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

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.

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Core-Proteomics-Based Annotation of Antigenic Targets and Reverse-Vaccinology-Assisted Design of Ensemble Immunogen against the Emerging Nosocomial Infection-Causing Bacterium Elizabethkingia meningoseptica

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph19010194 ◽

2021 ◽

Vol 19 (1) ◽

pp. 194

Author(s):

Muhammad Idrees ◽

Muhammad Yasir Noorani ◽

Kalim Ullah Altaf ◽

Eid A. Alatawi ◽

Faris F. Aba Alkhayl ◽

...

Keyword(s):

Immune Response ◽

Vaccine Development ◽

Dynamic Properties ◽

Dynamics Simulation ◽

Strong Immune Response ◽

Physiochemical Properties ◽

Hospital Acquired Infection ◽

Elizabethkingia Meningoseptica ◽

Structural Vaccinology ◽

Hospital Acquired

Elizabethkingia meningoseptica is a ubiquitous Gram-negative emerging pathogen that causes hospital-acquired infection in both immunocompromised and immunocompetent patients. It is a multi-drug-resistant bacterium; therefore, an effective subunit immunogenic candidate is of great interest to encounter the pathogenesis of this pathogen. A protein-wide annotation of immunogenic targets was performed to fast-track the vaccine development against this pathogen, and structural-vaccinology-assisted epitopes were predicted. Among the total proteins, only three, A0A1T3FLU2, A0A1T3INK9, and A0A1V3U124, were shortlisted, which are the essential vaccine targets and were subjected to immune epitope mapping. The linkers EAAK, AAY, and GPGPG were used to link CTL, HTL, and B-cell epitopes and an adjuvant was also added at the N-terminal to design a multi-epitope immunogenic construct (MEIC). The computationally predicted physiochemical properties of the ensemble immunogen reported a highly antigenic nature and produced multiple interactions with immune receptors. In addition, the molecular dynamics simulation confirmed stable binding and good dynamic properties. Furthermore, the computationally modeled immune response proposed that the immunogen triggered a strong immune response after several doses at different intervals. Neutralization of the antigen was observed on the 3rd day of injection. Conclusively, the immunogenic construct produces protection against Elizabethkingia meningoseptica; however, further immunological testing is needed to unveil its real efficacy.

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Recombinant Antigens Based on Non-Glycosylated Regions from RBD SARS-CoV-2 as Potential Vaccine Candidates against COVID-19

Vaccines ◽

10.3390/vaccines9080928 ◽

2021 ◽

Vol 9 (8) ◽

pp. 928

Author(s):

Leandro Núñez-Muñoz ◽

Gabriel Marcelino-Pérez ◽

Berenice Calderón-Pérez ◽

Miriam Pérez-Saldívar ◽

Karla Acosta-Virgen ◽

...

Keyword(s):

Immune Response ◽

Neutralizing Antibodies ◽

Vaccine Development ◽

Polyclonal Antibodies ◽

Igg Antibodies ◽

Mice Model ◽

Strong Immune Response ◽

Recombinant Antigens ◽

Glycosylation Sites ◽

Potential Vaccine

The Receptor-Binding Domain (RBD) of the Spike (S) protein from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has glycosylation sites which can limit the production of reliable antigens expressed in prokaryotic platforms, due to glycan-mediated evasion of the host immune response. However, protein regions without glycosylated residues capable of inducing neutralizing antibodies could be useful for antigen production in systems that do not carry the glycosylation machinery. To test this hypothesis, the potential antigens NG06 and NG19, located within the non-glycosylated S-RBD region, were selected and expressed in Escherichia coli, purified by FPLC and employed to determine their immunogenic potential through detection of antibodies in serum from immunized rabbits, mice, and COVID-19 patients. IgG antibodies from sera of COVID-19-recovered patients detected the recombinant antigens NG06 and NG19 (A450 nm = 0.80 ± 0.33; 1.13 ± 0.33; and 0.11 ± 0.08 for and negatives controls, respectively). Also, the purified antigens were able to raise polyclonal antibodies in animal models evoking a strong immune response with neutralizing activity in mice model. This research highlights the usefulness of antigens based on the non-N-glycosylated region of RBD from SARS-CoV-2 for candidate vaccine development.

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Interactions between Yersinia pestis V-antigen (LcrV) and human Toll-like receptor 2 (TLR2) in a modelled protein complex and potential mechanistic insights

BMC Immunology ◽

10.1186/s12865-019-0329-5 ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Tiandi Wei ◽

Jing Gong ◽

Guojing Qu ◽

Mingyu Wang ◽

Hai Xu

Keyword(s):

Immune Response ◽

Yersinia Pestis ◽

Mechanistic Model ◽

White Blood Cells ◽

Dynamics Simulation ◽

Structure Model ◽

Toll Like Receptor ◽

Toll Like Receptor 2 ◽

V Antigen

Abstract Background Yersinia pestis, the etiological pathogen of plague, is capable of repressing the immune response of white blood cells to evade phagocytosis. The V-antigen (LcrV) was found to be involved in this process by binding to human Toll-like Receptor 2 (TLR2). The detailed mechanism behind this LcrV and TLR2 mediated immune response repression, however, is yet to be fully elucidated due to the lack of structural information. Results In this work, with protein structure modelling, we were able to construct a structure model of the heterotetramer of Y. pestis LcrV and human TLR2. Molecular dynamics simulation suggests the stability of this structure in aquatic environment. The LcrV model has a dumbbell-like structure with two globule domains (G1 at N-terminus and G2 away from membrane) connected with a coiled-coil linker (CCL) domain. The two horseshoe-shape TLR2 subunits form a V-shape structure, are not in direct contact with each other, and are held together by the LcrV homodimer. In this structure model, both the G1 and CCL domains are involved in the formation of LcrV homodimer, while all three domains are involved in LcrV-TLR2 binding. A mechanistic model was proposed based on this heterotetrameric structure model: The LcrV homodimer separates the TLR2 subunits to inhibit the dimerization of TLR2 and subsequent signal transfer for immune response; while LcrV could also inhibit the formation of heterodimers of TLR2 with other TLRs, and leads to immune response repression. Conclusions A heterotetrameric structure of Y. pestis LcrV and human TLR2 was modelled in this work. Analysis of this modelled structure showed its stability in aquatic environments and the role of LcrV domains and residues in protein-protein interaction. A mechanistic model for the role of LcrV in Y. pestis pathogenesis is raised based on this heterotetrameric structure model. This work provides a hypothesis of LcrV function, with which further experimental validation may elucidate the role of LcrV in human immune response repression.

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Chimeric Vaccines Designed by Immunoinformatics-Activated Polyfunctional and Memory T Cells That Trigger Protection against Experimental Visceral Leishmaniasis

Vaccines ◽

10.3390/vaccines8020252 ◽

2020 ◽

Vol 8 (2) ◽

pp. 252 ◽

Cited By ~ 2

Author(s):

Rory Cristiane Fortes De Brito ◽

Jeronimo Conceição Ruiz ◽

Jamille Mirelle de Oliveira Cardoso ◽

Thais Lopes Valentim Di Paschoale Ostolin ◽

Levi Eduardo Soares Reis ◽

...

Keyword(s):

Immune Response ◽

T Cells ◽

Visceral Leishmaniasis ◽

Vaccine Development ◽

Memory T Cells ◽

Parasite Burden ◽

Effector Memory ◽

Potential Candidate ◽

Protective Mechanisms ◽

Strong Immune Response

Many vaccine candidates against visceral leishmaniasis (VL) have been proposed; however, to date, none of them have been efficacious for the human or canine disease. On this basis, the design of leishmaniasis vaccines has been constantly changing, and the use of approaches to select specific epitopes seems to be crucial in this scenario. The ability to predict T cell-specific epitopes makes immunoinformatics an even more necessary approach, as in VL an efficient immune response against the parasite is triggered by T lymphocytes in response to Leishmania spp. immunogenic antigens. Moreover, the success of vaccines depends on the capacity to generate long-lasting memory and polyfunctional cells that are able to eliminate the parasite. In this sense, our study used a combination of different approaches to develop potential chimera candidate vaccines against VL. The first point was to identify the most immunogenic epitopes of Leishmania infantum proteins and construct chimeras composed of Major histocompatibility complex (MHC) class I and II epitopes. For this, we used immunoinformatics features. Following this, we validated these chimeras in a murine model in a thorough memory study and multifunctionality of T cells that contribute to a better elucidation of the immunological protective mechanisms of polyepitope vaccines (chimera A and B) using multicolor flow cytometry. Our results showed that in silico-designed chimeras can elicit polyfunctional T cells producing T helper (Th)1 cytokines, a strong immune response against Leishmania antigen, and the generation of central and effector memory T cells in the spleen cells of vaccinated animals that was able to reduce the parasite burden in this organ. These findings contribute two potential candidate vaccines against VL that can be used in further studies, and help in this complex field of vaccine development against this challenging parasite.

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Immune Response to COVID-19: Can We Benefit from the SARS-CoV and MERS-CoV Pandemic Experience?

Pathogens ◽

10.3390/pathogens9090739 ◽

2020 ◽

Vol 9 (9) ◽

pp. 739

Author(s):

Emilia Sinderewicz ◽

Wioleta Czelejewska ◽

Katarzyna Jezierska-Wozniak ◽

Joanna Staszkiewicz-Chodor ◽

Wojciech Maksymowicz

Keyword(s):

Immune Response ◽

T Cell ◽

Vaccine Development ◽

T Cell Response ◽

High Fatality Rate ◽

Scientific World ◽

Specific Antibody Production ◽

Potential Vaccine ◽

Cellular Immune

The global range and high fatality rate of the newest human coronavirus (HCoV) pandemic has made SARS-CoV-2 the focus of the scientific world. Next-generation sequencing of the viral genome and a phylogenetic analysis have shown the high homology of SARS-CoV-2 to other HCoVs that have led to local epidemics in the past. The experience acquired in SARS and MERS epidemics may prove useful in understanding the SARS-CoV-2 pathomechanism and lead to effective treatment and potential vaccine development. This study summarizes the immune response to SARS-CoV, MERS-CoV, and SARS-CoV-2 and focuses on T cell response, humoral immunity, and complement system activation in different stages of HCoVs infections. The study also presents the quantity and frequency of T cell responses, particularly CD4+ and CD8+; the profile of cytokine production and secretion; and its relation to T cell type, disease severity, and utility in prognostics of the course of SARS, MERS, and COVID-19 outbreaks. The role of interferons in the therapy of these infections is also discussed. Moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural HCoVs proteins and their utility in the development of a vaccine against SARS, MERS, and COVID-19 has been updated.

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Development of a Conserved Chimeric Vaccine for Induction of Strong Immune Response against Staphylococcus aureus Using Immunoinformatics Approaches

Vaccines ◽

10.3390/vaccines9091038 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1038

Author(s):

Rahul Chatterjee ◽

Panchanan Sahoo ◽

Soumya Ranjan Mahapatra ◽

Jyotirmayee Dey ◽

Mrinmoy Ghosh ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Immune Response ◽

Multidrug Resistant ◽

Host Cells ◽

Dynamics Simulation ◽

Population Coverage ◽

Strong Immune Response ◽

Chimeric Vaccine

Staphylococcus aureus is one of the most notorious Gram-positive bacteria with a very high mortality rate. The WHO has listed S. aureus as one of the ESKAPE pathogens requiring urgent research and development efforts to fight against it. Yet there is a major layback in the advancement of effective vaccines against this multidrug-resistant pathogen. SdrD and SdrE proteins are attractive immunogen candidates as they are conserved among all the strains and contribute specifically to bacterial adherence to the host cells. Furthermore, these proteins are predicted to be highly antigenic and essential for pathogen survival. Therefore, in this study, using the immunoinformatics approach, a novel vaccine candidate was constructed using highly immunogenic conserved T-cell and B-cell epitopes along with specific linkers, adjuvants, and consequently modeled for docking with human Toll-like receptor 2. Additionally, physicochemical properties, secondary structure, disulphide engineering, and population coverage analysis were also analyzed for the vaccine. The constructed vaccine showed good results of worldwide population coverage and a promising immune response. For evaluation of the stability of the vaccine-TLR-2 docked complex, a molecular dynamics simulation was performed. The constructed vaccine was subjected to in silico immune simulations by C-ImmSim and Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells, and INF-γ. Lastly, upon cloning, the vaccine protein was reverse transcribed into a DNA sequence and cloned into a pET28a (+) vector to ensure translational potency and microbial expression. The overall results of the study showed that the designed novel chimeric vaccine can simultaneously elicit humoral and cell-mediated immune responses and is a reliable construct for subsequent in vivo and in vitro studies against the pathogen.

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New highly antigenic linear B cell epitope peptides from PvAMA-1 as potential vaccine candidates

PLoS ONE ◽

10.1371/journal.pone.0258637 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0258637

Author(s):

Raianna F. Fantin ◽

Vanessa G. Fraga ◽

Camila A. Lopes ◽

Isabella C. de Azevedo ◽

João L. Reis-Cunha ◽

...

Keyword(s):

Immune Response ◽

B Cell ◽

Structure Prediction ◽

Markov Models ◽

Vaccine Development ◽

Secondary Structure Prediction ◽

Cell Epitope ◽

B Cell Epitope ◽

Potential Vaccine ◽

Vaccine Approach

Peptide-based vaccines have demonstrated to be an important way to induce long-lived immune responses and, therefore, a promising strategy in the rational of vaccine development. As to malaria, among the classic vaccine targets, the Apical membrane antigen (AMA-1) was proven to have important B cell epitopes that can induce specific immune response and, hence, became key players for a vaccine approach. The peptides selection was carried out using a bioinformatic approach based on Hidden Markov Models profiles of known antigens and propensity scale methods based on hydrophilicity and secondary structure prediction. The antigenicity of the selected B-cell peptides was assessed by multiple serological assays using sera from acute P.vivax infected subjects. The synthetic peptides were recognized by 45.5%, 48.7% and 32.2% of infected subjects for peptides I, II and III respectively. Moreover, when synthetized together (tripeptide), the reactivity increases up to 62%, which is comparable to the reactivity found against the whole protein PvAMA-1 (57%). Furthermore, IgG reactivity against the tripeptide after depletion was reduced by 42%, indicating that these epitopes may be responsible for a considerable part of the protein immunogenicity. These results represent an excellent perspective regarding future chimeric vaccine constructions that may come to contemplate several targets with the potential to generate the robust and protective immune response that a vivax malaria vaccine needs to succeed.

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Immunoinformatics and System Biology Approaches for Potential Vaccine Candidates Against Burkholderia Pseudomallei

10.21203/rs.3.rs-38222/v1 ◽

2020 ◽

Author(s):

Asfiha Tarannum ◽

Md. Arif Khan ◽

Ahmad S. Sirajee ◽

Mahmuda Yasmin ◽

Chowdhury R. Ahsan

Keyword(s):

System Biology ◽

Burkholderia Pseudomallei ◽

Vaccine Development ◽

Cell Epitope ◽

Epitope Prediction ◽

Human Leukocyte ◽

Protein Molecule ◽

Dynamics Simulation ◽

Vaccine Candidates ◽

Potential Vaccine

Abstract Background: Burkholderia pseudomallei, an intracellular gram-negative bacterium, is the causative agent of melioidosis. It is a highly infectious disease that usually involves the lungs of humans as well as animals endemic in South-East Asia and Northern Australia. At present, we do not have any vaccine or treatment scheme at our disposal which is absolutely effective against this disease. There have been few advances in the development of vaccines against intracellular bacterial pathogens, making vaccine development against intracellular pathogen a more challenging arena. So, we opted for in-silico methods of drug designing intending to combat B. pseudomallei.Results: The whole proteome of B. pseudomallei was analyzed for determining immunogenic proteins. Combining B-cell and T-cell epitope prediction studies, the sequence ETAAADALY was considered as the most potential epitope for both T and B cells, followed by molecular docking against an MHC (major histocompatibility complex) Class I molecule, HLA-A*26:01 (human leukocyte antigens encoded by the HLA-A locus). Apart from epitope prediction, hydrogen bond study and target site analysis were carried out which concludes that ARG 237, ALA 234, ARG 236, ARG 262, GLN 226, ASP229, VAL 230, VAL 239, GLY 258, LEU259, ASN 225, and ILE 254 consist the best active site of the protein molecule. The study of the bacterial antigenic protein model's secondary structure and stereochemical properties provided an insight into the protein's stability as our epitope of choice. The post docking interactions were further subjected to molecular dynamics simulation and the system biology approach for validation. Conclusion: The goal of our endeavor is to delve into an integrative Immunoinformatics study combined with the system biology logistics of B. pseudomallei to detect potential vaccine candidates against this pathogen as well as providing a depiction of the bacterial immunome that could be insightful for vaccine generation in the future.

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HIV-1 Accessory Proteins: Which one is Potentially Effective in Diagnosis and Vaccine Development?

Protein and Peptide Letters ◽

10.2174/0929866528999201231213610 ◽

2020 ◽

Vol 28 ◽

Author(s):

Alireza Milani ◽

Kazem Baesi ◽

Elnaz Agi ◽

Ghazal Marouf ◽

Maryam Ahmadi ◽

...

Keyword(s):

Immune Response ◽

Vaccine Development ◽

Treated Group ◽

Vaccine Antigen ◽

Accessory Proteins ◽

Serological Method ◽

Th2 Immune Response ◽

Untreated Individuals ◽

Immunogenic Properties ◽

Hiv 1

Background:: The combination antiretroviral therapy (cART) could increase the number of circulating naive CD4 T lymphocytes, but was not able to eradicate human immunodeficiency virus-1 (HIV-1) infection. Objective:: Thus, induction of strong immune responses is important for control of HIV-1 infection. Furthermore, a simple and perfect serological method is required to detect virus in untreated-, treated- and drug resistant- HIV-1 infected individuals. Methods:: This study was conducted to assess and compare immunogenic properties of Nef, Vif, Vpr and Vpu accessory proteins as an antigen candidate in mice and their diagnostic importance in human as a biomarker. Results:: Our data showed that in mice, all heterologous prime/ boost regimens were more potent than homologous prime/ boost regimens in eliciting Th1 response and Granzyme B secretion as CTL activity. Moreover, the Nef, Vpu and Vif proteins could significantly increase Th1 immune response. In contrast, the Vpr protein could considerably induce Th2 immune response. On the other hand, among four accessory proteins, HIV-1 Vpu could significantly detect treated group from untreated group as a possible biomarker in human. Conclusion:: Generally, among accessory proteins, Nef, Vpu and Vif antigens were potentially more suitable vaccine antigen candidates than Vpr antigen. Human antibodies against all these proteins were higher in HIV-1 different groups than healthy group. Among them, Vpu was known as a potent antigen in diagnosis of treated from untreated individuals. The potency of accessory proteins as an antigen candidate in an animal model and a human cohort study are underway.

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Integrated IEW-TOPSIS and Fire Dynamics Simulation for Agent-Based Evacuation Modeling in Industrial Safety

Safety ◽

10.3390/safety7020047 ◽

2021 ◽

Vol 7 (2) ◽

pp. 47

Author(s):

Wattana Chanthakhot ◽

Kasin Ransikarbum

Keyword(s):

Emergency Evacuation ◽

Industrial Sector ◽

Industrial Safety ◽

Dynamics Simulation ◽

Entropy Weight ◽

Fire Dynamics ◽

Evacuation Simulation ◽

Evacuation Modeling ◽

Agent Based ◽

The Impact

Emergency events in the industrial sector have been increasingly reported during the past decade. However, studies that focus on emergency evacuation to improve industrial safety are still scarce. Existing evacuation-related studies also lack a perspective of fire assembly point’s analysis. In this research, location of assembly points is analyzed using the multi-criteria decision analysis (MCDA) technique based on the integrated information entropy weight (IEW) and techniques for order preference by similarity to ideal solution (TOPSIS) to support the fire evacuation plan. Next, we propose a novel simulation model that integrates fire dynamics simulation coupled with agent-based evacuation simulation to evaluate the impact of smoke and visibility from fire on evacuee behavior. Factors related to agent and building characteristics are examined for fire perception of evacuees, evacuees with physical disabilities, escape door width, fire location, and occupancy density. Then, the proposed model is applied to a case study of a home appliance factory in Chachoengsao, Thailand. Finally, results for the total evacuation time and the number of remaining occupants are statistically examined to suggest proper evacuation planning.

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