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Vaccines
Special Issues
Computer and Technology Supported Development of Vaccines
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Computer and Technology Supported Development of Vaccines

A special issue of Vaccines (ISSN 2076-393X).

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 22526

Special Issue Editors

Dr. Pedro A. Reche

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Chief Guest Editor
Laboratory of Immunomedicine, Department of Immunology & O2, School of Medicine, Complutense University of Madrid, Pza Ramon y Cajal, S/N, 28040 Madrid, Spain
Interests: immunity; immunomodulation; T cells; B cells; cytokines; epitopes
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Francesco Pappalardo

E-Mail Website
Guest Editor
Department of Drug Sciences, University of Catania, 95125 Catania, Italy
Interests: computational immunology; agent-based models; in silico trials; regulatory affairs; systems biomedicine
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Early vaccines were obtained with little knowledge or technology and required much time and effort for their development. In contrast, ongoing COVID-19 pandemics have underscored our current ability to develop vaccines quickly. In this context, the main aim of this issue is to put forward new knowledge, concepts, and technologies that can be recruited to facilitate vaccine design, including contributions from proteomics, immunology, structural biology, systems biology, and mathematical modeling. In this context, the adoption of modeling and simulation for the development and de-risking of vaccines will be the key to drastically reducing animal and human testing, lowering costs, and shortening marketing times.

We particularly welcome research articles and reviews on complete genome sequencing of pathogens, computational, and high-throughput technologies for antigen and epitope discovery, antigen receptor profiling, modeling of antigen–antigen receptor interactions, and computational simulation of immune responses. Likewise, contributions utilizing these technologies to develop vaccines and immunotherapeutics to treat cancer, allergies, and autoimmune diseases are also welcome

Dr. Pedro A. Reche
Prof. Francesco Pappalardo
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

  • antigen
  • epitope
  • immunoinformatics
  • vaccines
  • computational immune simulations

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Published Papers (6 papers)

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Research

17 pages, 6355 KiB  
Article
Designing a Multi-Epitope Vaccine against Toxoplasma gondii: An Immunoinformatics Approach
by Mutiat Hammed-Akanmu, Maria Mim, Abdinasir Yusuf Osman, Abdulrahman M. Sheikh, Esmaeil Behmard, Ali A. Rabaan, Rapeah Suppain and Khalid Hajissa
Vaccines 2022, 10(9), 1389; https://doi.org/10.3390/vaccines10091389 - 25 Aug 2022
Cited by 10 | Viewed by 3159
Abstract
Infection with the intracellular apicomplexan parasite Toxoplasma gondii causes serious clinical outcomes in both human and veterinary settings worldwide. Although approximately one-third of the world’s population is infected with T. gondii, an effective human vaccine for this disease remains unavailable. We aimed [...] Read more.
Infection with the intracellular apicomplexan parasite Toxoplasma gondii causes serious clinical outcomes in both human and veterinary settings worldwide. Although approximately one-third of the world’s population is infected with T. gondii, an effective human vaccine for this disease remains unavailable. We aimed to design a potential T. gondii vaccine candidate that consisted of the B- and T-lymphocyte epitopes of three parasite immunogenic antigens. Firstly, the immunodominant epitopes expressed within the ROP2, MIC3, and GRA7 proteins of T. gondii were identified. Subsequently, six B-cell epitopes, five CTL epitopes, and five HTL epitopes were combined to generate a multi-epitope vaccine, and the 50S ribosomal protein L7/L12 was added as an adjuvant to boost the vaccine’s immunogenicity. All these epitopes were found to be antigenic, nonallergenic, nontoxic, and nonhuman homologs. The designed vaccine construct has a molecular weight of 51 kDa, an antigenicity score of 0.6182, and a solubility of 0.903461. Likewise, the candidate vaccine was immunogenic, nonallergenic, and stable. Molecular docking analysis revealed stable interactions between the vaccine construct and the TLR-4 immune receptor. Meanwhile, the stability of the developed vaccine was validated using molecular dynamics simulation. In silico, the vaccine construct was able to trigger primary immune responses. However, further laboratory-based assessments are needed to confirm its efficacy and safety. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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17 pages, 5135 KiB  
Article
Execution and Design of an Anti HPIV-1 Vaccine with Multiple Epitopes Triggering Innate and Adaptive Immune Responses: An Immunoinformatic Approach
by Muhammad Naveed, Allah Rakha Yaseen, Hira Khalid, Urooj Ali, Ali A. Rabaan, Mohamed Garout, Muhammad A. Halwani, Abbas Al Mutair, Saad Alhumaid, Zainab Al Alawi, Yousef N. Alhashem, Naveed Ahmed and Chan Yean Yean
Vaccines 2022, 10(6), 869; https://doi.org/10.3390/vaccines10060869 - 29 May 2022
Cited by 20 | Viewed by 4097
Abstract
Human Parainfluenza Virus (HPIV) Type-1, which is an anti-sense ribonucleic acid (RNA) virus belonging to the paramyxoviridae family, induces upper and lower respiratory tract infections. The infections caused by the HPIV Type-1 virus are usually confined to northwestern regions of America. HPIV-1 causes [...] Read more.
Human Parainfluenza Virus (HPIV) Type-1, which is an anti-sense ribonucleic acid (RNA) virus belonging to the paramyxoviridae family, induces upper and lower respiratory tract infections. The infections caused by the HPIV Type-1 virus are usually confined to northwestern regions of America. HPIV-1 causes infections through the virulence of the hemagglutinin-neuraminidase (HN) protein, which plays a key role in the attachment of the viral particle with the host’s receptor cells. To the best of our knowledge, there is no effective antiviral drugs or vaccines being developed to combat the infection caused by HPIV-1. In the current study, a multiple epitope-based vaccine was designed against HPIV-1 by taking the viral HN protein as a probable vaccine candidate. The multiple epitopes were selected in accordance with their allergenicity, antigenicity and toxicity scoring. The determined epitopes of the HN protein were connected simultaneously using specific conjugates along with an adjuvant to construct the subunit vaccine, with an antigenicity score of 0.6406. The constructed vaccine model was docked with various Toll-like Receptors (TLRs) and was computationally cloned in a pET28a (+) vector to analyze the expression of vaccine sequence in the biological system. Immune stimulations carried out by the C-ImmSim Server showed an excellent result of the body’s defense system against the constructed vaccine model. The AllerTop tool predicted that the construct was non-allergen with and without the adjuvant sequence, and the VaxiJen 2.0 with 0.4 threshold predicted that the construct was antigenic, while the Toxinpred predicted that the construct was non-toxic. Protparam results showed that the selected protein was stable with 36.48 instability index (II) scores. The Grand average of Hydropathicity or GRAVY score indicated that the constructed protein was hydrophilic in nature. Aliphatic index values (93.53) confirmed that the construct was thermostable. This integrated computational approach shows that the constructed vaccine model has a potential to combat laryngotracheobronchitis infections caused by HPIV-I. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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19 pages, 4696 KiB  
Article
Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach
by Thamer H. Albekairi, Abdulrahman Alshammari, Metab Alharbi, Amal F. Alshammary, Muhammad Tahir ul Qamar, Asad Ullah, Muhammad Irfan and Sajjad Ahmad
Vaccines 2022, 10(5), 665; https://doi.org/10.3390/vaccines10050665 - 22 Apr 2022
Cited by 23 | Viewed by 3478
Abstract
Enterobacter hormaechei is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in E. hormaechei and lack of licensed vaccine availability, efforts are required to overcome the antibiotics crisis. In the current research study, [...] Read more.
Enterobacter hormaechei is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in E. hormaechei and lack of licensed vaccine availability, efforts are required to overcome the antibiotics crisis. In the current research study, a multi-epitope-based vaccine against E. hormaechei was designed using reverse vaccinology and immunoinformatic approaches. A total number of 50 strains were analyzed from which the core proteome was extracted. One extracellular (curlin minor subunit CsgB) and two periplasmic membrane proteins (flagellar basal-body rod protein (FlgF) and flagellar basal body P-ring protein (FlgI) were prioritized for B and T-cell epitope prediction. Only three filtered TPGKMDYTS, GADMTPGKM and RLSAESQAT epitopes were used when designing the vaccine construct. The epitopes were linked via GPGPG linkers and EAAAK linker-linked cholera toxin B-subunit adjuvant was used to enhance the immune stimulation efficacy of the vaccine. Docking studies of the vaccine construct with immune cell receptors revealed better interactions, vital for generating proper immune reactions. Docked complexes of vaccine with MHC-I, MHC-II and Tool-like receptor 4 (TLR-4) reported the lowest binding energy of −594.1 kcal/mol, −706.7 kcal/mol, −787.2 kcal/mol, respectively, and were further subjected to molecular dynamic simulations. Net binding free energy calculations also confirmed that the designed vaccine has a strong binding affinity for immune receptors and thus could be a good vaccine candidate for future experimental investigations. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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22 pages, 3302 KiB  
Article
A Vaccine Construction against COVID-19-Associated Mucormycosis Contrived with Immunoinformatics-Based Scavenging of Potential Mucoralean Epitopes
by Muhammad Naveed, Urooj Ali, Mohmed Isaqali Karobari, Naveed Ahmed, Roshan Noor Mohamed, Shahabe Saquib Abullais, Mohammed Abdul Kader, Anand Marya, Pietro Messina and Giuseppe Alessandro Scardina
Vaccines 2022, 10(5), 664; https://doi.org/10.3390/vaccines10050664 - 22 Apr 2022
Cited by 29 | Viewed by 3372
Abstract
Mucormycosis is a group of infections, caused by multiple fungal species, which affect many human organs and is lethal in immunocompromised patients. During the COVID-19 pandemic, the current wave of mucormycosis is a challenge to medical professionals as its effects are multiplied because [...] Read more.
Mucormycosis is a group of infections, caused by multiple fungal species, which affect many human organs and is lethal in immunocompromised patients. During the COVID-19 pandemic, the current wave of mucormycosis is a challenge to medical professionals as its effects are multiplied because of the severity of COVID-19 infection. The variant of concern, Omicron, has been linked to fatal mucormycosis infections in the US and Asia. Consequently, current postdiagnostic treatments of mucormycosis have been rendered unsatisfactory. In this hour of need, a preinfection cure is needed that may prevent lethal infections in immunocompromised individuals. This study proposes a potential vaccine construct targeting mucor and rhizopus species responsible for mucormycosis infections, providing immunoprotection to immunocompromised patients. The vaccine construct, with an antigenicity score of 0.75 covering, on average, 92–98% of the world population, was designed using an immunoinformatics approach. Molecular interactions with major histocompatibility complex-1 (MHC-I), Toll-like receptors-2 (TLR2), and glucose-regulated protein 78 (GRP78), with scores of −896.0, −948.4, and −925.0, respectively, demonstrated its potential to bind with the human immune receptors. It elicited a strong predicted innate and adaptive immune response in the form of helper T (Th) cells, cytotoxic T (TC) cells, B cells, natural killer (NK) cells, and macrophages. The vaccine cloned in the pBR322 vector showed positive amplification, further solidifying its stability and potential. The proposed construct holds a promising approach as the first step towards an antimucormycosis vaccine and may contribute to minimizing postdiagnostic burdens and failures. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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25 pages, 8322 KiB  
Article
Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis
by Roba Attar, Eid A. Alatawi, Faris F. Aba Alkhayl, Khloud Nawaf Alharbi, Khaled S. Allemailem and Ahmad Almatroudi
Vaccines 2022, 10(5), 637; https://doi.org/10.3390/vaccines10050637 - 19 Apr 2022
Cited by 2 | Viewed by 3259
Abstract
Due to the misuse of antibiotics in our daily lives, antimicrobial resistance (AMR) has become a major health problem. Penicillin, the first antibiotic, was used in the 1930s and led to the emergence of AMR. Due to alterations in the microbe’s genome and [...] Read more.
Due to the misuse of antibiotics in our daily lives, antimicrobial resistance (AMR) has become a major health problem. Penicillin, the first antibiotic, was used in the 1930s and led to the emergence of AMR. Due to alterations in the microbe’s genome and the evolution of new resistance mechanisms, antibiotics are losing efficacy against microbes. There are high rates of mortality and morbidity due to antibiotic resistance, so addressing this major health issue requires new approaches. Staphylococcus auricularis is a Gram-positive cocci and is capable of causing opportunistic infections and sepsis. S. auricularis is resistant to several antibiotics and does not currently have a licensed vaccine. In this study, we used bacterial pan-genome analysis (BPGA) to study S. auricularis pan-genome and applied a reverse immunology approach to prioritize vaccine targets against S. auricularis. A total of 15,444 core proteins were identified by BPGA analysis, which were then used to identify good vaccine candidates considering potential vaccine filters. Two vaccine candidates were evaluated for epitope prediction including the superoxide dismutase and gamma-glutamyl transferase protein. The epitope prediction phase involved the prediction of a variety of B-Cell and T-cell epitopes, and the epitopes that met certain criteria, such as antigenicity, immunogenicity, non-allergenicity, and non-toxicity were chosen. A multi-epitopes vaccine construct was then constructed from all the predicted epitopes, and a cholera toxin B-subunit adjuvant was also added to increase vaccine antigenicity. Three-dimensional models of the vaccine were used for downward analyses. Using the best-modeled structure, binding potency was tested with MHC-I, MHC-II and TLR-4 immune cells receptors, proving that the vaccine binds strongly with the receptors. Further, molecular dynamics simulations interpreted strong intermolecular binding between the vaccine and receptors and confirmed the vaccine epitopes exposed to the host immune system. The results support that the vaccine candidate may be capable of eliciting a protective immune response against S. auricularis and may be a promising candidate for experimental in vitro and in vivo studies. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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19 pages, 4803 KiB  
Article
Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against Yersinia pestis through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach
by Azaz Ul Haq, Abbas Khan, Jafar Khan, Shamaila Irum, Yasir Waheed, Sajjad Ahmad, N. Nizam-Uddin, Aqel Albutti, Nasib Zaman, Zahid Hussain, Syed Shujait Ali, Muhammad Waseem, Fariha Kanwal, Dong-Qing Wei and Qian Wang
Vaccines 2021, 9(11), 1327; https://doi.org/10.3390/vaccines9111327 - 15 Nov 2021
Cited by 5 | Viewed by 3940
Abstract
Yersinia pestis is responsible for plague and major pandemics in Asia and Europe. This bacterium has shown resistance to an array of drugs commonly used for the treatment of plague. Therefore, effective therapeutics measurements, such as designing a vaccine that can effectively and [...] Read more.
Yersinia pestis is responsible for plague and major pandemics in Asia and Europe. This bacterium has shown resistance to an array of drugs commonly used for the treatment of plague. Therefore, effective therapeutics measurements, such as designing a vaccine that can effectively and safely prevent Y. pestis infection, are of high interest. To fast-track vaccine development against Yersinia pestis, herein, proteome-wide vaccine target annotation was performed, and structural vaccinology-assisted epitopes were predicted. Among the total 3909 proteins, only 5 (rstB, YPO2385, hmuR, flaA1a, and psaB) were shortlisted as essential vaccine targets. These targets were then subjected to multi-epitope vaccine design using different linkers. EAAK, AAY, and GPGPG as linkers were used to link CTL, HTL, and B-cell epitopes, and an adjuvant (beta defensin) was also added at the N-terminal of the MEVC. Physiochemical characterization, such as determination of the instability index, theoretical pI, half-life, aliphatic index, stability profiling, antigenicity, allergenicity, and hydropathy of the ensemble, showed that the vaccine is highly stable, antigenic, and non-allergenic and produces multiple interactions with immune receptors upon docking. In addition, molecular dynamics simulation confirmed the stable binding and good dynamic properties of the vaccine–TLR complex. Furthermore, in silico and immune simulation of the developed MEVC for Y. pestis showed that the vaccine triggered strong immune response after several doses at different intervals. Neutralization of the antigen was observed at the third day of injection. Conclusively, the vaccine designed here for Y. pestis produces an immune response; however, further immunological testing is needed to unveil its real efficacy. Full article
(This article belongs to the Special Issue Computer and Technology Supported Development of Vaccines)
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