COMPUTATIONAL PROSPECTING FOR VALIDATION OF AN OPTICAL BIOSENSOR FOR THE DETECTION OF ESCHERICHIA COLI

Bruno Prado Sereno; Manuela Leal da Silva; Ana Carolina Silva Bulla

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Submission

Paper Title

COMPUTATIONAL PROSPECTING FOR VALIDATION OF AN OPTICAL BIOSENSOR FOR THE DETECTION OF ESCHERICHIA COLI

Authors

Bruno Prado Sereno
Manuela Leal da Silva
Ana Carolina Silva Bulla

Modality

Poster

Subject area

Systems Biology and Modeling

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/831844-computational-prospecting-for-validation-of-an-optical-biosensor-for-the-detection-of-escherichia-coli

ISBN

978-65-272-0843-3

Keywords

E. coli, Epitope, Immunoinformatics, Optical Biosensors.

Summary

Escherichia coli was responsible for 25.6% of all foodborne illness outbreaks in Brazil. In under-5 year olds, it's the main agent of diarrhea and it's estimated that 1.9 million deaths occur every year worldwide. Faced with possible new outbreaks, it is essential to have a diagnostic method that is fast, portable, inexpensive, sensitive and specific. Optical biosensors represent an alternative for identifying and detecting pathogens in biological samples. Then, Immunoinformatics can contribute to the identification of potential immunogenic targets. The purpose of this work is to identify antigenic epitopes, through computational predictions, for the validation of an optical biosensor focused on the detection of Escherichia coli in solutions. A search for protein targets present on the outer membrane of E. coli K-12 was initiated in the literature through the National Center for Biotechnology Information (NCBI), as well as in databases such as BV-BRC, PSORTdb and EcoCyc. Uniprot was consulted to access a protein sequence. To investigate the presence of these proteins in other Gram-negative bacteria, local alignments were conducted using the Protein Basic Local Alignment Search Tool (BLASTp), using BLOSUM 62 scoring matrix and non-redundant protein sequences (nr) as a database. Exclusion criteria were identity of more than 80% between E. coli and other organisms. To predict the antigenic levels of the targets, the Vaxijen 2.0 server was used with a Threshold of 0.5, any value above which is considered antigenic. To predict linear B cells, three web-servers with different algorithms were used: Ellipro, Bepipred and ABCpred respectively. As well as the conformational ones Discotope, Epitope3D and Ellipro. Only epitopes identified by two or more servers were considered. The NNAlign server was used to predict T cells (MHC II), with a default Threshold IC50 < 50nM. The loci selected were based on their highest presence in the population as described by Paul, S. et al 2015 (DR, DQ and DP). As a result, 290 proteins determined as outer membrane or extracellular for E. coli were found. By local alignment method, six proteins were identified that showed no correlation between other Proteobacteria phylum bacteria. However, only one protein qualifies as a candidate due to the limitations of a diagnostic method without sample preparation. A total of 16 linear B-cell consensus epitopes were identified, ranging from 13 residues to 54 in the same epitope. There were also two conformational consensus epitopes. The low number of conformational may be explained by consensus methodology, which reduces sensitivity at the cost of specificity and, consequently, less false positives. There were 83 positive T epitopes below the IC50. In addition, the candidate protein exhibited antigenic regions through prediction. Perspectives include in vitro tests with antibodies and antigenic peptides for application in the optical biosensor.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

SERENO, Bruno Prado; SILVA, Manuela Leal da; BULLA, Ana Carolina Silva. COMPUTATIONAL PROSPECTING FOR VALIDATION OF AN OPTICAL BIOSENSOR FOR THE DETECTION OF ESCHERICHIA COLI.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/831844-COMPUTATIONAL-PROSPECTING-FOR-VALIDATION-OF-AN-OPTICAL-BIOSENSOR-FOR-THE-DETECTION-OF-ESCHERICHIA-COLI. Access in: 13/06/2025