1
|
Deng H, Cao H, Wang Y, Li J, Dai J, Li LF, Qiu HJ, Li S. Viral replication organelles: the highly complex and programmed replication machinery. Front Microbiol 2024; 15:1450060. [PMID: 39144209 PMCID: PMC11322364 DOI: 10.3389/fmicb.2024.1450060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Viral infections usually induce the rearrangement of cellular cytoskeletal proteins and organelle membrane structures, thus creating independent compartments [termed replication organelles (ROs)] to facilitate viral genome replication. Within the ROs, viral replicases, including polymerases, helicases, and ligases, play functional roles during viral replication. These viral replicases are pivotal in the virus life cycle, and numerous studies have demonstrated that the viral replicases could be the potential targets for drugs development. Here, we summarize primarily the key replicases within viral ROs and emphasize the advancements of antiviral drugs targeting crucial viral replicases, providing novel insights into the future development of antiviral strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
2
|
Turner DL, Mathias RA. The human cytomegalovirus decathlon: Ten critical replication events provide opportunities for restriction. Front Cell Dev Biol 2022; 10:1053139. [PMID: 36506089 PMCID: PMC9732275 DOI: 10.3389/fcell.2022.1053139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous human pathogen that can cause severe disease in immunocompromised individuals, transplant recipients, and to the developing foetus during pregnancy. There is no protective vaccine currently available, and with only a limited number of antiviral drug options, resistant strains are constantly emerging. Successful completion of HCMV replication is an elegant feat from a molecular perspective, with both host and viral processes required at various stages. Remarkably, HCMV and other herpesviruses have protracted replication cycles, large genomes, complex virion structure and complicated nuclear and cytoplasmic replication events. In this review, we outline the 10 essential stages the virus must navigate to successfully complete replication. As each individual event along the replication continuum poses as a potential barrier for restriction, these essential checkpoints represent potential targets for antiviral development.
Collapse
Affiliation(s)
- Declan L. Turner
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Rommel A. Mathias
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia,*Correspondence: Rommel A. Mathias,
| |
Collapse
|
3
|
Birkmann A, Bonsmann S, Kropeit D, Pfaff T, Rangaraju M, Sumner M, Timmler B, Zimmermann H, Buschmann H, Ruebsamen-Schaeff H. Discovery, Chemistry, and Preclinical Development of Pritelivir, a Novel Treatment Option for Acyclovir-Resistant Herpes Simplex Virus Infections. J Med Chem 2022; 65:13614-13628. [PMID: 36202389 PMCID: PMC9620171 DOI: 10.1021/acs.jmedchem.2c00668] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
When the nucleoside analogue acyclovir was introduced
in the early
1980s, it presented a game-changing treatment modality for herpes
simplex virus infections. Since then, work has been ongoing to improve
the weaknesses that have now been identified: a narrow time window
for therapeutic success, resistance in immunocompromised patients,
little influence on frequency of recurrences, relatively fast elimination,
and poor bioavailability. The present Drug Annotation focuses on the
helicase–primase inhibitor pritelivir currently in development
for the treatment of acyclovir-resistant HSV infections and describes
how a change of the molecular target (from viral DNA polymerase to
the HSV helicase–primase complex) afforded improvement of the
shortcomings of nucleoside analogs. Details are presented for the
discovery process leading to the final drug candidate, the pivotal
preclinical studies on mechanism of action and efficacy, and on how
ongoing clinical research has been able to translate preclinical promises
into clinical use.
Collapse
Affiliation(s)
| | | | - Dirk Kropeit
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany
| | - Tamara Pfaff
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany
| | | | - Melanie Sumner
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany
| | | | | | | | | |
Collapse
|
4
|
Allen CNS, Arjona SP, Santerre M, Sawaya BE. Hallmarks of Metabolic Reprogramming and Their Role in Viral Pathogenesis. Viruses 2022; 14:602. [PMID: 35337009 PMCID: PMC8955778 DOI: 10.3390/v14030602] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks can be identified: (1) increased glycolysis and lactic acid, (2) increased glutaminolysis, (3) increased pentose phosphate pathway, (4) mitochondrial changes, (5) increased lipid metabolism, (6) changes in amino acid metabolism, and (7) changes in other biosynthetic and bioenergetic pathways. Viruses depend on metabolic reprogramming to increase biomass to fuel viral genome replication and production of new virions. Viruses take advantage of the non-metabolic effects of metabolic reprogramming, creating an anti-apoptotic environment and evading the immune system. Other non-metabolic effects can negatively affect cellular function. Understanding the role metabolic reprogramming plays in viral pathogenesis may provide better therapeutic targets for antivirals.
Collapse
Affiliation(s)
- Charles N. S. Allen
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Sterling P. Arjona
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Maryline Santerre
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Bassel E. Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
- Departments of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Cancer and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| |
Collapse
|
5
|
Raubenolt BA, Islam NN, Summa CM, Rick SW. Molecular dynamics simulations of the flexibility and inhibition of SARS-CoV-2 NSP 13 helicase. J Mol Graph Model 2022; 112:108122. [PMID: 35021142 PMCID: PMC8730789 DOI: 10.1016/j.jmgm.2022.108122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 11/25/2022]
Abstract
The helicase protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is both a good potential drug target and very flexible. The flexibility, and therefore its function, could be reduced through knowledge of these motions and identification of allosteric pockets. Using molecular dynamics simulations with enhanced sampling, we determined key modes of motion and sites on the protein that are at the interface between flexible domains of the proteins. We developed an approach to map the principal components of motion onto the surface of a potential binding pocket to help in the identification of allosteric sites.
Collapse
Affiliation(s)
- Bryan A Raubenolt
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
| | - Naeyma N Islam
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA
| | - Christoper M Summa
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Steven W Rick
- Department of Chemistry, University of New Orleans, New Orleans, LA, 70148, USA.
| |
Collapse
|
6
|
High conservation of varicella-zoster virus helicase-primase complex, the target of the new antiviral drug amenamevir. Antiviral Res 2021; 195:105189. [PMID: 34666108 DOI: 10.1016/j.antiviral.2021.105189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/08/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022]
Abstract
Varicella-zoster virus (VZV) resistance to current antiviral drugs, that all target the viral DNA polymerase, represents a growing concern, notably among immunocompromised patients. Amenamevir, a novel antiviral that inhibits the VZV helicase-primase (HP) complex, is approved in Japan for the treatment of herpes zoster. In this study, we describe the low natural polymorphism of VZV HP complex (interstrain identity >99.7% both at nucleotide and amino acid levels) among 44 VZV clinical isolates. This work enabled to settle the maps of natural polymorphisms of VZV HP complex and to provide the genotypic tools for the monitoring of the emergence of VZV resistance to amenamevir in patients.
Collapse
|
7
|
Bermek O, Williams RS. The three-component helicase/primase complex of herpes simplex virus-1. Open Biol 2021; 11:210011. [PMID: 34102080 PMCID: PMC8187027 DOI: 10.1098/rsob.210011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is one of the nine herpesviruses that infect humans. HSV-1 encodes seven proteins to replicate its genome in the hijacked human cell. Among these are the herpes virus DNA helicase and primase that are essential components of its replication machinery. In the HSV-1 replisome, the helicase-primase complex is composed of three components including UL5 (helicase), UL52 (primase) and UL8 (non-catalytic subunit). UL5 and UL52 subunits are functionally interdependent, and the UL8 component is required for the coordination of UL5 and UL52 activities proceeding in opposite directions with respect to the viral replication fork. Anti-viral compounds currently under development target the functions of UL5 and UL52. Here, we review the structural and functional properties of the UL5/UL8/UL52 complex and highlight the gaps in knowledge to be filled to facilitate molecular characterization of the structure and function of the helicase-primase complex for development of alternative anti-viral treatments.
Collapse
Affiliation(s)
- Oya Bermek
- Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| |
Collapse
|
8
|
Sweet C. Lessons from studies with murine cytomegalovirus that could lead to a safe live attenuated vaccine for human cytomegalovirus. Access Microbiol 2020; 2:acmi000147. [PMID: 33195979 PMCID: PMC7656186 DOI: 10.1099/acmi.0.000147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022] Open
Abstract
Studies with a murine cytomegalovirus mutant tsm5 suggested two possible approaches to producing a live attenuated human cytomegalovirus vaccine. One approach would be to use a combination of five to six mutants where an attenuating mutation in the gene of one mutant is compensated by the wild-type version in a second mutant, which in turn has a mutation in a different gene compensated by the wild-type version in a third mutant, etc. Important genes in this approach could include those involved in DNA replication. The importance of the carboxy terminase of the primase gene (M70/UL70) for its function suggested a second approach where some of the natural codons in this region could be substituted with synonymous non-preferred (minor) codons that would reduce the replication fitness of the mutant.
Collapse
Affiliation(s)
- Clive Sweet
- School of Biosciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
9
|
Mendes AF, Goncalves P, Serrano-Solis V, Silva PMD. Identification of candidate microRNAs from Ostreid herpesvirus-1 (OsHV-1) and their potential role in the infection of Pacific oysters (Crassostrea gigas). Mol Immunol 2020; 126:153-164. [PMID: 32853878 DOI: 10.1016/j.molimm.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022]
Abstract
Oyster production is an economic activity of great interest worldwide. Recently, oysters have been suffering significant mortalities from OsHV-1infection, which has resulted in substantial economic loses in several countries around the world. Understanding viral pathogenicity mechanisms is of central importance for the establishment of disease control measures. Thus, the present work aimed to identify and characterize miRNAs from OsHV-1 as well as to predict their target transcripts in the virus and the host. OsHV-1 genome was used for the in silico discovery of pre-miRNAs. Subsequently, viral and host target transcripts of the OsHV-1 miRNAs were predicted according to the base pairing interaction between mature miRNAs and mRNA 3' untranslated regions (UTRs). Six unique pre-miRNAs were found in different regions of the viral genome, ranging in length from 85 to 172 nucleotides. A complex network of self-regulation of viral gene expression mediated by the miRNAs was identified. These sequences also seem to have a broad ability to regulate the expression of host immune-related genes, especially those associated with pathogen recognition. Our results suggest that OsHV-1 encodes miRNAs with important functions in the infection process, inducing self-regulation of viral transcripts, as well as affecting the regulation of Pacific oyster transcripts related to immunity. Understanding the molecular basis of host-pathogen interactions can help mitigate the recurrent events of oyster mass mortalities by OsHV-1 observed worldwide.
Collapse
Affiliation(s)
- Andrei Félix Mendes
- Laboratório de Imunologia e Patologia de Invertebrados (LABIPI), Departamento de Biologia Molecular, Universidade Federal da Paraíba (UFPB), 58051-900, João Pessoa, Paraíba, Brazil
| | - Priscila Goncalves
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Victor Serrano-Solis
- Laboratório de Imunologia e Patologia de Invertebrados (LABIPI), Departamento de Biologia Molecular, Universidade Federal da Paraíba (UFPB), 58051-900, João Pessoa, Paraíba, Brazil
| | - Patricia Mirella da Silva
- Laboratório de Imunologia e Patologia de Invertebrados (LABIPI), Departamento de Biologia Molecular, Universidade Federal da Paraíba (UFPB), 58051-900, João Pessoa, Paraíba, Brazil.
| |
Collapse
|
10
|
Ligat G, Muller C, Alain S, Hantz S. [The terminase complex, a relevant target for the treatment of HCMV infection]. Med Sci (Paris) 2020; 36:367-375. [PMID: 32356713 DOI: 10.1051/medsci/2020063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human cytomegalovirus (HCMV) is an important ubiquitous opportunistic pathogen that belongs to the betaherpesviridae. Primary HCMV infection is generally asymptomatic in immunocompetent individuals. In contrast, HCMV infection causes serious disease in immunocompromised patients and is the leading cause of congenital viral infection. Although they are effective, the use of conventional molecules is limited by the emergence of resistance and by their toxicity. New antivirals targeting other replication steps and inducing fewer adverse effects are therefore needed. During HCMV replication, DNA packaging is performed by the terminase complex, which cleaves DNA to package the virus genome into the capsid. With no counterpart in mammalian cells, these terminase proteins are ideal targets for highly specific antivirals. A new terminase inhibitor, letermovir, recently proved effective against HCMV in phase III clinical trials. However, its mechanism of action is unclear and it has no significant activity against other herpesvirus or non-human CMV.
Collapse
Affiliation(s)
- Gaëtan Ligat
- Univ. Limoges, Inserm, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France - CHU Limoges, Laboratoire de bactériologie-virologie-hygiène, Centre national de référence des Herpèsvirus (NRCHV), 87000 Limoges, France - Adresse actuelle : Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 3 rue Koeberlé, 67000 Strasbourg, France
| | - Clotilde Muller
- Univ. Limoges, Inserm, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France - CHU Limoges, Laboratoire de bactériologie-virologie-hygiène, Centre national de référence des Herpèsvirus (NRCHV), 87000 Limoges, France
| | - Sophie Alain
- Univ. Limoges, Inserm, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France - CHU Limoges, Laboratoire de bactériologie-virologie-hygiène, Centre national de référence des Herpèsvirus (NRCHV), 87000 Limoges, France
| | - Sébastien Hantz
- Univ. Limoges, Inserm, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France - CHU Limoges, Laboratoire de bactériologie-virologie-hygiène, Centre national de référence des Herpèsvirus (NRCHV), 87000 Limoges, France
| |
Collapse
|
11
|
Highlighting of a LAGLIDADG and a Zing Finger Motifs Located in the pUL56 Sequence Crucial for HCMV Replication. Viruses 2019; 11:v11121093. [PMID: 31779110 PMCID: PMC6950143 DOI: 10.3390/v11121093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 02/05/2023] Open
Abstract
The human cytomegalovirus (HCMV) terminase complex is part of DNA-packaging machinery that delivers a unit-length genome into a procapsid. Sequence comparison of herpesvirus homologs allowed us to identify a potential LATLNDIERFL and zinc finger pattern in N-terminal part of pUL56. Recombinant viruses were generated with specific serine or alanine substitutions in these putative patterns. We identified a LATLNDIERFL pattern characteristic of LAGLIDADG homing endonucleases and a metal-binding pattern involving the cysteine and histidine residues C191-X2-C194-X22-C217-X-H219 (CCCH) close to the region conferring letermovir resistance. These patterns are crucial for viral replication, suggesting that they are essential for pUL56 structure and function. Thus, these patterns represent potential targets for the development of new antivirals such as small molecules or peptides and may allow to better understand the letermovir mechanism of action.
Collapse
|
12
|
Bai L, Dong J, Liu Z, Rao Y, Feng P, Lan K. Viperin catalyzes methionine oxidation to promote protein expression and function of helicases. SCIENCE ADVANCES 2019; 5:eaax1031. [PMID: 31489375 PMCID: PMC6713503 DOI: 10.1126/sciadv.aax1031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/25/2019] [Indexed: 05/29/2023]
Abstract
Helicases play pivotal roles in fundamental biological processes, and posttranslational modifications regulate the localization, function, and stability of helicases. Here, we report that methionine oxidation of representative helicases, including DNA and RNA helicases of viral (ORF44 of KSHV) and cellular (MCM7 and RIG-I) origin, promotes their expression and functions. Cellular viperin, a major antiviral interferon-stimulated gene whose functions beyond host defense remain largely unknown, catalyzes the methionine oxidation of these helicases. Moreover, biochemical studies entailing loss-of-function mutations of helicases and a pharmacological inhibitor interfering with lipid metabolism and, hence, decreasing viperin activity indicate that methionine oxidation potently increases the stability and enzyme activity of these helicases that are critical for DNA replication and immune activation. Our work uncovers a pivotal role of viperin in catalyzing the methionine oxidation of helicases that are implicated in diverse fundamental biological processes.
Collapse
Affiliation(s)
- Lei Bai
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan 430072, P.R. China
| | - Jiazhen Dong
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, P.R. China
| | - Zhenqiu Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Youliang Rao
- Section of Infection and Immunity, Herman Ostrow School of Dentistry and Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry and Norris Comprehensive Cancer Center, University of Southern California, 925 W 34th Street, Los Angeles, CA 90089, USA
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan 430072, P.R. China
| |
Collapse
|