scholarly journals Design of a candidate multi-epitope vaccine against SARS-CoV-2 using reverse vaccinology approach

Author(s):  
Amir Atapour ◽  
Ali Golestan

Abstract Coronavirus 2019 (COVID-19) infection as a global epidemic that is spreading dramatically day to day. Currently, many efforts have been made against COVID-19 through the designing or developing of specific vaccine or drug, worldwide. In this study, we used the bioinformatics approach to design an effective multi-epitope vaccine against COVID-19 based on Spike (S) protein. Here, we employed in silico tools to identify potential T and B cell epitopes from S protein that have the ability to induce cellular and humoral immunity. Then, the peptide sequence of potential T, B cell epitopes and flagellin (as adjuvant molecule) were joined together by suitable linkers to construct of candidate multi-epitope vaccine (MEV). Subsequently, immunological and structural evaluations such as antigenicity, allergenicity, 3D modeling, molecular docking, fast flexibility simulations as well as in silico cloning were performed. Immunological and structural computational data showed that designed MEV potentially has proper capacity for inducing of cellular and humoral immune responses against COVID-19. Based on the preliminary results, in vitro and in vivo experiments are required for validation in the future.

2021 ◽  
Author(s):  
Amir Atapour ◽  
Ali Golestan

Abstract Coronavirus 2019 (COVID-19) infection is a global epidemic that is spreading dramatically from day today. Currently, many efforts have been made against COVID-19 through the designing or developing of specific vaccines or drugs, worldwide. Unfortunately, to date, it has not been successful. Therefore, an effective vaccine against COVID-19 is mandatory. In this study, we used the bioinformatics approach to design an effective multi-epitope vaccine against COVID-19 based on Spike protein. Here, we implemented in silico tools to identify potential T and B cell epitopes that can induce cellular and humoral immunity. Then, the peptide sequence of potential T, B cell epitopes, and flagellin (as an adjuvant molecule) was joined together by suitable linkers to construct of candidate multi-epitope vaccine (MEV). Subsequently, immunological and structural evaluations such as antigenicity, 3D modeling, etc. were performed. In the following, molecular docking of vaccine constructs with Toll-Like Receptors 5 (TLR5), Molecular Dynamics (MD) simulation as well as in silico cloning were carried out. Immunological and structural computational data showed that designed MEV potentially has proper capacity for inducing cellular and humoral immune responses against COVID-19. Based on the preliminary results, in vitro and in vivo experiments are required for validation in the future. Keywords: COVID-19, Vaccine, Reverse Vaccinology, Multi-epitope, Molecular docking, MD Simulation.


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5056 ◽  
Author(s):  
Allan Wee Ren Ng ◽  
Pei Jun Tan ◽  
Winfrey Pui Yee Hoo ◽  
Dek Shen Liew ◽  
Michelle Yee Mun Teo ◽  
...  

Background Somatic point substitution mutations in the KRAS proto-oncogene primarily affect codons 12/13 where glycine is converted into other amino acids, and are highly prevalent in pancreatic, colorectal, and non-small cell lung cancers. These cohorts are non-responsive to anti-EGFR treatments, and are left with non-specific chemotherapy regimens as their sole treatment options. In the past, the development of peptide vaccines for cancer treatment was reported to have poor AT properties when inducing immune responses. Utilization of bioinformatics tools have since become an interesting approach in improving the design of peptide vaccines based on T- and B-cell epitope predictions. Methods In this study, the region spanning exon 2 from the 4th to 18th codon within the peptide sequence of wtKRAS was chosen for sequence manipulation. Mutated G12V and G13D K-ras controls were generated in silico, along with additional single amino acid substitutions flanking the original codon 12/13 mutations. IEDB was used for assessing human and mouse MHC class I/II epitope predictions, as well as linear B-cell epitopes predictions, while RNA secondary structure prediction was performed via CENTROIDFOLD. A scoring and ranking system was established in order to shortlist top mimotopes whereby normalized and reducing weighted scores were assigned to peptide sequences based on seven immunological parameters. Among the top 20 ranked peptide sequences, peptides of three mimotopes were synthesized and subjected to in vitro and in vivo immunoassays. Mice PBMCs were treated in vitro and subjected to cytokine assessment using CBA assay. Thereafter, mice were immunized and sera were subjected to IgG-based ELISA. Results In silico immunogenicity prediction using IEDB tools shortlisted one G12V mimotope (68-V) and two G13D mimotopes (164-D, 224-D) from a total of 1,680 candidates. Shortlisted mimotopes were predicted to promote high MHC-II and -I affinities with optimized B-cell epitopes. CBA assay indicated that: 224-D induced secretions of IL-4, IL-5, IL-10, IL-12p70, and IL-21; 164-D triggered IL-10 and TNF-α; while 68-V showed no immunological responses. Specific-IgG sera titers against mutated K-ras antigens from 164-D immunized Balb/c mice were also elevated post first and second boosters compared to wild-type and G12/G13 controls. Discussion In silico-guided predictions of mutated K-ras T- and B-cell epitopes were successful in identifying two immunogens with high predictive scores, Th-bias cytokine induction and IgG-specific stimulation. Developments of such immunogens are potentially useful for future immunotherapeutic and diagnostic applications against KRAS(+) malignancies, monoclonal antibody production, and various other research and development initiatives.


2021 ◽  
Vol 12 ◽  
Author(s):  
Mingkai Yu ◽  
Yuejie Zhu ◽  
Yujiao Li ◽  
Zhiqiang Chen ◽  
Tong Sha ◽  
...  

All the time, echinococcosis is a global zoonotic disease which seriously endangers public health all over the world. In order to speed up the development process of anti-Echinococcus granulosus vaccine, at the same time, it can also save economic cost. In this study, immunoinformatics tools and molecular docking methods were used to predict and screen the antigen epitopes of Echinococcus granulosus, to design a multi-epitope vaccine containing B- and T-cell epitopes. The multi-epitope vaccine could activate B lymphocytes to produce specific antibodies theoretically, which could protect the human body against Echinococcus granulosus infection. It also could activate T lymphocytes and clear the infected parasites in the body. In this study, four CD8+ T-cell epitopes, three CD4+ T-cell epitopes and four B-cell epitopes of Protein EgTeg were identified by immunoinformatics methods. Meanwhile, three CD8+ T-cell epitopes, two CD4+ T-cell epitopes and four B-cell epitopes of Protein EgFABP1 were identified. We constructed the multi-epitope vaccine using linker proteins. The study based on the traditional methods of antigen epitope prediction, further optimized the prediction results combined with molecular docking technology and improved the precision and accuracy of the results. Finally, in vivo and in vitro experiments had verified that the vaccine designed in this study had good antigenicity and immunogenicity.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samira Sanami ◽  
Fatemeh Azadegan-Dehkordi ◽  
Mahmoud Rafieian-Kopaei ◽  
Majid Salehi ◽  
Maryam Ghasemi-Dehnoo ◽  
...  

AbstractCervical cancer, caused by human papillomavirus (HPV), is the fourth most common type of cancer among women worldwide. While HPV prophylactic vaccines are available, they have no therapeutic effects and do not clear up existing infections. This study aims to design a therapeutic vaccine against cervical cancer using reverse vaccinology. In this study, the E6 and E7 oncoproteins from HPV16 were chosen as the target antigens for epitope prediction. Cytotoxic T lymphocytes (CTL) and helper T lymphocytes (HTL) epitopes were predicted, and the best epitopes were selected based on antigenicity, allergenicity, and toxicity. The final vaccine construct was composed of the selected epitopes, along with the appropriate adjuvant and linkers. The multi-epitope vaccine was evaluated in terms of physicochemical properties, antigenicity, and allergenicity. The tertiary structure of the vaccine construct was predicted. Furthermore, several analyses were also carried out, including molecular docking, molecular dynamics (MD) simulation, and in silico cloning of the vaccine construct. The results showed that the final proposed vaccine could be considered an effective therapeutic vaccine for HPV; however, in vitro and in vivo experiments are required to validate the efficacy of this vaccine candidate.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3017-3017
Author(s):  
Chiara Tarantelli ◽  
Eugenio Gaudio ◽  
Petra Hillmann ◽  
Filippo Spriano ◽  
Ivo Kwee ◽  
...  

Abstract Background. The PI3K/AKT/mTOR pathway is an important therapeutic target in lymphomas. PQR309 is a dual PI3K/mTOR inhibitor that has shown in vitroanti-lymphoma activity (Tarantelli et al, ASH2015) and is in phase 2 trial (NCT02249429, , NCT02723877, NCT02669511). PQR620 is a novel mTORC1/2 inhibitor that has shown preclinical activity in solid tumor models (Beaufils et al, AACR 2016). Here, we present the in vitro and in vivo anti-lymphoma activity of PQR620 as single agent and also the in vivo results of PQR620 or PQR309 containing combinations with the BCL2 inhibitor venetoclax. Materials and Methods. The drug concentration causing 50% inhibition of cell proliferation (IC50) was obtained in lymphoma cell lines [diffuse large B cell lymphoma (DLBCL), no.=26; mantle cell lymphoma (MCL), no.=8; anaplastic large T-cell lymphoma, no.=5; others, no=5] exposed to increasing doses of PQR620 for 72h using a Tecan D300e Digital Dispenser on 384well plates. For in vivo experiments, NOD-Scid (NOD.CB17-Prkdcscid/J) mice were subcutaneously inoculated with 10 x106 (RIVA) or with 5 x106(SU-DHL-6) cells. Results. PQR620 had a median IC50 of 250 nM (95%CI, 200-269 nM) when tested on 44 lymphoma cell lines. Activity was higher in B cell (no.=36) than in T cell tumors (no.=8) (median IC50s: 250 nM vs 450 nM; P=0.002). At 72h, anti-tumor activityof PQR620 was mostly cytostatic and apoptosis induction was seen only in 6/44 cell lines (13%), Sensitivity to PQR620 or apoptosis induction did not differ between DLBCL and MCL, and they were not affected by the DLBCL cell of origin, by TP53 status or by the presence of MYC or BCL2 translocations. The activity of PQR620 as single agent underwent in vivo evaluation in two DLBCL models, the germinal center B cell type DLBCL (GCB-DLBCL) SU-DHL-6 and the acivated B cell-like DLBCL (ABC-DLBCL) RIVA. Treatments with PQR620 (100mg/kg dose per day, Qdx7/w) started with 100-150 mm3 tumors and were carried for 14 (SU-DHL-6) or 21 days (RIVA). In both models, PQR620 determined a 2-fold decrease of the tumor volumes in comparison with control, with significant differences in both SU-DHL-6 (D7, D9, D11, D14; P < 0.005) and RIVA (D14, D16, D19, D21; P < 0.005). Based on the previously reported synergy between the dual PI3K/mTOR inhibitor PQR309 and venetoclax (Tarantelli et al, ASH 2015), we evaluated the combination of the PQR620 or PQR309 with the BCL2 inhibitor venetoclax (100 mg/kg, Qdx7/w) in the SU-DHL-6 model. Both the venetoclax combination with the dual PI3K/mTOR inhibitor and the venetoclax combination with mTORC1/2 inhibitor were superior to the compounds given as single agents, leading to the eradication of the xenografts. The combination of PQR620 with venetoclax showed highly significant differences either versus control or single agents during all days of the experiment (D4, D7, D9, D11, D14; P < 0.001). Similarly, the combination of PQR309 with venetoclax showed highly significant differences versus venetoclax (D7, D9, D11, D14; P < 0.001) and PQR309 (D7, D9, D11; P < 0.005) alone. Conclusions. The novel mTORC1/2 inhibitor PQR620 had in vitro and in vivo anti-lymphoma activity as single agent. In vivo experiments showed that both PQR620 and the dual PI3K/mTOR inhibitor PQR309 can strongly benefit from the combination with the BCL2 inhibitor venetoclax. Disclosures Hillmann: PIQUR Therapeutics AG: Employment. Fabbro:PIQUR Therapeutics AG: Employment. Cmiljanovic:PIQUR Therapeutics AG: Employment, Membership on an entity's Board of Directors or advisory committees.


Author(s):  
Neetu Agrawal ◽  
Ahsas Goyal

: Due to the extremely contagious nature of SARS-COV-2, it presents a significant threat to humans worldwide. A plethora of studies are going on all over the world to discover the drug to fight SARS-COV-2. One of the most promising targets is RNA-dependent RNA polymerase (RdRp), responsible for viral RNA replication in host cells. Since RdRp is a viral enzyme with no host cell homologs, it allows the development of selective SARS-COV-2 RdRp inhibitors. A variety of studies used in silico approaches for virtual screening, molecular docking, and repurposing of already existing drugs and phytochemicals against SARS-COV-2 RdRp. This review focuses on collating compounds possessing the potential to inhibit SARS-COV-2 RdRp based on in silico studies to give medicinal chemists food for thought so that the existing drugs can be repurposed for the control and treatment of ongoing COVID-19 pandemic after performing in vitro and in vivo experiments.


Author(s):  
Neetu Agrawal ◽  
Shilpi Pathak ◽  
Ahsas Goyal

: The entire world has been in a battle against the COVID-19 pandemic since its first appearance in December 2019. Thus researchers are desperately working to find an effective and safe therapeutic agent for its treatment. The multifunctional coronavirus enzyme papain-like protease (PLpro) is a potential target for drug discovery to combat the ongoing pandemic responsible for cleavage of the polypeptide, deISGylation, and suppression of host immune response. The present review collates the in silico studies performed on various FDA-approved drugs, chemical compounds, and phytochemicals from various drug databases and represents the compounds possessing the potential to inhibit PLpro. Thus this review can provide quick access to a potential candidate to medicinal chemists to perform in vitro and in vivo experiments who are thriving to find the effective agents for the treatment of COVID-19.


2021 ◽  
Author(s):  
Ravi Deval ◽  
Ayushi Saxena ◽  
Zeba Mueed ◽  
Dibyabhaba Pradhan ◽  
Pankaj Kumar Rai

BACKGROUND SARS-CoV-2, belonging to the Coronaviridae family, is a novel RNA virus, known for causing fatal disease in humans called COVID-19. Researchers all around the world are keen on developing a precise treatment or vaccine against this deadly disease. OBJECTIVE The main objective of this paper is to design a novel multi-epitope vaccine candidate against SARS-CoV-2 using immunoinformatics tools. METHODS A consensus sequence was generated from various genomes of SARS-Cov-2 available from various countries of the outbreak at the ViPR database using JalView software. T cell and B cell epitopes were predicted by restricting them to certain HLA alleles using various servers (nHLApred, NetMHCIIpan v.3.1, ABCpred) and were validated using IEDB tools. Using these epitopes and adjuvant, a multi-epitope vaccine was constructed in-silicoand was later subjected to allergenicity, antigenicity and physicochemical properties profiling along with identification of conformational B-cell epitopes. The designed vaccine was evaluated via codon optimization by the Jcat server and finally, it’s in-silicoexpression was done in pET-28a(+) vector using snap-gene software. RESULTS A total of 18 epitopes (both T and B cell) were predicted that constituted vaccine construct along with adjuvant and end tag. Vaccine construct was validated and its best structure model was successfully docked with human Toll-like receptors. In-silico expression of the designed vector was also seen in pET-28a(+) plasmid. CONCLUSIONS The designed novel vaccine candidate has been validated in-silico to elicit robust immune responses hence; it can be used as a potential model for further development of multi-epitope vaccines in the laboratory.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rahul Sharma ◽  
Vikrant Singh Rajput ◽  
Salma Jamal ◽  
Abhinav Grover ◽  
Sonam Grover

AbstractTuberculosis is one the oldest known affliction of mankind caused by the pathogen Mycobacterium tuberculosis. Till date, there is no absolute single treatment available to deal with the pathogen, which has acquired a great potential to develop drug resistance rapidly. BCG is the only anti-tuberculosis vaccine available till date which displays limited global efficacy due to genetic variation and concurrent pathogen infections. Extracellular vesicles or exosomes vesicle (EVs) lie at the frontier cellular talk between pathogen and the host, and therefore play a significant role in establishing pathogenesis. In the present study, an in-silico approach has been adopted to construct a multi-epitope vaccine from selected immunogenic EVs proteins to elicit a cellular as well as a humoral immune response. Our designed vaccine has wide population coverage and can effectively compensate for the genetic variation among different populations. For maximum efficacy and minimum adverse effects possibilities the antigenic, non-allergenic and non-toxic B-cell, HTL and CTL epitopes from experimentally proven EVs proteins were selected for the vaccine construct. TLR4 agonist RpfE served as an adjuvant for the vaccine construct. The vaccine construct structure was modelled, refined and docked on TLR4 immune receptor. The designed vaccine construct displayed safe usage and exhibits a high probability to elicit the critical immune regulators, like B cells, T-cells and memory cells as displayed by the in-silico immunization assays. Therefore, it can be further corroborated using in vitro and in vivo assays to fulfil the global need for a more efficacious anti-tuberculosis vaccine.


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