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Current Computer-Aided Drug Design


ISSN (Print): 1573-4099
ISSN (Online): 1875-6697

Research Article

A Novel in silico SELEX Method to Screen and Identify Aptamers against Vibrio cholerae

Author(s): Hamid Reza Rasouli Jazi, Mehdi Zeinoddini* and Seyed Shahriar Arab

Volume 19, Issue 6, 2023

Published on: 15 February, 2023

Page: [416 - 424] Pages: 9

DOI: 10.2174/1573409919666230126101635

Price: $65


Background: Vibrio cholerae, the causative agent of cholera, has been responsible for global epidemics and many other problems over the centuries. It is one of the main public health issues in less-developed and developing countries and is considered one of the deadliest infectious agents. Therefore, precise and susceptible detection of V. cholerae from environmental and biological samples is critical. Aptamers provide a rapid, sensitive, highly specific, and inexpensive alternative to traditional methods.

Objective: The present study develops a new protocol inspired by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to implement an in silico aptamer selection against V. cholerae, which can also be employed in the case of other pathogenic microorganisms.

Methods: First, we built an oligonucleotide pool and screened it based on the secondary structure. Following that, we modeled the tertiary structures of filtered sequences and performed RNAprotein dockings to assess binding affinities between RNA sequences and Outer Membrane Protein U (OmpU), an effective marker in distinguishing epidemic strains of V. cholerae, which constitute up to 60% of the total outer membrane protein. Finally, we used molecular dynamics simulation to validate the results.

Results: Three sequences (ChOmpUapta) were proposed as final aptameric candidates. Analysis of the top-ranked docking results revealed that these candidate aptamers bound to all subunits of OmpU at the extracellular side with high affinity. Moreover, ChOmpUapta-3 and ChOmpUapta-2 were fully stable and formed strong bonds under dynamic conditions.

Conclusion: We propose incorporating these candidate sequences into aptasensors for V. cholerae detection.

Keywords: Vibrio cholera, in silico SELEX, RNA aptamer screening, detection, OmpU, molecular dynamics simulation, highthroughput screening.

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