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Advances in Antibody Design and Antigenic Peptide Targeting 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (20 October 2022) | Viewed by 24686

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Prof. Dr. Gunnar Houen

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Guest Editor

Department of Neurology Rigshospitalet Glostrup, Valdemar Hansens vej 1-23, 2600 Glostrup, Denmark
Interests: antibodies; aptamers; peptides; peptide antibodies; recognition molecules; synthetic libraries
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Dr. Nicole H. Trier

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Guest Editor

Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens vej 1-23, 2600 Glostrup, Denmark
Interests: rheumatoid arthritis; anti-citrullinated protein antibodies; citrullinated epitopes; cyclic citrullinated peptides
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Antibodies are natural, large multimeric proteins with high affinities and specific recognition properties. Antibodies can be made in large amounts by recombinant technology and can be engineered in several ways to modify their properties, e.g., structure, immunogenicity, and effector functions. Moreover, antibodies are crucial components in diagnostics, therapeutics. and as research tools and can be directed to numerus targets, e.g., peptides, proteins, or other molecular components.

The majority of antibodies recognize three-dimensional structures of the antigen, composed of small parts of the primary structure which are brought together upon protein folding. Only a small number of antibodies recognize a small stretch of amino acids in the primary structure, referred to as continuous epitopes. Antibodies directed to peptides tend to recognize continuous epitopes, whereas antibodies to native protein structures primarily recognize three-dimensional structures. Nevertheless, a small number of protein antibodies do recognize continuous peptide epitopes, given that the epitope is accessible on the surface in a region of a flexible structure, or the protein is unfolded.

The advantage of using peptide antibodies is that peptides can be made synthetically in essentially unlimited amounts, with post-translational modifications, non-natural amino acids, and L- or D-amino acids. Based on a seemingly unlimited number of possible options for antigenic peptide targeting, peptide antibodies are valuable reagents for several purposes, e.g., for the targeting of modified targets for epitope mapping. However, as peptide antibodies typically recognize targets of very little defined structure, they are sometimes unsuitable as specific reagents for target recognition.

The use of synthetic peptides for the production of antibodies (peptide antibodies) has been extremely rewarding in all areas of biology and biotechnology and continues to be of major importance. Although peptide antibodies are particularly good at recognizing continuous epitopes, post-translationally modified epitopes, and denatured proteins, several goals remain to be achieved in relation to peptides and antibodies, such as the design and synthesis of (constrained) peptides with specific recognition properties and the use of peptides as therapeutic vaccines.

This issue of IJMS aims to describe current knowledge about specially designed peptides and antibodies with a particular emphasis on sophisticated peptide antibodies and peptide targeting in general.

Prof. Dr. Gunnar Houen
Dr. Nicole H. Trier
Guest Editors

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Editorial

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2 pages, 186 KiB

Open AccessEditorial

Advances in Antibody Design and Antigenic Peptide Targeting 2.0

by Nicole Hartwig Trier and Gunnar Houen

Int. J. Mol. Sci. 2023, 24(9), 8033; https://doi.org/10.3390/ijms24098033 - 28 Apr 2023

Viewed by 1157

Abstract

Antibodies possess numerous important functions in diagnostics, both as therapeutics and as research tools [...] Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

Research

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13 pages, 1450 KiB

Open AccessArticle

Comparative Evaluation of Reproducibility of Phage-Displayed Peptide Selections and NGS Data, through High-Fidelity Mapping of Massive Peptide Repertoires

by Klaus G. Petry, Eleftherios Pilalis and Aristotelis Chatziioannou

Int. J. Mol. Sci. 2023, 24(2), 1594; https://doi.org/10.3390/ijms24021594 - 13 Jan 2023

Cited by 2 | Viewed by 1903

Abstract

Phage-displayed peptide selections generate complex repertoires of several hundred thousand peptides as revealed by next-generation sequencing (NGS). In repeated peptide selections, however, even in identical experimental in vitro conditions, only a very small number of common peptides are found. The repertoire complexities are evidence of the difficulty of distinguishing between effective selections of specific peptide binders to exposed targets and the potential high background noise. Such investigation is even more relevant when considering the plethora of in vivo expressed targets on cells, in organs or in the entire organism to define targeting peptide agents. In the present study, we compare the published NGS data of three peptide repertoires that were obtained by phage display under identical experimental in vitro conditions. By applying the recently developed tool PepSimili we evaluate the calculated similarities of the individual peptides from each of these three repertoires and perform their mappings on the human proteome. The peptide-to-peptide mappings reveal high similarities among the three repertoires, confirming the desired reproducibility of phage-displayed peptide selections. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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17 pages, 2727 KiB

Open AccessArticle

Selective Silencing of Disease-Associated B Lymphocytes from Hashimoto’s Thyroiditis Patients by Chimeric Protein Molecules

by Nikola Ralchev Ralchev, Aleksandar Mishel Markovski, Inna Angelova Yankova, Iliyan Konstantinov Manoylov, Irini Atanas Doytchinova, Nikolina Mihaylova Mihaylova, Alexander Dimitrov Shinkov and Andrey Ivanov Tchorbanov

Int. J. Mol. Sci. 2022, 23(23), 15083; https://doi.org/10.3390/ijms232315083 - 1 Dec 2022

Cited by 2 | Viewed by 1983

Abstract

Hashimoto’s thyroiditis is one of the most common endocrine disorders, affecting up to 20% of the adult population. No treatment or prevention exists except hormonal substitution for hypothyroidism. We hypothesize that it may be possible to selectively suppress anti-thyroglobulin (Tg) IgG antibody-producing B lymphocytes from HT patients by a chimeric protein molecule containing a monoclonal antibody specific for the human inhibitory receptor CR1, coupled to peptide epitopes derived from Tg protein. We expect that this treatment will down-regulate B-cell autoreactivity by delivering a strong inhibitory signal. Three peptides—two epitope-predicted ones derived from Tg and another irrelevant peptide—were synthesized and then coupled with monoclonal anti-human CR1 antibody to construct three chimeric molecules. The binding to CD35 on human B cells and the effects of the chimeric constructs on PBMC and TMC from patients with HT were tested using flow cytometry, ELISpot assay, and immunoenzyme methods. We found that after the chemical conjugation, all chimeras retained their receptor-binding capacity, and the Tg epitopes could be recognized by anti-Tg autoantibodies in the patients’ sera. This treatment downregulated B-cell autoreactivity and cell proliferation, inhibited Tg-specific B-cell differentiation to plasmablasts and promoted apoptosis to the targeted cells. The treatment of PBMCs from HT patients with Tg-epitope-carrying chimeric molecules affects the activity of Tg-specific autoreactive B lymphocytes, delivering to them a strong suppressive signal. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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12 pages, 2767 KiB

Open AccessArticle

Potential Antigenic Candidates for the Development of Peptide-Based Vaccines to Induce Immunization against Helicobacter pylori Infection in BALB/c Mice

by Doaa M. AlEraky, Hatem M. Abuohashish, Amr S. Bugshan, Maha M. Abdelsalam, Hussain A. AlHawaj, Taleb T. AlKhamis, Fatimah A. AlDossary, Nabras M. Alrayes, Yasser M. Ragab, Zeinab AbdelKhalek, Omneya M. Helmy and Mohammed A. Ramadan

Int. J. Mol. Sci. 2022, 23(21), 12824; https://doi.org/10.3390/ijms232112824 - 24 Oct 2022

Cited by 3 | Viewed by 2599

Abstract

Helicobacter pylori (H. pylori) has been identified as a group-1 definite carcinogen. As of yet, there is no available vaccine for this microorganism. Our study aimed to identify antigenic peptides in H. pylori using an in silico proteomic approach, and to evaluate their effectiveness as potential vaccine candidates. Four different peptide sequences were prioritized using the reverse vaccinology, namely, CagA¹, CagA², VacA, and SabA. Peptides emulsified with Freunde’s adjuvant were used to immunize BALB/C mice. Subcutaneously immunized mice were challenged by oral administration of H. pylori. IgG, IgA, IL4, and IL17 were detected in mice sera. Histopathology of the dissected stomach of vaccinated and control mice were assessed using H&E stain. IgG was significantly higher in mice vaccinated with SabA. IL-4 was significantly increased in CagA¹, CagA², VacA, and SabA vaccinated mice compared to the adjuvant group. Additionally, histopathological examination of gastric tissue showed a protective effect in the vaccinated groups compared to adjuvant and PBS groups. Our findings indicate a promising effect of the tested epitopes, particularly the SabA antigen, to induce an immune response against H. pylori. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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14 pages, 2896 KiB

Open AccessArticle

Neutralizing Ability of a Single Domain VNAR Antibody: In Vitro Neutralization of SARS-CoV-2 Variants of Concern

by Blanca J. Valdovino-Navarro, Salvador Dueñas, G. Isaí Flores-Acosta, Jahaziel Gasperin-Bulbarela, Johanna Bernaldez-Sarabia, Olivia Cabanillas-Bernal, Karla E. Cervantes-Luevano and Alexei F. Licea-Navarro

Int. J. Mol. Sci. 2022, 23(20), 12267; https://doi.org/10.3390/ijms232012267 - 14 Oct 2022

Cited by 10 | Viewed by 2344

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 is the causal pathogen of coronavirus disease 2019 (COVID-19). The emergence of new variants with different mutational patterns has limited the therapeutic options available and complicated the development of effective neutralizing antibodies targeting the spike (S) protein. Variable New Antigen Receptors (VNARs) constitute a neutralizing antibody technology that has been introduced into the list of possible therapeutic options against SARS-CoV-2. The unique qualities of VNARs, such as high affinities for target molecules, capacity for paratope reformatting, and relatively high stability, make them attractive molecules to counteract the emerging SARS-CoV-2 variants. In this study, we characterized a VNAR antibody (SP240) that was isolated from a synthetic phage library of VNAR domains. In the phage display, a plasma with high antibody titers against SARS-CoV-2 was used to selectively displace the VNAR antibodies bound to the antigen SARS-CoV-2 receptor binding domain (RBD). In silico data suggested that the SP240 binding epitopes are located within the ACE2 binding interface. The neutralizing ability of SP240 was tested against live Delta and Omicron SARS-CoV-2 variants and was found to clear the infection of both variants in the lung cell line A549-ACE2-TMPRSS2. This study highlights the potential of VNARs to act as neutralizing antibodies against emerging SARS-CoV-2 variants. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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9 pages, 4031 KiB

Open AccessArticle

A New Neutralization Epitope in the Spike Protein of Porcine Epidemic Diarrhea Virus

by Jianbo Liu, Hongyan Shi, Jianfei Chen, Xin Zhang, Da Shi, Zhaoyang Ji, Zhaoyang Jing and Li Feng

Int. J. Mol. Sci. 2022, 23(17), 9674; https://doi.org/10.3390/ijms23179674 - 26 Aug 2022

Cited by 8 | Viewed by 2236

Abstract

Porcine epidemic diarrhea virus (PEDV) infects piglets and causes serious diarrhea as well as vomiting, dehydration, and death. The trimeric S protein plays a crucial role in the induction of neutralizing antibodies, and many neutralizing monoclonal antibodies (mAbs) against PEDV S protein have been developed. However, these mAbs exclusively target the S1 protein. In this study, we obtained a neutralizing mAb, 5F7, against the S2 protein of PEDV, and this mAb could neutralize new variant genotype 2 PEDV strains (LNCT2), as well as a genotype 1 PEDV strain (CV777), in vitro. The core sequence of the epitope was found in amino acid sequence 1261 aa~1337 aa. These findings confirm that the S2 protein possessed neutralizing epitopes and provided knowledge to aid further research on this virus. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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21 pages, 2491 KiB

Open AccessArticle

Production and Characterization of Peptide Antibodies to the C-Terminal of Frameshifted Calreticulin Associated with Myeloproliferative Diseases

by Farah Perveen Mughal, Ann Christina Bergmann, Ha Uyen Buu Huynh, Sarah Hyllekvist Jørgensen, Inaam Mansha, Meliha Kesmez, Patrick Mark Schürch, Alexandre Pierre André Theocharides, Paul Robert Hansen, Tina Friis, Morten Orebo Holmström, Evaldas Ciplys, Rimantas Slibinskas, Peter Højrup, Gunnar Houen and Nicole Hartwig Trier

Int. J. Mol. Sci. 2022, 23(12), 6803; https://doi.org/10.3390/ijms23126803 - 18 Jun 2022

Cited by 14 | Viewed by 3143

Abstract

Myeloproliferative Neoplasms (MPNs) constitute a group of rare blood cancers that are characterized by mutations in bone marrow stem cells leading to the overproduction of erythrocytes, leukocytes, and thrombocytes. Mutations in calreticulin (CRT) genes may initiate MPNs, causing a novel variable polybasic stretch terminating in a common C-terminal sequence in the frameshifted CRT (CRTfs) proteins. Peptide antibodies to the mutated C-terminal are important reagents for research in the molecular mechanisms of MPNs and for the development of new diagnostic assays and therapies. In this study, eight peptide antibodies targeting the C-terminal of CRTfs were produced and characterised by modified enzyme-linked immunosorbent assays using resin-bound peptides. The antibodies reacted to two epitopes: CREACLQGWTE for SSI-HYB 385-01, 385-02, 385-03, 385-04, 385-07, 385-08, and 385-09 and CLQGWT for SSI-HYB 385-06. For the majority of antibodies, the residues Cys¹, Trp⁹, and Glu¹¹ were essential for reactivity. SSI-HYB 385-06, with the highest affinity, recognised recombinant CRTfs produced in yeast and the MARIMO cell line expressing CRTfs when examined in Western immunoblotting. Moreover, SSI-HYB 385-06 occasionally reacted to CRTfs from MPN patients when analysed by flow cytometry. The characterized antibodies may be used to understand the role of CRTfs in the pathogenesis of MPNs and to design and develop new diagnostic assays and therapeutic targets. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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13 pages, 1523 KiB

Open AccessArticle

The Anti-Glucocorticoid Receptor Antibody Clone 5E4: Raising Awareness of Unspecific Antibody Binding

by Lisa Ehlers, Marieluise Kirchner, Philipp Mertins, Cindy Strehl, Frank Buttgereit and Timo Gaber

Int. J. Mol. Sci. 2022, 23(9), 5049; https://doi.org/10.3390/ijms23095049 - 2 May 2022

Cited by 1 | Viewed by 2157

Abstract

Unspecific antibody binding takes a significant toll on researchers in the form of both the economic burden and the disappointed hopes of promising new therapeutic targets. Despite recent initiatives promoting antibody validation, a uniform approach addressing this issue has not yet been developed. Here, we demonstrate that the anti-glucocorticoid receptor (GR) antibody clone 5E4 predominantly targets two different proteins of approximately the same size, namely AMP deaminase 2 (AMPD2) and transcription intermediary factor 1-beta (TRIM28). This paper is intended to generate awareness of unspecific binding of well-established reagents and advocate the use of more rigorous verification methods to improve antibody quality in the future. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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16 pages, 3551 KiB

Open AccessArticle

Peptide Antibody Reactivity to Homologous Regions in Glutamate Decarboxylase Isoforms and Coxsackievirus B4 P2C

by Nicole Hartwig Trier, Niccolo Valdarnini, Ilaria Fanelli, Paolo Rovero, Paul Robert Hansen, Claus Schafer-Nielsen, Evaldas Ciplys, Rimantas Slibinskas, Flemming Pociot, Tina Friis and Gunnar Houen

Int. J. Mol. Sci. 2022, 23(8), 4424; https://doi.org/10.3390/ijms23084424 - 17 Apr 2022

Cited by 7 | Viewed by 2430

Abstract

Two isoforms of the glutamate decarboxylase (GAD) enzyme exist, GAD65 and GAD67, which are associated with type 1 diabetes (T1D) and stiff-person syndrome (SPS), respectively. Interestingly, it has been reported that T1D patients seldom develop SPS, whereas patients with SPS occasionally develop T1D. In addition, coxsackievirus B4 (CVB4) has previously been proposed to be involved in the onset of T1D through molecular mimicry. On this basis, we aimed to examine antibody cross-reactivity between a specific region of GAD65 and GAD67, which has high sequence homology to the nonstructural P2C protein of CVB4 to determine potential correlations at antibody level. Monoclonal peptide antibodies generated in mice specific for a region with high similarity in all three proteins were screened for reactivity along with human sera in immunoassays. In total, six antibodies were generated. Two of the antibodies reacted to both GAD isoforms. However, none of the antibodies were cross-reactive to CVB, suggesting that antibody cross-reactivity between GAD65 and CVB, and GAD67 and CVB may not contribute to the onset of T1D and SPS, respectively. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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Review

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15 pages, 1130 KiB

Open AccessReview

Identification of B-Cell Epitopes for Eliciting Neutralizing Antibodies against the SARS-CoV-2 Spike Protein through Bioinformatics and Monoclonal Antibody Targeting

by Hui Xuan Lim, Malihe Masomian, Kanwal Khalid, Asqwin Uthaya Kumar, Paul A. MacAry and Chit Laa Poh

Int. J. Mol. Sci. 2022, 23(8), 4341; https://doi.org/10.3390/ijms23084341 - 14 Apr 2022

Cited by 13 | Viewed by 3453

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, especially in reducing the transmission of SARS-CoV-2 and hospitalization incidences. In view of the emergence of new SARS-CoV-2 variants, vaccines developed against the Wuhan strain were less effective against the variants. Neutralizing antibodies produced by B cells are a critical component of adaptive immunity, particularly in neutralizing viruses by blocking virus attachment and entry into cells. Therefore, the identification of protective linear B-cell epitopes can guide epitope-based peptide designs. This study reviews the identification of SARS-CoV-2 B-cell epitopes within the spike, membrane and nucleocapsid proteins that can be incorporated as potent B-cell epitopes into peptide vaccine constructs. The bioinformatic approach offers a new in silico strategy for the mapping and identification of potential B-cell epitopes and, upon in vivo validation, would be useful for the rapid development of effective multi-epitope-based vaccines. Potent B-cell epitopes were identified from the analysis of three-dimensional structures of monoclonal antibodies in a complex with SARS-CoV-2 from literature mining. This review provides significant insights into the elicitation of potential neutralizing antibodies by potent B-cell epitopes, which could advance the development of multi-epitope peptide vaccines against SARS-CoV-2. Full article

(This article belongs to the Special Issue Advances in Antibody Design and Antigenic Peptide Targeting 2.0)

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