B-Cell Epitope Prediction of Dengue Virus NS1 Protein Using Bioinformatics Tools

DOI

10.2991/978-94-6463-536-2_18How to use a DOI?

Keywords

B-cell epitopes; bioinformatics; dengue; NS1 protein; biomarkers

Abstract

Reinfection with different DENV serotypes might develop cross immunity that aggravates the illness via antibody-dependent enhancement. Identifying the DENV epitopes can help in the development of a tetravalent vaccine. However, the available prediction technologies (i.e., X-crystallography and NMR) are prohibitively expensive and time-consuming compared to the in silico-based methods. Hence, the main purpose of this study is to predict the linear B-cell epitopes (BCEs) of DENV NS1 protein using multiple prediction tools such as BepiPred 2.0, SVMTrip, and BCPred. BepiPred 2.0 is operated based on the crystal structures which uses a Random Forest algorithm trained on epitopes and non-epitope amino acids. SVMTrip applied the SVM model to improve prediction performance by combining tri-peptide similarity and propensity scores. BCPred predicts fixed length of linear BCEs using SVM models with the subsequence kernel. Forty-eight sequences from each serotype, representing four countries in Southeast Asia, were aligned using ClustalW. Further analysis using conservancy tools of the predicted epitopes were then analyzed using WebLogo 3.0 and Epitope conservancy Analysis tool. Finally, the predicted epitopes were evaluated by comparing the epitopes among the prediction tools and the data of the immunogenic epitopes from other studies. There were 24 linear BCEs on the NS1 protein obtained whereby most of them have nearly identical regions predicted as epitopes by three different prediction tools, indicating high agreement across all the prediction tools. EP12 (¹⁸²RLMSAAIKDSKAVHADMGYW²⁰¹) and EP15 (²¹⁷FIEVKTCIWPKSHTLWSNGV²³⁶) were predicted showing more than 85% conservancy across all four DENV serotypes, indicating their potential as a vaccine target or biomarker for the detection of four DENV groups. The epitopes also found overlapping or partially constituting immunogenic regions on the NS1 protein which had previously been identified by reference [1]. NS1 protein epitopes with therapeutic potential can be determined in silico due to its simplicity, cost-effectiveness, and speed.

Copyright

© 2024 The Author(s)

Open Access

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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TY  - CONF
AU  - Noor Saidah Abd Rohim
AU  - Roziah Hj. Kambol
PY  - 2024
DA  - 2024/10/17
TI  - B-Cell Epitope Prediction of Dengue Virus NS1 Protein Using Bioinformatics Tools
BT  - Proceedings of the International Conference on Science Technology and Social Sciences – Biology Track (ICONSTAS-BIO 2023)
PB  - Atlantis Press
SP  - 197
EP  - 209
SN  - 2468-5747
UR  - https://doi.org/10.2991/978-94-6463-536-2_18
DO  - 10.2991/978-94-6463-536-2_18
ID  - Rohim2024
ER  -