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Muhammad AM, Salum GM, Meguid MAE, Fotouh BE, Dawood RM. Bioinformatics analysis of multi-epitope peptide vaccines against Hepatitis C virus: a molecular docking study. J Genet Eng Biotechnol 2023; 21:117. [PMID: 37962693 PMCID: PMC10646107 DOI: 10.1186/s43141-023-00583-w] [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: 01/16/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Hepatitis C Virus (HCV) infection is one of the causal agents of liver disease burden. Six multiple antigenic peptides were synthesized including (P315, P412, and P517) plus (P1771, P2121, and P2941) to induce humoral and cellular responses, respectively against HCV infection. AIM This paper aimed to employ computational tools to evaluate the efficacy of each peptide individually and to determine the most effective one for better vaccine development and/or immunotherapy. METHODS VaxiJen web and AllerTOP servers were used for antigenicity and allergenicity prediction, respectively. The ToxinPred web server was used to investigate the peptide toxicity. Each peptide was docked with its corresponding receptors. RESULTS No peptides were expected to be toxic. P315 and P2941 are predicted to have robust antigenic properties, lowest allergenicity, and minimal sOPEP energies. In turn, P315 (derived from gpE1) formed the highest hydrophobic bonds with the BCR and CD81 receptors that will elicit B cell function. P2941 (derived from NS5B) was shown to strongly bind to both CD4 and CD8 receptors that will elicit T cell function. CONCLUSION P315 successfully bound to B cell (BCR and CD81) receptors. Also, P2941 is strongly bound to T cell (CD4 and CD8) receptors.
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Affiliation(s)
- Ashraf M Muhammad
- Applied Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Ghada M Salum
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt.
| | - Mai Abd El Meguid
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Basma E Fotouh
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Reham M Dawood
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
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Zahedipour F, Jamialahmadi K, Zamani P, Reza Jaafari M. Improving the efficacy of peptide vaccines in cancer immunotherapy. Int Immunopharmacol 2023; 123:110721. [PMID: 37543011 DOI: 10.1016/j.intimp.2023.110721] [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: 05/24/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
Peptide vaccines have shown great potential in cancer immunotherapy by targeting tumor antigens and activating the patient's immune system to mount a specific response against cancer cells. However, the efficacy of peptide vaccines in inducing a sustained immune response and achieving clinical benefit remains a major challenge. In this review, we discuss the current status of peptide vaccines in cancer immunotherapy and strategies to improve their efficacy. We summarize the recent advancements in the development of peptide vaccines in pre-clinical and clinical settings, including the use of novel adjuvants, neoantigens, nano-delivery systems, and combination therapies. We also highlight the importance of personalized cancer vaccines, which consider the unique genetic and immunological profiles of individual patients. We also discuss the strategies to enhance the immunogenicity of peptide vaccines such as multivalent peptides, conjugated peptides, fusion proteins, and self-assembled peptides. Although, peptide vaccines alone are weak immunogens, combining peptide vaccines with other immunotherapeutic approaches and developing novel approaches such as personalized vaccines can be promising methods to significantly enhance their efficacy and improve the clinical outcomes for cancer patients.
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Affiliation(s)
- Fatemeh Zahedipour
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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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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Inácio MM, Moreira ALE, Cruz-Leite VRM, Mattos K, Silva LOS, Venturini J, Ruiz OH, Ribeiro-Dias F, Weber SS, Soares CMDA, Borges CL. Fungal Vaccine Development: State of the Art and Perspectives Using Immunoinformatics. J Fungi (Basel) 2023; 9:633. [PMID: 37367569 DOI: 10.3390/jof9060633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Fungal infections represent a serious global health problem, causing damage to health and the economy on the scale of millions. Although vaccines are the most effective therapeutic approach used to combat infectious agents, at the moment, no fungal vaccine has been approved for use in humans. However, the scientific community has been working hard to overcome this challenge. In this sense, we aim to describe here an update on the development of fungal vaccines and the progress of methodological and experimental immunotherapies against fungal infections. In addition, advances in immunoinformatic tools are described as an important aid by which to overcome the difficulty of achieving success in fungal vaccine development. In silico approaches are great options for the most important and difficult questions regarding the attainment of an efficient fungal vaccine. Here, we suggest how bioinformatic tools could contribute, considering the main challenges, to an effective fungal vaccine.
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Affiliation(s)
- Moisés Morais Inácio
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia 74605-170, Brazil
- Estácio de Goiás University Center, Goiânia 74063-010, Brazil
| | - André Luís Elias Moreira
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia 74605-170, Brazil
| | | | - Karine Mattos
- Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Lana O'Hara Souza Silva
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia 74605-170, Brazil
| | - James Venturini
- Faculty of Medicine, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Orville Hernandez Ruiz
- MICROBA Research Group-Cellular and Molecular Biology Unit-CIB, School of Microbiology, University of Antioquia, Medellín 050010, Colombia
| | - Fátima Ribeiro-Dias
- Laboratório de Imunidade Natural (LIN), Instituto de Patologia Tropical e Saúde Pública, Federal University of Goiás, Goiânia 74001-970, Brazil
| | - Simone Schneider Weber
- Bioscience Laboratory, Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Célia Maria de Almeida Soares
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia 74605-170, Brazil
| | - Clayton Luiz Borges
- Laboratory of Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia 74605-170, Brazil
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Kalita P, Padhi AK, Tripathi T. Immunoinformatics Protocol to Design Multi-Epitope Subunit Vaccines. Methods Mol Biol 2023; 2673:357-369. [PMID: 37258927 DOI: 10.1007/978-1-0716-3239-0_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
With the development of scientific technologies, the accessibility of genomic data, computational tools, software, databases, and machine learning, the field of immunoinformatics has emerged as an effective technique for immunologists to design potential vaccines in a short time. A large number of tools and databases are available to screen the genome sequences of parasites/pathogens and identify the highly immunogenic peptides or epitopes that can be used to design effective vaccines. In this chapter, we provide an easy-to-use protocol for the design of multi-epitope-based subunit vaccines. Though the computational immunoinformatics-based approaches have demonstrated their competency in designing potentially effective vaccine candidates quickly, their immunogenicity and safety must be evaluated in laboratory settings before they are tested in clinical trials.
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Affiliation(s)
- Parismita Kalita
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, Meghalaya, India
- Regional Director's Office, Indira Gandhi National Open University, Regional Centre Kohima, Kohima, Nagaland, India
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Pogostin BH, Yu MH, Azares AR, Euliano EM, Lai CSE, Saenz G, Wu SX, Farsheed AC, Melhorn SM, Graf TP, Woodside DG, Hartgerink JD, McHugh KJ. Multidomain peptide hydrogel adjuvants elicit strong bias towards humoral immunity. Biomater Sci 2022; 10:6217-6229. [PMID: 36102692 PMCID: PMC9717470 DOI: 10.1039/d2bm01242a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adjuvants play a critical role in enhancing vaccine efficacy; however, there is a need to develop new immunomodulatory compounds to address emerging pathogens and to expand the use of immunotherapies. Multidomain peptides (MDPs) are materials composed of canonical amino acids that form injectable supramolecular hydrogels under physiological salt and pH conditions. MDP hydrogels are rapidly infiltrated by immune cells in vivo and have previously been shown to influence cytokine production. Therefore, we hypothesized that these immunostimulatory characteristics would allow MDPs to function as vaccine adjuvants. Herein, we demonstrate that loading antigen into MDP hydrogels does not interfere with their rheological properties and that positively charged MDPs can act as antigen depots, as demonstrated by their ability to release ovalbumin (OVA) over a period of 7-9 days in vivo. Mice vaccinated with MDP-adjuvanted antigen generated significantly higher IgG titers than mice treated with the unadjuvanted control, suggesting that these hydrogels potentiate humoral immunity. Interestingly, MDP hydrogels did not elicit a robust cellular immune response, as indicated by the lower production of IgG2c and smaller populations of tetramer-positive CD8+ T splenocytes compared to mice vaccinated alum-adjuvanted OVA. Together, the data suggest that MDP hydrogel adjuvants strongly bias the immune response towards humoral immunity while evoking a very limited cellular immune response. As a result, MDPs may have the potential to serve as adjuvants for applications that benefit exclusively from humoral immunity.
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Affiliation(s)
- Brett H Pogostin
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Marina H Yu
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Alon R Azares
- Molecular Cardiology Research Laboratories, Texas Heart Institute, Houston, TX, 77030, USA
| | - Erin M Euliano
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | | | - Gabriel Saenz
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Samuel X Wu
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Adam C Farsheed
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Sarah M Melhorn
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Tyler P Graf
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
| | - Darren G Woodside
- Molecular Cardiology Research Laboratories, Texas Heart Institute, Houston, TX, 77030, USA
| | - Jeffrey D Hartgerink
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Kevin J McHugh
- Department of Bioengineering, Rice University, Houston, TX, 77005, USA.
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