Login Register Cart 0
Generic placeholder image

Current Computer-Aided Drug Design

Editor-in-Chief

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

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
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

Abstract

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.

« Previous Next »
Graphical Abstract

[1]
Illness and Symptoms | Cholera | CDC. Available from: https://www.cdc.gov/cholera/illness.html (Accessed on: 2021-01-22).
[2]
Clemens, J.D.; Nair, G.B.; Ahmed, T.; Qadri, F.; Holmgren, J. Cholera. Lancet, 2017, 390(10101), 1539-1549.
[http://dx.doi.org/10.1016/S0140-6736(17)30559-7] [PMID: 28302312]
[3]
Legros, D. Global cholera epidemiology: Opportunities to reduce the burden of cholera by 2030. J. Infect. Dis., 2018, S137-S140.
[http://dx.doi.org/10.1093/infdis/jiy486]
[4]
Ali, M.; Nelson, A.R.; Lopez, A.L.; Sack, D.A. Updated global burden of cholera in endemic countries. PLoS Negl. Trop. Dis., 2015, 9(6)e0003832
[http://dx.doi.org/10.1371/journal.pntd.0003832] [PMID: 26043000]
[5]
Diagnosis and detection | Cholera | CDC. Available from:https://www.cdc.gov/cholera/diagnosis.html(Accessed on: 2021-10-06).
[6]
Yan, Y.; Zhan, L.; Zhu, G.; Zhang, J.; Li, P.; Chen, L.; He, P.; Luo, J.; Chen, Z. Direct and rapid identification of vibrio cholerae serogroup and toxigenicity by a novel multiplex real-time assay. Pathogens, 2022, 11(8), 865.
[http://dx.doi.org/10.3390/pathogens11080865] [PMID: 36014986]
[7]
Global Task Force on Cholera Control Interim Technical Note The Use of Cholera Rapid Diagnostic Tests., 2016, (November), 1-5.
[8]
Muzembo, B.A.; Kitahara, K.; Debnath, A.; Okamoto, K.; Miyoshi, S.I. Accuracy of cholera rapid diagnostic tests: A systematic review and meta-analysis. Clin. Microbiol. Infect., 2022, 28(2), 155-162.
[http://dx.doi.org/10.1016/j.cmi.2021.08.027] [PMID: 34506946]
[9]
Song, K.M.; Lee, S.; Ban, C. Aptamers and their biological applications. Sensors, 2012, 12(1), 612-631.
[http://dx.doi.org/10.3390/s120100612] [PMID: 22368488]
[10]
White, R.R.; Sullenger, B.A.; Rusconi, C.P. Developing aptamers into therapeutics. J. Clin. Invest., 2000, 106(8), 929-934.
[http://dx.doi.org/10.1172/JCI11325] [PMID: 11032851]
[11]
Citartan, M.; Ch’ng, E.S.; Rozhdestvensky, T.S.; Tang, T.H. Aptamers as the “capturing” agents in aptamer-based capture assays. Microchemical J., 2016, 187-197.
[http://dx.doi.org/10.1016/j.microc.2016.04.019]
[12]
Jo, H.; Ban, C. Aptamer-nanoparticle complexes as powerful diagnostic and therapeutic tools. Exp. Mol. Med., 2016, 48(5)e230
[http://dx.doi.org/10.1038/emm.2016.44] [PMID: 27151454]
[13]
Keefe, A.D.; Pai, S.; Ellington, A. Aptamers as therapeutics. Nat. Rev. Drug Discov., 2010, 9(7), 537-550.
[http://dx.doi.org/10.1038/nrd3141] [PMID: 20592747]
[14]
Ray, P.; White, R.R. Aptamers for targeted drug delivery. In: Pharmaceuticals; MDPI AG; , 2010; pp. 1761-1778.
[http://dx.doi.org/10.3390/ph3061761]
[15]
Sun, H.; Zhu, X.; Lu, P.Y.; Rosato, R.R.; Tan, W.; Zu, Y. Oligonucleotide aptamers: New tools for targeted cancer therapy. Mol. Ther. Nucleic Acids, 2014.e182
[http://dx.doi.org/10.1038/mtna.2014.32]
[16]
Wang, A.Z.; Farokhzad, O.C. Current progress of aptamer-based molecular imaging. J. Nucl. Med., 2014, 353-356.
[http://dx.doi.org/10.2967/jnumed.113.126144]
[17]
Cowperthwaite, M.C.; Ellington, A.D. Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J. Mol. Evol., 2008, 67(1), 95-102.
[http://dx.doi.org/10.1007/s00239-008-9130-4] [PMID: 18594898]
[18]
Zhuo, Z.; Yu, Y.; Wang, M.; Li, J.; Zhang, Z.; Liu, J.; Wu, X.; Lu, A.; Zhang, G.; Zhang, B. Recent advances in SELEX technology and aptamer applications in biomedicine. Int. J. Mol. Sci., 2017, 18(10), 2142.
[http://dx.doi.org/10.3390/ijms18102142] [PMID: 29036890]
[19]
Ishida, R.; Adachi, T.; Yokota, A.; Yoshihara, H.; Aoki, K.; Nakamura, Y.; Hamada, M. RaptRanker: In silico RNA aptamer selection from HT-SELEX experiment based on local sequence and structure information. bioRxiv, 2019.2019.12.31.890392
[http://dx.doi.org/10.1101/2019.12.31.890392]
[20]
Caroli, J.; Taccioli, C.; De La Fuente, A.; Serafini, P.; Bicciato, S. APTANI: A computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data. Bioinformatics, 2015, 32(2)btv545
[http://dx.doi.org/10.1093/bioinformatics/btv545] [PMID: 26395772]
[21]
Iwano, N.; Adachi, T.; Aoki, K.; Nakamura, Y.; Hamada, M. Generative aptamer discovery using RaptGen. Nature Computational Sci., 2022, 2(6), 378-386.
[http://dx.doi.org/10.1038/s43588-022-00249-6]
[22]
Chen, Z.; Hu, L.; Zhang, B.T.; Lu, A.; Wang, Y.; Yu, Y.; Zhang, G. Artificial intelligence in aptamer-target binding prediction. Int. J. Mol. Sci., 2021, 22(7), 3605.
[http://dx.doi.org/10.3390/ijms22073605] [PMID: 33808496]
[23]
Buglak, A.A.; Samokhvalov, A.V.; Zherdev, A.V.; Dzantiev, B.B. Methods and applications of in silico aptamer design and modeling. Int. J. Mol. Sci., 2020, 21(22), 8420.
[http://dx.doi.org/10.3390/ijms21228420] [PMID: 33182550]
[24]
Team:Heidelberg/Software/MAWS-2017.igem.org Available from: https://2017.igem.org/Team:Heidelberg/Software/MAWS (Accessed on: 2022-11-27)
[25]
Reidl, J.; Klose, K.E. Vibrio cholerae and cholera: Out of the water and into the host. FEMS Microbiol. Rev., 2002, 26(2), 125-139.
[http://dx.doi.org/10.1111/j.1574-6976.2002.tb00605.x] [PMID: 12069878]
[26]
Das, M.; Chopra, A.K.; Cantu, J.M.; Peterson, J.W. Antisera to selected outer membrane proteins of Vibrio cholerae protect against challenge with homologous and heterologous strains of V. cholerae. FEMS Immunol. Med. Microbiol., 1998, 22(4), 303-308.
[http://dx.doi.org/10.1111/j.1574-695X.1998.tb01219.x] [PMID: 9879921]
[27]
Provenzano, D.; Klose, K.E. Altered expression of the ToxR-regulated porins OmpU and OmpT diminishes Vibrio cholerae bile resistance, virulence factor expression, and intestinal colonization. Proc. Natl. Acad. Sci. USA, 2000, 97(18), 10220-10224.
[http://dx.doi.org/10.1073/pnas.170219997] [PMID: 10944196]
[28]
Provenzano, D.; Lauriano, C.M.; Klose, K.E. Characterization of the role of the ToxR-modulated outer membrane porins OmpU and OmpT in Vibrio cholerae virulence. J. Bacteriol., 2001, 183(12), 3652-3662.
[http://dx.doi.org/10.1128/JB.183.12.3652-3662.2001] [PMID: 11371530]
[29]
Goel, A.K.; Jain, M.; Kumar, P.; Jiang, S.C. Molecular characterization of Vibrio cholerae outbreak strains with altered El Tor biotype from southern India. World J. Microbiol. Biotechnol., 2010, 26(2), 281-287.
[http://dx.doi.org/10.1007/s11274-009-0171-7] [PMID: 20495624]
[30]
Chakrabarti, S.R.; Chaudhuri, K.; Sen, K.; Das, J. Porins of Vibrio cholerae: Purification and characterization of OmpU. J. Bacteriol., 1996, 178(2), 524-530.
[http://dx.doi.org/10.1128/jb.178.2.524-530.1996] [PMID: 8550475]
[31]
Paauw, A.; Trip, H.; Niemcewicz, M.; Sellek, R.; Heng, J.M.E.; Mars-Groenendijk, R.H.; de Jong, A.L.; Majchrzykiewicz-Koehorst, J.A.; Olsen, J.S.; Tsivtsivadze, E. OmpU as a biomarker for rapid discrimination between toxigenic and epidemic Vibrio cholerae O1/O139 and non-epidemic Vibrio cholerae in a modified MALDI-TOF MS assay. BMC Microbiol., 2014, 14(1), 158.
[http://dx.doi.org/10.1186/1471-2180-14-158] [PMID: 24943244]
[32]
Li, H.; Zhang, W.; Dong, C. Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 Å resolution. Acta Crystallogr. D Struct. Biol., 2018, 74(1), 21-29.
[http://dx.doi.org/10.1107/S2059798317017697] [PMID: 29372896]
[33]
Pathania, M.; Acosta-Gutierrez, S.; Bhamidimarri, S.P.; Baslé, A.; Winterhalter, M.; Ceccarelli, M.; van den Berg, B. Unusual constriction zones in the major porins OmpU and OmpT from Vibrio cholerae. Structure, 2018, 26(5), 708-721.e4.
[http://dx.doi.org/10.1016/j.str.2018.03.010] [PMID: 29657131]
[34]
Lorenz, R.; Bernhart, S.H.; Höner zu Siederdissen, C.; Tafer, H.; Flamm, C.; Stadler, P.F.; Hofacker, I.L. ViennaRNA package 2.0. Algorithms Mol. Biol., 2011, 6(1), 26.
[http://dx.doi.org/10.1186/1748-7188-6-26] [PMID: 22115189]
[35]
Yan, Y.; Zhang, D.; Zhou, P.; Li, B.; Huang, S.Y. HDOCK: A web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res., 2017, 45(W1), W365-W373.
[http://dx.doi.org/10.1093/nar/gkx407] [PMID: 28521030]
[36]
Lee, J.; Cheng, X.; Swails, J.M.; Yeom, M.S.; Eastman, P.K.; Lemkul, J.A.; Wei, S.; Buckner, J.; Jeong, J.C.; Qi, Y.; Jo, S.; Pande, V.S.; Case, D.A.; Brooks, C.L., III; MacKerell, A.D., Jr; Klauda, J.B. Im, W. CHARMM-GUI Input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J. Chem. Theory Comput., 2016, 12(1), 405-413.
[http://dx.doi.org/10.1021/acs.jctc.5b00935] [PMID: 26631602]
[37]
Jo, S.; Kim, T.; Iyer, V.G. Im, W. CHARMM-GUI: A web-based graphical user interface for CHARMM. J. Comput. Chem., 2008, 29(11), 1859-1865.
[http://dx.doi.org/10.1002/jcc.20945] [PMID: 18351591]
[38]
Wu, E.L.; Cheng, X.; Jo, S.; Rui, H.; Song, K.C.; Dávila-Contreras, E.M.; Qi, Y.; Lee, J.; Monje-Galvan, V.; Venable, R.M.; Klauda, J.B. Im, W. CHARMM-GUI Membrane builder toward realistic biological membrane simulations. J. Comput. Chem., 2014, 35(27), 1997-2004.
[http://dx.doi.org/10.1002/jcc.23702] [PMID: 25130509]
[39]
Lomize, M.A.; Pogozheva, I.D.; Joo, H.; Mosberg, H.I.; Lomize, A.L. OPM database and PPM web server: Resources for positioning of proteins in membranes. Nucleic Acids Res., 2012, 40(D1), D370-D376.
[http://dx.doi.org/10.1093/nar/gkr703] [PMID: 21890895]
[40]
Abraham, M.J.; van der Spoel, D.; Lindahl, E.; Hess, B. GROMACS user manual version 5.1.5; , 2017.
[41]
Luscombe, N.; Laskowski, R.A.; Thornton, J.M. NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Res., 1997, 25(24), 4940-4945.
[http://dx.doi.org/10.1093/nar/25.24.4940] [PMID: 9396800]
[42]
Gevertz, J.; Gan, H.H.; Schlick, T. In vitro RNA random pools are not structurally diverse: A computational analysis. RNA, 2005, 11(6), 853-863.
[http://dx.doi.org/10.1261/rna.7271405] [PMID: 15923372]
[43]
Fontana, W.; Konings, D.A.M.; Stadler, P.F.; Schuster, P. Statistics of RNA secondary structures. Biopolymers, 1993, 33(9), 1389-1404.
[http://dx.doi.org/10.1002/bip.360330909] [PMID: 7691201]
[44]
Schultes, E.; Hraber, P.T.; LaBean, T.H. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA, 1997, 3(7), 792-806.
[PMID: 9214661]
[45]
Knight, R.; De Sterck, H.; Markel, R.; Smit, S.; Oshmyansky, A.; Yarus, M. Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res., 2005, 33(18), 5924-5935.
[http://dx.doi.org/10.1093/nar/gki886] [PMID: 16237127]
[46]
Hasegawa, H.; Savory, N.; Abe, K.; Ikebukuro, K. Methods for improving aptamer binding affinity. Molecules, 2016, 21(4), 421.
[http://dx.doi.org/10.3390/molecules21040421] [PMID: 27043498]
[47]
Bonnet, E.; Wuyts, J.; Rouzé, P.; Van de Peer, Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 2004, 20(17), 2911-2917.
[http://dx.doi.org/10.1093/bioinformatics/bth374] [PMID: 15217813]
[48]
Seffens, W.; Digby, D. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res., 1999, 27(7), 1578-1584.
[http://dx.doi.org/10.1093/nar/27.7.1578] [PMID: 10075987]
[49]
Clote, P.; Ferré, F.; Kranakis, E.; Krizanc, D. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA, 2005, 11(5), 578-591.
[http://dx.doi.org/10.1261/rna.7220505] [PMID: 15840812]
[50]
Chushak, Y.; Stone, M.O. In silico selection of RNA aptamers. Nucleic Acids Res., 2009, 37(12)e87
[http://dx.doi.org/10.1093/nar/gkp408] [PMID: 19465396]
[51]
Lakhin, A.V.; Tarantul, V.Z.; Gening, L.V. Aptamers: Problems, solutions and prospects. Acta Nat., 2013, 5(4), 34-43.
[http://dx.doi.org/10.32607/20758251-2013-5-4-34-43] [PMID: 24455181]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy