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Yang Z, Wang C, Liu J, Xiao L, Guo L, Xie J. In Silico-Ex Vitro Iteration Strategy for Affinity Maturation of Anti-Ricin Peptides and the SPR Biosensing Application. Toxins (Basel) 2023; 15:490. [PMID: 37624247 PMCID: PMC10467137 DOI: 10.3390/toxins15080490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
The highly toxic plant toxin ricin is one of the most known threatening toxins. Accurate and sensitive biosensing methods for the first emergency response and intoxication treatment, are always pursued in the biodefense field. Screening affinity molecules is the fundamental mainstream approach for developing biosensing methods. Compared with common affinity molecules such as antibodies and oligonucleotide aptamers, peptides have great potential as biosensing modules with more accessible chemical synthesis capability and better batch-to-batch stability than antibodies, more abundant interaction sites, and robust sensing performance towards complex environments. However, anti-ricin peptides are so scant to be screened and discovered, and an advanced screening strategy is the utmost to tackle this issue. Here, we present a new in silico-in vitro iteration-assisted affinity maturation strategy of anti-ricin peptides. We first obtained affinity peptides targeting ricin through phage display with five panning rounds of "coating-elution-amplification-enrichment" procedures. The binding affinity and kinetic parameters characterized by surface plasmon resonance (SPR) showed that we had obtained four peptides owning dissociation constants (KD) around 2~35 μM, in which peptide PD-2-R5 has the lower KD of 4.7 μM and higher stable posture to interact with ricin. We then constructed a new strategy for affinity maturity, composing two rounds of in silico-in vitro iterations. Firstly, towards the single-site alanine scanning mutation peptide library, the molecular docking predictions match the SPR evaluation results well, laying a solid foundation for designing a full saturation mutated peptide library. Secondly, plenty of in silico saturation mutation prediction results guided the discovery of peptides PD2-R5-T3 and PD-2-R5-T4 with higher affinity from only a limited number of SPR evaluation experiments. Both evolved peptides had increased affinity by about 5~20 times, i.e., KD of 230 nM and 900 nM. A primary cellular toxicity assay indicated that both peptides could protect cells against ricin damage. We further established an SPR assay based on PD-2-R5-T3 and PD-2-R5-T4 elongated with an antifouling peptide linkage and achieved good linearity with a sensitivity of 1 nM and 0.5 nM, respectively. We hope this new affinity-mature strategy will find its favorable position in relevant peptide evolution, biosensing, and medical countermeasures for biotoxins to protect society's security and human life better.
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Affiliation(s)
- Zhifang Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Chuang Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
- Key Laboratory of Ethnomedicine Ministry of Education (Minzu University of China), School of Pharmacy, Minzu University of China, Beijing 100081, China
| | - Jia Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
- College of Pharmacy, Hebei Science and Technology University, Shijiazhuang 050018, China
| | - Lan Xiao
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
- Key Laboratory of Ethnomedicine Ministry of Education (Minzu University of China), School of Pharmacy, Minzu University of China, Beijing 100081, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
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Teixeira AAR, D'Angelo S, Erasmus MF, Leal-Lopes C, Ferrara F, Spector LP, Naranjo L, Molina E, Max T, DeAguero A, Perea K, Stewart S, Buonpane RA, Nastri HG, Bradbury ARM. Simultaneous affinity maturation and developability enhancement using natural liability-free CDRs. MAbs 2022; 14:2115200. [PMID: 36068722 PMCID: PMC9467613 DOI: 10.1080/19420862.2022.2115200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Affinity maturation is often a necessary step for the development of potent therapeutic molecules. Many different diversification strategies have been used for antibody affinity maturation, including error-prone PCR, chain shuffling, and targeted complementary-determining region (CDR) mutation. Although effective, they can negatively impact antibody stability or alter epitope recognition. Moreover, they do not address the presence of sequence liabilities, such as glycosylation, asparagine deamidation, aspartate isomerization, aggregation motifs, and others. Such liabilities, if present or inadvertently introduced, can potentially create the need for new rounds of engineering, or even abolish the value of the antibody as a therapeutic molecule. Here, we demonstrate a sequence agnostic method to improve antibody affinities, while simultaneously eliminating sequence liabilities and retaining the same epitope binding as the parental antibody. This was carried out using a defined collection of natural CDRs as the diversity source, purged of sequence liabilities, and matched to the antibody germline gene family. These CDRs were inserted into the lead molecule in one or two sites at a time (LCDR1-2, LCDR3, HCDR1-2) while retaining the HCDR3 and framework regions unchanged. The final analysis of 92 clones revealed 81 unique variants, with each of 24 tested variants having the same epitope specificity as the parental molecule. Of these, the average affinity improved by over 100 times (to 96 pM), and the best affinity improvement was 231-fold (to 32 pM).
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Smith K, Garman L, Norris K, Muther J, Duke A, Engler RJM, Nelson MR, Collins LC, Spooner C, Guthridge C, James JA. Insufficient Anthrax Lethal Toxin Neutralization Is Associated with Antibody Subclass and Domain Specificity in the Plasma of Anthrax-Vaccinated Individuals. Microorganisms 2021; 9:microorganisms9061204. [PMID: 34199431 PMCID: PMC8229884 DOI: 10.3390/microorganisms9061204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 11/17/2022] Open
Abstract
Anthrax vaccine adsorbed (AVA) is a significant line of defense against bioterrorist attack from Bacillus anthracis spores. However, in a subset of individuals, this vaccine may produce a suboptimal quantity of anti-protective antigen (PA), antibodies that are poorly neutralizing, and/or antibody titers that wane over time, necessitating annual boosters. To study individuals with such poor responses, we examine the properties of anti-PA in a subset of vaccinated individuals that make significant quantities of antibody but are still unable to neutralize toxin. In this cohort, characterized by poorly neutralizing antibody, we find that increased IgG4 to IgG1 subclass ratios, low antibody avidity, and insufficient antibody targeting domain 4 associate with improper neutralization. Thus, future vaccines and vaccination schedules should be formulated to improve these deficiencies.
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Affiliation(s)
- Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
- Correspondence: (K.S.); (J.A.J.); Tel.: +1-405-271-3275 (K.S.); +1-405-271-4987 (J.A.J.)
| | - Lori Garman
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA;
| | - Kathleen Norris
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
| | - Jennifer Muther
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
| | - Angie Duke
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
| | - Renata J. M. Engler
- Walter Reed National Military Medical Center, 8901 Wisconsin Ave, Bethesda, MD 20814, USA; (R.J.M.E.); (M.R.N.); (L.C.C.); (C.S.)
| | - Michael R. Nelson
- Walter Reed National Military Medical Center, 8901 Wisconsin Ave, Bethesda, MD 20814, USA; (R.J.M.E.); (M.R.N.); (L.C.C.); (C.S.)
| | - Limone C. Collins
- Walter Reed National Military Medical Center, 8901 Wisconsin Ave, Bethesda, MD 20814, USA; (R.J.M.E.); (M.R.N.); (L.C.C.); (C.S.)
| | - Christina Spooner
- Walter Reed National Military Medical Center, 8901 Wisconsin Ave, Bethesda, MD 20814, USA; (R.J.M.E.); (M.R.N.); (L.C.C.); (C.S.)
| | - Carla Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
| | - Judith A. James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, 825 NE 13th St., Oklahoma City, OK 73104, USA; (K.N.); (J.M.); (A.D.); (C.G.)
- Department of Microbiology and Immunology, Oklahoma University Health Science Center, 940 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Departments of Medicine and Pathology, Oklahoma University Health Science Center, 1000 Stanton L. Young Blvd, Oklahoma City, OK 73104, USA
- Correspondence: (K.S.); (J.A.J.); Tel.: +1-405-271-3275 (K.S.); +1-405-271-4987 (J.A.J.)
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Vajda S, Porter KA, Kozakov D. Progress toward improved understanding of antibody maturation. Curr Opin Struct Biol 2021; 67:226-231. [PMID: 33610066 DOI: 10.1016/j.sbi.2020.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Upon encountering an antigen, antibodies mature through various rounds of somatic mutations, resulting in higher affinities and specificities to the particular antigen. We review recent progress in four areas of antibody maturation studies. (1) Next-generation and single-cell sequencing have revolutionized the analysis of antibody repertoires by dramatically increasing the sequences available to study the state and evolution of the immune system. Computational methods, including machine learning tools, have been developed for reconstituting antibody clonal lineages and for general repertoire analysis. (2) The availability of X-ray structures, thermodynamic and kinetic data, and molecular dynamics simulations provide information on the biophysical mechanisms responsible for improved affinity. (3) In addition to improved binding to a specific antigen, providing affinity-independent diversity and self/nonself discrimination are fundamental functions of the immune system. Recent studies, including X-ray structures, yield improved understanding of both mechanisms. (4) Results from in vivo maturation help to develop methods of in vitro maturation to improve antibody properties for therapeutic applications, frequently combining computational and experimental approaches.
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Affiliation(s)
- Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston MA 02215, United States.
| | - Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston MA 02215, United States
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook NY 11794, United States; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook NY, 11790, United States.
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Orsini Delgado ML, Avril A, Prigent J, Dano J, Rouaix A, Worbs S, Dorner BG, Rougeaux C, Becher F, Fenaille F, Livet S, Volland H, Tournier JN, Simon S. Ricin Antibodies' Neutralizing Capacity against Different Ricin Isoforms and Cultivars. Toxins (Basel) 2021; 13:100. [PMID: 33573016 PMCID: PMC7911099 DOI: 10.3390/toxins13020100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
Ricin, a highly toxic protein from Ricinus communis, is considered a potential biowarfare agent. Despite the many data available, no specific treatment has yet been approved. Due to their ability to provide immediate protection, antibodies (Abs) are an approach of choice. However, their high specificity might compromise their capacity to protect against the different ricin isoforms (D and E) found in the different cultivars. In previous work, we have shown the neutralizing potential of different Abs (43RCA-G1 (anti ricin A-chain) and RB34 and RB37 (anti ricin B-chain)) against ricin D. In this study, we evaluated their protective capacity against both ricin isoforms. We show that: (i) RB34 and RB37 recognize exclusively ricin D, whereas 43RCA-G1 recognizes both isoforms, (ii) their neutralizing capacity in vitro varies depending on the cultivar, and (iii) there is a synergistic effect when combining RB34 and 43RCA-G1. This effect is also demonstrated in vivo in a mouse model of intranasal intoxication with ricin D/E (1:1), where approximately 60% and 40% of mice treated 0 and 6 h after intoxication, respectively, are protected. Our results highlight the importance of evaluating the effectiveness of the Abs against different ricin isoforms to identify the treatment with the broadest spectrum neutralizing effect.
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Affiliation(s)
- Maria Lucia Orsini Delgado
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Arnaud Avril
- Microbiology and Infectious Diseases Department, Anti-Infectious Biotherapies and Immunity Unit, Army Biomedical Research Institute, 91220 Brétigny-sur-Orge, France; (A.A.); (C.R.); (J.-N.T.)
| | - Julie Prigent
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Julie Dano
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Audrey Rouaix
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Sylvia Worbs
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute (RKI), 13353 Berlin, Germany; (S.W.); (B.G.D.)
| | - Brigitte G. Dorner
- Biological Toxins, Centre for Biological Threats and Special Pathogens, Robert Koch Institute (RKI), 13353 Berlin, Germany; (S.W.); (B.G.D.)
| | - Clémence Rougeaux
- Microbiology and Infectious Diseases Department, Anti-Infectious Biotherapies and Immunity Unit, Army Biomedical Research Institute, 91220 Brétigny-sur-Orge, France; (A.A.); (C.R.); (J.-N.T.)
| | - François Becher
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - François Fenaille
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Sandrine Livet
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Hervé Volland
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
| | - Jean-Nicolas Tournier
- Microbiology and Infectious Diseases Department, Anti-Infectious Biotherapies and Immunity Unit, Army Biomedical Research Institute, 91220 Brétigny-sur-Orge, France; (A.A.); (C.R.); (J.-N.T.)
| | - Stéphanie Simon
- Paris-Saclay University, CEA, INRAE, Medicines and Healthcare Technologies Department (DMTS), SPI, 91191 Gif-sur-Yvette, France; (J.P.); (J.D.); (A.R.); (F.B.); (F.F.); (S.L.); (H.V.)
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Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics 2019; 35:462-469. [PMID: 30020414 PMCID: PMC6361233 DOI: 10.1093/bioinformatics/bty635] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/17/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. Results We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. This version now contains manually curated binding data for 7085 mutations, an increase of 133%, including changes in kinetics for 1844 mutations, enthalpy and entropy changes for 443 mutations, and 440 mutations, which abolish detectable binding. Availability and implementation The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justina Jankauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Brian Jiménez-García
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Justas Dapkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institut de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Iain H Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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Mooney B, Torres‐Velez FJ, Doering J, Ehrbar DJ, Mantis NJ. Sensitivity of Kupffer cells and liver sinusoidal endothelial cells to ricin toxin and ricin toxin-Ab complexes. J Leukoc Biol 2019; 106:1161-1176. [PMID: 31313388 PMCID: PMC7008010 DOI: 10.1002/jlb.4a0419-123r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/03/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022] Open
Abstract
Ricin toxin is a plant-derived, ribosome-inactivating protein that is rapidly cleared from circulation by Kupffer cells (KCs) and liver sinusoidal endothelial cells (LSECs)-with fatal consequences. Rather than being inactivated, ricin evades normal degradative pathways and kills both KCs and LSECs with remarkable efficiency. Uptake of ricin by these 2 specialized cell types in the liver occurs by 2 parallel routes: a "lactose-sensitive" pathway mediated by ricin's galactose/N-acetylgalactosamine-specific lectin subunit (RTB), and a "mannose-sensitive" pathway mediated by the mannose receptor (MR; CD206) or other C-type lectins capable of recognizing the mannose-side chains displayed on ricin's A (RTA) and B subunits. In this report, we investigated the capacity of a collection of ricin-specific mouse MAb and camelid single-domain (VH H) antibodies to protect KCs and LSECs from ricin-induced killing. In the case of KCs, individual MAbs against RTA or RTB afforded near complete protection against ricin in ex vivo and in vivo challenge studies. In contrast, individual MAbs or VH Hs afforded little (<40%) or even no protection to LSECs against ricin-induced death. Complete protection of LSECs was only achieved with MAb or VH H cocktails, with the most effective mixtures targeting RTA and RTB simultaneously. Although the exact mechanisms of protection of LSECs remain unknown, evidence indicates that the Ab cocktails exert their effects on the mannose-sensitive uptake pathway without the need for Fcγ receptor involvement. In addition to advancing our understanding of how toxins and small immune complexes are processed by KCs and LSECs, our study has important implications for the development of Ab-based therapies designed to prevent or treat ricin exposure should the toxin be weaponized.
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Affiliation(s)
- Bridget Mooney
- Division of Infectious DiseasesWadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Fernando J. Torres‐Velez
- Division of Infectious DiseasesWadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Jennifer Doering
- Division of Infectious DiseasesWadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Dylan J. Ehrbar
- Division of Infectious DiseasesWadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
| | - Nicholas J. Mantis
- Division of Infectious DiseasesWadsworth CenterNew York State Department of HealthAlbanyNew YorkUSA
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Franke H, Scholl R, Aigner A. Ricin and Ricinus communis in pharmacology and toxicology-from ancient use and "Papyrus Ebers" to modern perspectives and "poisonous plant of the year 2018". Naunyn Schmiedebergs Arch Pharmacol 2019; 392:1181-1208. [PMID: 31359089 DOI: 10.1007/s00210-019-01691-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
While probably originating from Africa, the plant Ricinus communis is found nowadays around the world, grown for industrial use as a source of castor oil production, wildly sprouting in many regions, or used as ornamental plant. As regards its pharmacological utility, a variety of medical purposes of selected parts of the plant, e.g., as a laxative, an anti-infective, or an anti-inflammatory drug, have been described already in the sixteenth century BC in the famous Papyrus Ebers (treasured in the Library of the University of Leipzig). Quite in contrast, on the toxicological side, the native plant has become the "poisonous plant 2018" in Germany. As of today, a number of isolated components of the plant/seeds have been characterized, including, e.g., castor oil, ricin, Ricinus communis agglutinin, ricinin, nudiflorin, and several allergenic compounds. This review mainly focuses on the most toxic protein, ricin D, classified as a type 2 ribosome-inactivating protein (RIP2). Ricin is one of the most potent and lethal substances known. It has been considered as an important bioweapon (categorized as a Category B agent (second-highest priority)) and an attractive agent for bioterroristic activities. On the other hand, ricin presents great potential, e.g., as an anti-cancer agent or in cell-based research, and is even explored in the context of nanoparticle formulations in tumor therapy. This review provides a comprehensive overview of the pharmacology and toxicology-related body of knowledge on ricin. Toxicokinetic/toxicodynamic aspects of ricin poisoning and possibilities for analytical detection and therapeutic use are summarized as well.
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Affiliation(s)
- Heike Franke
- Rudolf-Boehm-Institute of Pharmacology and Toxicology, Medical Faculty, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
| | - Reinhold Scholl
- Department of History, University of Leipzig, Leipzig, Germany
| | - Achim Aigner
- Rudolf-Boehm-Institute of Pharmacology and Toxicology, Clinical Pharmacology, Medical Faculty, University of Leipzig, Leipzig, Germany
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9
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Antibody Cross-Reactivity in Antivenom Research. Toxins (Basel) 2018; 10:toxins10100393. [PMID: 30261694 PMCID: PMC6215175 DOI: 10.3390/toxins10100393] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/04/2022] Open
Abstract
Antivenom cross-reactivity has been investigated for decades to determine which antivenoms can be used to treat snakebite envenomings from different snake species. Traditionally, the methods used for analyzing cross-reactivity have been immunodiffusion, immunoblotting, enzyme-linked immunosorbent assay (ELISA), enzymatic assays, and in vivo neutralization studies. In recent years, new methods for determination of cross-reactivity have emerged, including surface plasmon resonance, antivenomics, and high-density peptide microarray technology. Antivenomics involves a top-down assessment of the toxin-binding capacities of antivenoms, whereas high-density peptide microarray technology may be harnessed to provide in-depth knowledge on which toxin epitopes are recognized by antivenoms. This review provides an overview of both the classical and new methods used to investigate antivenom cross-reactivity, the advantages and disadvantages of each method, and examples of studies using the methods. A special focus is given to antivenomics and high-density peptide microarray technology as these high-throughput methods have recently been introduced in this field and may enable more detailed assessments of antivenom cross-reactivity.
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Ledsgaard L, Kilstrup M, Karatt-Vellatt A, McCafferty J, Laustsen AH. Basics of Antibody Phage Display Technology. Toxins (Basel) 2018; 10:E236. [PMID: 29890762 PMCID: PMC6024766 DOI: 10.3390/toxins10060236] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 01/12/2023] Open
Abstract
Antibody discovery has become increasingly important in almost all areas of modern medicine. Different antibody discovery approaches exist, but one that has gained increasing interest in the field of toxinology and antivenom research is phage display technology. In this review, the lifecycle of the M13 phage and the basics of phage display technology are presented together with important factors influencing the success rates of phage display experiments. Moreover, the pros and cons of different antigen display methods and the use of naïve versus immunized phage display antibody libraries is discussed, and selected examples from the field of antivenom research are highlighted. This review thus provides in-depth knowledge on the principles and use of phage display technology with a special focus on discovery of antibodies that target animal toxins.
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Affiliation(s)
- Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark.
| | - Mogens Kilstrup
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark.
| | | | | | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby DK-2800, Denmark.
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Wang Z, Li Y, Liang W, Zheng J, Li S, Hu C, Chen A. A Highly Sensitive Detection System based on Proximity-dependent Hybridization with Computer-aided Affinity Maturation of a scFv Antibody. Sci Rep 2018; 8:3837. [PMID: 29497069 PMCID: PMC5832849 DOI: 10.1038/s41598-018-22111-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/14/2018] [Indexed: 01/10/2023] Open
Abstract
The hepatitis B virus (HBV) infection is a critical health problem worldwide, and HBV preS1 is an important biomarker for monitoring HBV infection. Previously, we found that a murine monoclonal antibody, mAb-D8, targets the preS1 (aa91-107) fragment of HBV. To improve its performance, we prepared the single-chain variable region of mAb-D8 (scFvD8) and constructed the three-dimensional structure of the scFvD8-preS1 (aa91-107) complex by computer modelling. The affinity of scFvD8 was markedly increased by the introduction of mutations L96Tyr to Ser and H98Asp to Ser. Furthermore, a highly sensitive immunosensor was designed based on a proximity-dependent hybridization strategy in which the preS1 antigen competitively reacts with an antibody labelled with DNA, resulting in decreased proximity-dependent hybridization and increased electrochemical signal from the Fc fragment, which can be used for the quantisation of preS1. The results showed a wide detection range from 1 pM to 50 pM with a detection limit of 0.1 pM. The sensitivity and specificity of this immunosensor in clinical serum samples were 100% and 96%, respectively. This study provides a novel system based on proximity-dependent hybridization and the scFv antibody fragment for the rapid quantisation of antigens of interest with a high sensitivity.
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Affiliation(s)
- Zhiheng Wang
- Department of Clinical Biochemistry, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - Yan Li
- Department of Clinical Laboratory Science, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - Wenbin Liang
- Department of Clinical Biochemistry, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - Junsong Zheng
- Department of Clinical Laboratory Science, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - Shuhui Li
- Department of Clinical Biochemistry, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - Chuanmin Hu
- Department of Clinical Biochemistry, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China
| | - An Chen
- Department of Clinical Biochemistry, College of Medical Laboratory, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, PR China.
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High-Definition Mapping of Four Spatially Distinct Neutralizing Epitope Clusters on RiVax, a Candidate Ricin Toxin Subunit Vaccine. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00237-17. [PMID: 29046307 DOI: 10.1128/cvi.00237-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
RiVax is a promising recombinant ricin toxin A subunit (RTA) vaccine antigen that has been shown to be safe and immunogenic in humans and effective at protecting rhesus macaques against lethal-dose aerosolized toxin exposure. We previously used a panel of RTA-specific monoclonal antibodies (MAbs) to demonstrate, by competition enzyme-linked immunosorbent assay (ELISA), that RiVax elicits similar serum antibody profiles in humans and macaques. However, the MAb binding sites on RiVax have yet to be defined. In this study, we employed hydrogen exchange-mass spectrometry (HX-MS) to localize the epitopes on RiVax recognized by nine toxin-neutralizing MAbs and one nonneutralizing MAb. Based on strong protection from hydrogen exchange, the nine MAbs grouped into four spatially distinct epitope clusters (namely, clusters I to IV). Cluster I MAbs protected RiVax's α-helix B (residues 94 to 107), a protruding immunodominant secondary structure element known to be a target of potent toxin-neutralizing antibodies. Cluster II consisted of two subclusters located on the "back side" (relative to the active site pocket) of RiVax. One subcluster involved α-helix A (residues 14 to 24) and α-helices F-G (residues 184 to 207); the other encompassed β-strand d (residues 62 to 69) and parts of α-helices D-E (154 to 164) and the intervening loop. Cluster III involved α-helices C and G on the front side of RiVax, while cluster IV formed a sash from the front to back of RiVax, spanning strands b, c, and d (residues 35 to 59). Having a high-resolution B cell epitope map of RiVax will enable the development and optimization of competitive serum profiling assays to examine vaccine-induced antibody responses across species.
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Vance DJ, Tremblay JM, Rong Y, Angalakurthi SK, Volkin DB, Middaugh CR, Weis DD, Shoemaker CB, Mantis NJ. High-Resolution Epitope Positioning of a Large Collection of Neutralizing and Nonneutralizing Single-Domain Antibodies on the Enzymatic and Binding Subunits of Ricin Toxin. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:e00236-17. [PMID: 29021300 PMCID: PMC5717184 DOI: 10.1128/cvi.00236-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/02/2017] [Indexed: 01/05/2023]
Abstract
We previously produced a heavy-chain-only antibody (Ab) VH domain (VHH)-displayed phage library from two alpacas that had been immunized with ricin toxoid and nontoxic mixtures of the enzymatic ricin toxin A subunit (RTA) and binding ricin toxin B subunit (RTB) (D. J. Vance, J. M. Tremblay, N. J. Mantis, and C. B. Shoemaker, J Biol Chem 288:36538-36547, 2013, https://doi.org/10.1074/jbc.M113.519207). Initial and subsequent screens of that library by direct enzyme-linked immunosorbent assay (ELISA) yielded more than two dozen unique RTA- and RTB-specific VHHs, including 10 whose structures were subsequently solved in complex with RTA. To generate a more complete antigenic map of ricin toxin and to define the epitopes associated with toxin-neutralizing activity, we subjected the VHH-displayed phage library to additional "pannings" on both receptor-bound ricin and antibody-captured ricin. We now report the full-length DNA sequences, binding affinities, and neutralizing activities of 68 unique VHHs: 31 against RTA, 33 against RTB, and 4 against ricin holotoxin. Epitope positioning was achieved through cross-competition ELISAs performed with a panel of monoclonal antibodies (MAbs) and verified, in some instances, with hydrogen-deuterium exchange mass spectrometry. The 68 VHHs grouped into more than 20 different competition bins. The RTA-specific VHHs with strong toxin-neutralizing activities were confined to bins that overlapped two previously identified neutralizing hot spots, termed clusters I and II. The four RTB-specific VHHs with potent toxin-neutralizing activity grouped within three adjacent bins situated at the RTA-RTB interface near cluster II. These results provide important insights into epitope interrelationships on the surface of ricin and delineate regions of vulnerability that can be exploited for the purpose of vaccine and therapeutic development.
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Affiliation(s)
- David J Vance
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Jacqueline M Tremblay
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Yinghui Rong
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Siva Krishna Angalakurthi
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, USA
| | - C Russell Middaugh
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, USA
| | - David D Weis
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Charles B Shoemaker
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Nicholas J Mantis
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, New York, USA
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A Supercluster of Neutralizing Epitopes at the Interface of Ricin's Enzymatic (RTA) and Binding (RTB) Subunits. Toxins (Basel) 2017; 9:toxins9120378. [PMID: 29168727 PMCID: PMC5744098 DOI: 10.3390/toxins9120378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/10/2017] [Accepted: 11/18/2017] [Indexed: 12/29/2022] Open
Abstract
As part of an effort to engineer ricin antitoxins and immunotherapies, we previously produced and characterized a collection of phage-displayed, heavy chain-only antibodies (VHHs) from alpacas that had been immunized with ricin antigens. In our initial screens, we identified nine VHHs directed against ricin toxin’s binding subunit (RTB), but only one, JIZ-B7, had toxin-neutralizing activity. Linking JIZ-B7 to different VHHs against ricin’s enzymatic subunit (RTA) resulted in several bispecific antibodies with potent toxin-neutralizing activity in vitro and in vivo. JIZ-B7 may therefore be an integral component of a future VHH-based neutralizing agent (VNA) for ricin toxin. In this study, we now localize, using competitive ELISA, JIZ-B7’s epitope to a region of RTB’s domain 2 sandwiched between the high-affinity galactose/N-acetylgalactosamine (Gal/GalNAc)-binding site and the boundary of a neutralizing hotspot on RTA known as cluster II. Analysis of additional RTB (n = 8)- and holotoxin (n = 4)-specific VHHs from a recent series of screens identified a “supercluster” of neutralizing epitopes at the RTA-RTB interface. Among the VHHs tested, toxin-neutralizing activity was most closely associated with epitope proximity to RTA, and not interference with RTB’s ability to engage Gal/GalNAc receptors. We conclude that JIZ-B7 is representative of a larger group of potent toxin-neutralizing antibodies, possibly including many described in the literature dating back several decades, that recognize tertiary and possibly quaternary epitopes located at the RTA-RTB interface and that target a region of vulnerability on ricin toxin.
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