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Krejčová K, Krafcikova P, Klima M, Chalupska D, Chalupsky K, Zilecka E, Boura E. Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase. Structure 2024; 32:1099-1109.e3. [PMID: 38781970 DOI: 10.1016/j.str.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Flaviviruses are single-stranded positive-sense RNA (+RNA) viruses that are responsible for several (re)emerging diseases such as yellow, dengue, or West Nile fevers. The Zika epidemic highlighted their dangerousness when a relatively benign virus known since the 1950s turned into a deadly pathogen. The central protein for their replication is NS5 (non-structural protein 5), which is composed of the N-terminal methyltransferase (MTase) domain and the C-terminal RNA-dependent RNA-polymerase (RdRp) domain. It is responsible for both RNA replication and installation of the 5' RNA cap. We structurally and biochemically analyzed the Ntaya virus MTase and RdRp domains and we compared their properties to other flaviviral NS5s. The enzymatic centers are well conserved across Flaviviridae, suggesting that the development of drugs targeting all flaviviruses is feasible. However, the enzymatic activities of the isolated proteins were significantly different for the MTase domains.
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Affiliation(s)
- Kateřina Krejčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic; Faculty of Sciences, Charles University, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Karel Chalupsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eva Zilecka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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2
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Shankar K, Sorin MN, Sharma H, Skoglund O, Dahmane S, Ter Beek J, Tesfalidet S, Nenzén L, Carlson LA. In vitro reconstitution reveals membrane clustering and RNA recruitment by the enteroviral AAA+ ATPase 2C. PLoS Pathog 2024; 20:e1012388. [PMID: 39102425 PMCID: PMC11326647 DOI: 10.1371/journal.ppat.1012388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/15/2024] [Accepted: 07/02/2024] [Indexed: 08/07/2024] Open
Abstract
Enteroviruses are a vast genus of positive-sense RNA viruses that cause diseases ranging from common cold to poliomyelitis and viral myocarditis. They encode a membrane-bound AAA+ ATPase, 2C, that has been suggested to serve several roles in virus replication, e.g. as an RNA helicase and capsid assembly factor. Here, we report the reconstitution of full-length, poliovirus 2C's association with membranes. We show that the N-terminal membrane-binding domain of 2C contains a conserved glycine, which is suggested by structure predictions to divide the domain into two amphipathic helix regions, which we name AH1 and AH2. AH2 is the main mediator of 2C oligomerization, and is necessary and sufficient for its membrane binding. AH1 is the main mediator of a novel function of 2C: clustering of membranes. Cryo-electron tomography reveal that several 2C copies mediate this function by localizing to vesicle-vesicle interfaces. 2C-mediated clustering is partially outcompeted by RNA, suggesting a way by which 2C can switch from an early role in coalescing replication organelles and lipid droplets, to a later role where 2C assists RNA replication and particle assembly. 2C is sufficient to recruit RNA to membranes, with a preference for double-stranded RNA (the replicating form of the viral genome). Finally, the in vitro reconstitution revealed that full-length, membrane-bound 2C has ATPase activity and ATP-independent, single-strand ribonuclease activity, but no detectable helicase activity. Together, this study suggests novel roles for 2C in membrane clustering, RNA membrane recruitment and cleavage, and calls into question a role of 2C as an RNA helicase. The reconstitution of functional, 2C-decorated vesicles provides a platform for further biochemical studies into this protein and its roles in enterovirus replication.
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Affiliation(s)
- Kasturika Shankar
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Marie N Sorin
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Himanshu Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Oskar Skoglund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Selma Dahmane
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | | | - Louise Nenzén
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
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3
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Xu C, Wang M, Cheng A, Yang Q, Huang J, Ou X, Sun D, He Y, Wu Z, Wu Y, Zhang S, Tian B, Zhao X, Liu M, Zhu D, Jia R, Chen S. Multiple functions of the nonstructural protein 3D in picornavirus infection. Front Immunol 2024; 15:1365521. [PMID: 38629064 PMCID: PMC11018997 DOI: 10.3389/fimmu.2024.1365521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
3D polymerase, also known as RNA-dependent RNA polymerase, is encoded by all known picornaviruses, and their structures are highly conserved. In the process of picornavirus replication, 3D polymerase facilitates the assembly of replication complexes and directly catalyzes the synthesis of viral RNA. The nuclear localization signal carried by picornavirus 3D polymerase, combined with its ability to interact with other viral proteins, viral RNA and cellular proteins, indicate that its noncatalytic role is equally important in viral infections. Recent studies have shown that 3D polymerase has multiple effects on host cell biological functions, including inducing cell cycle arrest, regulating host cell translation, inducing autophagy, evading immune responses, and triggering inflammasome formation. Thus, 3D polymerase would be a very valuable target for the development of antiviral therapies. This review summarizes current studies on the structure of 3D polymerase and its regulation of host cell responses, thereby improving the understanding of picornavirus-mediated pathogenesis caused by 3D polymerase.
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Affiliation(s)
- Chenxia Xu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu He
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhen Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Duchoslav V, Boura E. Structure of monkeypox virus poxin: implications for drug design. Arch Virol 2023; 168:192. [PMID: 37378908 DOI: 10.1007/s00705-023-05824-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Monkeypox, or mpox, is a disease that has recently resurfaced and spread across the globe. Despite the availability of an FDA-approved vaccine (JYNNEOS) and an effective drug (tecovirimat), concerns remain over the possible recurrence of a viral pandemic. Like any other virus, mpox virus must overcome the immune system to replicate. Viruses have evolved various strategies to overcome both innate and adaptive immunity. Poxviruses possess an unusual nuclease, poxin, which cleaves 2'-3'-cGAMP, a cyclic dinucleotide, which is an important second messenger in the cGAS-STING signaling pathway. Here, we present the crystal structure of mpox poxin. The structure reveals a conserved, predominantly β-sheet fold and highlights the high conservation of the cGAMP binding site and of the catalytic residues His17, Tyr138, and Lys142. This research suggests that poxin inhibitors could be effective against multiple poxviruses.
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Affiliation(s)
- Vojtech Duchoslav
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.
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McPhail JA, Burke JE. Molecular mechanisms of PI4K regulation and their involvement in viral replication. Traffic 2023; 24:131-145. [PMID: 35579216 DOI: 10.1111/tra.12841] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/07/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Lipid phosphoinositides are master signaling molecules in eukaryotic cells and key markers of organelle identity. Because of these important roles, the kinases and phosphatases that generate phosphoinositides must be tightly regulated. Viruses can manipulate this regulation, with the Type III phosphatidylinositol 4-kinases (PI4KA and PI4KB) being hijacked by many RNA viruses to mediate their intracellular replication through the formation of phosphatidylinositol 4-phosphate (PI4P)-enriched replication organelles (ROs). Different viruses have evolved unique approaches toward activating PI4K enzymes to form ROs, through both direct binding of PI4Ks and modulation of PI4K accessory proteins. This review will focus on PI4KA and PI4KB and discuss their roles in signaling, functions in membrane trafficking and manipulation by viruses. Our focus will be the molecular basis for how PI4KA and PI4KB are activated by both protein-binding partners and post-translational modifications, with an emphasis on understanding the different molecular mechanisms viruses have evolved to usurp PI4Ks. We will also discuss the chemical tools available to study the role of PI4Ks in viral infection.
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Affiliation(s)
- Jacob A McPhail
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
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Konkolova E, Krejčová K, Eyer L, Hodek J, Zgarbová M, Fořtová A, Jirasek M, Teply F, Reyes-Gutierrez PE, Růžek D, Weber J, Boura E. A Helquat-like Compound as a Potent Inhibitor of Flaviviral and Coronaviral Polymerases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061894. [PMID: 35335258 PMCID: PMC8953834 DOI: 10.3390/molecules27061894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
Abstract
Positive-sense single-stranded RNA (+RNA) viruses have proven to be important pathogens that are able to threaten and deeply damage modern societies, as illustrated by the ongoing COVID-19 pandemic. Therefore, compounds active against most or many +RNA viruses are urgently needed. Here, we present PR673, a helquat-like compound that is able to inhibit the replication of SARS-CoV-2 and tick-borne encephalitis virus in cell culture. Using in vitro polymerase assays, we demonstrate that PR673 inhibits RNA synthesis by viral RNA-dependent RNA polymerases (RdRps). Our results illustrate that the development of broad-spectrum non-nucleoside inhibitors of RdRps is feasible.
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Affiliation(s)
- Eva Konkolova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Kateřina Krejčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Luděk Eyer
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Michala Zgarbová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Andrea Fořtová
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
| | - Michael Jirasek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Filip Teply
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Paul E. Reyes-Gutierrez
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Daniel Růžek
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; (L.E.); (A.F.); (D.R.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 1160/31, 37005 Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague, Czech Republic; (E.K.); (K.K.); (J.H.); (M.Z.); (M.J.); (F.T.); (P.E.R.-G.); (J.W.)
- Correspondence:
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Eisenreichova A, Różycki B, Boura E, Humpolickova J. Osh6 Revisited: Control of PS Transport by the Concerted Actions of PI4P and Sac1 Phosphatase. Front Mol Biosci 2021; 8:747601. [PMID: 34712698 PMCID: PMC8546167 DOI: 10.3389/fmolb.2021.747601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/08/2021] [Indexed: 12/03/2022] Open
Abstract
Osh6, a member of the oxysterol-binding protein-related protein (ORP) family, is a lipid transport protein that is involved in the transport of phosphatidylserine (PS) between the endoplasmic reticulum (ER) and the plasma membrane (PM). We used a biophysical approach to characterize its transport mechanism in detail. We examined the transport of all potential ligands of Osh6. PI4P and PS are the best described lipid cargo molecules; in addition, we showed that PIP2 can be transported by Osh6 as well. So far, it was the exchange between the two cargo molecules, PS and PI4P, in the lipid-binding pocket of Osh6 that was considered an essential driving force for the PS transport. However, we showed that Osh6 can efficiently transport PS along the gradient without the help of PI4P and that PI4P inhibits the PS transport along its gradient. This observation highlights that the exchange between PS and PI4P is indeed crucial, but PI4P bound to the protein rather than intensifying the PS transport suppresses it. We considered this to be important for the transport directionality as it prevents PS from returning back from the PM where its concentration is high to the ER where it is synthesized. Our results also highlighted the importance of the ER resident Sac1 phosphatase that enables the PS transport and ensures its directionality by PI4P consumption. Furthermore, we showed that the Sac1 activity is regulated by the negative charge of the membrane that can be provided by PS or PI anions in the case of the ER membrane.
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Affiliation(s)
- Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czechia
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8
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Localization of SARS-CoV-2 Capping Enzymes Revealed by an Antibody against the nsp10 Subunit. Viruses 2021; 13:v13081487. [PMID: 34452352 PMCID: PMC8402843 DOI: 10.3390/v13081487] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease-19 pandemic. One of the key components of the coronavirus replication complex are the RNA methyltransferases (MTases), RNA-modifying enzymes crucial for RNA cap formation. Recently, the structure of the 2’-O MTase has become available; however, its biological characterization within the infected cells remains largely elusive. Here, we report a novel monoclonal antibody directed against the SARS-CoV-2 non-structural protein nsp10, a subunit of both the 2’-O RNA and N7 MTase protein complexes. Using this antibody, we investigated the subcellular localization of the SARS-CoV-2 MTases in cells infected with the SARS-CoV-2.
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9
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Coxsackievirus B3 Exploits the Ubiquitin-Proteasome System to Facilitate Viral Replication. Viruses 2021; 13:v13071360. [PMID: 34372566 PMCID: PMC8310229 DOI: 10.3390/v13071360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/18/2023] Open
Abstract
Infection by RNA viruses causes extensive cellular reorganization, including hijacking of membranes to create membranous structures termed replication organelles, which support viral RNA synthesis and virion assembly. In this study, we show that infection with coxsackievirus B3 entails a profound impairment of the protein homeostasis at virus-utilized membranes, reflected by an accumulation of ubiquitinylated proteins, including K48-linked polyubiquitin conjugates, known to direct proteins to proteasomal degradation. The enrichment of membrane-bound ubiquitin conjugates is attributed to the presence of the non-structural viral proteins 2B and 3A, which are known to perturb membrane integrity and can cause an extensive rearrangement of cellular membranes. The locally increased abundance of ubiquitinylated proteins occurs without an increase of oxidatively damaged proteins. During the exponential phase of replication, the oxidative damage of membrane proteins is even diminished, an effect we attribute to the recruitment of glutathione, which is known to be required for the formation of infectious virus particles. Furthermore, we show that the proteasome contributes to the processing of viral precursor proteins. Taken together, we demonstrate how an infection with coxsackievirus B3 affects the cellular protein and redox homeostasis locally at the site of viral replication and virus assembly.
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10
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Structural analysis of the putative SARS-CoV-2 primase complex. J Struct Biol 2020; 211:107548. [PMID: 32535228 PMCID: PMC7289108 DOI: 10.1016/j.jsb.2020.107548] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
Abstract
We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the heterotetramer formed by both nsp7 and nsp8 that is flanked with two symmetry-related nsp8 β-sheet subdomains. It was also revealed that two hydrophobic interfaces one of approx. 1340 Å2 connects the nsp7 to nsp8 and a second one of approx. 950 Å2 connects the dimers and form the observed heterotetramer. Interestingly, analysis of the surface electrostatic potential revealed a putative RNA binding site that is formed only within the heterotetramer.
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11
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Lu Y, Song S, Zhang L. Emerging Role for Acyl-CoA Binding Domain Containing 3 at Membrane Contact Sites During Viral Infection. Front Microbiol 2020; 11:608. [PMID: 32322249 PMCID: PMC7156584 DOI: 10.3389/fmicb.2020.00608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
Acyl-coenzyme A binding domain containing 3 (ACBD3) is a multifunctional protein residing in the Golgi apparatus and is involved in several signaling pathways. The current knowledge on ACBD3 has been extended to virology. ACBD3 has recently emerged as a key factor subverted by viruses, including kobuvirus, enterovirus, and hepatitis C virus. The ACBD3-PI4KB complex is critical for the role of ACBD3 in viral replication. In most cases, ACBD3 plays a positive role in viral infection. ACBD3 associates with viral 3A proteins from a variety of Picornaviridae family members at membrane contact sites (MCSs), which are used by diverse viruses to ensure lipid transfer to replication organelles (ROs). In this review, we discuss the mechanisms underlying the involvement of ACBD3 in viral infection at MCSs. Our review will highlight the current research and reveal potential avenues for future research.
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Affiliation(s)
- Yue Lu
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, China.,Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Siqi Song
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Leiliang Zhang
- Institute of Basic Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
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12
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Škerle J, Humpolíčková J, Johnson N, Rampírová P, Poláchová E, Fliegl M, Dohnálek J, Suchánková A, Jakubec D, Strisovsky K. Membrane Protein Dimerization in Cell-Derived Lipid Membranes Measured by FRET with MC Simulations. Biophys J 2020; 118:1861-1875. [PMID: 32246901 DOI: 10.1016/j.bpj.2020.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/06/2020] [Accepted: 03/13/2020] [Indexed: 11/19/2022] Open
Abstract
Many membrane proteins are thought to function as dimers or higher oligomers, but measuring membrane protein oligomerization in lipid membranes is particularly challenging. Förster resonance energy transfer (FRET) and fluorescence cross-correlation spectroscopy are noninvasive, optical methods of choice that have been applied to the analysis of dimerization of single-spanning membrane proteins. However, the effects inherent to such two-dimensional systems, such as the excluded volume of polytopic transmembrane proteins, proximity FRET, and rotational diffusion of fluorophore dipoles, complicate interpretation of FRET data and have not been typically accounted for. Here, using FRET and fluorescence cross-correlation spectroscopy, we introduce a method to measure surface protein density and to estimate the apparent Förster radius, and we use Monte Carlo simulations of the FRET data to account for the proximity FRET effect occurring in confined two-dimensional environments. We then use FRET to analyze the dimerization of human rhomboid protease RHBDL2 in giant plasma membrane vesicles. We find no evidence for stable oligomers of RHBDL2 in giant plasma membrane vesicles of human cells even at concentrations that highly exceed endogenous expression levels. This indicates that the rhomboid transmembrane core is intrinsically monomeric. Our findings will find use in the application of FRET and fluorescence correlation spectroscopy for the analysis of oligomerization of transmembrane proteins in cell-derived lipid membranes.
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Affiliation(s)
- Jan Škerle
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.
| | - Nicholas Johnson
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Petra Rampírová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Edita Poláchová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Monika Fliegl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Jan Dohnálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic; University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Anna Suchánková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.
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13
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Dubankova A, Horova V, Klima M, Boura E. Structures of kobuviral and siciniviral polymerases reveal conserved mechanism of picornaviral polymerase activation. J Struct Biol 2019; 208:92-98. [PMID: 31415898 DOI: 10.1016/j.jsb.2019.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 01/03/2023]
Abstract
RNA-dependent RNA polymerase 3Dpol is a key enzyme for the replication of picornaviruses. The viral genome is translated into a single polyprotein that is subsequently proteolytically processed into matured products. The 3Dpol enzyme arises from a stable 3CD precursor that has high proteolytic activity but no polymerase activity. Upon cleavage of the precursor the newly established N-terminus of 3Dpol is liberated and inserts itself into a pocket on the surface of the 3Dpol enzyme. The essential residue for this mechanism is the very first glycine that is conserved among almost all picornaviruses. However, kobuviruses and siciniviruses have a serine residue instead. Intrigued by this anomaly we sought to solve the crystal structure of these 3Dpol enzymes. The structures revealed a unique fold of the 3Dpol N-termini but the very first serine residues were inserted into a charged pocket in a similar manner as the glycine residue in other picornaviruses. These structures revealed a common underlying mechanism of 3Dpol activation that lies in activation of the α10 helix containing a key catalytical residue Asp238 that forms a hydrogen bond with the 2' hydroxyl group of the incoming NTP nucleotide.
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Affiliation(s)
- Anna Dubankova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Vladimira Horova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2., 166 10 Prague 6, Czech Republic.
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14
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Chalupska D, Różycki B, Klima M, Boura E. Structural insights into Acyl-coenzyme A binding domain containing 3 (ACBD3) protein hijacking by picornaviruses. Protein Sci 2019; 28:2073-2079. [PMID: 31583778 DOI: 10.1002/pro.3738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 01/20/2023]
Abstract
Many picornaviruses hijack the Golgi resident Acyl-coenzyme A binding domain containing 3 (ACBD3) protein in order to recruit the phosphatidylinositol 4-kinase B (PI4KB) to viral replication organelles (ROs). PI4KB, once recruited and activated by ACBD3 protein, produces the lipid phosphatidylinositol 4-phosphate (PI4P), which is a key step in the biogenesis of viral ROs. To do so, picornaviruses use their small nonstructural protein 3A that binds the Golgi dynamics domain of the ACBD3 protein. Here, we present the analysis of the highly flexible ACBD3 proteins and the viral 3A protein in solution using small-angle X-ray scattering and computer simulations. Our analysis revealed that both the ACBD3 protein and the 3A:ACBD3 protein complex have an extended and flexible conformation in solution.
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Affiliation(s)
- Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Bartosz Różycki
- Institute of Physics of the Polish Academy of Sciences, Warsaw, Poland
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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15
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Convergent evolution in the mechanisms of ACBD3 recruitment to picornavirus replication sites. PLoS Pathog 2019; 15:e1007962. [PMID: 31381608 PMCID: PMC6695192 DOI: 10.1371/journal.ppat.1007962] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/15/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022] Open
Abstract
Enteroviruses, members of the family of picornaviruses, are the most common viral infectious agents in humans causing a broad spectrum of diseases ranging from mild respiratory illnesses to life-threatening infections. To efficiently replicate within the host cell, enteroviruses hijack several host factors, such as ACBD3. ACBD3 facilitates replication of various enterovirus species, however, structural determinants of ACBD3 recruitment to the viral replication sites are poorly understood. Here, we present a structural characterization of the interaction between ACBD3 and the non-structural 3A proteins of four representative enteroviruses (poliovirus, enterovirus A71, enterovirus D68, and rhinovirus B14). In addition, we describe the details of the 3A-3A interaction causing the assembly of the ACBD3-3A heterotetramers and the interaction between the ACBD3-3A complex and the lipid bilayer. Using structure-guided identification of the point mutations disrupting these interactions, we demonstrate their roles in the intracellular localization of these proteins, recruitment of downstream effectors of ACBD3, and facilitation of enterovirus replication. These structures uncovered a striking convergence in the mechanisms of how enteroviruses and kobuviruses, members of a distinct group of picornaviruses that also rely on ACBD3, recruit ACBD3 and its downstream effectors to the sites of viral replication. Enteroviruses are the most common viruses infecting humans. They cause a broad spectrum of diseases ranging from common cold to life-threatening diseases, such as poliomyelitis. To date, no effective antiviral therapy for enteroviruses has been approved yet. To ensure efficient replication, enteroviruses hijack several host factors, recruit them to the sites of virus replication, and use their physiological functions for their own purposes. Here, we characterize the complexes composed of the host protein ACBD3 and the ACBD3-binding viral proteins (called 3A) of four representative enteroviruses. Our study reveals the atomic details of these complexes and identifies the amino acid residues important for the interaction. We found out that the 3A proteins of enteroviruses bind to the same regions of ACBD3 as the 3A proteins of kobuviruses, a distinct group of viruses that also rely on ACBD3, but are oriented in the opposite directions. This observation reveals a striking case of convergent evolutionary pathways that have evolved to allow enteroviruses and kobuviruses (which are two distinct groups of the Picornaviridae family) to recruit a common host target, ACBD3, and its downstream effectors to the sites of viral replication.
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16
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Dubankova A, Boura E. Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses. Antiviral Res 2019; 169:104536. [PMID: 31202975 DOI: 10.1016/j.antiviral.2019.104536] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/23/2022]
Abstract
Yellow fever virus (YFV) is responsible for devastating outbreaks of Yellow fever (YF) in humans and is associated with high mortality rates. Recent large epidemics and epizootics and exponential increases in the numbers of YF cases in humans and non-human primates highlight the increasing threat YFV poses, despite the availability of an effective YFV vaccine. YFV is the first human virus discovered, but the structures of several of the viral proteins remain poorly understood. Here we report the structure of the full-length NS5 protein, a key enzyme for the replication of flaviviruses that contains both a methyltransferase domain and an RNA dependent RNA polymerase domain, at 3.1 Å resolution. The viral polymerase adopts right-hand fold, demonstrating the similarities of the Yellow fever, Dengue and Zika polymerases. Together this data suggests NS5 as a prime and ideal target for the design of pan-flavivirus inhibitors.
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Affiliation(s)
- Anna Dubankova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nam. 2, 166 10, Prague 6, Czech Republic.
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17
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Šebera J, Dubankova A, Sychrovský V, Ruzek D, Boura E, Nencka R. The structural model of Zika virus RNA-dependent RNA polymerase in complex with RNA for rational design of novel nucleotide inhibitors. Sci Rep 2018; 8:11132. [PMID: 30042483 PMCID: PMC6057956 DOI: 10.1038/s41598-018-29459-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022] Open
Abstract
Zika virus is a global health threat due to significantly elevated risk of fetus malformations in infected pregnant women. Currently, neither an effective therapy nor a prophylactic vaccination is available for clinical use, desperately necessitating novel therapeutics and approaches to obtain them. Here, we present a structural model of the Zika virus RNA-dependent RNA polymerase (ZIKV RdRp) in complex with template and nascent RNAs, Mg2+ ions and accessing nucleoside triphosphate. The model allowed for docking studies aimed at effective pre-screening of potential inhibitors of ZIKV RdRp. Applicability of the structural model for docking studies was illustrated with the NITD008 artificial nucleotide that is known to effectively inhibit the function of the ZIKV RdRp. The ZIKV RdRp – RNA structural model is provided for all possible variations of the nascent RNA bases pairs to enhance its general utility in docking and modelling experiments. The developed model makes the rational design of novel nucleosides and nucleotide analogues feasible and thus provides a solid platform for the development of advanced antiviral therapy.
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Affiliation(s)
- Jakub Šebera
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Anna Dubankova
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Daniel Ruzek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic.
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic.
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18
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Reuberson J, Horsley H, Franklin RJ, Ford D, Neuss J, Brookings D, Huang Q, Vanderhoydonck B, Gao LJ, Jang MY, Herdewijn P, Ghawalkar A, Fallah-Arani F, Khan AR, Henshall J, Jairaj M, Malcolm S, Ward E, Shuttleworth L, Lin Y, Li S, Louat T, Waer M, Herman J, Payne A, Ceska T, Doyle C, Pitt W, Calmiano M, Augustin M, Steinbacher S, Lammens A, Allen R. Discovery of a Potent, Orally Bioavailable PI4KIIIβ Inhibitor (UCB9608) Able To Significantly Prolong Allogeneic Organ Engraftment in Vivo. J Med Chem 2018; 61:6705-6723. [PMID: 29952567 DOI: 10.1021/acs.jmedchem.8b00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The primary target of a novel series of immunosuppressive 7-piperazin-1-ylthiazolo[5,4- d]pyrimidin-5-amines was identified as the lipid kinase, PI4KIIIβ. Evaluation of the series highlighted their poor solubility and unwanted off-target activities. A medicinal chemistry strategy was put in place to optimize physicochemical properties within the series, while maintaining potency and improving selectivity over other lipid kinases. Compound 22 was initially identified and profiled in vivo, before further modifications led to the discovery of 44 (UCB9608), a vastly more soluble, selective compound with improved metabolic stability and excellent pharmacokinetic profile. A co-crystal structure of 44 with PI4KIIIβ was solved, confirming the binding mode of this class of inhibitor. The much-improved in vivo profile of 44 positions it as an ideal tool compound to further establish the link between PI4KIIIβ inhibition and prolonged allogeneic organ engraftment, and suppression of immune responses in vivo.
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Affiliation(s)
- James Reuberson
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Helen Horsley
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Richard J Franklin
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Daniel Ford
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Judi Neuss
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Daniel Brookings
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Qiuya Huang
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Bart Vanderhoydonck
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Ling-Jie Gao
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Mi-Yeon Jang
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Anant Ghawalkar
- SAI Life Sciences Ltd , International Biotech Park , Hinjewadi, Pune 411 057 , India
| | | | - Adnan R Khan
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Jamie Henshall
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Mark Jairaj
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Sarah Malcolm
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Eleanor Ward
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | | | - Yuan Lin
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Shengqiao Li
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Thierry Louat
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Mark Waer
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Jean Herman
- Interface Valorization Platform , KU Leuven , Campus St.-Rafaël, Blok I, 8°, Kapucijnenvoer 33 B 7001 , 3000 Leuven , Belgium
| | - Andrew Payne
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Tom Ceska
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Carl Doyle
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Will Pitt
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Mark Calmiano
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
| | - Martin Augustin
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Stefan Steinbacher
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Alfred Lammens
- Proteros Biostructures GmbH , Bunsenstrasse 7a , 82152 Martinsried , Germany
| | - Rodger Allen
- UCB Pharma , 208 Bath Road , Slough , Berkshire SL1 3WE , United Kingdom
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