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Myburgh L, van Loon K, Huijbers EJM, van Beijnum JR, Russell CA, Griffioen AW. Guided design for the development of an evolution-proof influenza vaccine. Vaccine 2025; 59:127281. [PMID: 40398325 DOI: 10.1016/j.vaccine.2025.127281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 04/24/2025] [Accepted: 05/15/2025] [Indexed: 05/23/2025]
Abstract
Influenza remains a significant public health concern, particularly among high-risk populations, due to its capacity to cause annual epidemics and potentially trigger global pandemics. Despite the availability of countermeasures such as vaccines and antiviral treatments, their effectiveness is hindered by factors such as resistance development with manufacturing of the influenza vaccine still heavily relying on decades-old technologies. This review therefore examines the mechanisms by which influenza viruses evade host immunity and evaluates current and emerging approaches to enhance vaccine-mediated protection. Advances targeting the conserved hemagglutinin (HA) stem, incorporating multiple HA subtypes, and the use of adjuvants are discussed, alongside increased attention to neuraminidase (NA) and other viral components as immunogenic targets. Strategic epitope prediction, through glycan masking, evolutionary forecasting, and consensus sequence design, offer promising frameworks for rational vaccine design. Furthermore, delivery platforms, including recombinant protein, mRNA, and conjugate vaccines are explored for their potential to elicit broad and durable immunity. Collectively, these developments highlight a multifaceted approach towards the design of effective interventions against this persistent healthcare challenge.
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Affiliation(s)
- Lauren Myburgh
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Karlijn van Loon
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Elisabeth J M Huijbers
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Amsterdam, UMC, the Netherlands
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands.
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Prashar N, Mohammed SB, Raja NS, Mohideen HS. Rerouting therapeutic peptides and unlocking their potential against SARS-CoV2. 3 Biotech 2025; 15:116. [PMID: 40191455 PMCID: PMC11971104 DOI: 10.1007/s13205-025-04270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2025] [Accepted: 03/10/2025] [Indexed: 04/09/2025] Open
Abstract
The COVID-19 pandemic highlighted the potential of peptide-based therapies as an alternative to traditional pharmaceutical treatments for SARS-CoV-2 and its variants. Our review explores the role of therapeutic peptides in modulating immune responses, inhibiting viral entry, and disrupting replication. Despite challenges such as stability, bioavailability, and the rapid mutation of the virus, ongoing research and clinical trials show that peptide-based treatments are increasingly becoming integral to future viral outbreak responses. Advancements in computational modelling methods in combination with artificial intelligence will enable mass screening of therapeutic peptides and thereby, comprehending a peptide repurposing strategy similar to the small molecule repurposing. These findings suggest that peptide-based therapies play a critical and promising role in future pandemic preparedness and outbreak management.
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Affiliation(s)
- Namrata Prashar
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
| | - Saharuddin Bin Mohammed
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - N. S. Raja
- Deparmtent of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
| | - Habeeb Shaik Mohideen
- Bioinformatics and Entomoinformatics Lab, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Chennai, Tamil Nadu 603203 India
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Myburgh L, Karsjens H, Blanas A, de Ligt A, van Loon K, Huijbers EJM, van Beijnum JR, Engbersen DJM, Rekiki A, Mignon C, Vratskikh O, Griffioen AW. Targeting the early life stages of SARS-CoV-2 using a multi-peptide conjugate vaccine. Vaccine 2025; 54:126989. [PMID: 40088511 DOI: 10.1016/j.vaccine.2025.126989] [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: 10/16/2024] [Revised: 02/26/2025] [Accepted: 03/01/2025] [Indexed: 03/17/2025]
Abstract
The spike glycoprotein is a key factor in the infection cycle of SARS-CoV-2, as it mediates both receptor recognition and membrane fusion by the virus. Therefore, in this study, we aimed to design a multi-peptide conjugate vaccine against SARS-CoV-2, targeting the early stages of the virus's life cycle. We used iBoost technology, which is designed to induce immune responses against low- or non-immunogenic epitopes. We selected six peptide sequences, each representing a key domain of the spike protein (i.e., receptor binding domain (RBM), subdomain 1 (SD1), subdomain 2 (SD2), S1/S2, fusion peptide and the S2' sequences (FP + S2'), heptad repeat 1 (HR1)). Immunization studies in mice displayed targeted humoral and cellular immune responses against specific peptides of the spike protein simultaneously, while inducing cross-protection against the Delta and Omicron coronavirus variants. Moreover, vaccinated hamsters challenged with SARS-CoV-2 elicited high antibody levels against key peptides, induced early neutralizing antibody responses and resulted in less weight loss compared to controls. This highlights the potential for improving viral control and disease outcomes when utilizing this strategy. Therefore, by using iBoost technology in conjunction with our peptide design strategy, we were able to successfully target non-immunodominant regions in the spike protein while activating both arms of the adaptive immune system.
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MESH Headings
- Animals
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- COVID-19 Vaccines/immunology
- COVID-19 Vaccines/administration & dosage
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Mice
- COVID-19/prevention & control
- COVID-19/immunology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/administration & dosage
- Cricetinae
- Vaccines, Conjugate/immunology
- Vaccines, Conjugate/administration & dosage
- Female
- Mice, Inbred BALB C
- Immunity, Cellular
- Humans
- Cross Protection
- Immunity, Humoral
- Epitopes/immunology
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Affiliation(s)
- Lauren Myburgh
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Haiko Karsjens
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Athanasios Blanas
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Aafke de Ligt
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Karlijn van Loon
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Elisabeth J M Huijbers
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands
| | | | | | | | | | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands; CimCure BV, Amsterdam, the Netherlands.
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Zhang Y, Bailey TS, Hittmeyer P, Dubois LJ, Theys J, Lambin P. Multiplex genetic manipulations in Clostridium butyricum and Clostridium sporogenes to secrete recombinant antigen proteins for oral-spore vaccination. Microb Cell Fact 2024; 23:119. [PMID: 38659027 PMCID: PMC11040787 DOI: 10.1186/s12934-024-02389-y] [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: 02/13/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Clostridium spp. has demonstrated therapeutic potential in cancer treatment through intravenous or intratumoral administration. This approach has expanded to include non-pathogenic clostridia for the treatment of various diseases, underscoring the innovative concept of oral-spore vaccination using clostridia. Recent advancements in the field of synthetic biology have significantly enhanced the development of Clostridium-based bio-therapeutics. These advancements are particularly notable in the areas of efficient protein overexpression and secretion, which are crucial for the feasibility of oral vaccination strategies. Here, we present two examples of genetically engineered Clostridium candidates: one as an oral cancer vaccine and the other as an antiviral oral vaccine against SARS-CoV-2. RESULTS Using five validated promoters and a signal peptide derived from Clostridium sporogenes, a series of full-length NY-ESO-1/CTAG1, a promising cancer vaccine candidate, expression vectors were constructed and transformed into C. sporogenes and Clostridium butyricum. Western blotting analysis confirmed efficient expression and secretion of NY-ESO-1 in clostridia, with specific promoters leading to enhanced detection signals. Additionally, the fusion of a reported bacterial adjuvant to NY-ESO-1 for improved immune recognition led to the cloning difficulties in E. coli. The use of an AUU start codon successfully mitigated potential toxicity issues in E. coli, enabling the secretion of recombinant proteins in C. sporogenes and C. butyricum. We further demonstrate the successful replacement of PyrE loci with high-expression cassettes carrying NY-ESO-1 and adjuvant-fused NY-ESO-1, achieving plasmid-free clostridia capable of secreting the antigens. Lastly, the study successfully extends its multiplex genetic manipulations to engineer clostridia for the secretion of SARS-CoV-2-related Spike_S1 antigens. CONCLUSIONS This study successfully demonstrated that C. butyricum and C. sporogenes can produce the two recombinant antigen proteins (NY-ESO-1 and SARS-CoV-2-related Spike_S1 antigens) through genetic manipulations, utilizing the AUU start codon. This approach overcomes challenges in cloning difficult proteins in E. coli. These findings underscore the feasibility of harnessing commensal clostridia for antigen protein secretion, emphasizing the applicability of non-canonical translation initiation across diverse species with broad implications for medical or industrial biotechnology.
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Affiliation(s)
- Yanchao Zhang
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands.
| | - Tom S Bailey
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Philip Hittmeyer
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
- LivingMed Biotech BV, Clos Chanmurly 13, Liège, 4000, Belgium
| | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Jan Theys
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands
| | - Philippe Lambin
- The M-Lab, Department of Precision Medicine, GROW - Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, 6229 ER, the Netherlands.
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