Supplementary Material - In-silico characterization of conserved epitopes in Alphavirus E2 proteins: A promising approach for pan-vaccine design

This file contains supplementary materials related to the study "In-silico characterization of conserved epitopes in Alphavirus E2 proteins: A promising approach for pan-vaccine design." The study introduces a novel approach for identifying conserved epitopes within the E2 protein, shared by both arthritogenic and encephalitogenic alphaviruses, through a semi-automated computational pipeline named POA. By integrating structural analysis, the study identifies high-potential candidates within a novel set of linear epitopes targeting the E2 proteins of CHIKV and EEEV, providing insights for the development of a pan-alphavirus vaccine. These findings advance the field of integrative therapeutic interventions, offering innovative strategies to address the global burden of zoonotic and vector-borne diseases. The supplementary materials include the reference FASTA sequences of the E2 proteins from CHIKV and EEEV, used for epitope prediction, as well as the output files from the online prediction tools: Bepipred 2.0 (in JSON format), Predicted Antigenic Peptides (PAP) (in TEXT format), NetCTL 1.2, and MHC-II Binding Predictions (in HTML format). These materials support the conclusions of our study and provide additional resources to ensure reproducibility and facilitate further research. These files are an integral part of the study: In-silico characterization of conserved epitopes in Alphavirus E2 proteins: A promising approach for pan-vaccine designdoi: XXXXXXXXX Ubiratan da Silva Batista¹ᵟ Ana Clara Gomes de Souza¹, Breno de Mello Silva¹*, and Ricardo Lemes Gonçalves¹* 1. Laboratory of Biology and Technology of Microorganisms (LBTM), Department of Biological Sciences, Federal University of Ouro Preto (UFOP), 35400-000 Ouro Preto, MG, Brazil *Corresponding authors: [email protected] and [email protected] Present address: ᵟU.S.B.: Renewable Carbon and Biological Systems (ReCABS) Laboratory, Department of Biotechnology, Lorena School of Engineering, University of São Paulo (EEL-USP), 12602-810 Lorena, SP, Brazil Included Materials 1 – Reference sequences of E2 proteins from CHIKV and EEEV alphaviruses Format: FASTA file This file contains the amino acid sequences of the E2 proteins from the arthritogenic CHIKV (NCBI Accession: NP_690589.2) and the encephalitogenic EEEV (NCBI Accession: NP_632022.1), derived from the structural polyprotein sequences available in the NCBI GenBank database (https://www.ncbi.nlm.nih.gov/genbank/). 2 – Predicted B Cell epitopes from E2 proteins using the Bepipred 2.0 tool Format: JSON file This file contains the output from the Bepipred 2.0 tool, which predicts B cell epitopes. The JSON file organizes the protein sequences and identifies amino acids most likely to be part of antigenic epitopes. For further details on the methodology, refer to Jespersen et al., 2017. 3 – Predicted B Cell epitopes from E2 proteins using the Predicted Antigenic Peptides (PAP) tool Format: TXT file This file contains the output from the Predicted Antigenic Peptides (PAP) tool, which predicts B cell epitopes. The TXT file organizes the predicted epitopes for the E2 proteins in a tabular format. For further details on the epitope selection method, refer to Kolaskar and Tongaonkar, 1990. 4 – Predicted cytotoxic T Cell (Tc) epitopes from E2 proteins using the NetCTL 1.2 tool Format: HTML file This file contains the output from the NetCTL 1.2 tool, which predicts cytotoxic T cell (Tc) epitopes. The tool generates a web-based output, saved here in HTML format, organizing predicted epitopes based on their likelihood of binding to MHC class I molecules. For further details on the methodology, refer to Larsen et al., 2007. 5 – Predicted T helper (Th) Cell epitopes from CHIKV E2 protein using the MHC-II Binding Predictions Tool Format: HTML file This file contains the output from the MHC-II Binding Predictions tool, which predicts T helper (Th) cell epitopes for the CHIKV E2 protein. The tool generates a web-based output, saved here in HTML format, which organizes predicted epitopes and assigns scores based on their likelihood of binding to MHC class II molecules. For further details on the methodology, refer to Greenbaum et al., 2011. 6 – Predicted T helper (Th) Cell epitopes from EEEV E2 protein using the MHC-II Binding Predictions Tool Format: HTML file This file contains the output from the MHC-II Binding Predictions tool, which predicts T helper (Th) cell epitopes for the EEEV E2 protein. The tool generates a web-based output, saved here in HTML format, which organizes predicted epitopes and assigns scores based on their likelihood of binding to MHC class II molecules. For further details on the methodology, refer to Greenbaum et al., 2011.