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Ratishvili T, Quach HQ, Haralambieva IH, Suryawanshi YR, Ovsyannikova IG, Kennedy RB, Poland GA. A multifaceted approach for identification, validation, and immunogenicity of naturally processed and in silico-predicted highly conserved SARS-CoV-2 peptides. Vaccine 2024; 42:162-174. [PMID: 38105139 DOI: 10.1016/j.vaccine.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
SARS-CoV-2 remains a major global public health concern. Antibody waning and immune escape variant emergence necessitate the development of next generation vaccines that induce cross-reactive durable immune responses. T cell responses to SARS-CoV-2 demonstrate higher conservation, antigenic breadth, and longevity than antibody responses. Therefore, we sought to identify pathogen-derived T cell epitopes for a potential peptide-based vaccine. We pursued an approach leveraging: 1) liquid chromatography and tandem mass spectrometry (LC-MS/MS)-based identification of peptides from ancestral SARS-CoV-2-infected cell lines, 2) epitope prediction algorithms, and 3) overlapping peptide libraries. From this strategy, we identified 380 unique SARS-CoV-2-derived peptide sequences, including 53 antigenic HLA class I and class II peptides from multiple structural and non-structural/accessory viral proteins. These peptide sequences were highly conserved across variants of concern/interest (VoC/VoIs), and are estimated to achieve coverage of >96% of the world population. Our findings validate this discovery pipeline for peptide identification and immunogenicity testing, and are a crucial step toward the development of a next-generation multi-epitope SARS-CoV-2 peptide vaccine, and a novel vaccine platform methodology.
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Affiliation(s)
- Tamar Ratishvili
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iana H Haralambieva
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yogesh R Suryawanshi
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Department of General Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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Traut CC, Jones JL, Sanders RA, Clark LR, Hamill MM, Stavrakis G, Sop J, Beckey TP, Keller SC, Gilliams EA, Cochran WV, Laeyendecker O, Manabe YC, Mostafa HH, Thomas DL, Hansoti B, Gebo KA, Blankson JN. Orthopoxvirus-Specific T-Cell Responses in Convalescent Mpox Patients. J Infect Dis 2024; 229:54-58. [PMID: 37380166 PMCID: PMC10786252 DOI: 10.1093/infdis/jiad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/24/2023] [Indexed: 06/30/2023] Open
Abstract
Orthopoxvirus-specific T-cell responses were analyzed in 10 patients who had recovered from Mpox including 7 people with human immunodeficiency virus (PWH). Eight participants had detectable virus-specific T-cell responses, including a PWH who was not on antiretroviral therapy and a PWH on immunosuppressive therapy. These 2 participants had robust polyfunctional CD4+ T-cell responses to peptides from the 121L vaccinia virus (VACV) protein. T-cells from 4 of 5 HLA-A2-positive participants targeted at least 1 previously described HLA-A2-restricted VACV epitope, including an epitope targeted in 2 participants. These results advance our understanding of immunity in convalescent Mpox patients.
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Affiliation(s)
- Caroline C Traut
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Renata A Sanders
- Department of Pediatrics, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Laura R Clark
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Matthew M Hamill
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Georgia Stavrakis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Joel Sop
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Tyler P Beckey
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Sara C Keller
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | | | - Willa V Cochran
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
- Intramural Research Program, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Yukari C Manabe
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Bhakti Hansoti
- Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Kelly A Gebo
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins Medicine, Baltimore, Maryland, USA
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Tripathi T. Advances in vaccines: revolutionizing disease prevention. Sci Rep 2023; 13:11748. [PMID: 37474542 PMCID: PMC10359443 DOI: 10.1038/s41598-023-38798-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Affiliation(s)
- Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Liang J, Wu Y, Lan K, Dong C, Wu S, Li S, Zhou HB. Antiviral PROTACs: Opportunity borne with challenge. CELL INSIGHT 2023; 2:100092. [PMID: 37398636 PMCID: PMC10308200 DOI: 10.1016/j.cellin.2023.100092] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 07/04/2023]
Abstract
Proteolysis targeting chimera (PROTAC) degradation of pathogenic proteins by hijacking of the ubiquitin-proteasome-system has become a promising strategy in drug design. The overwhelming advantages of PROTAC technology have ensured a rapid and wide usage, and multiple PROTACs have entered clinical trials. Several antiviral PROTACs have been developed with promising bioactivities against various pathogenic viruses. However, the number of reported antiviral PROTACs is far less than that of other diseases, e.g., cancers, immune disorders, and neurodegenerative diseases, possibly because of the common deficiencies of PROTAC technology (e.g., limited available ligands and poor membrane permeability) plus the complex mechanism involved and the high tendency of viral mutation during transmission and replication, which may challenge the successful development of effective antiviral PROTACs. This review highlights the important advances in this rapidly growing field and critical limitations encountered in developing antiviral PROTACs by analyzing the current status and representative examples of antiviral PROTACs and other PROTAC-like antiviral agents. We also summarize and analyze the general principles and strategies for antiviral PROTAC design and optimization with the intent of indicating the potential strategic directions for future progress.
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Affiliation(s)
- Jinsen Liang
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Yihe Wu
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chune Dong
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shu Li
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
| | - Hai-Bing Zhou
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430071, China
- Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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