Reducing the Immunogenicity of Pulchellin A-Chain, Ribosome-Inactivating Protein Type 2, by Computational Protein Engineering for Potential New Immunotoxins

Maleki, R; Fu, L; Diaz, RS; Guimarães, FEG; Cabral-Marques, O; Cabral-Miranda, G; Sadraeian, M

Reducing the Immunogenicity of Pulchellin A-Chain, Ribosome-Inactivating Protein Type 2, by Computational Protein Engineering for Potential New Immunotoxins

Maleki, R Fu, L Diaz, RS Guimarães, FEG Cabral-Marques, O Cabral-Miranda, G Sadraeian, M

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Publisher:: MDPI
Publication Type:: Journal Article
Citation:: J — Multidisciplinary Scientific Journal, 6, (1), pp. 85-101

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Field	Value	Language
dc.contributor.author	Maleki, R
dc.contributor.author	Fu, L
dc.contributor.author	Diaz, RS
dc.contributor.author	Guimarães, FEG
dc.contributor.author	Cabral-Marques, O
dc.contributor.author	Cabral-Miranda, G
dc.contributor.author	Sadraeian, M https://orcid.org/0000-0002-7384-2247
dc.date.accessioned	2023-12-05T08:11:37Z
dc.date.available	2023-12-05T08:11:37Z
dc.identifier.citation	J — Multidisciplinary Scientific Journal, 6, (1), pp. 85-101
dc.identifier.issn	2571-8800
dc.identifier.issn	2571-8800
dc.identifier.uri	http://hdl.handle.net/10453/173723
dc.description.abstract	<jats:p>Pulchellin is a plant biotoxin categorized as a type 2 ribosome-inactivating protein (RIPs) which potentially kills cells at very low concentrations. Biotoxins serve as targeting immunotoxins (IT), consisting of antibodies conjugated to toxins. ITs have two independent protein components, a human antibody and a toxin with a bacterial or plant source; therefore, they pose unique setbacks in immunogenicity. To overcome this issue, the engineering of epitopes is one of the beneficial methods to elicit an immunological response. Here, we predicted the tertiary structure of the pulchellin A-chain (PAC) using five common powerful servers and adopted the best model after refining. Then, predicted structure using four distinct computational approaches identified conformational B-cell epitopes. This approach identified some amino acids as a potential for lowering immunogenicity by point mutation. All mutations were then applied to generate a model of pulchellin containing all mutations (so-called PAM). Mutants’ immunogenicity was assessed and compared to the wild type as well as other mutant characteristics, including stability and compactness, were computationally examined in addition to immunogenicity. The findings revealed a reduction in immunogenicity in all mutants and significantly in N146V and R149A. Furthermore, all mutants demonstrated remarkable stability and validity in Molecular Dynamic (MD) simulations. During docking and simulations, the most homologous toxin to pulchellin, Abrin-A was applied as a control. In addition, the toxin candidate containing all mutations (PAM) disclosed a high level of stability, making it a potential model for experimental deployment. In conclusion, by eliminating B-cell epitopes, our computational approach provides a potential less immunogenic IT based on PAC.</jats:p>
dc.language	en
dc.publisher	MDPI
dc.relation	University of Melbourne
dc.relation.ispartof	J — Multidisciplinary Scientific Journal
dc.relation.isbasedon	10.3390/j6010006
dc.rights	info:eu-repo/semantics/openAccess
dc.title	Reducing the Immunogenicity of Pulchellin A-Chain, Ribosome-Inactivating Protein Type 2, by Computational Protein Engineering for Potential New Immunotoxins
dc.type	Journal Article
utslib.citation.volume	6
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - IBMD - Initiative for Biomedical Devices
utslib.copyright.status	open_access	*
dc.date.updated	2023-12-05T08:11:36Z
pubs.issue	1
pubs.publication-status	Published online
pubs.volume	6
utslib.citation.issue	1

Abstract:

Pulchellin is a plant biotoxin categorized as a type 2 ribosome-inactivating protein (RIPs) which potentially kills cells at very low concentrations. Biotoxins serve as targeting immunotoxins (IT), consisting of antibodies conjugated to toxins. ITs have two independent protein components, a human antibody and a toxin with a bacterial or plant source; therefore, they pose unique setbacks in immunogenicity. To overcome this issue, the engineering of epitopes is one of the beneficial methods to elicit an immunological response. Here, we predicted the tertiary structure of the pulchellin A-chain (PAC) using five common powerful servers and adopted the best model after refining. Then, predicted structure using four distinct computational approaches identified conformational B-cell epitopes. This approach identified some amino acids as a potential for lowering immunogenicity by point mutation. All mutations were then applied to generate a model of pulchellin containing all mutations (so-called PAM). Mutants’ immunogenicity was assessed and compared to the wild type as well as other mutant characteristics, including stability and compactness, were computationally examined in addition to immunogenicity. The findings revealed a reduction in immunogenicity in all mutants and significantly in N146V and R149A. Furthermore, all mutants demonstrated remarkable stability and validity in Molecular Dynamic (MD) simulations. During docking and simulations, the most homologous toxin to pulchellin, Abrin-A was applied as a control. In addition, the toxin candidate containing all mutations (PAM) disclosed a high level of stability, making it a potential model for experimental deployment. In conclusion, by eliminating B-cell epitopes, our computational approach provides a potential less immunogenic IT based on PAC.

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http://hdl.handle.net/10453/173723