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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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2
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Bouin A, Vu MN, Al-Hakeem A, Tran GP, Nguyen JHC, Semler BL. Enterovirus-Cardiomyocyte Interactions: Impact of Terminally Deleted Genomic RNAs on Viral and Host Functions. J Virol 2023; 97:e0142622. [PMID: 36475766 PMCID: PMC9888282 DOI: 10.1128/jvi.01426-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Group B enteroviruses, including coxsackievirus B3 (CVB3), can persistently infect cardiac tissue and cause dilated cardiomyopathy. Persistence is linked to 5' terminal deletions of viral genomic RNAs that have been detected together with minor populations of full-length genomes in human infections. In this study, we explored the functions and interactions of the different viral RNA forms found in persistently infected patients and their putative role(s) in pathogenesis. Since enterovirus cardiac pathogenesis is linked to the viral proteinase 2A, we investigated the effect of different terminal genomic RNA deletions on 2A activity. We discovered that 5' terminal deletions in CVB3 genomic RNAs decreased the levels of 2A proteinase activity but could not abrogate it. Using newly generated viral reporters encoding nano-luciferase, we found that 5' terminal deletions resulted in decreased levels of viral protein and RNA synthesis in singly transfected cardiomyocyte cultures. Unexpectedly, when full-length and terminally deleted forms were cotransfected into cardiomyocytes, a cooperative interaction was observed, leading to increased viral RNA and protein production. However, when viral infections were carried out in cells harboring 5' terminally deleted CVB3 RNAs, a decrease in infectious particle production was observed. Our results provide a possible explanation for the necessity of full-length viral genomes during persistent infection, as they would stimulate efficient viral replication compared to that of the deleted genomes alone. To avoid high levels of viral particle production that would trigger cellular immune activation and host cell death, the terminally deleted RNA forms act to limit the production of viral particles, possibly as trans-dominant inhibitors. IMPORTANCE Enteroviruses like coxsackievirus B3 are able to initiate acute infections of cardiac tissue and, in some cases, to establish a long-term persistent infection that can lead to serious disease sequelae, including dilated cardiomyopathy. Previous studies have demonstrated the presence of 5' terminally deleted forms of enterovirus RNAs in heart tissues derived from patients with dilated cardiomyopathy. These deleted RNAs are found in association with very low levels of full-length enterovirus genomic RNAs, an interaction that may facilitate continued persistence while limiting virus particle production. Even in the absence of detectable infectious virus particle production, these deleted viral RNA forms express viral proteinases at levels capable of causing viral pathology. Our studies provide mechanistic insights into how full-length and deleted forms of enterovirus RNA cooperate to stimulate viral protein and RNA synthesis without stimulating infectious viral particle production. They also highlight the importance of targeting enteroviral proteinases to inhibit viral replication while at the same time limiting the long-term pathologies they trigger.
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Affiliation(s)
- Alexis Bouin
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Michelle N. Vu
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Ali Al-Hakeem
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Genevieve P. Tran
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Joseph H. C. Nguyen
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
| | - Bert L. Semler
- Department of Microbiology & Molecular Genetics, School of Medicine and Center for Virus Research, University of California, Irvine, California, USA
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bin Umair M, Akusa FN, Kashif H, Seerat-e-Fatima, Butt F, Azhar M, Munir I, Ahmed M, Khalil W, Sharyar H, Rafique S, Shahid M, Afzal S. Viruses as tools in gene therapy, vaccine development, and cancer treatment. Arch Virol 2022; 167:1387-1404. [PMID: 35462594 PMCID: PMC9035288 DOI: 10.1007/s00705-022-05432-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/28/2022] [Indexed: 12/11/2022]
Abstract
Using viruses to our advantage has been a huge leap for humanity. Their ability to mediate horizontal gene transfer has made them useful tools for gene therapy, vaccine development, and cancer treatment. Adenoviruses, adeno-associated viruses, retroviruses, lentiviruses, alphaviruses, and herpesviruses are a few of the most common candidates for use as therapeutic agents or efficient gene delivery systems. Efforts are being made to improve and perfect viral-vector-based therapies to overcome potential or reported drawbacks. Some preclinical trials of viral vector vaccines have yielded positive results, indicating their potential as prophylactic or therapeutic vaccine candidates. Utilization of the oncolytic activity of viruses is the future of cancer therapy, as patients will then be free from the harmful effects of chemo- or radiotherapy. This review discusses in vitro and in vivo studies showing the brilliant therapeutic potential of viruses.
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Affiliation(s)
- Musab bin Umair
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fujimura Nao Akusa
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hadia Kashif
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Seerat-e-Fatima
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Fatima Butt
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Marium Azhar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Iqra Munir
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Ahmed
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Wajeeha Khalil
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Hafiz Sharyar
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Muhammad Shahid
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
| | - Samia Afzal
- Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, 87-West Canal Bank Road, Thokar Niaz Baig, Lahore, Pakistan
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Persistent Enterovirus Infection: Little Deletions, Long Infections. Vaccines (Basel) 2022; 10:vaccines10050770. [PMID: 35632526 PMCID: PMC9143164 DOI: 10.3390/vaccines10050770] [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: 04/01/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Enteroviruses have now been shown to persist in cell cultures and in vivo by a novel mechanism involving the deletion of varying amounts of the 5′ terminal genomic region termed domain I (also known as the cloverleaf). Molecular clones of coxsackievirus B3 (CVB3) genomes with 5′ terminal deletions (TD) of varying length allow the study of these mutant populations, which are able to replicate in the complete absence of wildtype virus genomes. The study of TD enteroviruses has revealed numerous significant differences from canonical enteroviral biology. The deletions appear and become the dominant population when an enterovirus replicates in quiescent cell populations, but can also occur if one of the cis-acting replication elements of the genome (CRE-2C) is artificially mutated in the element’s stem and loop structures. This review discusses how the TD genomes arise, how they interact with the host, and their effects on host biology.
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