Elsevier

Journal of Theoretical Biology

Volume 465, 21 March 2019, Pages 34-44
Journal of Theoretical Biology

Computational analysis in designing T cell epitopes enriched peptides of Ebola glycoprotein exhibiting strong binding interaction with HLA molecules

https://doi.org/10.1016/j.jtbi.2019.01.016Get rights and content

Highlights

  • Four peptides containing multiple epitopes of Ebola glycoprotein identified.

  • In most of Ebola virus strains infecting humans, peptides are highly conserved.

  • Peptides have strong binding potential with diverse array of HLA molecules.

  • Peptides exhibit wide population coverage across the globe.

  • Selected peptides may act as synthetic vaccine candidates against Ebola virus.

Abstract

Computational approach has shown remarkable progress in epitope mapping, paving the way to finding vaccine candidates against different viruses. In the current study, prediction algorithms and molecular docking were applied to select peptides containing multiple Ebola glycoprotein epitopes showing interaction with different HLA molecules. Six peptides containing overlapping multiple HLA I (CD8+) and II (CD4+) restricted T cell epitopes were generated via consensus approach applying six different prediction tools. Four (P1, P2, P5 and P6) out of six peptides were selected after screening for absence of undesirable responses and presence of B cell epitopes. Peptide-HLA interaction analysis based on Autodock Vina and CABS-dock showed strong binding of these four peptides with eighteen HLA molecules. HLA coverage analysis from each prediction tool showed that these peptides were able to bind to diverse HLA-A, HLA-B, HLA-DP, HLA-DQ and HLA-DR alleles. Population coverage analysis of peptides for expected immune response in four different continents (Africa, America, Asia and Europe) have shown average population coverage viz, P1 (95%), P2 (96%), P5 (91%) and P6 (94%). Further, these peptides were found to be nearly 100% conserved in Zaire Ebola virus while LANETTQALQLF (P5) was found to be 100% conserved in Zaire, Sudan, Bundibugyo and Tai Forest species. Therefore, these peptides capable of inducing T and B cell response and being presented by a wide range of HLA molecules have a strong potential to be part of diagnostic and preventive tools against Ebola virus disease.

Introduction

Ebola virus (EBOV) is an enveloped, non-segmented, negative-stranded RNA virus which belongs to the Filoviridae family (Lee et al., 2008). Five Ebola virus species (Zaire, Reston, Sudan, Bundibugyo, and Tai Forest) are known of which, Zaire is the most pathogenic and Reston is non-pathogenic in humans (Groseth et al., 2012). The mortality rate of Ebola virus disease (EVD) varies from 25%–90% with an average of 50% (Peters et al., 1999). More than 28,000 cases with over 11,000 deaths have been reported during its latest breakout (Cherpillod et al., 2016).

The 19 kb genome of Ebola virus consists of seven genes which are present in a defined order viz. nucleoprotein (NP), polymerase cofactors (VP35 and VP40), glycoprotein (GP), transcription activators (VP30 and VP24) and RNA-dependent RNA polymerase (L) (Brauburger et al., 2014). The fourth gene from the 3′ end of EBOV genome results in the formation of three proteins viz. secreted glycoprotein (sGP), soluble secreted glycoprotein (ssGP) and surface glycoprotein (GP) (Ito et al., 2001) which is cleaved post-translationally to yield GP1 and GP2 subunits connected by a disulfide link (Jeffers et al., 2002). GP1 plays an important role in attachment to host cells with the help of 54-201 residues that form a highly conserved putative receptor-binding site (RBS) (Kuhn et al., 2006, Manicassamy et al., 2005, Lee et al., 2008). GP2 is indispensable for viral and host membrane fusion (Volchkov et al., 1998, Feldmann et al., 1993, Takada et al., 1997). Presence of both GP1 and GP2 is critical for recognition by an antibody. GP1 is required to maintain the proper pre-fusion conformation of GP2 for antibody binding. Studies have revealed that antibodies bind to a non-glycosylated epitope at the base of the GP2 subunit where they interact with residues 42-43 at the N terminus of GP1 and 505-514 and 549-556 at the N terminus of GP2 (Lee et al., 2008). As EBOV GP is the first protein to interact with the immune system, it is considered as a potential candidate for vaccine and anti-filoviral therapeutic development (Madara et al., 2015).

sGP is the most abundant product of the glycoprotein gene (Iwasa et al., 2011) and it has been proven to result in antigenic subversion (a process wherein sGP acts as a barrier between the virus GP and anti-GP12 antibodies, thus, preventing contact between the virus GP and the antibodies) (Mohan et al., 2012). It has been reported that sGP shares 295 amino acids with GP1 (Iwasa et al., 2011). Hence, sGP may be an important target for vaccine development.

An effective prophylaxis or treatment for EVD is not yet available (Takada et al., 2015). Among the vaccines in various stages of clinical trials are recombinant adenoviruses, recombinant vesicular stomatitis viruses, recombinant human para influenza viruses and virus-like particles (Sykes and Reisman, 2015, Sridhar, 2015). Efficient and prolonged response to the vaccine candidate and protection against different strains of the virus represent the current challenges faced by the scientific community (Sridhar, 2015, Hoenen et al., 2012).

A safer alternative route to live-attenuated or inactivated vaccines is the development of peptide based vaccines. They are relatively easier to produce and handle as there is no need to culture any pathogenic organisms. With the advancement in immunoinformatics tools focusing on epitope mapping, it has become easy to select peptides containing immunogenic epitopes. Immunoinformatics utilizes sequence and structure based approaches and has shown promising results in peptide based vaccine development. The immunogenic peptides obtained using this approach were validated in in vitro and in vivo system (Lohia and Baranwal, 2017, Oliveira et al., 2016, Kovjazin et al., 2013, Duvvuri et al., 2013). One of the noteworthy examples is in silico based selected influenza peptides which are the constituents of an influenza vaccine currently undergoing phase II clinical trial with the concept name of FluV (Pleguezuelos et al., 2012, van Doorn et al., 2017).

In the present study, consensus based predictions and molecular docking tools were employed to obtain the peptides containing multiple epitopes of Ebola glycoprotein which have the potential to interact with a wide range of HLA molecules.

Section snippets

Conserved peptides identification

1092 sequences belonging to various Ebola species (1976–30th January 2018) pathogenic to humans were downloaded from Ebola virus database (viprbrc). 173 unique full length (676 amino acids) Ebola glycoprotein sequences (164, 5, 3 and 1 sequences of Zaire, Sudan, Bundibugyo and Tai Forest species respectively) were screened out after removing redundancy.

22 sGP sequences (364 amino acids) belonging to various Ebola species (1976–April 2015) pathogenic to humans were downloaded from the Ebola

Results

The goal of this study was in silico elucidation of conserved peptide fragments capable of eliciting T (CD8+ and CD4+) and B cell response. Also, the identified fragments must be devoid of undesirable (autoimmune, allergic and toxic) responses. Further, these peptides should be presented by diverse HLA molecules and exhibit wide population coverage.

Discussion

Peptide as a choice of vaccine candidate has made remarkable headway in vaccine development against virus, bacteria and cancer. Peptides can be a recombinant or synthetic construct of epitopes which are targeted against cell surface or intracellular proteins (Kumai et al., 2017). GMP grade peptides are easy to synthesize and cost effective as compared to whole organism vaccine or recombinant proteins. Although peptide vaccines are still not translated into clinics, the promising results have

Conclusion

Four peptides containing multiple T and B cell epitopes of Ebola glycoprotein which are highly conserved in different Ebola strains infecting humans were identified. These peptides were found to be predicted for a large number of HLA molecules and have shown strong binding interactions with 18 HLA molecules. Hence, these peptides are proposed as candidates for synthetic vaccine design against Ebola virus and need to be validated experimentally in vitro or in vivo.

Disclosure and funding

This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors.

Declarations of interest

None.

Author's contribution

Dr. Manoj Baranwal was involved in design of study, results analysis and writing the manuscript. Sahil Jain carried out all the work and helped in writing the manuscript.

Acknowledgement

I express my sincere thanks to the scientific community for developing in silico tools.

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