Rep 2020; 10:13761. [PMID: 32792520 PMCID: PMC7427094 DOI: 10.1038/s41598-020-70436-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/21/2020] [Indexed: 12/29/2022] Open
Abstract
Coxsackievirus A24 variant (CVA24v) is a major causative agent of acute hemorrhagic conjunctivitis outbreaks worldwide, yet the evolutionary and transmission dynamics of the virus remain unclear. To address this, we analyzed and compared the 3C and partial VP1 gene regions of CVA24v isolates obtained from five outbreaks in Cuba between 1986 and 2009 and strains isolated worldwide. Here we show that Cuban strains were homologous to those isolated in Africa, the Americas and Asia during the same time period. Two genotypes of CVA24v (GIII and GIV) were repeatedly introduced into Cuba and they arose about two years before the epidemic was detected. The two genotypes co-evolved with a population size that is stable over time. However, nucleotide substitution rates peaked during pandemics with 4.39 × 10-3 and 5.80 × 10-3 substitutions per site per year for the 3C and VP1 region, respectively. The phylogeographic analysis identified 25 and 19 viral transmission routes based on 3C and VP1 regions, respectively. Pandemic viruses usually originated in Asia, and both China and Brazil were the major hub for the global dispersal of the virus. Together, these data provide novel insight into the epidemiological dynamics of this virus and possibly other pandemic viruses.
Collapse
Affiliation(s)
- Magilé C Fonseca
- Virology Department, Center for Research, Diagnosis and Reference, Institute of Tropical Medicine "Pedro Kourí" (IPK), Novia del Mediodía Km 61/2, La Lisa, Marianao 13, P.O. Box: 601, Havana, Cuba.
| | - Mario Pupo-Meriño
- Departamento de Bioinformática, Centro de Matemática Computacional, Universidad de las Ciencias Informáticas (UCI), Havana, Cuba
| | - Luis A García-González
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
| | - Sonia Resik
- Virology Department, Center for Research, Diagnosis and Reference, Institute of Tropical Medicine "Pedro Kourí" (IPK), Novia del Mediodía Km 61/2, La Lisa, Marianao 13, P.O. Box: 601, Havana, Cuba
| | - Lai Heng Hung
- Virology Department, Center for Research, Diagnosis and Reference, Institute of Tropical Medicine "Pedro Kourí" (IPK), Novia del Mediodía Km 61/2, La Lisa, Marianao 13, P.O. Box: 601, Havana, Cuba
| | - Mayra Muné
- Virology Department, Center for Research, Diagnosis and Reference, Institute of Tropical Medicine "Pedro Kourí" (IPK), Novia del Mediodía Km 61/2, La Lisa, Marianao 13, P.O. Box: 601, Havana, Cuba
| | - Hermis Rodríguez
- Cell Culture Laboratory, Center for Research, Diagnosis and Reference, Institute of Tropical Medicine "Pedro Kourí" (IPK), Havana, Cuba
| | - Luis Morier
- Department of Microbiology and Virology, Biology Faculty, Havana University, Havana, Cuba
| | - Heléne Norder
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Luis Sarmiento
- Immunovirology Unit, Department of Clinical Sciences, Skåne University Hospital, Lund University, Malmö, Sweden
| |
Collapse
|
22
|
Malik S, Sinclair A, Ryan A, Le Gresley A. Synthesis and Initial Evaluation of a Novel Fluorophore for Selective FMDV 3C Protease Detection. Molecules 2020; 25:E3599. [PMID: 32784761 PMCID: PMC7465021 DOI: 10.3390/molecules25163599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
The development and evaluation of a Boc-AL(Boc)Q(Trt)-AMC fluorophore to detect 3C Protease, produced by Foot and Mouth Disease Virus (FMDV) is reported, with a view to a potential use as a rapid screen for FMDV infected livestock The peptide-linked conjugate fluorophore is evaluated in vitro for sensitivity, specificity, stability and rapidity and shows statistically significant increases in fluorescence when exposed to physiologically relevant concentrations of 3C Protease and selectivity when compared with other common proteases likely to be located, typically in the absence of FMDV. The stability of deprotected Boc-AL(Boc)Q(Trt)-AMC is reported as a limitation of this probe.
Collapse
Affiliation(s)
| | | | | | - Adam Le Gresley
- Chemical and Pharmaceutical Sciences, SEC Faculty, Kingston University, Kingston-upon-Thames, London KT1 2EE, UK; (S.M.); (A.S.); (A.R.)
| |
Collapse
|
23
|
Meng B, Lan K, Xie J, Lerner RA, Wilson IA, Yang B. Inhibitory antibodies identify unique sites of therapeutic vulnerability in rhinovirus and other enteroviruses. Proc Natl Acad Sci U S A 2020; 117:13499-13508. [PMID: 32467165 PMCID: PMC7306783 DOI: 10.1073/pnas.1918844117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The existence of multiple serotypes renders vaccine development challenging for most viruses in the Enterovirus genus. An alternative and potentially more viable strategy for control of these viruses is to develop broad-spectrum antivirals by targeting highly conserved proteins that are indispensable for the virus life cycle, such as the 3C protease. Previously, two single-chain antibody fragments, YDF and GGVV, were reported to effectively inhibit human rhinovirus 14 proliferation. Here, we found that both single-chain antibody fragments target sites on the 3C protease that are distinct from its known drug site (peptidase active site) and possess different mechanisms of inhibition. YDF does not block the active site but instead noncompetitively inhibits 3C peptidase activity through an allosteric effect that is rarely seen for antibody protease inhibitors. Meanwhile, GGVV antagonizes the less-explored regulatory function of 3C in genome replication. The interaction between 3C and the viral genome 5' noncoding region has been reported to be important for enterovirus genome replication. Here, the interface between human rhinovirus 14 3C and its 5' noncoding region was probed by hydrogen-deuterium exchange coupled mass spectrometry and found to partially overlap with the interface between GGVV and 3C. Consistently, prebinding of GGVV completely abolishes interaction between human rhinovirus 14 3C and its 5' noncoding region. The epitopes of YDF and GGVV, therefore, represent two additional sites of therapeutic vulnerability in rhinovirus. Importantly, the GGVV epitope appears to be conserved across many enteroviruses, suggesting that it is a promising target for pan-enterovirus inhibitor screening and design.
Collapse
Affiliation(s)
- Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, People's Republic of China
| | - Keke Lan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, People's Republic of China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, People's Republic of China
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Ian A Wilson
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, People's Republic of China;
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210 Shanghai, People's Republic of China;
| |
Collapse
|
24
|
Zhang L, Lin D, Kusov Y, Nian Y, Ma Q, Wang J, von Brunn A, Leyssen P, Lanko K, Neyts J, de Wilde A, Snijder EJ, Liu H, Hilgenfeld R. α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment. J Med Chem 2020; 63:4562-4578. [PMID: 32045235 PMCID: PMC7098070 DOI: 10.1021/acs.jmedchem.9b01828] [Citation(s) in RCA: 376] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/26/2022]
Abstract
The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.
Collapse
Affiliation(s)
- Linlin Zhang
- Institute of Biochemistry, Center for Structural and
Cell Biology in Medicine, University of Lübeck, 23562
Lübeck, Germany
- German Center for Infection Research (DZIF),
Hamburg-Lübeck-Borstel-Riems Site, University of
Lübeck, 23562 Lübeck, Germany
| | - Daizong Lin
- Institute of Biochemistry, Center for Structural and
Cell Biology in Medicine, University of Lübeck, 23562
Lübeck, Germany
- German Center for Infection Research (DZIF),
Hamburg-Lübeck-Borstel-Riems Site, University of
Lübeck, 23562 Lübeck, Germany
- Shanghai Institute of Materia
Medica, 201203 Shanghai, China
| | - Yuri Kusov
- Institute of Biochemistry, Center for Structural and
Cell Biology in Medicine, University of Lübeck, 23562
Lübeck, Germany
| | - Yong Nian
- Shanghai Institute of Materia
Medica, 201203 Shanghai, China
| | - Qingjun Ma
- Institute of Biochemistry, Center for Structural and
Cell Biology in Medicine, University of Lübeck, 23562
Lübeck, Germany
| | - Jiang Wang
- Shanghai Institute of Materia
Medica, 201203 Shanghai, China
| | - Albrecht von Brunn
- Max von Pettenkofer Institute,
Ludwig-Maximilians-University Munich, 80336 Munich,
Germany
| | - Pieter Leyssen
- Rega Institute for Medical Research,
University of Leuven, 3000 Leuven,
Belgium
| | - Kristina Lanko
- Rega Institute for Medical Research,
University of Leuven, 3000 Leuven,
Belgium
| | - Johan Neyts
- Rega Institute for Medical Research,
University of Leuven, 3000 Leuven,
Belgium
| | - Adriaan de Wilde
- Leiden University Medical Center,
2333 ZA Leiden, The Netherlands
| | - Eric J. Snijder
- Leiden University Medical Center,
2333 ZA Leiden, The Netherlands
| | - Hong Liu
- Shanghai Institute of Materia
Medica, 201203 Shanghai, China
| | - 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),
Hamburg-Lübeck-Borstel-Riems Site, University of
Lübeck, 23562 Lübeck, Germany
- Shanghai Institute of Materia
Medica, 201203 Shanghai, China
| |
Collapse
|
25
|
Fan X, Li X, Zhou Y, Mei M, Liu P, Zhao J, Peng W, Jiang ZB, Yang S, Iverson BL, Zhang G, Yi L. Quantitative Analysis of the Substrate Specificity of Human Rhinovirus 3C Protease and Exploration of Its Substrate Recognition Mechanisms. ACS Chem Biol 2020; 15:63-73. [PMID: 31613083 DOI: 10.1021/acschembio.9b00539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human rhinovirus 3C protease (HRV 3C-P) is a high-value commercial cysteine protease that could specifically recognize the short peptide sequence of LEVLFQ↓GP. In here, a strategy based on our previous Yeast Endoplasmic Reticulum Sequestration Screening (YESS) approach was developed in Saccharomyces cerevisiae, a model microorganism, to fully characterize the substrate specificity of a typical human virus protease, HRV 3C-P, in a quantitative and fast manner. Our results demonstrated that HRV 3C-P had very high specificity at P1 and P1' positions, only recognizing Gln/Glu at the P1 position and Gly/Ala/Cys/Ser at the P1' position, respectively. Comparably, it exhibited efficient recognition of most residues at the P2' position, except Trp. Further biochemical characterization through site mutagenesis, enzyme structural modeling, and comparison with other 3C proteases indicated that the S1 pocket of HRV 3C-P was constituted by neutral and basic amino acids, in which His160 and Thr141 specifically interacted with Gln or Glu residues at the substrate P1 position. Additionally, the stringent S1' pocket determined its unique property of only accommodating residues without or with short side chains. Based on our characterization, LEVLFQ↓GM was identified as a more favorable substrate than the original LEVLFQ↓GP at high temperature, which might be caused by the conversion of random coils to β-turns in HRV 3C-P along with the temperature increase. Our studies prompted a further understanding of the substrate specificity and recognition mechanism of HRV 3C-P. Besides, the YESS-PSSC combined with the enzyme modeling strategy in this study provides a general strategy for deciphering the substrate specificities of proteases.
Collapse
Affiliation(s)
- Xian Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Xinzhi Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Yu Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin 300308 , China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Zheng-Bing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Brent L Iverson
- Department of Chemistry , University of Texas , Austin , Texas 78712 , United States
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences , Hubei University , Wuhan , 430062 , China
| |
Collapse
|
26
|
Saarinen NVV, Stone VM, Hankaniemi MM, Mazur MA, Vuorinen T, Flodström-Tullberg M, Hyöty H, Hytönen VP, Laitinen OH. Antibody Responses against Enterovirus Proteases are Potential Markers for an Acute Infection. Viruses 2020; 12:E78. [PMID: 31936473 PMCID: PMC7020046 DOI: 10.3390/v12010078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Enteroviruses are a group of common non-enveloped RNA viruses that cause symptoms ranging from mild respiratory infections to paralysis. Due to the abundance of enterovirus infections it is hard to distinguish between on-going and previous infections using immunological assays unless the IgM fraction is studied. METHODS In this study we show using Indirect ELISA and capture IgM ELISA that an IgG antibody response against the nonstructural enteroviral proteins 2A and 3C can be used to distinguish between IgM positive (n = 22) and IgM negative (n = 20) human patients with 83% accuracy and a diagnostic odds ratio of 30. Using a mouse model, we establish that the antibody response to the proteases is short-lived compared to the antibody response to the structural proteins in. As such, the protease antibody response serves as a potential marker for an acute infection. CONCLUSIONS Antibody responses against enterovirus proteases are shorter-lived than against structural proteins and can differentiate between IgM positive and negative patients, and therefore they are a potential marker for acute infections.
Collapse
Affiliation(s)
- Niila V. V. Saarinen
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
| | - Virginia M. Stone
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
- Karolinska Institutet, The Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska University Hospital, 14152 Stockholm, Sweden;
| | - Minna M. Hankaniemi
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
| | - Magdalena A. Mazur
- Karolinska Institutet, The Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska University Hospital, 14152 Stockholm, Sweden;
| | - Tytti Vuorinen
- Turku University Hospital, Clinical Microbiology and University of Turku, Institute of Biomedicine, 20520 Turku, Finland;
| | - Malin Flodström-Tullberg
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
- Karolinska Institutet, The Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska University Hospital, 14152 Stockholm, Sweden;
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
| | - Vesa P. Hytönen
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
| | - Olli H. Laitinen
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (N.V.V.S.); (V.M.S.); (M.M.H.); (M.F.-T.); (H.H.); (V.P.H.)
| |
Collapse
|
27
|
Jain S, Amin SA, Adhikari N, Jha T, Gayen S. Good and bad molecular fingerprints for human rhinovirus 3C protease inhibition: identification, validation, and application in designing of new inhibitors through Monte Carlo-based QSAR study. J Biomol Struct Dyn 2020; 38:66-77. [PMID: 30646829 DOI: 10.1080/07391102.2019.1566093] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/01/2019] [Indexed: 01/12/2023]
Abstract
HRV 3 C protease (HRV 3Cpro) is an important target for common cold and upper respiratory tract infection. Keeping in view of the non-availability of drug for the treatment, newer computer-based modelling strategies should be applied to rationalize the process of antiviral drug discovery in order to decrease the valuable time and huge expenditure of the process. The present work demonstrates a structure wise optimization using Monte Carlo-based QSAR method that decomposes ligand compounds (in SMILES format) into several molecular fingerprints/descriptors. The current state-of-the-art in QSAR study involves the balance of correlation approach using four different sets: training, invisible training, calibration, and validation. The final models were also validated through mean absolute error, index of ideality of correlation, Y-randomization and applicability domain analysis. R2 and Q2 values for the best model were 0.8602, 0.8507 (training); 0.8435, 0.8331 (invisible training); 0.7424, 0.7020 (calibration); 0.5993, 0.5216 (validation), respectively. The process identified some molecular substructures as good and bad fingerprints depending on their effect to increase or decrease the HRV 3Cpro inhibition. Finally, new inhibitors were designed based on the fundamental concept to replace the bad fragments with the good fragments as well as including more good fragments into the structure. The study points out the importance of the fingerprint based drug design strategy through Monte Carlo optimization method in the modelling of HRV 3Cpro inhibitors.
Collapse
Affiliation(s)
- Sanskar Jain
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, India
| | - Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, India
| |
Collapse
|
28
|
Sun Y, Zheng Q, Wang Y, Pang Z, Liu J, Yin Z, Lou Z. Activity-Based Protein Profiling Identifies ATG4B as a Key Host Factor for Enterovirus 71 Proliferation. J Virol 2019; 93:e01092-19. [PMID: 31554687 PMCID: PMC6880168 DOI: 10.1128/jvi.01092-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/18/2019] [Indexed: 01/11/2023] Open
Abstract
Virus-encoded proteases play diverse roles in the efficient replication of enterovirus 71 (EV71), which is the causative agent of human hand, foot, and mouth disease (HFMD). However, it is unclear how host proteases affect viral proliferation. Here, we designed activity-based probes (ABPs) based on an inhibitor of the main EV71 protease (3Cpro), which is responsible for the hydrolysis of the EV71 polyprotein, and successfully identified host candidates that bind to the ABPs. Among the candidates, the host cysteine protease autophagy-related protein 4 homolog B (ATG4B), a key component of the autophagy machinery, was demonstrated to hydrolytically process the substrate of EV71 3Cpro and had activity comparable to that of the viral protease. Genetic disruption of ATG4B confirmed that the enzyme is indispensable for viral proliferation in vivo Our results not only further the understanding of host-virus interactions in EV71 biology but also provide a sample for the usage of activity-based proteomics to reveal host-pathogen interactions.IMPORTANCE Enterovirus 71 (EV71), one of the major pathogens of human HFMD, has caused outbreaks worldwide. How EV71 efficiently assesses its life cycle with elaborate interactions with multiple host factors remains to be elucidated. In this work, we deconvoluted that the host ATG4B protein processes the viral polyprotein with its cysteine protease activity and helps EV71 replicate through a chemical biology strategy. Our results not only further the understanding of the EV71 life cycle but also provide a sample for the usage of activity-based proteomics to reveal host-pathogen interactions.
Collapse
Affiliation(s)
- Yang Sun
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qizhen Zheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Yaxin Wang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
- School of Life Science, Tianjin University, Tianjin, China
| | - Zhengyuan Pang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Jingwei Liu
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zheng Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiyong Lou
- Collaborative Innovation Center of Biotherapy, School of Medicine, Tsinghua University, Beijing, China
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
29
|
Le VD, Phan TTP, Nguyen TM, Brunsveld L, Schumann W, Nguyen HD. Using the IPTG-Inducible Pgrac212 Promoter for Overexpression of Human Rhinovirus 3C Protease Fusions in the Cytoplasm of Bacillus subtilis Cells. Curr Microbiol 2019; 76:1477-1486. [PMID: 31612259 DOI: 10.1007/s00284-019-01783-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/27/2019] [Indexed: 01/19/2023]
Abstract
Expression and secretion of recombinant proteins in the endotoxin-free bacterium, Bacillus subtilis, has been thoroughly studied, but overexpression in the cytoplasm has been limited to only a few proteins. Here, we used the robust IPTG-inducible promoter, Pgrac212, to overexpress human rhinovirus 3C protease (HRV3C) in the cytoplasm of B. subtilis cells. A novel solubility tag, the N-terminal domain of the lysS gene of B. subtilis coding for a lysyl-tRNA synthetase was placed at the N terminus with a cleavage site for the endoprotease HRV3C, followed by His-HRV3C or His-GST-HRV3C. The recombinant protease was purified by using a Ni-NTA column. In this study, the His-HRV3C and His-GST-HRV3C proteases were overexpressed in the cytoplasm of B. subtilis at 11% and 16% of the total cellular proteins, respectively. The specific protease activities were 8065 U/mg for His-HRV3C and 3623 U/mg for His-GST-HRV3C. The purified enzymes were used to cleave two different substrates followed by purification of the two different protein targets, the green fluorescent protein and the beta-galactosidase. In conclusion, the combination of an inducible promoter Pgrac212 and a solubility tag allowed the overexpression of the HRV3C protease in the cytoplasm of B. subtilis. The resulting fusion protein was purified using a nickel column and was active in cleaving target proteins to remove the fusion tags. This study offers an effective method for producing recombinant proteins in the cytoplasm of endotoxin-free bacteria.
Collapse
Affiliation(s)
- Vuong Duong Le
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Trang Thi Phuong Phan
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Laboratory of Molecular Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
| | - Tri Minh Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Str., Binh Thanh Dist., Hochiminh, Vietnam
| | - Luc Brunsveld
- Laboratory of Chemical Biology & Institute of Complex Molecular Systems, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, Netherlands
| | - Wolfgang Schumann
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam
- Institute of Genetics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Hoang Duc Nguyen
- Center for Bioscience and Biotechnology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
- Department of Microbiology, University of Science-VNUHCM, 227 Nguyen Van Cu Dist. 5, Hochiminh, Vietnam.
| |
Collapse
|
30
|
Zhou J, Fang L, Yang Z, Xu S, Lv M, Sun Z, Chen J, Wang D, Gao J, Xiao S. Identification of novel proteolytically inactive mutations in coronavirus 3C-like protease using a combined approach. FASEB J 2019; 33:14575-14587. [PMID: 31690127 DOI: 10.1096/fj.201901624rr] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022]
Abstract
Coronaviruses (CoVs) infect humans and multiple other animal species, causing highly prevalent and severe diseases. 3C-like proteases (3CLpros) from CoVs (also called main proteases) are essential for viral replication and are also involved in polyprotein cleavage and immune regulation, making them attractive and effective targets for the development of antiviral drugs. Herein, the 3CLpro from the porcine epidemic diarrhea virus, an enteropathogenic CoV, was used as a model to identify novel crucial residues for enzyme activity. First, we established a rapid, sensitive, and efficient luciferase-based biosensor to monitor the activity of PDEV 3CLproin vivo. Using this luciferase biosensor, along with confirming the well-known catalytic residues (His41 and Cys144), we identified 4 novel proteolytically inactivated mutants of PDEV 3CLpro, which was also confirmed in mammalian cells by biochemical experiments. Our molecular dynamics (MD) simulations showed that the hydrogen bonding interactions occurring within and outside of the protease's active site and the dynamic fluctuations of the substrate, especially the van der Waals contacts, were drastically altered, a situation related to the loss of 3CLpro activity. These data suggest that changing the intermolecular dynamics in protein-substrate complexes eliminates the mechanism underlying the protease activity. The discovery of novel crucial residues for enzyme activity in the binding pocket could potentially provide more druggable sites for the design of protease inhibitors. In addition, our in-depth study of the dynamic substrate's envelope model using MD simulations is an approach that could augment the discovery of new inhibitors against 3CLpro in CoVs and other viral 3C proteases.-Zhou, J., Fang, L., Yang, Z., Xu, S., Lv, M., Sun, Z., Chen, J., Wang, D., Gao, J., Xiao, S. Identification of novel proteolytically inactive mutations in coronavirus 3C-like protease using a combined approach.
Collapse
Affiliation(s)
- Junwei Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhixiang Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shangen Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Mengting Lv
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zheng Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiyao Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jun Gao
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| |
Collapse
|
31
|
Li ML, Lin JY, Chen BS, Weng KF, Shih SR, Calderon JD, Tolbert BS, Brewer G. EV71 3C protease induces apoptosis by cleavage of hnRNP A1 to promote apaf-1 translation. PLoS One 2019; 14:e0221048. [PMID: 31498791 PMCID: PMC6733512 DOI: 10.1371/journal.pone.0221048] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/29/2019] [Indexed: 12/20/2022] Open
Abstract
Enterovirus 71 (EV71) induces apoptosis to promote viral particle release. Earlier work showed that EV71 utilizes its 3C protease to induce apoptosis in a caspase-3-dependent pathway, though the mechanism is unknown. However, work from Vagner, Holcik and colleagues showed that host protein heterogeneous ribonucleoprotein A1 (hnRNP A1) binds the IRES of cellular apoptotic peptidase activating factor 1 (apaf-1) mRNA to repress its translation. In this work, we show that apaf-1 expression is essential for EV71-induced apoptosis. EV71 infection or ectopic expression of 3C protease cleaves hnRNP A1, which abolishes its binding to the apaf-1 IRES. This allows IRES-dependent synthesis of apaf-1, activation of caspase-3, and apoptosis. Thus, we reveal a novel mechanism that EV71 utilizes for virus release via a 3C protease-hnRNP A1-apaf-1-caspase-3-apoptosis axis.
Collapse
Affiliation(s)
- Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States of America
| | - Jing-Yi Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bo-Shiun Chen
- Research Center for Emerging Viral Infections, Chang Gung University, Tao-Yuan, Taiwan
| | - Kuo-Feng Weng
- Research Center for Emerging Viral Infections, Chang Gung University, Tao-Yuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Tao-Yuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan
| | - Jesse Davila Calderon
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, United States of America
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States of America
| |
Collapse
|
32
|
Ma Y, Li L, He S, Shang C, Sun Y, Liu N, Meek TD, Wang Y, Shang L. Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease. J Med Chem 2019; 62:6146-6162. [PMID: 31184893 DOI: 10.1021/acs.jmedchem.9b00387] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors (TCIs) have attracted growing attention from the pharmaceutical industry in recent decades because they have potential advantages in terms of efficacy, selectivity, and safety. TCIs have recently evolved into a new version with reversibility that can be systematically modulated. This feature may diminish the risk of haptenization and help optimize the drug-target residence time as needed. The enteroviral 3C protease (3Cpro) is a valuable therapeutic target, but the development of 3Cpro inhibitors is far from satisfactory. Therefore, we aimed to apply a reversible TCI approach to the design of novel 3Cpro inhibitors. The introduction of various substituents onto the α-carbon of classical Michael acceptors yielded inhibitors bearing several classes of warheads. Using steady-state kinetics and biomolecular mass spectrometry, we confirmed the mode of reversible covalent inhibition and elucidated the mechanism by which the potency and reversibility were affected by electronic and steric factors. This research produced several potent inhibitors with good selectivity and suitable reversibility; moreover, it validated the reversible TCI approach in the field of viral infection, suggesting broader applications in the design of reversible covalent inhibitors for other proteases.
Collapse
Affiliation(s)
- Yuying Ma
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300350 , China
| | - Linfeng Li
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Shuai He
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300350 , China
| | - Chengyou Shang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300350 , China
| | - Yang Sun
- Center of Basic Molecular Science, Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Ning Liu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300350 , China
| | - Thomas D Meek
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Yaxin Wang
- School of Life Sciences , Tianjin University , Tianjin 300110 , China
| | - Luqing Shang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300350 , China
| |
Collapse
|
33
|
Onyeogaziri FC, Papaneophytou C. A General Guide for the Optimization of Enzyme Assay Conditions Using the Design of Experiments Approach. SLAS Discov 2019; 24:587-596. [PMID: 30802413 DOI: 10.1177/2472555219830084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Many factors must be considered during the optimization of an enzyme assay. These include the choice of buffer and its composition, the type of enzyme and its concentration, as well as the type of substrate and concentrations, the reaction conditions, and the appropriate assay technology. The process of an enzyme assay optimization, in our experience, can take more than 12 weeks using the traditional one-factor-at-a-time approach. In contrast, the design of experiments (DoE) approaches have the potential to speed up the assay optimization process and provide a more detailed evaluation of tested variables. However, not all researchers are aware of DoE approaches or believe that it is easy to employ a DoE approach for the optimization of an assay. In order to facilitate enzyme assay developers to use DoE methodologies, we present in detail the steps required to identify in less than 3 days (1) the factors that significantly affect the activity of an enzyme and (2) the optimal assay conditions using a fractional factorial approach and response surface methodology. This is exemplified with the optimization of assay conditions for the human rhinovirus-3C protease, and the methodology used could be employed as a basic guide for the speedy identification of the optimum assay conditions for any enzyme.
Collapse
Affiliation(s)
- Favour Chinyere Onyeogaziri
- 1 Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Christos Papaneophytou
- 1 Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| |
Collapse
|
34
|
Abstract
The engineering of enzymes for the purpose of controlling their activity represents a valuable approach to address challenges in both fundamental and applied research. Here, we describe and compare different design strategies for the generation of a human rhinovirus-14 (HRV14) 3C protease-inducible caspase-3 (CASP3). We exemplify the application potential of the resulting protease by controlling the activity of a synthetic enzyme cascade, which represents an important motif for the design of artificial signal transduction networks. In addition, we use our engineered CASP3 to characterize the effect of aspartate mutations on enzymatic activity. Besides the identification of mutations that render the enzyme inactive, we find the CASP3-D192E mutant (aspartate-to-glutamate exchange at position 192) to be inaccessible for 3C protease-mediated cleavage. This indicates a structural change of CASP3 that goes beyond a slight misalignment of the catalytic triad. This study could inspire the design of additional engineered proteases that could be used to unravel fundamental research questions or to expand the collection of biological parts for the design of synthetic signaling pathways.
Collapse
Affiliation(s)
- Hanna J Wagner
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany.
| |
Collapse
|
35
|
Dial CN, Tate PM, Kicmal TM, Mounce BC. Coxsackievirus B3 Responds to Polyamine Depletion via Enhancement of 2A and 3C Protease Activity. Viruses 2019; 11:E403. [PMID: 31052199 PMCID: PMC6563312 DOI: 10.3390/v11050403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 01/16/2023] Open
Abstract
Polyamines are small positively-charged molecules abundant in eukaryotic cells that are crucial to RNA virus replication. In eukaryotic cells, polyamines facilitate processes such as transcription, translation, and DNA replication, and viruses similarly rely on polyamines to facilitate transcription and translation. Whether polyamines function at additional stages in viral replication remains poorly understood. Picornaviruses, including Coxsackievirus B3 (CVB3), are sensitive to polyamine depletion both in vitro and in vivo; however, precisely how polyamine function in picornavirus infection has not been described. Here, we describe CVB3 mutants that arise with passage in polyamine-depleted conditions. We observe mutations in the 2A and 3C proteases, and we find that these mutant proteases confer resistance to polyamine depletion. Using a split luciferase reporter system to measure protease activity, we determined that polyamines facilitate viral protease activity. We further observe that the 2A and 3C protease mutations enhance reporter protease activity in polyamine-depleted conditions. Finally, we find that these mutations promote cleavage of cellular eIF4G during infection of polyamine-depleted cells. In sum, our results suggest that polyamines are crucial to protease function during picornavirus infection. Further, these data highlight viral proteases as potential antiviral targets and highlight how CVB3 may overcome polyamine-depleting antiviral therapies.
Collapse
Affiliation(s)
- Courtney N Dial
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
| | - Patrick M Tate
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
| | - Thomas M Kicmal
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
| | - Bryan C Mounce
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA.
| |
Collapse
|
36
|
Sun D, Wang M, Wen X, Mao S, Cheng A, Jia R, Yang Q, Wu Y, Zhu D, Chen S, Liu M, Zhao X, Zhang S, Chen X, Liu Y, Yu Y, Zhang L. Biochemical characterization of recombinant Avihepatovirus 3C protease and its localization. Virol J 2019; 16:54. [PMID: 31036013 PMCID: PMC6489322 DOI: 10.1186/s12985-019-1155-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The picornaviral 3C protease mediates viral polyprotein maturation and multiple cleavages of host proteins to modulate viral translation and transcription. The 3C protease has been regarded as a valid target due to its structural similarity among different picornaviruses and minimal sequence similarity with host proteins; therefore, the development of potent inhibitors against the 3C protease as an antiviral drug is ongoing. Duck hepatitis A virus (DHAV) belongs to the Picornavidea family and is a major threat to the poultry industry. To date, little is known about the roles of the DHAV 3C protease plays during infection. METHODS In this study, we compared the full-length DHAV 3C protein sequence with other 3C sequences to obtain an alignment for the construction of a phylogenetic tree. Then, we expressed and purified recombinant DHAV 3C protease in the BL21 expression system using nickel-NTA affinity chromatography. The optimization of the cleavage assay conditions and the kinetic analysis for DHAV 3C protease were done by in vitro cleavage assays with a fluorogenic peptide respectively. The inhibitory activity of rupintrivir against the DHAV 3C protease was further evaluated. The localization of the 3C protease in infected and transfected cells was determined using immunofluorescence and confocal microscopy. RESULTS Under different expression conditions, the 3C protease was found to be highly expressed after induction with 1 mM IPTG at 16 °C for 10 h. We synthesized a fluorogenic peptide derived from the cleavage site of the DHAV polyprotein and evaluated the protease activity of the DHAV 3C protease for the first time. We used fluorimetric based kinetic analysis to determine kinetic parameters, and Vmax and Km values were determined to be 16.52 nmol/min and 50.78 μM, respectively. Rupintrivir was found to exhibit inhibitory activity against the DHAV 3C protease. Using polyclonal antibody and an indirect immunofluorescence microscopy assay (IFA), it was determined that the DHAV 3C protease was found in the nucleus during infection. In addition, the DHAV 3C protease can enter into the nucleus without the cooperation of viral proteins. CONCLUSIONS This is the first study to examine the activity of the DHAV 3C protease, and the activity of the DHAV 3C protease is temperature-, pH- and NaCl concentration- dependent. The DHAV 3C protease localizes throughout DHAV-infected cells and can enter into the nucleus in the absence of other viral proteins. The kinetic analysis was calculated, and the Vmax and Km values were 16.52 nmol/min and 50.78 μM, respectively, using the Lineweaver-Burk plot.
Collapse
Affiliation(s)
- Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Xingjian Wen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Xiaoyue Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130 People’s Republic of China
| |
Collapse
|
37
|
Kassem AF, Batran RZ, Abbas EMH, Elseginy SA, Shaheen MNF, Elmahdy EM. New 4-phenylcoumarin derivatives as potent 3C protease inhibitors: Design, synthesis, anti-HAV effect and molecular modeling. Eur J Med Chem 2019; 168:447-460. [PMID: 30844608 DOI: 10.1016/j.ejmech.2019.02.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Abstract
A new series of 4-phenylcoumarin derivatives was synthesized starting from (2-oxo-4-phenyl-2H-chromen-7-yloxy) acetic acid hydrazide 3. Evaluation of the target compounds for their antiviral activity against hepatitis A virus revealed that the ethylthiosemicarbazide derivative 7b was the most potent virucidal agent (IC50 = 3.1 μg/ml, TI = 83). The Schiff's bases 14c and 14b demonstrated the highest virustatic effects against viral adsorption and replication, respectively (14c; IC50 = 8.5 μg/ml, TI = 88 and 14b; IC50 = 10.7 μg/ml, TI = 91). Furthermore, compounds 7b, 14b and 14c were tested against HAV 3C protease and showed significant inhibition effects (Ki = 1.903, 0.104 and 0.217 μM, respectively). The remarkable inhibitory effect expressed by the three target compounds against HAV 3C protease prompted us to expand our research on HRV 3C protease, a structurally related enzyme of the same family, and interestingly, the three target compounds displayed significant inhibitory effect against HRV 3C protease (IC50 = 16.10, 4.13 and 6.30 μM, respectively). Moreover, the active compounds 7b, 14b and 14c were docked within the pocket site of HAV 3C protease (PDB code: 2HAL) illustrating a strong H-profile with the key amino acids Gly170 and Cys172 similar to the co-crystallized ligand. Furthermore, 3D-pharmacophore and quantitative structure activity relationship (QSAR) models were generated to explore the structural requirements for the observed antiviral activity.
Collapse
Affiliation(s)
- Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o.box 12622, Egypt
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt.
| | - Eman M H Abbas
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o.box 12622, Egypt
| | - Samia A Elseginy
- Green Chemistry Department, Chemical Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
| | - Mohamed N F Shaheen
- Environmental Virology Laboratory, Water pollution Research Department, Environmental Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
| | - Elmahdy M Elmahdy
- Environmental Virology Laboratory, Water pollution Research Department, Environmental Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
| |
Collapse
|
38
|
Xu H, Wang Q, Zhang Z, Yi L, Ma L, Zhai C. A simplified method to remove fusion tags from a xylanase of Bacillus sp. HBP8 with HRV 3C protease. Enzyme Microb Technol 2019; 123:15-20. [PMID: 30686346 DOI: 10.1016/j.enzmictec.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 10/19/2018] [Accepted: 01/04/2019] [Indexed: 02/06/2023]
Abstract
Human rhinovirus 3C protease (HRV 3C protease) is commonly used as a tool to remove fusion tags from recombinant proteins in gene engineering due to its distinguished specificity and high activity at low temperature. This paper is aimed to simplify the strategy of removing epitope tags from target proteins with HRV 3C protease. Fusion proteins composed of a xylanase from Bacillus sp. HBP8 (xylHB) and double tags (MBP/Nus and 6×His, with an HRV 3C protease recognition site between them) were applied as substrates. To perform the cleavage and purification, strains expressing HRV 3C protease and the substrates were mixed before (co-fermentation method) or after (post-fermentation method) inducing with IPTG, followed by cell disruption and incubation at 4℃, overnight for cleavage. The soluble cytoplasmic fraction was added to Ni-NTA resin to recover the cleaved target protein. Because the process was carried out in the cell lysate, it was named as cell lysate purification system based on HRV 3C protease (CLP3C). Our data indicated small number of cells expressing HRV 3C protease was enough to remove the fusion tags efficiently with both co-fermentation and post-fermentation methods. More importantly, the tags were cleaved precisely with no obvious non-specific degradation to the target protein. Hence, active xylanase was recovered easily with this strategy.
Collapse
Affiliation(s)
- Hu Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China; School of Chucai honors, Hubei University, Wuhan, People's Republic of China
| | - Zhiwei Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, People's Republic of China.
| |
Collapse
|
39
|
Emamipour N, Vossoughi M, Mahboudi F, Golkar M, Fard-Esfahani P. Soluble expression of IGF1 fused to DsbA in SHuffle™ T7 strain: optimization of expression and purification by Box-Behnken design. Appl Microbiol Biotechnol 2019; 103:3393-3406. [PMID: 30868206 DOI: 10.1007/s00253-019-09719-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
Production of insulin-like growth factor 1 (IGF1) in Escherichia coli mostly results in the formation of inclusion bodies. In the present study, IGF1 was fused to disulfide bond oxidoreductase A (DsbA) and expressed in SHuffle™ T7 strain, in order to obtain correctly folded protein. Soluble expression and IMAC purification of DsbA-IGF1 were optimized by applying the Box-Behnken design of response surface methodology. The optimization greatly increased concentration of soluble protein from 317 to 2600 mg/L, and IMAC yield from 400 to 1900 mg/L. Results of ANOVA showed induction OD600 and temperature had significant effects on the soluble protein expression while isopropyl-β-d thiogalactoside, in the concentrations tested, displayed no significant effect. Moreover, the three parameters of the binding buffer including, pH, concentration of NaCl, and imidazole displayed significant effects on the IMAC yield. Then, purified DsbA-IGF1 was cleaved by human rhinovirus 3C protease, and authentic IGF1 was obtained in flow through of a subtractive IMAC. Final polishing of the protein by reversed-phase HPLC yielded IGF1 with purity of 96%. The quality attributes of purified IGF1 such as purity, identity, molecular size, molecular weight, secondary structure, and biological activity were assessed and showed to be comparable to the standard IGF1. The final yield of purified IGF1 was estimated to be 120 ± 18 mg from 1 L of the culture. Our results demonstrated a simple and easily scalable strategy for production of large amounts of bioactive IGF1 by rational designing soluble protein expression, and further optimization of expression and purification methods.
Collapse
Affiliation(s)
- Nabbi Emamipour
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Manouchehr Vossoughi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Fereidoun Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran
| | - Majid Golkar
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran.
| | | |
Collapse
|
40
|
Fernandes MHV, Maggioli MF, Otta J, Joshi LR, Lawson S, Diel DG. Senecavirus A 3C Protease Mediates Host Cell Apoptosis Late in Infection. Front Immunol 2019; 10:363. [PMID: 30918505 PMCID: PMC6424860 DOI: 10.3389/fimmu.2019.00363] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 12/22/2022] Open
Abstract
Senecavirus A (SVA), an oncolytic picornavirus used for cancer treatment in humans, has recently emerged as a vesicular disease (VD)-causing agent in swine worldwide. Notably, SVA-induced VD is indistinguishable from foot-and-mouth disease (FMD) and other high-consequence VDs of pigs. Here we investigated the role of apoptosis on infection and replication of SVA. Given the critical role of the nuclear factor-kappa B (NF-κB) signaling pathway on modulation of cell death, we first assessed activation of NF-κB during SVA infection. Results here show that while early during infection SVA induces activation of NF-κB, as evidenced by nuclear translocation of NF-κB-p65 and NF-κB-mediated transcription, late in infection a cleaved product corresponding to the C-terminus of NF-κB-p65 is detected in infected cells, resulting in lower NF-κB transcriptional activity. Additionally, we assessed the potential role of SVA 3C protease (3Cpro) in SVA-induced host-cell apoptosis and cleavage of NF-κB-p65. Transient expression of SVA 3Cpro was associated with cleavage of NF-κB-p65 and Poly (ADP-ribose) polymerase (PARP), suggesting its involvement in virus-induced apoptosis. Most importantly, we showed that while cleavage of NF-κB-p65 is secondary to caspase activation, the proteolytic activity of SVA 3Cpro is essential for induction of apoptosis. Experiments using the pan-caspase inhibitor Z-VAD-FMK confirmed the relevance of late apoptosis for SVA infection, indicating that SVA induces apoptosis, presumably, as a mechanism to facilitate virus release and/or spread from infected cells. Together, these results suggest an important role of apoptosis for SVA infection biology.
Collapse
Affiliation(s)
| | | | | | | | | | - Diego G. Diel
- Animal Disease Research And Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States
| |
Collapse
|
41
|
Martel E, Forzono E, Kurker R, Clark BA, Neilan JG, Puckette M. Effect of foot-and-mouth disease virus 3C protease B2 β-strand proline mutagenesis on expression and processing of the P1 polypeptide using a plasmid expression vector. J Gen Virol 2019; 100:446-456. [PMID: 30702422 DOI: 10.1099/jgv.0.001204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The production of experimental molecular vaccines against foot-and-mouth disease virus utilizes the viral encoded 3C protease for processing of the P1 polyprotein. Expression of wild type 3C protease is detrimental to host cells. The molecular vaccine constructs containing the 3C protease L127P mutant significantly reduce adverse effects associated with protease expression while retaining the ability to process and assemble virus-like particles. In published 3C protease crystal structures, the L127 residue is contained within the B2 β-strand as part of the A2-B2 β-sheet. To provide insight into the mechanism by which the L127P mutant alters the properties of the 3C protease, we performed scanning proline mutagenesis of residues 123-128 of the B2 β-strand and monitored expression and P1 processing. Simultaneously, we utilized random mutagenesis of the full 3C sequence to identify additional mutations presenting a phenotype similar to the L127P mutation. Six of the tested mutants enhanced expression over wild type, and the I22P, T100P and V124P mutations surpassed the L127P mutation in certain cell lines. These data areinterpreted in conjunction with published 3C protease crystal structures to provide insight into the mechanism by which these mutations enhance expression.
Collapse
Affiliation(s)
- Erica Martel
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
| | - Emily Forzono
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
- †Present address: Coastal Carolina University, 100 Chanticleer Dr W, Conway, SC 29528, USA
| | - Richard Kurker
- 1Oak Ridge Institute for Science and Education, Plum Island Animal Disease Center Research Participation Program, Oak Ridge, TN, USA
- ‡Present address: Bard High School Early College Baltimore, 2801 N. Dukeland Street, Baltimore, MD 21216, USA
| | - Benjamin A Clark
- 2Leidos, Inc., Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - John G Neilan
- 3U. S. Department of Homeland Security Science and Technology Directorate, Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - Michael Puckette
- 3U. S. Department of Homeland Security Science and Technology Directorate, Plum Island Animal Disease Center, Greenport, NY 11944, USA
| |
Collapse
|
42
|
Meister SW, Hendrikse NM, Löfblom J. Directed evolution of the 3C protease from coxsackievirus using a novel fluorescence-assisted intracellular method. Biol Chem 2019; 400:405-415. [PMID: 30521472 DOI: 10.1515/hsz-2018-0362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/21/2018] [Indexed: 01/08/2023]
Abstract
Proteases are crucial for regulating biological processes in organisms through hydrolysis of peptide bonds. Recombinant proteases have moreover become important tools in biotechnological, and biomedical research and as therapeutics. We have developed a label-free high-throughput method for quantitative assessment of proteolytic activity in Escherichia coli. The screening method is based on co-expression of a protease of interest and a reporter complex. This reporter consists of an aggregation-prone peptide fused to a fluorescent protein via a linker that contains the corresponding substrate sequence. Cleavage of the substrate rescues the fluorescent protein from aggregation, resulting in increased fluorescence that correlates to proteolytic activity, which can be monitored using flow cytometry. In one round of flow-cytometric cell sorting, we isolated an efficiently cleaved tobacco etch virus (TEV) substrate from a 1:100 000 background of non-cleavable sequences, with around 6000-fold enrichment. We then engineered the 3C protease from coxsackievirus B3 (CVB3 3Cpro) towards improved proteolytic activity on the substrate LEVLFQ↓GP. We isolated highly proteolytic active variants from a randomly mutated CVB3 3Cpro library with up to 4-fold increase in activity. The method enables simultaneous measurement of proteolytic activity and protease expression levels and can therefore be applied for protease substrate profiling, as well as directed evolution of proteases.
Collapse
Affiliation(s)
- Sebastian W Meister
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Natalie M Hendrikse
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - John Löfblom
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| |
Collapse
|
43
|
Zhu Z, Grady LC, Ding Y, Lind KE, Davie CP, Phelps CB, Evindar G. Development of a Selection Method for Discovering Irreversible (Covalent) Binders from a DNA-Encoded Library. SLAS Discov 2019; 24:169-174. [PMID: 30383465 PMCID: PMC7221453 DOI: 10.1177/2472555218808454] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/12/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
Abstract
DNA-encoded libraries (DELs) have been broadly applied to identify chemical probes for target validation and lead discovery. To date, the main application of the DEL platform has been the identification of reversible ligands using multiple rounds of affinity selection. Irreversible (covalent) inhibition offers a unique mechanism of action for drug discovery research. In this study, we report a developing method of identifying irreversible (covalent) ligands from DELs. The new method was validated by using 3C protease (3CP) and on-DNA irreversible tool compounds (rupintrivir derivatives) spiked into a library at the same concentration as individual members of that library. After affinity selections against 3CP, the irreversible tool compounds were specifically enriched compared with the library members. In addition, we compared two immobilization methods and concluded that microscale columns packed with the appropriate affinity resin gave higher tool compound recovery than magnetic beads.
Collapse
Affiliation(s)
| | | | - Yun Ding
- GlaxoSmithKline, Cambridge,
Massachusetts, USA
| | | | | | | | | |
Collapse
|
44
|
Fujita M, Adachi K, Nagasawa M. Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA. Anal Biochem 2019; 566:46-49. [PMID: 30352199 PMCID: PMC7172543 DOI: 10.1016/j.ab.2018.10.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 11/18/2022]
Abstract
The group of positive-sense single-stranded RNA ((+) ssRNA) viruses includes many important human pathogens. However, specific antiviral agents are not currently available for many RNA viruses. For screening of antiviral agents, methods that are simple, rapid, and compatible with high-throughput are required. Here, we describe a novel method for measurement of double-stranded RNA using a homogeneous time-resolved fluorescence assay. This method allowed detection of human rhinovirus (HRV), enterovirus, coxsackievirus, and murine norovirus. Furthermore, this method detected antiviral activity of a HRV 3C protease inhibitor. The assay may be useful for discovery of antiviral agents against (+) ssRNA viruses.
Collapse
Affiliation(s)
- Motomichi Fujita
- Pharmacology Research Laboratory, Watarase Research Center, Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Koji Adachi
- Cisbio K. K., Makuhari Techno Garden, Building D 11F, 1-3 Nakase Mihama-ku, Chiba-shi, Chiba 261-8501, Japan
| | - Michiaki Nagasawa
- Pharmacology Research Laboratory, Watarase Research Center, Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| |
Collapse
|
45
|
Ma Y, Cong W, Huang H, Sun L, Mai AH, Boonen K, Maryam W, De Borggraeve W, Luo G, Liu Q, Schoofs L, Van Kuppeveld F, Neyts J, Mirabelli C, Luyten W. Identification of fukinolic acid from Cimicifuga heracleifolia and its derivatives as novel antiviral compounds against enterovirus A71 infection. Int J Antimicrob Agents 2019; 53:128-136. [PMID: 30063999 DOI: 10.1016/j.ijantimicag.2018.07.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 06/17/2018] [Accepted: 07/14/2018] [Indexed: 01/07/2023]
Abstract
Human enterovirus 71 (EV-A71) infections cause a wide array of diseases ranging from diarrhoea and rashes to hand-foot-and-mouth disease and, in rare cases, severe neurological disorders. No specific antiviral drug therapy is currently available. Extracts from 75 Chinese medicinal plants selected for antiviral activity based on the Chinese pharmacopeia and advice from traditional Chinese medicine clinicians were tested for activity against EV-A71. The aqueous extract of the rhizome of Cimicifuga heracleifolia (Sheng Ma) and Arnebia euchroma (Zi Cao) showed potent antiviral activity. The active fractions were isolated by bioassay-guided purification, and identified by a combination of high-resolution mass spectrometry and nuclear magnetic resonance. Fukinolic acid and cimicifugic acid A and J, were identified as active anti-EV-A71 compounds for C. heracleifolia, whereas for A. euchroma, two caffeic acid derivatives were tentatively deduced. Commercially available fukinolic acid analogues such as L-chicoric acid and D-chicoric also showed in vitro micromolar activity against EV-A71 lab-strain and clinical isolates.
Collapse
Affiliation(s)
- Yipeng Ma
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Belgium; Laboratory of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Belgium
| | - Wenjuan Cong
- Wolfson Wohl Cancer Research Centre, University of Glasgow, Scotland, UK
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou, China
| | - Liang Sun
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Anh Hung Mai
- R&D Department, PolymerExpert,1 Allée du Doyen Georges Brus, Pessac, France
| | - Kurt Boonen
- Laboratory of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Belgium
| | - Wahedi Maryam
- Departement of infection and immunology, University of Utrecht, the Netherlands
| | - Wim De Borggraeve
- Molecular Design and Synthesis unit, Chemistry department, KU Leuven, Belgium
| | - Guoan Luo
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Qingfei Liu
- School of Medicine, Tsinghua University, Beijing, China
| | - Liliane Schoofs
- Laboratory of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Belgium
| | - Frank Van Kuppeveld
- Departement of infection and immunology, University of Utrecht, the Netherlands
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Carmen Mirabelli
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Belgium
| | - Walter Luyten
- Laboratory of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Belgium.
| |
Collapse
|
46
|
Banerjee K, Bhat R, Rao VUB, Nain A, Rallapalli KL, Gangopadhyay S, Singh RP, Banerjee M, Jayaram B. Toward development of generic inhibitors against the 3C proteases of picornaviruses. FEBS J 2019; 286:765-787. [PMID: 30461192 PMCID: PMC7164057 DOI: 10.1111/febs.14707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 09/20/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022]
Abstract
Development of novel antivirals, which requires knowledge of the viral life cycle in molecular detail, is a daunting task, involving extensive investments, and frequently resulting in failure. As there exist significant commonalities among virus families in the manner of host interaction, identifying and targeting common rather than specific features may lead to the development of broadly useful antivirals. Here, we have targeted the 3C protease of Hepatitis A Virus (HAV), a feco-orally transmitted virus of the family Picornaviridae, for identification of potential antivirals. The 3C protease is a viable drug target as it is required by HAV, as well as by other picornaviruses, for post-translational proteolysis of viral polyproteins and for inhibiting host innate immune pathways. Computational screening, followed by chemical synthesis and experimental validation resulted in identification of a few compounds which, at low micromolar concentrations, could inhibit HAV 3C activity. These compounds were further tested experimentally against the 3C protease of Human Rhinovirus, another member of the Picornaviridae family, with comparable results. Computational studies on 3C proteases from other members of the picornavirus family have indicated that the compounds identified could potentially be generic inhibitors for picornavirus 3C proteases.
Collapse
Affiliation(s)
- Kamalika Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Ruchika Bhat
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
| | | | - Anshu Nain
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Kartik Lakshmi Rallapalli
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Department of Chemistry and BiochemistryUniversity of California San Diego9500 Gilman DrLa JollaCA92093USA
| | - Sohona Gangopadhyay
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Chemical DivisionGeological Survey of India15‐16 Jhalana DungriWestern RegionJaipur302004India
| | - R. P. Singh
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
| | - Manidipa Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
| |
Collapse
|
47
|
Rasti M, Khanbabaei H, Teimoori A. An update on enterovirus 71 infection and interferon type I response. Rev Med Virol 2019; 29:e2016. [PMID: 30378208 PMCID: PMC7169063 DOI: 10.1002/rmv.2016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022]
Abstract
Enteroviruses are members of Pichornaviridae family consisting of human enterovirus group A, B, C, and D as well as nonhuman enteroviruses. Hand, foot, and mouth disease (HFMD) is a serious disease which is usually seen in the Asia-Pacific region in children. Enterovirus 71 and coxsackievirus A16 are two important viruses responsible for HFMD which are members of group A enterovirus. IFN α and β are two cytokines, which have a major activity in the innate immune system against viral infections. Most of the viruses have some weapons against these cytokines. EV71 has two main proteases called 2A and 3C, which are important for polyprotein processing and virus maturation. Several studies have indicated that they have a significant effect on different cellular pathways such as interferon production and signaling pathway. The aim of this study was to investigate the latest findings about the interaction of 2A and 3C protease of EV71 and IFN production/signaling pathway and their inhibitory effects on this pathway.
Collapse
Affiliation(s)
- Mojtaba Rasti
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Hashem Khanbabaei
- Medical Physics Department, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Ali Teimoori
- Department of Virology, Faculty of MedicineHamadan University of Medical SciencesHamadanIran
| |
Collapse
|
48
|
Komissarov AA, Kostrov SV, Demidyuk IV. In Vitro Assay for the Evaluation of Cytotoxic Effects Provided by a Combination of Suicide and Killer Genes in a Bicistronic Vector. Methods Mol Biol 2019; 1895:135-147. [PMID: 30539535 DOI: 10.1007/978-1-4939-8922-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
When using bicistronic expression constructs the issue arises concerning proper evaluation of the cytotoxic efficiency of a combination of therapeutic genes. For this purpose, an approach can be applied based on the transient transfection of cultured human cells with a specifically designed set of mono- and bicistronic expression constructs and on the comparison of their cytotoxic effects. Here the application of this approach is described using an example of the evaluation of the combined cytotoxic action of bifunctional yeast cytosine deaminase/uracil phosphoribosyltransferase fusion protein (FCU1) and hepatitis A virus 3C protease in a bicistronic plasmid construct.
Collapse
Affiliation(s)
- Alexey A Komissarov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Kostrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V Demidyuk
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
49
|
Xue Q, Liu H, Zhu Z, Yang F, Xue Q, Cai X, Liu X, Zheng H. Seneca Valley Virus 3C protease negatively regulates the type I interferon pathway by acting as a viral deubiquitinase. Antiviral Res 2018; 160:183-189. [PMID: 30408499 PMCID: PMC7111287 DOI: 10.1016/j.antiviral.2018.10.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/26/2018] [Accepted: 10/31/2018] [Indexed: 02/05/2023]
Abstract
The mechanisms that enable Seneca Valley Virus (SVV) to escape the host innate immune response are not well known. Previous studies demonstrated that SVV 3Cpro suppresses innate immune responses by cleavage of host proteins and degradation of IRF3 and IRF7 protein expression. Here, we showed that SVV 3C protease (3Cpro) has deubiquitinating activity. Overexpressed 3Cpro inhibits the ubiquitination of cellular substrates, acting on both lysine-48- and lysine-63-linked polyubiquitin chains. SVV infection also possessed deubiquitinating activity. The ubiquitin-proteasome system was significantly involved in SVV replication. Furthermore, 3Cpro inhibited the ubiquitination of retinoic acid-inducible gene I (RIG-I), TANK-binding kinase 1 (TBK1), and TNF receptor-associated factor 3 (TRAF3), thereby blocking the expression of interferon (IFN)-β and IFN stimulated gene 54 (ISG54) mRNAs. A detailed analysis revealed that mutations (H48A, C160A, or H48A/C160A) that ablate the Cys and His residues of 3Cpro abrogated its deubiquitinating activity and the ability of 3Cpro to block IFN-β induction. Together, our results demonstrate a novel mechanism developed by SVV 3Cpro to promote viral replication, and may also provide a novel strategy for improving ubiquitination-based therapy.
Collapse
Affiliation(s)
- Qiao Xue
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Huisheng Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Qinghong Xue
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Xuepeng Cai
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
| |
Collapse
|
50
|
Perera KD, Galasiti Kankanamalage AC, Rathnayake AD, Honeyfield A, Groutas W, Chang KO, Kim Y. Protease inhibitors broadly effective against feline, ferret and mink coronaviruses. Antiviral Res 2018; 160:79-86. [PMID: 30342822 PMCID: PMC6240502 DOI: 10.1016/j.antiviral.2018.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/25/2018] [Accepted: 10/17/2018] [Indexed: 12/14/2022]
Abstract
Ferret and mink coronaviruses typically cause catarrhal diarrhea in ferrets and minks, respectively. In recent years, however, systemic fatal coronavirus infection has emerged in ferrets, which resembles feline infectious peritonitis (FIP) in cats. FIP is a highly fatal systemic disease caused by a virulent feline coronavirus infection in cats. Despite the importance of coronavirus infections in these animals, there are no effective commercial vaccines or antiviral drugs available for these infections. We have previously reported the efficacy of a protease inhibitor in cats with FIP, demonstrating that a virally encoded 3C-like protease (3CLpro) is a valid target for antiviral drug development for coronavirus infections. In this study, we extended our previous work on coronavirus inhibitors and investigated the structure-activity relationships of a focused library of protease inhibitors for ferret and mink 3CLpro. Using the fluorescence resonance energy transfer assay, we identified potent inhibitors broadly effective against feline, ferret and mink coronavirus 3CLpro. Multiple amino acid sequence analysis and modelling of 3CLpro of ferret and mink coronaviruses were conducted to probe the structural basis for these findings. The results of this study provide support for further research to develop broad-spectrum antiviral agents for multiple coronavirus infections. To the best of our knowledge, this is the first report on small molecule inhibitors of ferret and mink coronaviruses.
Collapse
Affiliation(s)
- Krishani Dinali Perera
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | | | - Amanda Honeyfield
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - William Groutas
- Department of Chemistry, Wichita State University, Wichita, KS, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|