Immunoinformatics aided designing of a next generation poly-epitope vaccine against uropathogenic Escherichia coli to combat urinary tract infections

Article

Author: Waseem, Maaz ; Ali, Amjad ; Shahwar Awan, Hayeqa ; Ishaq, Zaara ; Ullah, Nimat ; Zaheer, Tahreem ; AlAsmari, Fawaz ; AlAsmari, Abdullah F.

Urinary tract infections (UTIs) are the second most prevalent bacterial infections and uropathogenic Escherichia coli (UPEC) stands among the primary causative agents of UTIs. The usage of antibiotics is the routine therapy being used in various countries to treat UTIs but becoming ineffective because of increasing antibiotic resistance among UPEC strains. Thus, there must be the development of some alternative treatment strategies such as vaccine development against UPEC. In the following study, pan-genomics along with reverse vaccinology approaches is used under the framework of bioinformatics for the identification of core putative vaccine candidates, employing 307 UPEC genomes (complete and draft), available publicly. A total of nine T-cell epitopes (derived from B-cells) of both MHC classes (I and II), were prioritized among three potential protein candidates. These epitopes were then docked together by using linkers (GPGPG and AAY) and an adjuvant (Cholera Toxin B) to form a poly-valent vaccine construct. The chimeric vaccine construct was undergone by molecular modelling, further refinement and energy minimization. We predicted positive results of the vaccine construct in immune simulations with significantly high levels of immune cells. The protein-protein docking analysis of vaccine construct with toll-like receptors predicted efficient binding, which was further validated by molecular dynamics simulation of vaccine construct with TLR-2 and TLR-4 at 120 ns, resulting in stable complexes' conformation throughout the simulation run. Overall, the vaccine construct demonstrated positive antigenic response. In future, this chimeric vaccine construct or the identified epitopes could be experimentally validated for the development of UPEC vaccines against UTIs.Communicated by Ramaswamy H. Sarma.

06 Dec 2024·Journal of Biomolecular Structure and Dynamics

Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins

Article

Author: Alizadeh, Akram ; Irfan, Muhammad ; Ghatrehsamani, Mahdi ; Alharbi, Metab ; Ahmad, Sajjad ; Sanami, Samira ; Tahmasebian, Shahram ; Alasmari, Abdullah F. ; Pashapour Hajialilou, Maryam ; Pazoki-Toroudi, Hamidreza ; Shojaeian, Ali ; Nazarian, Shahin

In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.

06 Dec 2024·Journal of Biomolecular Structure and Dynamics

Designing a novel multi-epitopes pan-vaccine against SARS-CoV-2 and seasonal influenza: in silico and immunoinformatics approach

Article

Author: Moradi, Jale ; Shahlaei, Mohsen ; Abiri, Ramin ; Hossainpour, Hadi ; Moradi, Sajad ; Dashtbin, Shirin ; Alvandi, Amirhooshang ; Motamedi, Hamid ; Fathollahi, Matin

The merger of COVID-19 and seasonal influenza infections is considered a potentially serious threat to public health. These two viral agents can cause extensive and severe lower and upper respiratory tract infections with lung damage with host factors. Today, the development of vaccination has been shown to reduce the risk of hospitalization and mortality from the COVID-19 virus and influenza epidemics. Therefore, this study contributes to an immunoinformatics approach to producing a vaccine that can elicit strong and specific immune responses against COVID-19 and influenza A and B viruses. The NCBI, GISAID, and Uniprot databases were used to retrieve sequences. Linear B cell, Cytotoxic T lymphocyte, and Helper T lymphocyte epitopes were predicted using the online servers. Population coverage of MHC I epitopes worldwide for SARS-CoV-2, Influenza virus H3N2, H3N2, and Yamagata/Victoria were 99.93%, 68.67%, 68.38%, and 85.45%, respectively. Candidate epitopes were linked by GGGGS, GPGPG, and KK linkers. Different epitopes were permutated several times to form different peptides and then screened for antigenicity, allergenicity, and toxicity. The vaccine construct was analyzed for physicochemical properties, conformational B-cell epitopes, interaction with Toll-like receptors, and IFN-gamma-induced. Immune stimulation response of final construct was evaluated using C-IMMSIM. Eventually, the final construct sequence was codon-optimized for Escherichia coli K12 and Homo sapiens to design a multi-epitope vaccine and mRNA vaccine. In conclusion, due to the variable nature of SARS-CoV-2 and influenza proteins, the design of a multi-epitope vaccine can protect against all their standard variants, but laboratory validation is required.Communicated by Ramaswamy H. Sarma.

100 Deals associated with Leishmania multi-epitope vaccine(Shiraz University of Medical Sciences)

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Indication	Highest Phase	Country/Location	Organization	Date
Leishmaniasis	Preclinical	IR	Shiraz University of Medical Sciences	27 Oct 2022

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Leishmania multi-epitope vaccine(Shiraz University of Medical Sciences)

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