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Jiang H, Lin C, Chang J, Zou X, Zhang J, Li J. Crystal structures of the 3C proteases from Coxsackievirus B3 and B4. Acta Crystallogr F Struct Biol Commun 2024; 80:183-190. [PMID: 39052022 PMCID: PMC11299732 DOI: 10.1107/s2053230x24006915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Enteroviruses cause a wide range of disorders with varying presentations and severities, and some enteroviruses have emerged as serious public health concerns. These include Coxsackievirus B3 (CVB3), an active causative agent of viral myocarditis, and Coxsackievirus B4 (CVB4), which may accelerate the progression of type 1 diabetes. The 3C proteases from CVB3 and CVB4 play important roles in the propagation of these viruses. In this study, the 3C proteases from CVB3 and CVB4 were expressed in Escherichia coli and purified by affinity chromatography and gel-filtration chromatography. The crystals of the CVB3 and CVB4 3C proteases diffracted to 2.10 and 2.01 Å resolution, respectively. The crystal structures were solved by the molecular-replacement method and contained a typical chymotrypsin-like fold and a conserved His40-Glu71-Cys147 catalytic triad. Comparison with the structures of 3C proteases from other enteroviruses revealed high similarity with minor differences, which will guide the design of 3C-targeting inhibitors with broad-spectrum properties.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Cheng Lin
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
| | - Jingyi Chang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Xiaofang Zou
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
| | - Jin Zhang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang UniversityNanchang330031People’s Republic of China
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical UniversityGanzhou341000People’s Republic of China
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2
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Papaneophytou C. Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management. Int J Mol Sci 2024; 25:8105. [PMID: 39125676 PMCID: PMC11311956 DOI: 10.3390/ijms25158105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Respiratory viral infections (VRTIs) rank among the leading causes of global morbidity and mortality, affecting millions of individuals each year across all age groups. These infections are caused by various pathogens, including rhinoviruses (RVs), adenoviruses (AdVs), and coronaviruses (CoVs), which are particularly prevalent during colder seasons. Although many VRTIs are self-limiting, their frequent recurrence and potential for severe health complications highlight the critical need for effective therapeutic strategies. Viral proteases are crucial for the maturation and replication of viruses, making them promising therapeutic targets. This review explores the pivotal role of viral proteases in the lifecycle of respiratory viruses and the development of protease inhibitors as a strategic response to these infections. Recent advances in antiviral therapy have highlighted the effectiveness of protease inhibitors in curtailing the spread and severity of viral diseases, especially during the ongoing COVID-19 pandemic. It also assesses the current efforts aimed at identifying and developing inhibitors targeting key proteases from major respiratory viruses, including human RVs, AdVs, and (severe acute respiratory syndrome coronavirus-2) SARS-CoV-2. Despite the recent identification of SARS-CoV-2, within the last five years, the scientific community has devoted considerable time and resources to investigate existing drugs and develop new inhibitors targeting the virus's main protease. However, research efforts in identifying inhibitors of the proteases of RVs and AdVs are limited. Therefore, herein, it is proposed to utilize this knowledge to develop new inhibitors for the proteases of other viruses affecting the respiratory tract or to develop dual inhibitors. Finally, by detailing the mechanisms of action and therapeutic potentials of these inhibitors, this review aims to demonstrate their significant role in transforming the management of respiratory viral diseases and to offer insights into future research directions.
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Affiliation(s)
- Christos Papaneophytou
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia 2417, Cyprus
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3
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Gao X, Wang B, Zhu K, Wang L, Qin B, Shang K, Ding W, Wang J, Cui S. The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction. Nat Commun 2024; 15:4176. [PMID: 38755176 PMCID: PMC11099015 DOI: 10.1038/s41467-024-48504-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
SETD3 is an essential host factor for the replication of a variety of enteroviruses that specifically interacts with viral protease 2A. However, the interaction between SETD3 and the 2A protease has not been fully characterized. Here, we use X-ray crystallography and cryo-electron microscopy to determine the structures of SETD3 complexed with the 2A protease of EV71 to 3.5 Å and 3.1 Å resolution, respectively. We find that the 2A protease occupies the V-shaped central cleft of SETD3 through two discrete sites. The relative positions of the two proteins vary in the crystal and cryo-EM structures, showing dynamic binding. A biolayer interferometry assay shows that the EV71 2A protease outcompetes actin for SETD3 binding. We identify key 2A residues involved in SETD3 binding and demonstrate that 2A's ability to bind SETD3 correlates with EV71 production in cells. Coimmunoprecipitation experiments in EV71 infected and 2A expressing cells indicate that 2A interferes with the SETD3-actin complex, and the disruption of this complex reduces enterovirus replication. Together, these results reveal the molecular mechanism underlying the interplay between SETD3, actin, and viral 2A during virus replication.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Linyue Wang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Kun Shang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Medical School, Yan'an University, Yan'an, China
| | - Wei Ding
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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4
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Li X, Rahim K, Shen X, Cui X, Du C, Zhang G. Development of a Universal One-Step Purification and Activation Method to Engineer Protein-Glutaminase through Rational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10477-10486. [PMID: 38657166 DOI: 10.1021/acs.jafc.4c01406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cytotoxic enzymes often exist as zymogens containing prodomains to keep them in an inactive state. Protein-glutaminase (PG), which can enhance various functional characteristics of food proteins, is an enzyme containing pro-PG and mature-PG (mPG). However, poor activity and stability limit its application while tedious purification and activation steps limit its high-throughput engineering. Here, based on structural analysis, we replaced the linker sequence between pro-PG and mPG with the HRV3C protease recognition sequence and then coexpressed it with HRV3C protease in Escherichia coli to develop an efficient one-step purification and activation method for PG. We then used this method to obtain several mutants designed by a combination of computer-aided approach and beneficial point mutations. The specific activity (131.6 U/mg) of the best variant D1 was 4.14-fold that of the wild type, and t1/2 and T5010 increased by 13 min and 7 °C, respectively. D1 could effectively improve the solubility and emulsification of wheat proteins, more than twice the effect of the wild type. We also discussed the mechanism underlying the improved properties of D1. In summary, we not only provide a universal one-step purification and activation method to facilitate zymogen engineering but also obtain an excellent PG mutant.
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Affiliation(s)
- Xiaodi Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Kashif Rahim
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xingyu Shen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xin Cui
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Du
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guimin Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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5
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Tsilimingkra NT, Papaneophytou C. Phytochemicals: Promising Inhibitors of Human Rhinovirus Type 14 3C Protease as a Strategy to Fight the Common Cold. Curr Top Med Chem 2024; 24:1343-1358. [PMID: 38698747 DOI: 10.2174/0115680266308561240427065854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND Human rhinovirus 3C protease (HRV-3Cpro) plays a crucial role in viral proliferation, establishing it as a prime target for antiviral therapy. However, research on identifying HRV-3Cpro inhibitors is still limited. OBJECTIVE This study had two primary objectives: first, to validate the efficacy of an end-point colorimetric assay, previously developed by our team, for identifying potential inhibitors of HRV-3Cpro; and second, to discover phytochemicals in medicinal plants that inhibit the enzyme's activity. METHODS Rupintrivir, a well-known inhibitor of HRV-3Cpro, was used to validate the colorimetric assay. Following this, we conducted a two-step in silico screening of 2532 phytochemicals, which led to the identification of eight active compounds: apigenin, carnosol, chlorogenic acid, kaempferol, luteolin, quercetin, rosmarinic acid, and rutin. We subsequently evaluated these candidates in vitro. To further investigate the inhibitory potential of the most promising candidates, namely, carnosol and rosmarinic acid, molecular docking studies were performed to analyze their binding interactions with HRV-3Cpro. RESULTS The colorimetric assay we previously developed is effective in identifying compounds that selectively inhibit HRV-3Cpro. Carnosol and rosmarinic acid emerged as potent inhibitors, inhibiting HRV-3Cpro activity in vitro by over 55%. Our analysis indicated that carnosol and rosmarinic acid exert their inhibitory effects through a competitive mechanism. Molecular docking confirmed their competitive binding to the enzyme's active site. CONCLUSION Carnosol and rosmarinic acid warrant additional investigation for their potential in the development of common cold treatment. By highlighting these compounds as effective HRV-3Cpro inhibitors, our study presents a promising approach for discovering phytochemical inhibitors against proteases from similar pathogens.
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Affiliation(s)
| | - Christos Papaneophytou
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, 2417, Nicosia, Cyprus
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6
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Mondal S, Sarvari G, Boehr DD. Picornavirus 3C Proteins Intervene in Host Cell Processes through Proteolysis and Interactions with RNA. Viruses 2023; 15:2413. [PMID: 38140654 PMCID: PMC10747604 DOI: 10.3390/v15122413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
The Picornaviridae family comprises a large group of non-enveloped viruses with enormous impact on human and animal health. The picornaviral genome contains one open reading frame encoding a single polyprotein that can be processed by viral proteases. The picornaviral 3C proteases share similar three-dimensional structures and play a significant role in the viral life cycle and virus-host interactions. Picornaviral 3C proteins also have conserved RNA-binding activities that contribute to the assembly of the viral RNA replication complex. The 3C protease is important for regulating the host cell response through the cleavage of critical host cell proteins, acting to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and inactivating key factors in innate immunity signaling pathways. The protease and RNA-binding activities of 3C are involved in viral polyprotein processing and the initiation of viral RNA synthesis. Most importantly, 3C modifies critical molecules in host organelles and maintains virus infection by subtly subverting host cell death through the blocking of transcription, translation, and nucleocytoplasmic trafficking to modulate cell physiology for viral replication. Here, we discuss the molecular mechanisms through which 3C mediates physiological processes involved in promoting virus infection, replication, and release.
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Affiliation(s)
| | | | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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7
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Reuscher CM, Barth S, Gockel F, Netsch A, Seitz K, Rümenapf T, Lamp B. Processing of the 3C/D Region of the Deformed Wing Virus (DWV). Viruses 2023; 15:2344. [PMID: 38140585 PMCID: PMC10748302 DOI: 10.3390/v15122344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The deformed wing virus (DWV) belongs to the genus Iflavirus and the family Iflaviridae within the order Picornavirales. It is an important pathogen of the Western honey bee, Apis mellifera, causing major losses among honey bee colonies in association with the ectoparasitic mite Varroa destructor. Although DWV is one of the best-studied insect viruses, the mechanisms of viral replication and polyprotein processing have been poorly studied in the past. We investigated the processing of the protease-polymerase region at the C-terminus of the polyprotein in more detail using recombinant expression, novel serological reagents, and virus clone mutagenesis. Edman degradation of purified maturated polypeptides uncovered the C- and N-termini of the mature 3C-like (3CL) protease and RNA-dependent RNA polymerase (3DL, RdRp), respectively. Autocatalytic processing of the recombinant DWV 3CL protease occurred at P1 Q2118 and P1' G2119 (KPQ/GST) as well as P1 Q2393 and P1' S2394 (HAQ/SPS) cleavage sites. New monoclonal antibodies (Mab) detected the mature 3CL protease with an apparent molecular mass of 32 kDa, mature 3DL with an apparent molecular mass of 55 kDa as well as a dominant 3CDL precursor of 90 kDa in DWV infected honey bee pupae. The observed pattern corresponds well to data obtained via recombinant expression and N-terminal sequencing. Finally, we were able to show that 3CL protease activity and availability of the specific protease cleavage sites are essential for viral replication, protein synthesis, and establishment of infection using our molecular clone of DWV-A.
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Affiliation(s)
- Carina Maria Reuscher
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany (S.B.); (F.G.)
| | - Sandra Barth
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany (S.B.); (F.G.)
| | - Fiona Gockel
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany (S.B.); (F.G.)
- Institute of Medical Virology, Justus Liebig University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
| | - Anette Netsch
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany (S.B.); (F.G.)
| | - Kerstin Seitz
- Department for Pathobiology, Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria; (K.S.); (T.R.)
| | - Till Rümenapf
- Department for Pathobiology, Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria; (K.S.); (T.R.)
| | - Benjamin Lamp
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany (S.B.); (F.G.)
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8
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Li X, Song Y. Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review. Eur J Med Chem 2023; 260:115772. [PMID: 37659195 PMCID: PMC10529944 DOI: 10.1016/j.ejmech.2023.115772] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/04/2023]
Abstract
Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) identified in 2003 infected ∼8000 people in 26 countries with 800 deaths, which was soon contained and eradicated by syndromic surveillance and enhanced quarantine. A closely related coronavirus SARS-CoV-2, the causative agent of COVID-19 identified in 2019, has been dramatically more contagious and catastrophic. It has infected and caused various flu-like symptoms of billions of people in >200 countries, including >6 million people died of or with the virus. Despite the availability of several vaccines and antiviral drugs against SARS-CoV-2, finding new therapeutics is needed because of viral evolution and a possible emerging coronavirus in the future. The main protease (Mpro) of these coronaviruses plays important roles in their life cycle and is essential for the viral replication. This article represents a comprehensive review of the function, structure and inhibition of SARS-CoV and -CoV-2 Mpro, including structure-activity relationships, protein-inhibitor interactions and clinical trial status.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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9
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Parida PP, Saraswathi D, Mopidevi SM, Raran-Kurussi S. Advancing large-scale production of TEV protease through an innovative NT* tag-based fusion construct. Curr Res Struct Biol 2023; 6:100106. [PMID: 37822550 PMCID: PMC10563009 DOI: 10.1016/j.crstbi.2023.100106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023] Open
Abstract
Tobacco etch virus Protease (TEVp), a cysteine protease, is renowned for its remarkable specific proteolysis, making it an invaluable tool for removing fusion tags from recombinant proteins. However, TEV protease's inherent insolubility limits its broad application. Fusion constructs like an N-terminal MBP fusion, known for its improved solubility, have been employed for TEVp production to address this issue. In this study, we fused the TEVp with the N-terminal domain of the spider silk protein, specifically utilizing a charge-reversed mutant (D40K/K65D) of the N-terminal domain of major ampullate spidroin-1 protein from Euprosthenops australis, referred to as NT*. This fusion construct contains a TEVp cleavage site, enabling intracellular self-processing and the release of a His7-tagged protease. The significant increase in soluble protein expression allowed us to purify approximately 90-100 mg of TEVp from a 1-L E. coli culture, surpassing previous findings by a considerable margin. The enzyme remained stable and catalytically active even after several months of storage in a deep freezer (-80 °C).
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Affiliation(s)
- Pragyan P. Parida
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Deepa Saraswathi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Subbarao M.V. Mopidevi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad, 500046, Telangana, India
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10
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Stubbing LA, Hubert JG, Bell-Tyrer J, Hermant YO, Yang SH, McSweeney AM, McKenzie-Goldsmith GM, Ward VK, Furkert DP, Brimble MA. P 1 Glutamine isosteres in the design of inhibitors of 3C/3CL protease of human viruses of the Pisoniviricetes class. RSC Chem Biol 2023; 4:533-547. [PMID: 37547456 PMCID: PMC10398354 DOI: 10.1039/d3cb00075c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Viral infections are one of the leading causes of acute morbidity in humans and much endeavour has been made by the synthetic community for the development of drugs to treat associated diseases. Peptide-based enzyme inhibitors, usually short sequences of three or four residues, are one of the classes of compounds currently under development for enhancement of their activity and pharmaceutical properties. This review reports the advances made in the design of inhibitors targeting the family of highly conserved viral proteases 3C/3CLpro, which play a key role in viral replication and present minimal homology with mammalian proteases. Particular focus is put on the reported development of P1 glutamine isosteres to generate potent inhibitors mimicking the natural substrate sequence at the site of recognition.'
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Affiliation(s)
- Louise A Stubbing
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Jonathan G Hubert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Joseph Bell-Tyrer
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Yann O Hermant
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Sung Hyun Yang
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Alice M McSweeney
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Geena M McKenzie-Goldsmith
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Vernon K Ward
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
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11
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Arnaiz A, Guirado-Moreno JC, Guembe-García M, Barros R, Tamayo-Ramos JA, Fernández-Pampín N, García JM, Vallejos S. Lab-on-a-chip for the easy and visual detection of SARS-CoV-2 in saliva based on sensory polymers. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 379:133165. [PMID: 36536612 PMCID: PMC9751010 DOI: 10.1016/j.snb.2022.133165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The initial stages of the pandemic caused by SARS-CoV-2 showed that early detection of the virus in a simple way is the best tool until the development of vaccines. Many different tests are invasive or need the patient to cough up or even drag a sample of mucus from the throat area. Besides, the manufacturing time has proven insufficient in pandemic conditions since they were out of stock in many countries. Here we show a new method of manufacturing virus sensors and a proof of concept with SARS-CoV-2. We found that a fluorogenic peptide substrate of the main protease of the virus (Mpro) can be covalently immobilized in a polymer, with which a cellulose-based material can be coated. These sensory labels fluoresce with a single saliva sample of a positive COVID-19 patient. The results matched with that of the antigen tests in 22 of 26 studied cases (85% success rate).
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Affiliation(s)
- Ana Arnaiz
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
- Universidad Politécnica de Madrid, Calle Ramiro de Maeztu, 7, 28040 Madrid, Spain
| | - José Carlos Guirado-Moreno
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Marta Guembe-García
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Rocio Barros
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Juan Antonio Tamayo-Ramos
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Fernández-Pampín
- International Research Center in Critical Raw Materials for Advanced Industrial Technologies (ICCRAM), R&D Center, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - José M García
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Saúl Vallejos
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza de Misael Bañuelos s/n, 09001 Burgos, Spain
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12
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Wan L, Wang X, Wang T, Yuan X, Liu W, Huang Y, Deng C, Cao S. Comparison of Target Pocket Similarity and Progress into Research on Inhibitors of Picornavirus 3C Proteases. Chem Biodivers 2023; 20:e202201100. [PMID: 36808685 DOI: 10.1002/cbdv.202201100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/21/2023]
Abstract
The 3C protease (3C Pro) plays a significant role in the life cycle of picornaviruses from replication to translation, making it an attractive target for structure-based design of drugs against picornaviruses. The structurally related 3C-like protease (3CL Pro) is an important protein involved in the replication of coronaviruses. With the emergence of COVID-19 and consequent intensive research into 3CL Pro, development of 3CL Pro inhibitors has emerged as a popular topic. This article compares the similarities of the target pockets of various 3C and 3CL Pros from numerous pathogenic viruses. This article also reports several types of 3C Pro inhibitors that are currently undergoing extensive studies and introduces various structural modifications of 3C Pro inhibitors to provide a reference for the development of new and more effective inhibitors of 3C Pro and 3CL Pro.
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Affiliation(s)
- Li Wan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaobo Wang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Tangle Wang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xiaolan Yuan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Wei Liu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Yan Huang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Changyong Deng
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Shuang Cao
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
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13
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Mone K, Lasrado N, Sur M, Reddy J. Vaccines against Group B Coxsackieviruses and Their Importance. Vaccines (Basel) 2023; 11:vaccines11020274. [PMID: 36851152 PMCID: PMC9961666 DOI: 10.3390/vaccines11020274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
The group B coxsackieviruses (CVBs) exist in six serotypes (CVB1 to CVB6). Disease associations have been reported for most serotypes, and multiple serotypes can cause similar diseases. For example, CVB1, CVB3, and CVB5 are generally implicated in the causation of myocarditis, whereas CVB1 and CVB4 could accelerate the development of type 1 diabetes (T1D). Yet, no vaccines against these viruses are currently available. In this review, we have analyzed the attributes of experimentally tested vaccines and discussed their merits and demerits or limitations, as well as their impact in preventing infections, most importantly myocarditis and T1D.
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Affiliation(s)
- Kiruthiga Mone
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Ninaad Lasrado
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Meghna Sur
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Correspondence: ; Tel.: +1-(402)-472-8541
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14
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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] [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.
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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.
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15
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Chen Q, Zhou J, Yang Z, Guo J, Liu Z, Sun X, Jiang Q, Fang L, Wang D, Xiao S. An intermolecular salt bridge linking substrate binding and P1 substrate specificity switch of arterivirus 3C-like proteases. Comput Struct Biotechnol J 2022; 20:3409-3421. [PMID: 35832618 PMCID: PMC9271976 DOI: 10.1016/j.csbj.2022.06.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022] Open
Abstract
Equine arteritis virus (EAV) and porcine reproductive and respiratory syndrome virus (PRRSV) represent two members of the family Arteriviridae and pose a major threat to the equine- and swine-breeding industries throughout the world. Previously, we and others demonstrated that PRRSV 3C-like protease (3CLpro) had very high glutamic acid (Glu)-specificity at the P1 position (P1-Glu). Comparably, EAV 3CLpro exhibited recognition of both Glu and glutamine (Gln) at the P1 position. However, the underlying mechanisms of the P1 substrate specificity shift of arterivirus 3CLpro remain unclear. We systematically screened the specific amino acids in the S1 subsite of arterivirus 3CLpro using a cyclized luciferase-based biosensor and identified Gly116, His133 and Ser136 (using PRRSV 3CLpro numbering) are important for recognition of P1-Glu, whereas Ser136 is nonessential for recognition of P1-Gln. Molecular dynamics simulations and biochemical experiments highlighted that the PRRSV 3CLpro and EAV 3CLpro formed distinct S1 subsites for the P1 substrate specificity switch. Mechanistically, a specific intermolecular salt bridge between PRRSV 3CLpro and substrate P1-Glu (Lys138/P1-Glu) are invaluable for high Glu-specificity at the P1 position, and the exchange of K138T (salt bridge interruption, from PRRSV to EAV) shifted the specificity of PRRSV 3CLpro toward P1-Gln. In turn, the T139K exchange of EAV 3CLpro showed a noticeable shift in substrate specificity, such that substrates containing P1-Glu are likely to be recognized more efficiently. These findings identify an evolutionarily accessible mechanism for disrupting or reorganizing salt bridge with only a single mutation of arterivirus 3CLpro to trigger a substrate specificity switch.
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Affiliation(s)
- Qian Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Junwei Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zhixiang Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Jiahui Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zimin Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Xinyi Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Qingshi Jiang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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16
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Yuan X, Kadowaki T. DWV 3C Protease Uncovers the Diverse Catalytic Triad in Insect RNA Viruses. Microbiol Spectr 2022; 10:e0006822. [PMID: 35575593 PMCID: PMC9241925 DOI: 10.1128/spectrum.00068-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/20/2022] Open
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.
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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
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17
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Structure of Senecavirus A 3C Protease Revealed the Cleavage Pattern of 3C Protease in Picornaviruses. J Virol 2022; 96:e0073622. [PMID: 35727031 DOI: 10.1128/jvi.00736-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Senecavirus A (SVA) is an emerging picornavirus infecting porcine of all age groups and causing foot and mouth disease (FMD)-like symptoms. One of its key enzymes is the 3C protease (3Cpro), which is similar to other picornaviruses and essential for virus maturation by controlling polyprotein cleavage and RNA replication. In this study, we reported the crystal structure of SVA 3Cpro at a resolution of 1.9 Å and a thorough structural comparison against all published picornavirus 3Cpro structures. Using statistical and graphical visualization techniques, we also investigated the sequence specificity of the 3Cpro. The structure revealed that SVA 3Cpro adopted a typical chymotrypsin-like fold with the S1 subsite as the most conservative site among picornavirus 3Cpro. The surface loop, A1-B1 hairpin, adopted a novel conformation in SVA 3Cpro and formed a positively charged protrusion around S' subsites. Correspondingly, SVA scissile bonds preferred Asp rather than neutral amino acids at P3' and P4'. Moreover, SVA 3Cpro showed a wide range tolerance to P4 residue volume (acceptable range: 67 Å3 to 141 Å3), such as aromatic side chain, in contrast to other picornaviruses. In summary, our results provided valuable information for understanding the cleavage pattern of 3Cpro. IMPORTANCE Picornaviridae is a group of RNA viruses that harm both humans and livestock. 3Cpro is an essential enzyme for picornavirus maturation, which makes it a promising target for antiviral drug development and a critical component for virus-like particle (VLP) production. However, the current challenge in the development of antiviral drugs and VLP vaccines includes the limited knowledge of how subsite structure determines the 3Cpro cleavage pattern. Thus, an extensive comparative study of various picornaviral 3Cpro was required. Here, we showed the 1.9 Å crystal structure of SVA 3Cpro. The structure revealed similarities and differences in the substrate-binding groove among picornaviruses, providing new insights into the development of inhibitors and VLP.
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18
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Surgical Strikes on Host Defenses: Role of the Viral Protease Activity in Innate Immune Antagonism. Pathogens 2022; 11:pathogens11050522. [PMID: 35631043 PMCID: PMC9145062 DOI: 10.3390/pathogens11050522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
As a frontline defense mechanism against viral infections, the innate immune system is the primary target of viral antagonism. A number of virulence factors encoded by viruses play roles in circumventing host defenses and augmenting viral replication. Among these factors are viral proteases, which are primarily responsible for maturation of viral proteins, but in addition cause proteolytic cleavage of cellular proteins involved in innate immune signaling. The study of these viral protease-mediated host cleavages has illuminated the intricacies of innate immune networks and yielded valuable insights into viral pathogenesis. In this review, we will provide a brief summary of how proteases of positive-strand RNA viruses, mainly from the Picornaviridae, Flaviviridae and Coronaviridae families, proteolytically process innate immune components and blunt their functions.
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19
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Miao M, Deng G, Xiong X, Qiu Y, Huang W, Yuan M, Yu F, Bai S, Zhou X, Zhao X. Enterovirus 71 3C proteolytically processes the histone H3 N-terminal tail during infection. Virol Sin 2022; 37:314-317. [PMID: 35256288 PMCID: PMC9170973 DOI: 10.1016/j.virs.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
•The N-terminal tail of histone H3 is specifically cleaved during EV71 infection. •Viral protease 3C is identified as a protease responsible for proteolytically processing the N-terminal H3 tail. •Our finding reveals a new epigenetic regulatory mechanism for Enterovirus 71 in virus-host interactions.
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Affiliation(s)
- Meng Miao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Gang Deng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaobei Xiong
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Yang Qiu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Wenda Huang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meng Yuan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Yu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shimei Bai
- Institute of Biochemistry, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xi Zhou
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China.
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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20
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Dai W, Jochmans D, Xie H, Yang H, Li J, Su H, Chang D, Wang J, Peng J, Zhu L, Nian Y, Hilgenfeld R, Jiang H, Chen K, Zhang L, Xu Y, Neyts J, Liu H. Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2. J Med Chem 2022; 65:2794-2808. [PMID: 33872498 PMCID: PMC8084273 DOI: 10.1021/acs.jmedchem.0c02258] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Indexed: 12/30/2022]
Abstract
A novel series of peptidomimetic aldehydes was designed and synthesized to target 3C protease (3Cpro) of enterovirus 71 (EV71). Most of the compounds exhibited high antiviral activity, and among them, compound 18p demonstrated potent enzyme inhibitory activity and broad-spectrum antiviral activity on a panel of enteroviruses and rhinoviruses. The crystal structure of EV71 3Cpro in complex with 18p determined at a resolution of 1.2 Å revealed that 18p covalently linked to the catalytic Cys147 with an aldehyde group. In addition, these compounds also exhibited good inhibitory activity against the 3CLpro and the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially compound 18p (IC50 = 0.034 μM, EC50 = 0.29 μM). According to our previous work, these compounds have no reasons for concern regarding acute toxicity. Compared with AG7088, compound 18p also exhibited good pharmacokinetic properties and more potent anticoronavirus activity, making it an excellent lead for further development.
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Affiliation(s)
- Wenhao Dai
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hang Xie
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
| | - Hang Yang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Jian Li
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Haixia Su
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Di Chang
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Jiang Wang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Jingjing Peng
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Yong Nian
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine,
University of Lübeck, 23562 Lübeck,
Germany
- German Center for Infection Research (DZIF),
University of Lübeck, 23562 Lübeck,
Germany
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hong Liu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
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21
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Ekanayaka P, Shin SH, Weeratunga P, Lee H, Kim TH, Chathuranga K, Subasinghe A, Park JH, Lee JS. Foot-and-Mouth Disease Virus 3C Protease Antagonizes Interferon Signaling and C142T Substitution Attenuates the FMD Virus. Front Microbiol 2021; 12:737031. [PMID: 34867853 PMCID: PMC8639872 DOI: 10.3389/fmicb.2021.737031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
3C protease (3Cpro), a chymotrypsin-like cysteine protease encoded by the foot-and-mouth disease virus (FMDV), plays an essential role in processing the FMDV P1 polyprotein into individual viral capsid proteins in FMDV replication. Previously, it has been shown that 3Cpro is involved in the blockage of the host type-I interferon (IFN) responses by FMDV. However, the underlying mechanisms are poorly understood. Here, we demonstrated that the protease activity of 3Cpro contributed to the degradation of RIG-I and MDA5, key cytosolic sensors of the type-I IFN signaling cascade in proteasome, lysosome and caspase-independent manner. And also, we examined the degradation ability on RIG-I and MDA5 of wild-type FMDV 3Cpro and FMDV 3Cpro C142T mutant which is known to significantly alter the enzymatic activity of 3Cpro. The results showed that the FMDV 3Cpro C142T mutant dramatically reduce the degradation of RIG-I and MDA5 due to weakened protease activity. Thus, the protease activity of FMDV 3Cpro governs its RIG-I and MDA5 degradation ability and subsequent negative regulation of the type-I IFN signaling. Importantly, FMD viruses harboring 3Cpro C142T mutant showed the moderate attenuation of FMDV in a pig model. In conclusion, our results indicate that a novel mechanism evolved by FMDV 3Cpro to counteract host type-I IFN responses and a rational approach to virus attenuation that could be utilized for future vaccine development.
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Affiliation(s)
- Pathum Ekanayaka
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Sung Ho Shin
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, South Korea
| | - Prasanna Weeratunga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyuncheol Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - Tae-Hwan Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Ashan Subasinghe
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Jong-Hyeon Park
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, South Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
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22
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Zhang T, Li C, Cao M, Wang D, Wang Q, Xie Y, Gao S, Fu S, Zhou X, Wu J. A Novel Rice Curl Dwarf-Associated Picornavirus Encodes a 3C Serine Protease Recognizing Uncommon EPT/S Cleavage Sites. Front Microbiol 2021; 12:757451. [PMID: 34721366 PMCID: PMC8549817 DOI: 10.3389/fmicb.2021.757451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Picornaviruses cause diseases in a wide range of vertebrates, invertebrates and plants. Here, a novel picornavirus was identified by RNA-seq technology from rice plants showing dwarfing and curling symptoms, and the name rice curl dwarf-associated virus (RCDaV) is tentatively proposed. The RCDaV genome consists of an 8,987 nt positive-stranded RNA molecule, excluding a poly(A) tail, that encodes two large polyproteins. Using in vitro cleavage assays, we have identified that the RCDaV 3C protease (3Cpro) as a serine protease recognizes the conserved EPT/S cleavage site which differs from the classic Q(E)/G(S) sites cleaved by most picornaviral 3C chymotrypsin-like cysteine proteases. Therefore, we comprehensively deciphered the RCDaV genome organization and showed that the two polyproteins of RCDaV can be cleaved into 12 mature proteins. We found that seven unclassified picornaviruses also encode a 3Cpro similar to RCDaV, and use the highly conserved EPT/S as the cleavage site. The precise genome organizations of these viruses were illustrated. Moreover, RCDaV and the seven unclassified picornaviruses share high sequence identities and similar genome organizations, and cluster into a distinct clade in the order Picornavirales. Our study provides valuable information for the understanding of picornaviral 3Cpros, deciphers the genome organization of a few relatively obscure picornaviruses, and lays the foundation for further pathogenesis research on these viruses.
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Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, China
| | - Dan Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yi Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shibo Gao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Hainan Research Institute of Zhejiang University, Hainan, China
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23
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Real-Hohn A, Blaas D. Rhinovirus Inhibitors: Including a New Target, the Viral RNA. Viruses 2021; 13:1784. [PMID: 34578365 PMCID: PMC8473194 DOI: 10.3390/v13091784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Rhinoviruses (RVs) are the main cause of recurrent infections with rather mild symptoms characteristic of the common cold. Nevertheless, RVs give rise to enormous numbers of absences from work and school and may become life-threatening in particular settings. Vaccination is jeopardised by the large number of serotypes eliciting only poorly cross-neutralising antibodies. Conversely, antivirals developed over the years failed FDA approval because of a low efficacy and/or side effects. RV species A, B, and C are now included in the fifteen species of the genus Enteroviruses based upon the high similarity of their genome sequences. As a result of their comparably low pathogenicity, RVs have become a handy model for other, more dangerous members of this genus, e.g., poliovirus and enterovirus 71. We provide a short overview of viral proteins that are considered potential drug targets and their corresponding drug candidates. We briefly mention more recently identified cellular enzymes whose inhibition impacts on RVs and comment novel approaches to interfere with infection via aggregation, virus trapping, or preventing viral access to the cell receptor. Finally, we devote a large part of this article to adding the viral RNA genome to the list of potential drug targets by dwelling on its structure, folding, and the still debated way of its exit from the capsid. Finally, we discuss the recent finding that G-quadruplex stabilising compounds impact on RNA egress possibly via obfuscating the unravelling of stable secondary structural elements.
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Affiliation(s)
- Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria
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24
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Yi J, Peng J, Yang W, Zhu G, Ren J, Li D, Zheng H. Picornavirus 3C - a protease ensuring virus replication and subverting host responses. J Cell Sci 2021; 134:134/5/jcs253237. [PMID: 33692152 DOI: 10.1242/jcs.253237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The protease 3C is encoded by all known picornaviruses, and the structural features related to its protease and RNA-binding activities are conserved; these contribute to the cleavage of viral polyproteins and the assembly of the viral RNA replication complex during virus replication. Furthermore, 3C performs functions in the host cell through its interaction with host proteins. For instance, 3C has been shown to selectively 'hijack' host factors involved in gene expression, promoting picornavirus replication, and to inactivate key factors in innate immunity signaling pathways, inhibiting the production of interferon and inflammatory cytokines. Importantly, 3C maintains virus infection by subtly subverting host cell death and modifying critical molecules in host organelles. This Review focuses on the molecular mechanisms through which 3C mediates physiological processes involved in virus-host interaction, thus highlighting the picornavirus-mediated pathogenesis caused by 3C.
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Affiliation(s)
- Jiamin Yi
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jiangling Peng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Wenping Yang
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Guoqiang Zhu
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Jingjing Ren
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology and OIE/National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
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25
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Jin Z, Wang H, Duan Y, Yang H. The main protease and RNA-dependent RNA polymerase are two prime targets for SARS-CoV-2. Biochem Biophys Res Commun 2021; 538:63-71. [PMID: 33288200 PMCID: PMC7680044 DOI: 10.1016/j.bbrc.2020.10.091] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an unprecedented global health crisis. It is particularly urgent to develop clinically effective therapies to contain the pandemic. The main protease (Mpro) and the RNA-dependent RNA polymerase (RdRP), which are responsible for the viral polyprotein proteolytic process and viral genome replication and transcription, respectively, are two attractive drug targets for SARS-CoV-2. This review summarizes up-to-date progress in the structural and pharmacological aspects of those two key targets above. Different classes of inhibitors individually targeting Mpro and RdRP are discussed, which could promote drug development to treat SARS-CoV-2 infection.
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Affiliation(s)
- Zhenming Jin
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,School of Life Sciences, Tianjin University, Tianjin, China,Corresponding author. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China,Corresponding author
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26
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Yang H, Rao Z. Structural biology of SARS-CoV-2 and implications for therapeutic development. Nat Rev Microbiol 2021; 19:685-700. [PMID: 34535791 PMCID: PMC8447893 DOI: 10.1038/s41579-021-00630-8] [Citation(s) in RCA: 253] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 02/04/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an unprecedented global health crisis. However, therapeutic options for treatment are still very limited. The development of drugs that target vital proteins in the viral life cycle is a feasible approach for treating COVID-19. Belonging to the subfamily Orthocoronavirinae with the largest RNA genome, SARS-CoV-2 encodes a total of 29 proteins. These non-structural, structural and accessory proteins participate in entry into host cells, genome replication and transcription, and viral assembly and release. SARS-CoV-2 proteins can individually perform essential physiological roles, be components of the viral replication machinery or interact with numerous host cellular factors. In this Review, we delineate the structural features of SARS-CoV-2 from the whole viral particle to the individual viral proteins and discuss their functions as well as their potential as targets for therapeutic interventions.
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Affiliation(s)
- Haitao Yang
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zihe Rao
- grid.440637.20000 0004 4657 8879Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China ,grid.12527.330000 0001 0662 3178Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China ,grid.216938.70000 0000 9878 7032State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China ,grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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27
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Cisneros-Martínez AM, Becerra A, Lazcano A. Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons. Virus Evol 2021; 7:veab019. [PMID: 33758672 PMCID: PMC7967035 DOI: 10.1093/ve/veab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses.
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Affiliation(s)
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- El Colegio Nacional, Donceles 104, Centro Histórico, Mexico City, Mexico
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28
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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: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [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.
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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
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29
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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: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [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.
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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;
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30
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Structural Biology of the Enterovirus Replication-Linked 5'-Cloverleaf RNA and Associated Virus Proteins. Microbiol Mol Biol Rev 2020; 84:84/2/e00062-19. [PMID: 32188627 DOI: 10.1128/mmbr.00062-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although enteroviruses are associated with a wide variety of diseases and conditions, their mode of replication is well conserved. Their genome is carried as a single, positive-sense RNA strand. At the 5' end of the strand is an approximately 90-nucleotide self-complementary region called the 5' cloverleaf, or the oriL. This noncoding region serves as a platform upon which host and virus proteins, including the 3B, 3C, and 3D virus proteins, assemble in order to initiate replication of a negative-sense RNA strand. The negative strand in turn serves as a template for synthesis of multiple positive-sense RNA strands. Building on structural studies of individual RNA stem-loops, the structure of the intact 5' cloverleaf from rhinovirus has recently been determined via nuclear magnetic resonance/small-angle X-ray scattering (NMR/SAXS)-based methods, while structures have also been determined for enterovirus 3A, 3B, 3C, and 3D proteins. Analysis of these structures, together with structural and modeling studies of interactions between host and virus proteins and RNA, has begun to provide insight into the enterovirus replication mechanism and the potential to inhibit replication by blocking these interactions.
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31
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Saraswat S, Chaudhary M, Sehgal D. Hepatitis E Virus Cysteine Protease Has Papain Like Properties Validated by in silico Modeling and Cell-Free Inhibition Assays. Front Cell Infect Microbiol 2020; 9:478. [PMID: 32039053 PMCID: PMC6989534 DOI: 10.3389/fcimb.2019.00478] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/27/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatitis E virus (HEV) has emerged as a global health concern during the last decade. In spite of a high mortality rate in pregnant women with fulminant hepatitis, no antiviral drugs or licensed vaccine is available in India. HEV-protease is a pivotal enzyme responsible for ORF1 polyprotein processing leading to cleavage of the non-structural enzymes involved in virus replication. HEV-protease region encoding 432–592 amino acids of Genotype-1 was amplified, expressed in Sf21 cells and purified in its native form. The recombinant enzyme was biochemically characterized using SDS-PAGE, Western blotting and Immunofluorescence. The enzyme activity and the inhibition studies were conducted using Zymography, FTC-casein based protease assay and ORF1 polyprotein digestion. To conduct ORF1 digestion assay, the polyprotein, natural substrate of HEV-protease, was expressed in E. coli and purified. Cleavage of 186 kDa ORF1 polyprotein by the recombinant HEV-protease lead to appearance of non-structural proteins viz. Methyltransferase, Protease, Helicase and RNA dependent RNA polymerase which were confirmed through immunoblotting using antibodies generated against specific epitopes of the enzymes. FTC-casein substrate was used for kinetic studies to determine Km and Vmax of the enzyme and also the effect of different metal ions and other protease inhibitors. A 95% inhibition was observed with E-64 which was validated through in silico analysis. The correlation coefficient between inhibition and docking score of Inhibitors was found to have a significant value of r2 = 0.75. The predicted 3D model showed two domain architecture structures similar to Papain like cysteine protease though they differed in arrangements of alpha helices and beta sheets. Hence, we propose that HEV-protease has characteristics of “Papain-like cysteine protease,” as determined through structural homology, active site residues and class-specific inhibition. However, conclusive nature of the enzyme remains to be established.
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Affiliation(s)
- Shweta Saraswat
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Meenakshi Chaudhary
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
| | - Deepak Sehgal
- Virology Lab, Department of Life Sciences, Shiv Nadar University, Greater Noida, India
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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] [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.
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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
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Li F, Chen J, Leier A, Marquez-Lago T, Liu Q, Wang Y, Revote J, Smith AI, Akutsu T, Webb GI, Kurgan L, Song J. DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinformatics 2019; 36:1057-1065. [PMID: 31566664 PMCID: PMC8215920 DOI: 10.1093/bioinformatics/btz721] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/13/2019] [Accepted: 09/25/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Proteases are enzymes that cleave target substrate proteins by catalyzing the hydrolysis of peptide bonds between specific amino acids. While the functional proteolysis regulated by proteases plays a central role in the 'life and death' cellular processes, many of the corresponding substrates and their cleavage sites were not found yet. Availability of accurate predictors of the substrates and cleavage sites would facilitate understanding of proteases' functions and physiological roles. Deep learning is a promising approach for the development of accurate predictors of substrate cleavage events. RESULTS We propose DeepCleave, the first deep learning-based predictor of protease-specific substrates and cleavage sites. DeepCleave uses protein substrate sequence data as input and employs convolutional neural networks with transfer learning to train accurate predictive models. High predictive performance of our models stems from the use of high-quality cleavage site features extracted from the substrate sequences through the deep learning process, and the application of transfer learning, multiple kernels and attention layer in the design of the deep network. Empirical tests against several related state-of-the-art methods demonstrate that DeepCleave outperforms these methods in predicting caspase and matrix metalloprotease substrate-cleavage sites. AVAILABILITY AND IMPLEMENTATION The DeepCleave webserver and source code are freely available at http://deepcleave.erc.monash.edu/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - André Leier
- Department of Genetics, USA,Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tatiana Marquez-Lago
- Department of Genetics, USA,Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Quanzhong Liu
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Yanze Wang
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Jerico Revote
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - A Ian Smith
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Geoffrey I Webb
- Monash Centre for Data Science, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia
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Kanitz M, Blanck S, Heine A, Gulyaeva AA, Gorbalenya AE, Ziebuhr J, Diederich WE. Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus. Virology 2019; 533:21-33. [PMID: 31078932 PMCID: PMC7111312 DOI: 10.1016/j.virol.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023]
Abstract
Cavally virus (CavV) is a mosquito-borne plus-strand RNA virus in the family Mesoniviridae (order Nidovirales). We present X-ray structures for the CavV 3C-like protease (3CLpro), as a free enzyme and in complex with a peptide aldehyde inhibitor mimicking the P4-to-P1 residues of a natural substrate. The 3CLpro structure (refined to 1.94 Å) shows that the protein forms dimers. The monomers are comprised of N-terminal domains I and II, which adopt a chymotrypsin-like fold, and a C-terminal α-helical domain III. The catalytic Cys-His dyad is assisted by a complex network of interactions involving a water molecule that mediates polar contacts between the catalytic His and a conserved Asp located in the domain II-III junction and is suitably positioned to stabilize the developing positive charge of the catalytic His in the transition state during catalysis. The study also reveals the structural basis for the distinct P2 Asn-specific substrate-binding pocket of mesonivirus 3CLpros. First structure of a 3CLpro of an invertebrate RNA virus. Structural basis of the unique substrate specificity defined by Asn at the P2 position of mesonivirus 3CLpro substrates. Emerging role of a conserved Asp residue that assists the Cys-His catalytic dyad in vertebrate and invertebrate 3CLpros.
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Affiliation(s)
- Manuel Kanitz
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Sandra Blanck
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Wibke E Diederich
- Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany; Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany.
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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] [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.
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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.
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Validating Enterovirus D68-2A pro as an Antiviral Drug Target and the Discovery of Telaprevir as a Potent D68-2A pro Inhibitor. J Virol 2019; 93:JVI.02221-18. [PMID: 30674624 DOI: 10.1128/jvi.02221-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/11/2019] [Indexed: 02/08/2023] Open
Abstract
Enterovirus D68 (EV-D68) is a viral pathogen that leads to severe respiratory illness and has been linked with the development of acute flaccid myelitis (AFM) in children. No vaccines or antivirals are currently available for EV-D68 infection, and treatment options for hospitalized patients are limited to supportive care. Here, we report the expression of the EV-D68 2A protease (2Apro) and characterization of its enzymatic activity. Furthermore, we discovered that telaprevir, an FDA-approved drug used for the treatment of hepatitis C virus (HCV) infections, is a potent antiviral against EV-D68 by targeting the 2Apro enzyme. Using a fluorescence resonance energy transfer-based substrate cleavage assay, we showed that the purified EV-D68 2Apro has proteolytic activity selective against a peptide sequence corresponding to the viral VP1-2A polyprotein junction. Telaprevir inhibits EV-D68 2Apro through a nearly irreversible, biphasic binding mechanism. In cell culture, telaprevir showed submicromolar-to-low-micromolar potency against several recently circulating neurotropic strains of EV-D68 in different human cell lines. To further confirm the antiviral drug target, serial viral passage experiments were performed to select for resistance against telaprevir. An N84T mutation near the active site of 2Apro was identified in resistant viruses, and this mutation reduced the potency of telaprevir in both the enzymatic and cellular antiviral assays. Collectively, we report for the first time the in vitro enzymatic activity of EV-D68 2Apro and the identification of telaprevir as a potent EV-D68 2Apro inhibitor. These findings implicate EV-D68 2Apro as an antiviral drug target and highlight the repurposing potential of telaprevir to treat EV-D68 infection.IMPORTANCE A 2014 EV-D68 outbreak in the United States has been linked to the development of acute flaccid myelitis in children. Unfortunately, no treatment options against EV-D68 are currently available, and the development of effective therapeutics is urgently needed. Here, we characterize and validate a new EV-D68 drug target, the 2Apro, and identify telaprevir-an FDA-approved drug used to treat hepatitis C virus (HCV) infections-as a potent antiviral with a novel mechanism of action toward 2Apro 2Apro functions as a viral protease that cleaves a peptide sequence corresponding to the VP1-2A polyprotein junction. The binding of telaprevir potently inhibits its enzymatic activity, and using drug resistance selection, we show that the potent antiviral activity of telaprevir was due to 2Apro inhibition. This is the first inhibitor to selectively target the 2Apro from EV-D68 and can be used as a starting point for the development of therapeutics with selective activity against EV-D68.
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GII.4 Norovirus Protease Shows pH-Sensitive Proteolysis with a Unique Arg-His Pairing in the Catalytic Site. J Virol 2019; 93:JVI.01479-18. [PMID: 30626675 DOI: 10.1128/jvi.01479-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses (NoVs) are the main cause of epidemic and sporadic gastroenteritis. Phylogenetically, noroviruses are divided into seven genogroups, with each divided into multiple genotypes. NoVs belonging to genogroup II and genotype 4 (GII.4) are globally most prevalent. Genetic diversity among the NoVs and the periodic emergence of novel strains present a challenge for the development of vaccines and antivirals to treat NoV infection. NoV protease is essential for viral replication and is an attractive target for the development of antivirals. The available structure of GI.1 protease provided a basis for the design of inhibitors targeting the active site of the protease. These inhibitors, although potent against the GI proteases, poorly inhibit the GII proteases, for which structural information is lacking. To elucidate the structural basis for this difference in the inhibitor efficiency, we determined the crystal structure of a GII.4 protease. The structure revealed significant changes in the S2 substrate-binding pocket, making it noticeably smaller, and in the active site, with the catalytic triad residues showing conformational changes. Furthermore, a conserved arginine is found inserted into the active site, interacting with the catalytic histidine and restricting substrate/inhibitor access to the S2 pocket. This interaction alters the relationships between the catalytic residues and may allow for a pH-dependent regulation of protease activity. The changes we observed in the GII.4 protease structure may explain the reduced potency of the GI-specific inhibitors against the GII protease and therefore must be taken into account when designing broadly cross-reactive antivirals against NoVs.IMPORTANCE Human noroviruses (NoVs) cause sporadic and epidemic gastroenteritis worldwide. They are divided into seven genogroups (GI to GVII), with each genogroup further divided into several genotypes. Human NoVs belonging to genogroup II and genotype 4 (GII.4) are the most prevalent. Currently, there are no vaccines or antiviral drugs available for NoV infection. The protease encoded by NoV is considered a valuable target because of its essential role in replication. NoV protease structures have only been determined for the GI genogroup. We show here that the structure of the GII.4 protease exhibits several significant changes from GI proteases, including a unique pairing of an arginine with the catalytic histidine that makes the proteolytic activity of GII.4 protease pH sensitive. A comparative analysis of NoV protease structures may provide a rational framework for structure-based drug design of broadly cross-reactive inhibitors targeting NoVs.
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Mann KS, Sanfaçon H. Expanding Repertoire of Plant Positive-Strand RNA Virus Proteases. Viruses 2019; 11:v11010066. [PMID: 30650571 PMCID: PMC6357015 DOI: 10.3390/v11010066] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/13/2022] Open
Abstract
Many plant viruses express their proteins through a polyprotein strategy, requiring the acquisition of protease domains to regulate the release of functional mature proteins and/or intermediate polyproteins. Positive-strand RNA viruses constitute the vast majority of plant viruses and they are diverse in their genomic organization and protein expression strategies. Until recently, proteases encoded by positive-strand RNA viruses were described as belonging to two categories: (1) chymotrypsin-like cysteine and serine proteases and (2) papain-like cysteine protease. However, the functional characterization of plant virus cysteine and serine proteases has highlighted their diversity in terms of biological activities, cleavage site specificities, regulatory mechanisms, and three-dimensional structures. The recent discovery of a plant picorna-like virus glutamic protease with possible structural similarities with fungal and bacterial glutamic proteases also revealed new unexpected sources of protease domains. We discuss the variety of plant positive-strand RNA virus protease domains. We also highlight possible evolution scenarios of these viral proteases, including evidence for the exchange of protease domains amongst unrelated viruses.
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Affiliation(s)
- Krin S Mann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
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Amin SA, Adhikari N, Gayen S, Jha T. First Report on the Validated Classification-Based Chemometric Modeling of Human Rhinovirus 3C Protease (HRV 3Cpro) Inhibitors. ACTA ACUST UNITED AC 2018. [DOI: 10.4018/ijqspr.2018070101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Human rhinoviruses (HRVs), a major cause of common cold and upper respiratory infections, may trigger severe respiratory complications like asthma and COPD. To date, no drugs are available in the market which are designed as novel HRV inhibitors despite the involvement of some pharmaceutical companies' due to economical and clinical constraints. HRV 3C protease may be a potential target for drug design as it plays crucial role in viral RNA replication and virion assembly process. Therefore, designing novel HRV 3Cpro inhibitors is necessary and demanding in the field of antiviral drug design. In this article, statistically significant and validated classification-based QSARs of a series of HRV 3Cpro inhibitors were performed for the first time as per the authors' knowledge. Results suggest that oxopyrrolidine and piperidinone rings are favored whereas carboxybenzyl and unsubstituted benzyl functions may be unfavorable. Moreover, this group, along with cyclic alkyl or aryl ring structures may favor HRV 3Cpro inhibition. These observations may be utilized for the design of a higher active anti-HRV agent in future.
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Affiliation(s)
| | | | | | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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40
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Namoto K, Sirockin F, Sellner H, Wiesmann C, Villard F, Moreau RJ, Valeur E, Paulding SC, Schleeger S, Schipp K, Loup J, Andrews L, Swale R, Robinson M, Farady CJ. Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors. Bioorg Med Chem Lett 2018; 28:906-909. [PMID: 29433930 DOI: 10.1016/j.bmcl.2018.01.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/28/2018] [Accepted: 01/30/2018] [Indexed: 01/09/2023]
Abstract
The design and synthesis of macrocyclic inhibitors of human rhinovirus 3C protease is described. A macrocyclic linkage of the P1 and P3 residues, and the subsequent structure-based optimization of the macrocycle conformation and size led to the identification of a potent biochemical inhibitor 10 with sub-micromolar antiviral activity.
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Affiliation(s)
- Kenji Namoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
| | - Finton Sirockin
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Holger Sellner
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Christian Wiesmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Robert J Moreau
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Eric Valeur
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Stephanie C Paulding
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Simone Schleeger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Kathrin Schipp
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Joachim Loup
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Lori Andrews
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Ryann Swale
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Michael Robinson
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA 94608-2916, USA
| | - Christopher J Farady
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
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The Medicinal Chemistry of Antihepatitis Agents I. STUDIES ON HEPATITIS VIRUSES 2018. [PMCID: PMC7149832 DOI: 10.1016/b978-0-12-813330-9.00005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since viral hepatitis, as discussed in preceding chapters, has emerged as a major public health problem throughout the world affecting several hundreds of millions of people, and since no effective chemotherapy has been developed so far that can completely treat viral hepatitis, attempts are continued to find potential drugs against this disease. In this respect, the development of medicinal chemistry has been rewarding, as it covers all aspects of drug design such as recognition of important drug targets, computational chemistry, optimization of drug activity based on their structure-activity relationship, finding the three-dimensional structures of compounds by X-ray crystallography, NMR, molecular dynamics, and then synthesis of the drugs and evaluating their activity. The present chapter, thus, presents such medicinal chemistry study on anti-HAV, anti-HDV, and anti-HEV drugs.
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Affiliation(s)
- Kimi Azad
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;,
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India;,
| | - John E. Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037
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43
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Lei J, Hilgenfeld R. RNA-virus proteases counteracting host innate immunity. FEBS Lett 2017; 591:3190-3210. [PMID: 28850669 PMCID: PMC7163997 DOI: 10.1002/1873-3468.12827] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/20/2023]
Abstract
Virus invasion triggers host immune responses, in particular, innate immune responses. Pathogen‐associated molecular patterns of viruses (such as dsRNA, ssRNA, or viral proteins) released during virus replication are detected by the corresponding pattern‐recognition receptors of the host, and innate immune responses are induced. Through production of type‐I and type‐III interferons as well as various other cytokines, the host innate immune system forms the frontline to protect host cells and inhibit virus infection. Not surprisingly, viruses have evolved diverse strategies to counter this antiviral system. In this review, we discuss the multiple strategies used by proteases of positive‐sense single‐stranded RNA viruses of the families Picornaviridae, Coronaviridae, and Flaviviridae, when counteracting host innate immune responses.
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Affiliation(s)
- Jian Lei
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Germany.,German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, Germany
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44
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Pang LL, Yuan XH, Shao CS, Li MZ, Wang Y, Wang HM, Xie GC, Xie ZP, Yuan Y, Zhou DM, Sun XM, Zhang Q, Xin Y, Li DD, Duan ZJ. The suppression of innate immune response by human rhinovirus C. Biochem Biophys Res Commun 2017; 490:22-28. [PMID: 28576493 DOI: 10.1016/j.bbrc.2017.05.169] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/29/2017] [Indexed: 12/20/2022]
Abstract
Rhinovirus C (RV-C), a newly identified group of human rhinoviruses (RVs), is associated with exacerbation of severe asthma. The type I interferon (IFN) response induced by this virus and the mechanisms of evasion of IFN-mediated innate immunity for RV-C remain unclear. In this study, we constructed a full-length cDNA clone of RV-C (LZ651) from a clinical sample. IFN-β mRNA and protein levels were not elevated in differentiated Human bronchial epithelial (HBE) cells at the air-liquid interface infected with RV-C, except in the early stage of infection. The ability to attenuate IFN-β activation was ascribed to 3Cpro of RV-C, and the 40-His site of 3Cpro played an important role. Furthermore, RIG-I was degraded by 3Cpro in a caspase-dependent manner and 3Cpro cleaved MAVS at 148 Q/A, which inhibited IFN signaling. Taken together, our results demonstrate the mechanism by which RV-C circumvents the production of type I IFN in infected cells.
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Affiliation(s)
- Li-Li Pang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin-Hui Yuan
- The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Chang-Sheng Shao
- Anhui Engineering Research Center of Recombinant Protein Pharmaceutical Biotechnology, Institute of Advanced Technology, University of Science and Technology of China, Hefei 230026, China
| | - Mao-Zhong Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Institute for Immunization and Prevention, Beijing CDC, Beijing 100013, China
| | - Ying Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Basic Medical College, Inner Mongolia Medical University, Hohhot 010000, China
| | - Hui-Min Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Basic Medical College, Inner Mongolia Medical University, Hohhot 010000, China
| | - Guang-Cheng Xie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Department of Pathogenic Biology, Chengde Medical University, Chengde 067000, China
| | - Zhi-Ping Xie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yue Yuan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Basic Medical College, Inner Mongolia Medical University, Hohhot 010000, China
| | - Dong-Mei Zhou
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiao-Man Sun
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yan Xin
- Basic Medical College, Inner Mongolia Medical University, Hohhot 010000, China
| | - Dan-di Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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45
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Abstract
Viruses are major pathogenic agents that can cause a variety of diseases, such as AIDS, hepatitis, respiratory diseases, and many more, in humans, plants, and animals. The most prominent of them have been adenoviruses, alphaviruses, flaviviruses, hepatitis C virus, herpesviruses, human immunodeficiency virus of type 1, and picornaviruses. This chapter presents an introductory remark on such viruses, mechanisms of their invasion, and diseases related to them. The inhibition of these viruses is of great concern to human beings. Each of these viruses encodes one or more proteases that play crucial roles in their replication, and thus they are important targets for the design and development of potent antiviral agents. The chapter, therefore, also introduces the readers to such proteases and their structures and functions. This chapter is thus a prelude to the remaining chapters in the book, which present in detail about the different viruses and their proteases.
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Affiliation(s)
- Anjana Sharma
- Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh, India
| | - Satya P. Gupta
- National Institute of Technical Teachers’ Training and Research, Bhopal, Madhya Pradesh, India
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46
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Ma GH, Ye Y, Zhang D, Xu X, Si P, Peng JL, Xiao YL, Cao RY, Yin YL, Chen J, Zhao LX, Zhou Y, Zhong W, Liu H, Luo XM, Chen LL, Shen X. Identification and biochemical characterization of DC07090 as a novel potent small molecule inhibitor against human enterovirus 71 3C protease by structure-based virtual screening. Eur J Med Chem 2016; 124:981-991. [PMID: 27776325 DOI: 10.1016/j.ejmech.2016.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/21/2016] [Accepted: 10/10/2016] [Indexed: 11/28/2022]
Abstract
Hand, foot and mouth disease (HFMD) is a serious, highly contagious disease. HFMD caused by Enterovirus 71 (EV71), results in severe complications and even death. The pivotal role of EV71 3Cpro in the viral life cycle makes it an attractive target for drug discovery and development to treat HFMD. In this study, we identified novel EV71 3Cpro inhibitors by docking-based virtual screening. Totally 50 compounds were selected to test their inhibitory activity against EV71 3Cpro. The best inhibitor DC07090 exhibited the inhibition potency with an IC50 value of 21.72 ± 0.95 μM without apparent toxicity (CC50 > 200 μM). To explore structure-activity relationship of DC07090, 15 new derivatives were designed, synthesized and evaluated in vitro enzyme assay accordingly. Interestingly, four compounds showed inhibitory activities against EV71 3Cpro and only DC07090 inhibited EV71 replication with an EC50 value of 22.09 ± 1.07 μM. Enzyme inhibition kinetic experiments showed that the compound was a reversible and competitive inhibitor. The Ki value was determined to be 23.29 ± 12.08 μM. Further molecular docking, MD simulation and mutagenesis studies confirmed the binding mode of DC07090 and EV71 3Cpro. Besides, DC07090 could also inhibit coxsackievirus A16 (CVA16) replication with an EC50 value of 27.76 ± 0.88 μM. Therefore, DC07090 represents a new non-peptidyl small molecule inhibitor for further development of antiviral therapy against EV71 or other picornaviruses.
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Affiliation(s)
- Guang-Hui Ma
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Rd, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd, Pudong, Shanghai 201210, China
| | - Yan Ye
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Rd, Beijing 100191, China; University of Chinese Academy of Sciences, No.19A Yuquan Rd, Beijing 100049, China
| | - Dan Zhang
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, 103 Culture Rd, Shenyang 110016, China
| | - Xin Xu
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Pei Si
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; College of Life and Environmental Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Jian-Long Peng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yong-Long Xiao
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Rui-Yuan Cao
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Rd., Beijing 100850, China
| | - Yu-Ling Yin
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jing Chen
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin-Xiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, 103 Culture Rd, Shenyang 110016, China
| | - Yu Zhou
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Wu Zhong
- Beijing Institute of Pharmacology and Toxicology, 27 Taiping Rd., Beijing 100850, China
| | - Hong Liu
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xiao-Min Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Rd, Beijing 100191, China.
| | - Li-Li Chen
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Xu Shen
- Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Abstract
The need for antiviral drugs is growing rapidly as more viral diseases are recognized. The methods used to discover these drugs have evolved considerably over the past 40 years and the overall process of discovery can be broken down into sub-processes which include lead generation, lead optimization and lead development. Various methods are now employed to ensure these processes are carried out efficiently. For lead generation, screening methodologies have developed to the extent where hundreds of thousands of compounds can be screened against a particular target. An alternative approach is to use the structures of enzyme substrates as a starting point for drug discovery. Much use is now made of X-ray crystallographic data of target–inhibitor complexes for the optimization of lead structures, and methods for preparing libraries of compounds to assist both generation and optimization of leads are welldeveloped. The methods used to predict and improve the pharmacokinetic properties of compounds are also changing rapidly. Finally, novel approaches to antiviral therapy using oligonucleotide-based compounds or modulating the host immune response are also being explored. This review discusses these approaches, provides examples of where their application has been successful and sets them against a historical background.
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Affiliation(s)
- PS Jones
- Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, UK
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48
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Wang QM, Johnson RB, Cohen JD, Voy GT, Richardson JM, Jungheim LN. Development of a Continuous Fluorescence Assay for Rhinovirus 14 3C Protease Using Synthetic Peptides. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rhinovirus 3C protease is an attractive target for therapeutic intervention owing to its important role in virion maturation and infectivity. In order to facilitate the identification of potential 3C protease inhibitors, we have developed a continuous fluorescence assay using 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid (Edans) as a fluorescent donor and 4-(4-dimethylaminophenylazo)benzoic acid (Dabcyl) as a quenching acceptor. Several fluorogenic peptide substrates for 3C protease were synthesized by both solution chemistry and solid phase peptide synthesis. One of the synthetic Edans/Dabcyl substrates, with an amino acid sequence derived from the 2C/3A site of the virus polyprotein, yielded a 24-fold increase in fluorescence intensity after 3C cleavage. Data regarding substrate cleavage kinetics, assay sensitivity and optimization are presented. The application of this assay to the evaluation of 3C protease inhibitors is also shown.
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Affiliation(s)
- QM Wang
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - RB Johnson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JD Cohen
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - GT Voy
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JM Richardson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - LN Jungheim
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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49
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Yang J, Leen EN, Maree FF, Curry S. Crystal structure of the 3C protease from Southern African Territories type 2 foot-and-mouth disease virus. PeerJ 2016; 4:e1964. [PMID: 27168976 PMCID: PMC4860321 DOI: 10.7717/peerj.1964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/02/2016] [Indexed: 11/23/2022] Open
Abstract
The replication of foot-and-mouth disease virus (FMDV) is dependent on the virus-encoded 3C protease (3Cpro). As in other picornaviruses, 3Cpro performs most of the proteolytic processing of the polyprotein expressed from the large open reading frame in the RNA genome of the virus. Previous work revealed that the 3Cpro from serotype A—one of the seven serotypes of FMDV—adopts a trypsin-like fold. On the basis of capsid sequence comparisons the FMDV serotypes are grouped into two phylogenetic clusters, with O, A, C, and Asia 1 in one, and the three Southern African Territories serotypes, (SAT-1, SAT-2 and SAT-3) in another, a grouping pattern that is broadly, but not rigidly, reflected in 3Cpro amino acid sequences. We report here the cloning, expression and purification of 3C proteases from four SAT serotype viruses (SAT2/GHA/8/91, SAT1/NIG/5/81, SAT1/UGA/1/97, and SAT2/ZIM/7/83) and the crystal structure at 3.2 Å resolution of 3Cpro from SAT2/GHA/8/91.
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Affiliation(s)
- Jingjie Yang
- Departmet of Life Sciences, Imperial College , London , United Kingdom
| | - Eoin N Leen
- Departmet of Life Sciences, Imperial College , London , United Kingdom
| | - Francois F Maree
- Transboundary Animal Disease Programme, Agricultural Research Council, Onderstepoort Veterinary Institute , Onderstepoort , South Africa
| | - Stephen Curry
- Departmet of Life Sciences, Imperial College , London , United Kingdom
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50
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Khaw YS, Chan YF, Jafar FL, Othman N, Chee HY. Comparative Genetic Analyses of Human Rhinovirus C (HRV-C) Complete Genome from Malaysia. Front Microbiol 2016; 7:543. [PMID: 27199901 PMCID: PMC4851184 DOI: 10.3389/fmicb.2016.00543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/04/2016] [Indexed: 11/17/2022] Open
Abstract
Human rhinovirus-C (HRV-C) has been implicated in more severe illnesses than HRV-A and HRV-B, however, the limited number of HRV-C complete genomes (complete 5′ and 3′ non-coding region and open reading frame sequences) has hindered the in-depth genetic study of this virus. This study aimed to sequence seven complete HRV-C genomes from Malaysia and compare their genetic characteristics with the 18 published HRV-Cs. Seven Malaysian HRV-C complete genomes were obtained with newly redesigned primers. The seven genomes were classified as HRV-C6, C12, C22, C23, C26, C42, and pat16 based on the VP4/VP2 and VP1 pairwise distance threshold classification. Five of the seven Malaysian isolates, namely, 3430-MY-10/C22, 8713-MY-10/C23, 8097-MY-11/C26, 1570-MY-10/C42, and 7383-MY-10/pat16 are the first newly sequenced complete HRV-C genomes. All seven Malaysian isolates genomes displayed nucleotide similarity of 63–81% among themselves and 63–96% with other HRV-Cs. Malaysian HRV-Cs had similar putative immunogenic sites, putative receptor utilization and potential antiviral sites as other HRV-Cs. The genomic features of Malaysian isolates were similar to those of other HRV-Cs. Negative selections were frequently detected in HRV-Cs complete coding sequences indicating that these sequences were under functional constraint. The present study showed that HRV-Cs from Malaysia have diverse genetic sequences but share conserved genomic features with other HRV-Cs. This genetic information could provide further aid in the understanding of HRV-C infection.
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Affiliation(s)
- Yam Sim Khaw
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Faizatul Lela Jafar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya Kuala Lumpur, Malaysia
| | - Norlijah Othman
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
| | - Hui Yee Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia Serdang, Malaysia
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