Computational Design of Peptide Ligands for Ochratoxin A

Heurich, Meike ORCID: https://orcid.org/0000-0003-0105-2702, Altintas, Zeynep and Tothill, Ibtisam 2013. Computational Design of Peptide Ligands for Ochratoxin A. Toxins 5 (6) , pp. 1202-1218. 10.3390/toxins5061202

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Abstract

In this paper, we describe a peptide library designed by computational modelling and the selection of two peptide sequences showing affinity towards the mycotoxin, ochratoxin A (OTA). A virtual library of 20 natural amino acids was used as building blocks to design a short peptide library against ochratoxin A template using the de novo design program, LeapFrog, and the dynamic modelling software, FlexiDock. Peptide sequences were ranked according to calculated binding scores in their capacity to bind to ochratoxin A. Two high scoring peptides with the sequences N'-Cys-Ser-Ile-Val-Glu-Asp-Gly-Lys-C' (octapeptide) and N'-Gly-Pro-Ala-Gly-Ile-Asp-Gly-Pro-Ala-Gly-Ile-Arg-Cys-C' (13-mer) were selected for synthesis from the resulting database. These synthesized peptides were characterized using a microtitre plate-based binding assay and a surface plasmon resonance biosensor (Biacore 3000). The binding assay confirmed that both de novo designed peptides did bind to ochratoxin A in vitro. SPR analysis confirmed that the peptides bind to ochratoxin A, with calculated KD values of ~15.7 μM (13-mer) and ~11.8 μM (octamer). The affinity of the peptides corresponds well with the molecular modelling results, as the 13-mer peptide affinity is about 1.3-times weaker than the octapeptide; this is in accordance with the binding energy values modelled by FlexiDock. This work illustrates the potential of using computational modelling to design a peptide sequence that exhibits in vitro binding affinity for a small molecular weight toxin.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Pharmacy
Uncontrolled Keywords:	ochratoxin A; mycotoxins; peptide; computational modelling; surface plasmon resonance; biosensor
Publisher:	MDPI Publishing
ISSN:	2072-6651
Date of First Compliant Deposit:	19 April 2017
Date of Acceptance:	13 June 2013
Last Modified:	05 May 2023 03:50
URI:	https://orca.cardiff.ac.uk/id/eprint/99972

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