Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches

Aslam, Sidra; Ahmad, Sajjad; Fatima, Nosheen; Ashfaq, Usman Ali; Shahid, Farah; Rehman, Abdur; Qamar, Muhammad Tahir ul; Alatawi, Eid A.; Alshabrmi, Fahad M.; Allemailem, Khaled S.

doi:10.3390/biology10100997

Cited by 31 publications

(19 citation statements)

References 95 publications

(118 reference statements)

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“…The EAAAK linker is a rigid linker that, due to its helix formation properties, helped improve the immunogenic properties 43 , 67 . AAY, GPGPG, and KK linkers are typically made up of flexible and hydrophilic amino acids, which could help to prevent domain disruption 68 .…”

Section: Discussionmentioning

confidence: 99%

Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach

Alizadeh

Amini‐Khoei

Tahmasebian

et al. 2022

Sci Rep

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Ebola virus (EBOV) is a dangerous zoonotic infectious disease. To date, more than 25 EBOV outbreaks have been documented, the majority of which have occurred in Central Africa. The rVSVG-ZEBOV-GP vaccine (ERVEBO), a live attenuated vaccine, has been approved by the US Food and Drug Administration (FDA) to combat EBOV. Because of the several drawbacks of live attenuated vaccines, multi-epitope vaccines probably appear to be safer than live attenuated vaccines. In this work, we employed immunoinformatics tools to design a multi-epitope vaccine against EBOV. We collected sequences of VP35, VP24, VP30, VP40, GP, and NP proteins from the NCBI database. T-cell and linear B-cell epitopes from target proteins were identified and tested for antigenicity, toxicity, allergenicity, and conservancy. The selected epitopes were then linked together in the vaccine's primary structure using appropriate linkers, and the 50S ribosomal L7/L12 (Locus RL7 MYCTU) sequence was added as an adjuvant to the vaccine construct's N-terminal. The physicochemical, antigenicity, and allergenicity parameters of the vaccine were all found to be satisfactory. The 3D model of the vaccine was predicted, refined, and validated. The vaccine construct had a stable and strong interaction with toll-like receptor 4 (TLR4) based on molecular docking and molecular dynamic simulation (MD) analysis. The results of codon optimization and in silico cloning revealed that the proposed vaccine was highly expressed in Escherichia coli (E. coli). The findings of this study are promising; however, experimental validations should be carried out to confirm these findings.

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Section: Discussionmentioning

confidence: 99%

Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach

Alizadeh

Amini‐Khoei

Tahmasebian

et al. 2022

Sci Rep

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show abstract

“…However, these vaccines could be allergenic and poisonous because of toxic and potent allergic components. While recombinant vaccines (subunit and conjugates) were developed for targeting a particular protein or toxin, the existence of non-antigenic or allergic factors could result in severe toxicity and vaccine failure [ 91 , 92 ]. Bioinformatics resources are being used to develop multi-epitope vaccines employing a reverse vaccinology strategy [ 93 , 94 ].…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis

et al. 2022

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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.

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“…In vitro and in vivo are generally considered the most viable methods, but these methods are time-consuming and require a high cost to yield correct results. However, with the emergence of high-throughput technologies and advancement in the genomic era, various in silico approaches have been designed, providing a handy platform for validation of results [ 99 ]. Lastly, both experimental and virtual methods are available to validate the predicted results.…”

Section: Methodology Of Network Pharmacology Researchmentioning

confidence: 99%

Network Pharmacology Approach for Medicinal Plants: Review and Assessment

et al. 2022

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Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.

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Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches

Cited by 31 publications

References 95 publications

Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach

Designing a novel multi‑epitope vaccine against Ebola virus using reverse vaccinology approach

Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis

Network Pharmacology Approach for Medicinal Plants: Review and Assessment

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