Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study

The cytolethal distending toxin (CDT), <i>Haemophilus ducreyi</i>, is one of the bacterial toxins that have recently been considered for targeted therapies, especially in cancer therapies. CDT is an A-B2 exotoxin. Its catalytic subunit (CdtB) is capable of inducing DNA double strand brea...

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Autores principales:	Maryam Keshtvarz, Mahdieh Mahboobi, Marek Kieliszek, Antoni Miecznikowski, Hamid Sedighian, Milad Rezaei, Mohammad Ali Haghighi, Zahra Zareh, Ehsan Rezaei
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	cytolethal distending toxin immunogenicity stability tumor therapy mutation Medicine R
Acceso en línea:	https://doaj.org/article/148446ce389d4c62b5445fcaf8876908
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spelling	oai:doaj.org-article:148446ce389d4c62b5445fcaf88769082021-11-25T19:08:49ZEngineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study10.3390/toxins131107852072-6651https://doaj.org/article/148446ce389d4c62b5445fcaf88769082021-11-01T00:00:00Zhttps://www.mdpi.com/2072-6651/13/11/785https://doaj.org/toc/2072-6651The cytolethal distending toxin (CDT), <i>Haemophilus ducreyi</i>, is one of the bacterial toxins that have recently been considered for targeted therapies, especially in cancer therapies. CDT is an A-B2 exotoxin. Its catalytic subunit (CdtB) is capable of inducing DNA double strand breaks, cell cycle arrest and apoptosis in host eukaryotic cells. The sequence alignment indicates that the CdtB is structurally homologyr to phosphatases and deoxyribonucleases I (DNase I). Recently, it has been found that CdtB toxicity is mainly related to its nuclease activity. The immunogenicity of CDT can reduce its effectiveness in targeted therapies. However, the toxin can be very useful if its immunogenicity is significantly reduced. Detecting hotspot ectopic residues by computational servers and then mutating them to eliminate B-cell epitopes is a promising approach to reduce the immunogenicity of foreign protein-based therapeutics. By the mentioned method, in this study, we try to reduce the immunogenicity of the CdtB- protein sequence. This study initially screened residue of the CdtB is B-cell epitopes both linearly and conformationally. By overlapping the B-cell epitopes with the excluded conserve residues, and active and enzymatic sites, four residues were allowed to be mutated. There were two mutein options that show reduced antigenicity probability. Option one was N19F, G74I, and S161F with a VaxiJen score of 0.45 and the immune epitope database (IEDB) score of 1.80, and option two was N19F, G74I, and S161W with a VaxiJen score of 0.45 and IEDB score of 1.88. The 3D structure of the proposed sequences was evaluated and refined. The structural stability of native and mutant proteins was accessed through molecular dynamic simulation. The results showed that the mutations in the mutants caused no considerable changes in their structural stability. However, mutant 1 reveals more thermodynamic stability during the simulation. The applied approaches in this study can be used as rough guidelines for finding hot spot immunogen regions in the therapeutic proteins. Our results provide a new version of CdtB that, due to reduced immunogenicity and increased stability, can be used in toxin-based drugs such as immunotoxins.Maryam KeshtvarzMahdieh MahboobiMarek KieliszekAntoni MiecznikowskiHamid SedighianMilad RezaeiMohammad Ali HaghighiZahra ZarehEhsan RezaeiMDPI AGarticlecytolethal distending toxinimmunogenicitystabilitytumor therapymutationMedicineRENToxins, Vol 13, Iss 785, p 785 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cytolethal distending toxin immunogenicity stability tumor therapy mutation Medicine R
spellingShingle	cytolethal distending toxin immunogenicity stability tumor therapy mutation Medicine R Maryam Keshtvarz Mahdieh Mahboobi Marek Kieliszek Antoni Miecznikowski Hamid Sedighian Milad Rezaei Mohammad Ali Haghighi Zahra Zareh Ehsan Rezaei Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
description	The cytolethal distending toxin (CDT), <i>Haemophilus ducreyi</i>, is one of the bacterial toxins that have recently been considered for targeted therapies, especially in cancer therapies. CDT is an A-B2 exotoxin. Its catalytic subunit (CdtB) is capable of inducing DNA double strand breaks, cell cycle arrest and apoptosis in host eukaryotic cells. The sequence alignment indicates that the CdtB is structurally homologyr to phosphatases and deoxyribonucleases I (DNase I). Recently, it has been found that CdtB toxicity is mainly related to its nuclease activity. The immunogenicity of CDT can reduce its effectiveness in targeted therapies. However, the toxin can be very useful if its immunogenicity is significantly reduced. Detecting hotspot ectopic residues by computational servers and then mutating them to eliminate B-cell epitopes is a promising approach to reduce the immunogenicity of foreign protein-based therapeutics. By the mentioned method, in this study, we try to reduce the immunogenicity of the CdtB- protein sequence. This study initially screened residue of the CdtB is B-cell epitopes both linearly and conformationally. By overlapping the B-cell epitopes with the excluded conserve residues, and active and enzymatic sites, four residues were allowed to be mutated. There were two mutein options that show reduced antigenicity probability. Option one was N19F, G74I, and S161F with a VaxiJen score of 0.45 and the immune epitope database (IEDB) score of 1.80, and option two was N19F, G74I, and S161W with a VaxiJen score of 0.45 and IEDB score of 1.88. The 3D structure of the proposed sequences was evaluated and refined. The structural stability of native and mutant proteins was accessed through molecular dynamic simulation. The results showed that the mutations in the mutants caused no considerable changes in their structural stability. However, mutant 1 reveals more thermodynamic stability during the simulation. The applied approaches in this study can be used as rough guidelines for finding hot spot immunogen regions in the therapeutic proteins. Our results provide a new version of CdtB that, due to reduced immunogenicity and increased stability, can be used in toxin-based drugs such as immunotoxins.
format	article
author	Maryam Keshtvarz Mahdieh Mahboobi Marek Kieliszek Antoni Miecznikowski Hamid Sedighian Milad Rezaei Mohammad Ali Haghighi Zahra Zareh Ehsan Rezaei
author_facet	Maryam Keshtvarz Mahdieh Mahboobi Marek Kieliszek Antoni Miecznikowski Hamid Sedighian Milad Rezaei Mohammad Ali Haghighi Zahra Zareh Ehsan Rezaei
author_sort	Maryam Keshtvarz
title	Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
title_short	Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
title_full	Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
title_fullStr	Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
title_full_unstemmed	Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study
title_sort	engineering of cytolethal distending toxin b by its reducing immunogenicity and maintaining stability as a new drug candidate for tumor therapy; an in silico study
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/148446ce389d4c62b5445fcaf8876908
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Engineering of Cytolethal Distending Toxin B by Its Reducing Immunogenicity and Maintaining Stability as a New Drug Candidate for Tumor Therapy; an In Silico Study

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