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Vaccines
Special Issues
Advances in Epitope-Based Vaccine Design
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Advances in Epitope-Based Vaccine Design

A special issue of Vaccines (ISSN 2076-393X). This special issue belongs to the section "Vaccine Adjuvants".

Deadline for manuscript submissions: closed (31 May 2023) | Viewed by 13727

Special Issue Editors

Dr. Sajjad Ahmad

E-Mail Website
Guest Editor
Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
Interests: computer aided vaccine design for bacterial; viral and parasitic pathogens; computational biology; Artificial Intelligence in vaccine design
Special Issues, Collections and Topics in MDPI journals
Dr. Muhammad Khurram

E-Mail Website
Guest Editor
Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
Interests: computer aided vaccine design for bacterial; viral and parasitic pathogens; medical microbiology; computational biology; Artificial Intelligence in vaccine design
Special Issues, Collections and Topics in MDPI journals
Dr. Sumra Wajid Abbasi

E-Mail Website
Guest Editor
Department of Biological Science, National University of Medical Sciences, Rawalpindi, Pakistan
Interests: computer aided vaccine design for bacterial; viral and parasitic pathogens; medical microbiology; computational biology; Artificial Intelligence in vaccine design

Special Issue Information

Dear Colleagues,

Conventional vaccines are developed from live attenuated or inactivated organisms, which elicit strong humoral and cellular immunity, resulting in long lasting immunity. However, the use of such vaccines has been questioned due to crucial safety concerns, as the used pathogen may become reactivated. Similarly, subunit-based vaccines containing a single whole protein are also not a good choice because of non-specific immune responses, which may occur due to the presence of multiple antigenic determinants. In addition, the formulation of such vaccines often lead to reactogenic and/or allergenic responses that are often not desired. The design of epitope-driven or peptide-based vaccines is more attractive; they are comparatively easier to produce and construct, they lack any infectious potential, and offer chemical stability. Moreover, for proper engagement of cellular and humoral immunity, a combining task for different peptides is more appreciated. The construction of multi-epitope vaccines by linking the safest and B-cell derived T-cell antigenic epitope offers many significant benefits. These include broader intrinsic immunogenicity, both humoral and cellular immunity can properly be engaged and improve T-cell epitopes population coverage. The novel combination of immuno-informative approaches, together with the knowledge of host immune responses and the exponential increase in complete genome sequencing of pathogen strains, now makes it possible to select the most antigenic epitopes. As such, it is conceived that cocktails of selected and defined epitopes may provide foundations for the rational design of vaccines capable of eliciting convenient cellular and humoral immunity.

This Special Issue aims to detail the advancemes in the epitope-based vaccines development. The Special Issue covers said vaccine development both on computational and experimetnal techniques for variety of pathogens as well as cancer diseases.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but not limited to) the following:

  • Computational design of epitope based vaccines;
  • Experimental design of epitopes based vaccines. 

We look forward to receiving your contributions.

Dr. Sajjad Ahmad
Dr. Muhammad Khurram
Dr. Sumra Wajid Abbasi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Vaccines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • vaccines
  • Eptiope vaccines
  • bacteria
  • viruses
  • parasites
  • cancer
  • animal model
  • immunity
  • cellular immunity
  • bioinformatics

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Published Papers (5 papers)

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Research

22 pages, 4366 KiB  
Article
Immunoinformatics Approach to Design a Multi-Epitope Vaccine against Cutaneous Leishmaniasis
by Shumaila Naz, Aiman Aroosh, Ayse Caner, Esra Atalay Şahar, Seray Toz, Yusuf Ozbel and Sumra Wajid Abbasi
Vaccines 2023, 11(2), 339; https://doi.org/10.3390/vaccines11020339 - 2 Feb 2023
Cited by 4 | Viewed by 2857
Abstract
Cutaneous Leishmaniasis (CL), a neglected vector-borne disease caused by protozoan parasite Leishmania major (L. major), is a major public health concern, and the development of new strategies to reduce the disease incidence has become a top priority. Advances in immunoinformatics and [...] Read more.
Cutaneous Leishmaniasis (CL), a neglected vector-borne disease caused by protozoan parasite Leishmania major (L. major), is a major public health concern, and the development of new strategies to reduce the disease incidence has become a top priority. Advances in immunoinformatics and in-silico epitope prediction could be a promising approach to designing a finest vaccine candidate. In this study, we aimed to design a peptide-based vaccine against CL using computational tools and identified ten B-cell-derived T-cell epitopes from the glycoprotein gp63 of L. major. All of the potential immunodominant epitopes were used to design a vaccine construct along with a linker and an adjuvant at the N-terminal for enhancing its immunogenicity. Additionally, many characteristics of the proposed vaccine were examined, and it was confirmed to be non-allergenic, non-toxic, and thermally stable. To assess the vaccine interaction with the innate immune toll-like receptor-4 (TLR-4), a 3D structure of the vaccine construct was developed. Molecular docking and molecular dynamic simulation were used to confirm the binding and to assess the stability of the vaccine-TLR4 complex and interactions, respectively. In conclusion, our multi-epitope vaccine will provide a gateway to analyze the protein function of a potential vaccine candidate against CL. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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15 pages, 3340 KiB  
Article
Targeted Protein-Specific Multi-Epitope-Based Vaccine Designing against Human Cytomegalovirus by Using Immunoinformatics Approaches
by Mohammed Ali Bakkari
Vaccines 2023, 11(2), 203; https://doi.org/10.3390/vaccines11020203 - 17 Jan 2023
Cited by 5 | Viewed by 2041
Abstract
Cytomegaloviruses are emerging pathogenic agents known to cause congenital disorders in humans. In this study, immune epitopes (CTL, B cell and HTL) were screened for highly antigenic target proteins of the Human Cytomegalovirus. These shortlisted epitopes were then joined together through suitable linkers [...] Read more.
Cytomegaloviruses are emerging pathogenic agents known to cause congenital disorders in humans. In this study, immune epitopes (CTL, B cell and HTL) were screened for highly antigenic target proteins of the Human Cytomegalovirus. These shortlisted epitopes were then joined together through suitable linkers to construct multi epitope-based vaccine constructs (MEVCs). The functionality of each vaccine construct was evaluated through tertiary vaccine structure modelling and validations. Furthermore, physio-chemical properties including allergenicity, antigenicity molecular weight and many others were also predicted. The vaccine designs were also docked with the human TLR-4 receptor to demonstrate the receptor specific affinity and formed interactions. The vaccine peptides sequences were also subjected to codon optimization to confirm the potential vaccines expression in E. coli hosts. Additionally, all the MEVCs were also evaluated for immune response (IgG and IgM) induction. However, further in vivo tests are needed to ensure the efficacy of these vaccine designs. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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31 pages, 11916 KiB  
Article
Identification of a Potential Vaccine against Treponema pallidum Using Subtractive Proteomics and Reverse-Vaccinology Approaches
by Siyab Khan, Muhammad Rizwan, Adnan Zeb, Muhammad Alaa Eldeen, Said Hassan, Ashfaq Ur Rehman, Refaat A. Eid, Mohamed Samir A. Zaki, Ghadeer M. Albadrani, Ahmed E. Altyar, Nehal Ahmed Talaat Nouh, Mohamed M. Abdel-Daim and Amin Ullah
Vaccines 2023, 11(1), 72; https://doi.org/10.3390/vaccines11010072 - 28 Dec 2022
Cited by 5 | Viewed by 2627
Abstract
Syphilis, a sexually transmitted infection, is a deadly disease caused by Treponema pallidum. It is a Gram-negative spirochete that can infect nearly every organ of the human body. It can be transmitted both sexually and perinatally. Since syphilis is the second most [...] Read more.
Syphilis, a sexually transmitted infection, is a deadly disease caused by Treponema pallidum. It is a Gram-negative spirochete that can infect nearly every organ of the human body. It can be transmitted both sexually and perinatally. Since syphilis is the second most fatal sexually transmitted disease after AIDS, an efficient vaccine candidate is needed to establish long-term protection against infections by T. pallidum. This study used reverse-vaccinology-based immunoinformatic pathway subtractive proteomics to find the best antigenic proteins for multi-epitope vaccine production. Six essential virulent and antigenic proteins were identified, including the membrane lipoprotein TpN32 (UniProt ID: O07950), DNA translocase FtsK (UniProt ID: O83964), Protein Soj homolog (UniProt ID: O83296), site-determining protein (UniProt ID: F7IVD2), ABC transporter, ATP-binding protein (UniProt ID: O83930), and Sugar ABC superfamily ATP-binding cassette transporter, ABC protein (UniProt ID: O83782). We found that the multiepitope subunit vaccine consisting of 4 CTL, 4 HTL, and 11 B-cell epitopes mixed with the adjuvant TLR-2 agonist ESAT6 has potent antigenic characteristics and does not induce an allergic response. Before being docked at Toll-like receptors 2 and 4, the developed vaccine was modeled, improved, and validated. Docking studies revealed significant binding interactions, whereas molecular dynamics simulations demonstrated its stability. Furthermore, the immune system simulation indicated significant and long-lasting immunological responses. The vaccine was then reverse-transcribed into a DNA sequence and cloned into the pET28a (+) vector to validate translational activity as well as the microbial production process. The vaccine developed in this study requires further scientific consensus before it can be used against T. pallidum to confirm its safety and efficacy. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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24 pages, 3867 KiB  
Article
Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches
by Mahreen Nawaz, Asad Ullah, Alhanouf I. Al-Harbi, Mahboob Ul Haq, Alaa R. Hameed, Sajjad Ahmad, Aamir Aziz, Khadija Raziq, Saifullah Khan, Muhammad Irfan and Riaz Muhammad
Vaccines 2022, 10(10), 1729; https://doi.org/10.3390/vaccines10101729 - 16 Oct 2022
Cited by 7 | Viewed by 2993
Abstract
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for [...] Read more.
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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22 pages, 86568 KiB  
Article
Vaccinomics-Aided Development of a Next-Generation Chimeric Vaccine against an Emerging Threat: Mycoplasma genitalium
by Kashaf Khalid, Tajamul Hussain, Zubia Jamil, Khalid Salman Alrokayan, Bashir Ahmad and Yasir Waheed
Vaccines 2022, 10(10), 1720; https://doi.org/10.3390/vaccines10101720 - 14 Oct 2022
Cited by 3 | Viewed by 2276
Abstract
Mycoplasma genitalium, besides urethritis, causes a number of other sexually transmitted diseases, posing a significant health threat to both men and women, particularly in developing countries. In light of the rapid appearance of multidrug-resistant strains, M. genitalium is regarded as an emerging [...] Read more.
Mycoplasma genitalium, besides urethritis, causes a number of other sexually transmitted diseases, posing a significant health threat to both men and women, particularly in developing countries. In light of the rapid appearance of multidrug-resistant strains, M. genitalium is regarded as an emerging threat and has been placed on the CDC’s “watch list”. Hence, a protective vaccine is essential for combating this pathogen. In this study, we utilized reverse vaccinology to develop a chimeric vaccine against M. genitalium by identifying vaccine targets from the reference proteome (Strain G-37) of this pathogen. A multiepitope vaccine was developed using proteins that are non-toxic, non-allergic, and non-homologous to human proteins. Several bioinformatic tools identified linear and non-linear B-cell epitopes, as well as MHC epitopes belonging to classes I and II, from the putative vaccine target proteins. The epitopes that showed promiscuity among the various servers were shortlisted and subsequently selected for further investigation based on an immunoinformatic analysis. Using GPGPG, AAY, and KK linkers, the shortlisted epitope sequences were assembled to create a chimeric construct. A GPI anchor protein immunomodulating adjuvant was adjoined to the vaccine construct’s N-terminus through the EAAK linker so as to improve the overall immunogenicity. For further investigations of the designed construct, various bioinformatic tools were employed to study the physicochemical properties, immune profile, solubility, and allergenicity profile. A tertiary chimeric design was computationally modeled using I-TASSER and Robetta and was subsequently refined through GalaxyRefine. ProSA-Web was exploited to corroborate the quality of the construct by detecting errors and the Ramachandran plot was used to identify possible quality issues. Simulation studies of the molecular dynamics demonstrated the robustness and flexibility of the designed construct. Following the successful docking of the designed model to the immune receptors, the construct was computationally cloned into Escherichia coli plasmids to affirm the efficient expression of the designed construct in a biological system. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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