1
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Alvarez JAE, Dean SN. TEMPRO: nanobody melting temperature estimation model using protein embeddings. Sci Rep 2024; 14:19074. [PMID: 39154093 PMCID: PMC11330463 DOI: 10.1038/s41598-024-70101-6] [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: 06/21/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024] Open
Abstract
Single-domain antibodies (sdAbs) or nanobodies have received widespread attention due to their small size (~ 15 kDa) and diverse applications in bio-derived therapeutics. As many modern biotechnology breakthroughs are applied to antibody engineering and design, nanobody thermostability or melting temperature (Tm) is crucial for their successful utilization. In this study, we present TEMPRO which is a predictive modeling approach for estimating the Tm of nanobodies using computational methods. Our methodology integrates various nanobody biophysical features to include Evolutionary Scale Modeling (ESM) embeddings, NetSurfP3 structural predictions, pLDDT scores per sdAb region from AlphaFold2, and each sequence's physicochemical characteristics. This approach is validated with our combined dataset containing 567 unique sequences with corresponding experimental Tm values from a manually curated internal data and a recently published nanobody database, NbThermo. Our results indicate the efficacy of protein embeddings in reliably predicting the Tm of sdAbs with mean absolute error (MAE) of 4.03 °C and root mean squared error (RMSE) of 5.66 °C, thus offering a valuable tool for the optimization of nanobodies for various biomedical and therapeutic applications. Moreover, we have validated the models' performance using experimentally determined Tms from nanobodies not found in NbThermo. This predictive model not only enhances nanobody thermostability prediction, but also provides a useful perspective of using embeddings as a tool for facilitating a broader applicability of downstream protein analyses.
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Affiliation(s)
- Jerome Anthony E Alvarez
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA
| | - Scott N Dean
- Naval Research Laboratory, Center for Bio/Molecular Science and Engineering, Washington, DC, USA.
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2
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Niazi SK, Magoola M, Mariam Z. Innovative Therapeutic Strategies in Alzheimer's Disease: A Synergistic Approach to Neurodegenerative Disorders. Pharmaceuticals (Basel) 2024; 17:741. [PMID: 38931409 PMCID: PMC11206655 DOI: 10.3390/ph17060741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Alzheimer's disease (AD) remains a significant challenge in the field of neurodegenerative disorders, even nearly a century after its discovery, due to the elusive nature of its causes. The development of drugs that target multiple aspects of the disease has emerged as a promising strategy to address the complexities of AD and related conditions. The immune system's role, particularly in AD, has gained considerable interest, with nanobodies representing a new frontier in biomedical research. Advances in targeting antibodies against amyloid-β (Aβ) and using messenger RNA for genetic translation have revolutionized the production of antibodies and drug development, opening new possibilities for treatment. Despite these advancements, conventional therapies for AD, such as Cognex, Exelon, Razadyne, and Aricept, often have limited long-term effectiveness, underscoring the need for innovative solutions. This necessity has led to the incorporation advanced technologies like artificial intelligence and machine learning into the drug discovery process for neurodegenerative diseases. These technologies help identify therapeutic targets and optimize lead compounds, offering a more effective approach to addressing the challenges of AD and similar conditions.
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Affiliation(s)
| | | | - Zamara Mariam
- Centre for Health and Life Sciences, Coventry University, Coventry CV1 5FB, UK
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3
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Gordon GL, Raybould MIJ, Wong A, Deane CM. Prospects for the computational humanization of antibodies and nanobodies. Front Immunol 2024; 15:1399438. [PMID: 38812514 PMCID: PMC11133524 DOI: 10.3389/fimmu.2024.1399438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
To be viable therapeutics, antibodies must be tolerated by the human immune system. Rational approaches to reduce the risk of unwanted immunogenicity involve maximizing the 'humanness' of the candidate drug. However, despite the emergence of new discovery technologies, many of which start from entirely human gene fragments, most antibody therapeutics continue to be derived from non-human sources with concomitant humanization to increase their human compatibility. Early experimental humanization strategies that focus on CDR loop grafting onto human frameworks have been critical to the dominance of this discovery route but do not consider the context of each antibody sequence, impacting their success rate. Other challenges include the simultaneous optimization of other drug-like properties alongside humanness and the humanization of fundamentally non-human modalities such as nanobodies. Significant efforts have been made to develop in silico methodologies able to address these issues, most recently incorporating machine learning techniques. Here, we outline these recent advancements in antibody and nanobody humanization, focusing on computational strategies that make use of the increasing volume of sequence and structural data available and the validation of these tools. We highlight that structural distinctions between antibodies and nanobodies make the application of antibody-focused in silico tools to nanobody humanization non-trivial. Furthermore, we discuss the effects of humanizing mutations on other essential drug-like properties such as binding affinity and developability, and methods that aim to tackle this multi-parameter optimization problem.
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Affiliation(s)
| | | | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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4
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Manzanares-Guzmán A, Lugo-Fabres PH, Camacho-Villegas TA. vNARs as Neutralizing Intracellular Therapeutic Agents: Glioblastoma as a Target. Antibodies (Basel) 2024; 13:25. [PMID: 38534215 DOI: 10.3390/antib13010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Glioblastoma is the most prevalent and fatal form of primary brain tumors. New targeted therapeutic strategies for this type of tumor are imperative given the dire prognosis for glioblastoma patients and the poor results of current multimodal therapy. Previously reported drawbacks of antibody-based therapeutics include the inability to translocate across the blood-brain barrier and reach intracellular targets due to their molecular weight. These disadvantages translate into poor target neutralization and cancer maintenance. Unlike conventional antibodies, vNARs can permeate tissues and recognize conformational or cryptic epitopes due to their stability, CDR3 amino acid sequence, and smaller molecular weight. Thus, vNARs represent a potential antibody format to use as intrabodies or soluble immunocarriers. This review comprehensively summarizes key intracellular pathways in glioblastoma cells that induce proliferation, progression, and cancer survival to determine a new potential targeted glioblastoma therapy based on previously reported vNARs. The results seek to support the next application of vNARs as single-domain antibody drug-conjugated therapies, which could overcome the disadvantages of conventional monoclonal antibodies and provide an innovative approach for glioblastoma treatment.
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Affiliation(s)
- Alejandro Manzanares-Guzmán
- Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
| | - Pavel H Lugo-Fabres
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)-Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
| | - Tanya A Camacho-Villegas
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)-Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico
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5
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Garg U, Jain N, Kaul S, Nagaich U. Role of Albumin as a Targeted Drug Carrier in the Management of Rheumatoid Arthritis: A Comprehensive Review. Mol Pharm 2023; 20:5345-5358. [PMID: 37870420 DOI: 10.1021/acs.molpharmaceut.3c00581] [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] [Indexed: 10/24/2023]
Abstract
An endogenous transporter protein called albumin interacts with the Fc receptor to provide it with multiple substrate-binding domains, cell membrane receptor activation, and an extended circulating half-life. Albumin has the remarkable ability to bind with receptors viz. secreted protein acidic and rich in cysteine (SPARC) and scavenger protein-A (SR-A) that are overexpressed during rheumatoid arthritis (RA), enabling active targeting of the disease site instead of requiring specialized substrates to be added to the nanocarrier. RA, a chronic autoimmune illness, is characterized by the presence of a severe inflammatory response. RA patients have low serum albumin concentration, which signifies the high uptake of albumin at the inflammatory sites, giving a rationale to use albumin as a drug carrier for RA therapy. Albumin has the capacity for both passive and active targeting. It is an abundantly available protein in the bloodstream showing excellent cellular compatibility, degradability in biological tissues, nonantigenicity, and safety. There are three strategies of albumin mediated drug delivery as encapsulating therapeutics in albumin nanoparticles, chemically conjugating drugs with functional proteins, and albumin itself which is used as a targeting ligand to deliver drugs specifically to cells or tissues that express albumin-binding receptors. In the current review, an attempt has been made to highlight the significant evidence of albumin as a drug delivery carrier for the safe and effective management of RA. Evidence has been provided in the form of recent research advances, clinical trials, and patents. Additionally, this review will outline the prospective for the potential utilization of albumin as a drug vehicle for RA and suggest possible future avenues to provide the perspective for subsequent studies.
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Affiliation(s)
- Unnati Garg
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Neha Jain
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Shreya Kaul
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
| | - Upendra Nagaich
- Department of Pharmaceutics, Amity Institute of Pharmacy, Amity University, Noida, Uttar Pradesh 201303, India
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6
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Koerselman M, Morshuis LCM, Karperien M. The use of peptides, aptamers, and variable domains of heavy chain only antibodies in tissue engineering and regenerative medicine. Acta Biomater 2023; 170:1-14. [PMID: 37517622 DOI: 10.1016/j.actbio.2023.07.045] [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: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Over the years, much research has been focused on the use of small molecules such as peptides or aptamers or more recently on the use of variable antigen-binding domain of heavy chain only antibodies in the field of tissue engineering and regenerative medicine. The use of these molecules originated as an alternative for the larger conventional antibodies, of which most drawbacks are derived from their size and complex structure. In the field of tissue engineering and regenerative medicine, biological functionalities are often conjugated to biomaterials in order to (re-)create an in vivo like situation, especially when bioinert biomaterials are used. Those biomaterials are functionalized with these functionalities for instance for the purpose of cell attachment or cell targeting for targeted drug delivery but also for local enrichment or blocking of ligands such as growth factors or cytokines on the biomaterial surface. In this review, we further refer to peptides, aptamers, and variable antigen-binding domain of heavy chain only antibodies as biological functionalities. Here, we compare these biological functionalities within the field of tissue engineering and regenerative medicine and give an overview of recent work in which these biological functionalities have been explored. We focus on the previously mentioned purposes of the biological functionalities. We will compare structural differences, possible modifications and (chemical) conjugation strategies. In addition, we will provide an overview of biologicals that are, or have been, involved in clinical trials. Finally, we will highlight the challenges of each of these biologicals. STATEMENT OF SIGNIFICANCE: In the field of tissue engineering there is broad application of functionalized biomaterials for cell attachment, targeted drug delivery and local enrichment or blocking of growth factors. This was previously mostly done via conventional antibodies, but their large size and complex structure impose various challenges with respect of retaining biological functionality. Peptides, aptamers and VHHs may provide an alternative solution for the use of conventional antibodies. This review discusses the use of these molecules for biological functionalization of biomaterials. For each of the molecules, their characteristics, conjugation possibilities and current use in research and clinical trials is described. Furthermore, this review sets out the benefits and challenges of using these types of molecules for different fields of application.
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Affiliation(s)
- Michelle Koerselman
- Department of Developmental BioEngineering, TechMed Institute, University of Twente, The Netherlands. Drienerlolaan 5, 7522 NB, Enschede, the Netherlands
| | - Lisanne C M Morshuis
- Department of Developmental BioEngineering, TechMed Institute, University of Twente, The Netherlands. Drienerlolaan 5, 7522 NB, Enschede, the Netherlands
| | - Marcel Karperien
- Department of Developmental BioEngineering, TechMed Institute, University of Twente, The Netherlands. Drienerlolaan 5, 7522 NB, Enschede, the Netherlands.
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7
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Arras P, Yoo HB, Pekar L, Clarke T, Friedrich L, Schröter C, Schanz J, Tonillo J, Siegmund V, Doerner A, Krah S, Guarnera E, Zielonka S, Evers A. AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study. Front Mol Biosci 2023; 10:1249247. [PMID: 37842638 PMCID: PMC10575757 DOI: 10.3389/fmolb.2023.1249247] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and nextgeneration sequencing (NGS) in combination with artificial intelligence and machine learning methods (AI/ML) for the identification of de novo humanized single domain antibodies (sdAbs) with favorable early developability profiles. Methods: The display library was derived from a novel approach, in which VHH-based CDR3 regions obtained from a llama (Lama glama), immunized against NKp46, were grafted onto a humanized VHH backbone library that was diversified in CDR1 and CDR2. Following NGS analysis of sequence pools from two rounds of fluorescence-activated cell sorting we focused on four sequence clusters based on NGS frequency and enrichment analysis as well as in silico developability assessment. For each cluster, long short-term memory (LSTM) based deep generative models were trained and used for the in silico sampling of new sequences. Sequences were subjected to sequence- and structure-based in silico developability assessment to select a set of less than 10 sequences per cluster for production. Results: As demonstrated by binding kinetics and early developability assessment, this procedure represents a general strategy for the rapid and efficient design of potent and automatically humanized sdAb hits from screening selections with favorable early developability profiles.
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Affiliation(s)
- Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Thomas Clarke
- Bioinformatics, EMD Serono, Billerica, MA, United States
| | - Lukas Friedrich
- Computational Chemistry and Biologics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Jennifer Schanz
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Jason Tonillo
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Enrico Guarnera
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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8
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Lim HT, Kok BH, Leow CY, Leow CH. Exploring shark VNAR antibody against infectious diseases using phage display technology. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108986. [PMID: 37541634 DOI: 10.1016/j.fsi.2023.108986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.
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Affiliation(s)
- Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
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9
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Gordon GL, Capel HL, Guloglu B, Richardson E, Stafford RL, Deane CM. A comparison of the binding sites of antibodies and single-domain antibodies. Front Immunol 2023; 14:1231623. [PMID: 37533864 PMCID: PMC10392943 DOI: 10.3389/fimmu.2023.1231623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Antibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sdAbs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sdAbs, suggesting that they include non-specific interactions to achieve comparable affinity. Furthermore, the epitopes of sdAbs are only marginally less accessible than those of Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.
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Affiliation(s)
- Gemma L. Gordon
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Henriette L. Capel
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eve Richardson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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10
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Mrštná K, Kujovská Krčmová L, Švec F. Advances in kynurenine analysis. Clin Chim Acta 2023:117441. [PMID: 37321530 DOI: 10.1016/j.cca.2023.117441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
Kynurenine, the first product of tryptophan degradation via the kynurenine pathway, has become one of the most frequently mentioned biomarkers in recent years. Its levels in the body indicate the state of the human physiology. Human serum and plasma are the main matrixes used to evaluate kynurenine levels and liquid chromatography is the dominant technique for its determination. However, their concentrations in blood do not always correspond to the levels in other matrixes obtained from the affected individuals. It is therefore important to decide when it is appropriate to analyse kynurenine in alternative matrices. However, liquid chromatography may not be the best option for the analysis. This review presents alternatives that can be used and summarizes the features that need to be considered prior to kynurenine determination. Possible approaches to kynurenine analysis in a variety of human matrixes, their challenges, and limitations are critically discussed.
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Affiliation(s)
- K Mrštná
- The Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 50005 Hradec Králové, Czech Republic; The Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Sokolská 581, 50005 Hradec Králové, Czech Republic
| | - L Kujovská Krčmová
- The Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 50005 Hradec Králové, Czech Republic; The Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, Sokolská 581, 50005 Hradec Králové, Czech Republic.
| | - F Švec
- The Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203/8, 50005 Hradec Králové, Czech Republic
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11
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Smith CN, Kihn K, Williamson ZA, Chow KM, Hersh LB, Korotkov KV, Deredge D, Blackburn JS. Development and characterization of nanobodies that specifically target the oncogenic Phosphatase of Regenerating Liver-3 (PRL-3) and impact its interaction with a known binding partner, CNNM3. PLoS One 2023; 18:e0285964. [PMID: 37220097 PMCID: PMC10204944 DOI: 10.1371/journal.pone.0285964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Phosphatase of Regenerating Liver-3 (PRL-3) is associated with cancer progression and metastasis. The mechanisms that drive PRL-3's oncogenic functions are not well understood, partly due to a lack of research tools available to study this protein. We have begun to address these issues by developing alpaca-derived single domain antibodies, or nanobodies, targeting PRL-3 with a KD of 30-300 nM and no activity towards highly homologous family members PRL-1 and PRL-2. We found that longer and charged N-terminal tags on PRL-3, such as GFP and FLAG, changed PRL-3 localization compared to untagged protein, indicating that the nanobodies may provide new insights into PRL-3 trafficking and function. The nanobodies perform equally, if not better, than commercially available antibodies in immunofluorescence and immunoprecipitation. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed that the nanobodies bind partially within the PRL-3 active site and can interfere with PRL-3 phosphatase activity. Co-immunoprecipitation with a known PRL-3 active site binding partner, the CBS domain of metal transporter CNNM3, showed that the nanobodies reduced the amount of PRL-3:CBS inter-action. The potential of blocking this interaction is highly relevant in cancer, as multiple research groups have shown that PRL-3 binding to CNNM proteins is sufficient to promote metastatic growth in mouse models. The anti-PRL-3 nanobodies represent an important expansion of the research tools available to study PRL-3 function and can be used to define the role of PRL-3 in cancer progression.
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Affiliation(s)
- Caroline N. Smith
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- University of Kentucky Markey Cancer Center, Lexington, Kentucky, United States of America
| | - Kyle Kihn
- University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Zachary A. Williamson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - K. Martin Chow
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Louis B. Hersh
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Daniel Deredge
- University of Maryland School of Pharmacy, Baltimore, Maryland, United States of America
| | - Jessica S. Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- University of Kentucky Markey Cancer Center, Lexington, Kentucky, United States of America
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12
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Lipinski B, Arras P, Pekar L, Klewinghaus D, Boje AS, Krah S, Zimmermann J, Klausz K, Peipp M, Siegmund V, Evers A, Zielonka S. NKp46-specific single domain antibodies enable facile engineering of various potent NK cell engager formats. Protein Sci 2023; 32:e4593. [PMID: 36775946 PMCID: PMC9951198 DOI: 10.1002/pro.4593] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Herein, we describe the generation of potent NK cell engagers (NKCEs) based on single domain antibodies (sdAbs) specific for NKp46 harboring the humanized Fab version of Cetuximab for tumor targeting. After immunization of camelids, a plethora of different VHH domains were retrieved by yeast surface display. Upon reformatting into Fc effector-silenced NKCEs targeting NKp46 and EGFR in a strictly monovalent fashion, the resulting bispecific antibodies elicited potent NK cell-mediated killing of EGFR-overexpressing tumor cells with potencies (EC50 killing) in the picomolar range. This was further augmented via co-engagement of Fcγ receptor IIIa (FcγRIIIa). Importantly, NKp46-specific sdAbs enabled the construction of various NKCE formats with different geometries and valencies which displayed favorable biophysical and biochemical properties without further optimization. By this means, killing capacities were further improved significantly. Hence, NKp46-specific sdAbs are versatile building blocks for the construction of different NKCE formats.
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Affiliation(s)
- Britta Lipinski
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Paul Arras
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniel Klewinghaus
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Ammelie Svea Boje
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Jasmin Zimmermann
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Katja Klausz
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Vanessa Siegmund
- Protein and Cell Sciences, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Evers
- Computational Chemistry and Biology, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.,Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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13
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Xi X, Xiao G, An G, Liu L, Liu X, Hao P, Wang JY, Song D, Yu W, Gu Y. A novel shark single-domain antibody targeting OGT as a tool for detection and intracellular localization. Front Immunol 2023; 14:1062656. [PMID: 36855630 PMCID: PMC9968394 DOI: 10.3389/fimmu.2023.1062656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/09/2023] [Indexed: 02/14/2023] Open
Abstract
Introduction O-GlcNAcylation is a type of reversible post-translational modification on Ser/Thr residues of intracellular proteins in eukaryotic cells, which is generated by the sole O-GlcNAc transferase (OGT) and removed by O-GlcNAcase (OGA). Thousands of proteins, that are involved in various physiological and pathological processes, have been found to be O-GlcNAcylated. However, due to the lack of favorable tools, studies of the O-GlcNAcylation and OGT were impeded. Immunoglobulin new antigen receptor (IgNAR) derived from shark is attractive to research tools, diagnosis and therapeutics. The variable domain of IgNARs (VNARs) have several advantages, such as small size, good stability, low-cost manufacture, and peculiar paratope structure. Methods We obtained shark single domain antibodies targeting OGT by shark immunization, phage display library construction and panning. ELISA and BIACORE were used to assess the affinity of the antibodies to the antigen and three shark single-domain antibodies with high affinity were successfully screened. The three antibodies were assessed for intracellular function by flow cytometry and immunofluorescence co-localization. Results In this study, three anti-OGT VNARs (2D9, 3F7 and 4G2) were obtained by phage display panning. The affinity values were measured using surface plasmon resonance (SPR) that 2D9, 3F7 and 4G2 bound to OGT with KD values of 35.5 nM, 53.4 nM and 89.7 nM, respectively. Then, the VNARs were biotinylated and used for the detection and localization of OGT by ELISA, flow cytometry and immunofluorescence. 2D9, 3F7 and 4G2 were exhibited the EC50 values of 102.1 nM, 40.75 nM and 120.7 nM respectively. VNAR 3F7 was predicted to bind the amino acid residues of Ser375, Phe377, Cys379 and Tyr 380 on OGT. Discussion Our results show that shark single-domain antibodies targeting OGT can be used for in vitro detection and intracellular co-localization of OGT, providing a powerful tool for the study of OGT and O-GlcNAcylation.
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Affiliation(s)
- Xiaozhi Xi
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Guiqi An
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Lin Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Peiyu Hao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Jennifer Yiyang Wang
- College of Letters and Science Dept. of Microbiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Dandan Song
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
| | - Yuchao Gu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Ocean University of China, Qingdao, China
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14
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Arras P, Yoo HB, Pekar L, Schröter C, Clarke T, Krah S, Klewinghaus D, Siegmund V, Evers A, Zielonka S. A library approach for the de novo high-throughput isolation of humanized VHH domains with favorable developability properties following camelid immunization. MAbs 2023; 15:2261149. [PMID: 37766540 PMCID: PMC10540653 DOI: 10.1080/19420862.2023.2261149] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we generated a novel library approach for high throughput de novo identification of humanized single-domain antibodies following camelid immunization. To achieve this, VHH-derived complementarity-determining regions-3 (CDR3s) obtained from an immunized llama (Lama glama) were grafted onto humanized VHH backbones comprising moderately sequence-diversified CDR1 and CDR2 regions similar to natural immunized and naïve antibody repertoires. Importantly, these CDRs were tailored toward favorable in silico developability properties, by considering human-likeness as well as excluding potential sequence liabilities and predicted immunogenic motifs. Target-specific humanized single-domain antibodies (sdAbs) were readily obtained by yeast surface display. We demonstrate that, by exploiting this approach, high affinity sdAbs with an optimized in silico developability profile can be generated. These sdAbs display favorable biophysical, biochemical, and functional attributes and do not require any further sequence optimization. This approach is generally applicable to any antigen upon camelid immunization and has the potential to significantly accelerate candidate selection and reduce risks and attrition rates in sdAb development.
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Affiliation(s)
- Paul Arras
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | | | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniel Klewinghaus
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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15
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Bauer C, Ciesielski E, Pekar L, Krah S, Toleikis L, Zielonka S, Sellmann C. Facile One-Step Generation of Camelid VHH and Avian scFv Libraries for Phage Display by Golden Gate Cloning. Methods Mol Biol 2023; 2681:47-60. [PMID: 37405642 DOI: 10.1007/978-1-0716-3279-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Since its development in the 1980s, the Nobel Prize-awarded phage display technology has been one of the most commonly used in vitro selection technologies for the discovery of therapeutic and diagnostic antibodies. Besides the importance of selection strategy, one key component of the successful isolation of highly specific recombinant antibodies is the construction of high-quality phage display libraries. However, previous cloning protocols relied on a tedious multistep process with subsequent cloning steps for the introduction of first heavy and then light chain variable genetic antibody fragments (VH and VL). This resulted in reduced cloning efficiency, higher frequency of missing VH or VL sequences, as well as truncated antibody fragments. With the emergence of Golden Gate Cloning (GGC) for the generation of antibody libraries, the possibility of more facile library cloning has arisen. Here, we describe a streamlined one-step GGC strategy for the generation of camelid heavy chain only variable phage display libraries as well as the simultaneous introduction of heavy chain and light chain variable regions from the chicken into a scFv phage display vector.
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Affiliation(s)
- Christina Bauer
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Elke Ciesielski
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Carolin Sellmann
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany.
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16
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Kolmar H, Grzeschik J, Könning D, Krah S, Zielonka S. Construction of Semisynthetic Shark vNAR Yeast Surface Display Antibody Libraries. Methods Mol Biol 2023; 2702:227-243. [PMID: 37679622 DOI: 10.1007/978-1-0716-3381-6_11] [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] [Indexed: 09/09/2023]
Abstract
The adaptive immune system of sharks comprises a unique heavy chain-only antibody isotype, termed immunoglobulin new antigen receptor (IgNAR), in which antigen binding is mediated by a single variable domain, referred to as vNAR. In recent years, efforts were made to harness these domains for biomedical and biotechnological applications particularly due to their high affinity and specificity combined with a small size and high stability. Herein, we describe protocols for the construction of semisynthetic, CDR3-randomized vNAR libraries for the isolation of target-specific paratopes by yeast surface display. Additionally, we provide guidance for affinity maturation of a panel of antigen-enriched vNAR domains through CDR1 diversification of the FACS-selected, antigen-enriched population and sublibrary establishment.
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Affiliation(s)
- Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
- Antibody Discovery & Protein Engineering, Merck KGaA, Darmstadt, Germany.
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17
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Klausz K, Pekar L, Boje AS, Gehlert CL, Krohn S, Gupta T, Xiao Y, Krah S, Zaynagetdinov R, Lipinski B, Toleikis L, Poetzsch S, Rabinovich B, Peipp M, Zielonka S. Multifunctional NK Cell–Engaging Antibodies Targeting EGFR and NKp30 Elicit Efficient Tumor Cell Killing and Proinflammatory Cytokine Release. THE JOURNAL OF IMMUNOLOGY 2022; 209:1724-1735. [DOI: 10.4049/jimmunol.2100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 08/23/2022] [Indexed: 01/04/2023]
Abstract
Abstract
In this work, we have generated novel Fc-comprising NK cell engagers (NKCEs) that bridge human NKp30 on NK cells to human epidermal growth factor receptor (EGFR) on tumor cells. Camelid-derived VHH single-domain Abs specific for human NKp30 and a humanized Fab derived from the EGFR-specific therapeutic Ab cetuximab were used as binding arms. By combining camelid immunization with yeast surface display, we were able to isolate a diverse panel of NKp30-specific VHHs against different epitopes on NKp30. Intriguingly, NKCEs built with VHHs that compete for binding to NKp30 with B7-H6, the natural ligand of NKp30, were significantly more potent in eliciting tumor cell lysis of EGFR-positive tumor cells than NKCEs harboring VHHs that target different epitopes on NKp30 from B7-H6. We demonstrate that the NKCEs can be further improved with respect to killing capabilities by concomitant engagement of FcγRIIIa and that soluble B7-H6 does not impede cytolytic capacities of all scrutinized NKCEs at significantly higher B7-H6 concentrations than observed in cancer patients. Moreover, we show that physiological processes requiring interactions between membrane-bound B7-H6 and NKp30 on NK cells are unaffected by noncompeting NKCEs still eliciting tumor cell killing at low picomolar concentrations. Ultimately, the NKCEs generated in this study were significantly more potent in eliciting NK cell–mediated tumor cell lysis than cetuximab and elicited a robust release of proinflammatory cytokines, both features which might be beneficial for antitumor therapy.
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Affiliation(s)
- Katja Klausz
- *Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian Albrechts University Kiel, Kiel, Germany
| | - Lukas Pekar
- †Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Ammelie Svea Boje
- *Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian Albrechts University Kiel, Kiel, Germany
| | - Carina Lynn Gehlert
- *Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian Albrechts University Kiel, Kiel, Germany
| | - Steffen Krohn
- *Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian Albrechts University Kiel, Kiel, Germany
| | - Tushar Gupta
- ‡Protein Engineering and Antibody Technologies, EMD Serono Research & Development Institute, Inc., Billerica, MA
| | - Yanping Xiao
- §Department of Oncology and Immuno-oncology, EMD Serono Research & Development Institute, Inc., Billerica, MA
| | - Simon Krah
- †Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Rinat Zaynagetdinov
- §Department of Oncology and Immuno-oncology, EMD Serono Research & Development Institute, Inc., Billerica, MA
| | - Britta Lipinski
- †Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
- ¶Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany; and
| | - Lars Toleikis
- †Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Sven Poetzsch
- ‖Strategic Innovation, Merck Healthcare KGaA, Darmstadt, Germany
| | - Brian Rabinovich
- §Department of Oncology and Immuno-oncology, EMD Serono Research & Development Institute, Inc., Billerica, MA
| | - Matthias Peipp
- *Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian Albrechts University Kiel, Kiel, Germany
| | - Stefan Zielonka
- †Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
- ¶Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany; and
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18
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Hu Y, Lin J, Wang Y, Wu S, Wu J, Lv H, Ji X, Muyldermans S, Zhang Y, Wang S. Identification of Serum Ferritin-Specific Nanobodies and Development towards a Diagnostic Immunoassay. Biomolecules 2022; 12:biom12081080. [PMID: 36008974 PMCID: PMC9406126 DOI: 10.3390/biom12081080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/28/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022] Open
Abstract
Serum ferritin (SF) is an iron-rich protein tightly connected with iron homeostasis, and the variations are frequently observed in diseased states, including iron-deficiency anemia, inflammation, liver disease, and tumors, which renders SF level an indicator of potential malignancies in clinical practice. Nanobodies (Nbs) have been widely explored and developed into theranostic reagents. Surprisingly, no reports stated the identification of anti-SF Nbs, nor the potential of such Nbs as a diagnostic tool. In this study, we generated SF-specific Nbs and provided novel clinical diagnostic approaches to develop an immunoassay. An immune library was constructed after immunizing an alpaca with SF, and five Nbs specifically targeting human SF were retrieved. The obtained Nbs exhibited robust properties including high stability, affinity, and specificity. Then, an ELISA-based test using a heterologous Nb-pair was developed. The calibration curve demonstrated a linear range of SF between 9.0 to 1100 ng/mL, and a limit of detection (LOD) of 1.01 ng/mL. The detecting recovery and coefficient variation (CV) were determined by spiking different concentrations of SF into the serum sample, to verify the successful application of our selected Nbs for SF monitoring. In general, this study generated SF-specific Nbs and demonstrated their potential as diagnostic immunoassay tools.
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Affiliation(s)
- Yaozhong Hu
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Jing Lin
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Sihao Wu
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Jing Wu
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Huan Lv
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xuemeng Ji
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Yan Zhang
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
- Correspondence: (Y.Z.); (S.W.); Tel.: +86-22-8535-8445 (S.W.)
| | - Shuo Wang
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin 300071, China
- Correspondence: (Y.Z.); (S.W.); Tel.: +86-22-8535-8445 (S.W.)
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19
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Zhang X, Liao X, Wu Y, Xiong W, Du J, Tu Z, Yang W, Wang D. A sensitive electrochemical immunosensing interface for label-free detection of aflatoxin B 1 by attachment of nanobody to MWCNTs-COOH@black phosphorene. Anal Bioanal Chem 2021; 414:1129-1139. [PMID: 34719746 DOI: 10.1007/s00216-021-03738-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022]
Abstract
A label-free electrochemical immunosensor has advantages of real-time and rapid detection, but it is weak in detection of small molecular toxins such as aflatoxin B1 (AFB1). The greatest obstacle to achieving this is that small molecules bound to a common immunosensing interface cannot interfere with electron transfer effectively and the detection signal is so weak. Therefore, a sensitive electrochemical immunosensing interface for small molecules is urgently needed. Here, we employed functionalized black phosphorene (BP) as electrode modification materials and anti-AFB1 nanobody (Nb) as a biorecognition element to construct a very sensitive immunosensing interface towards small molecular AFB1. The BP functionalized by carboxylic multi-walled carbon nanotubes (MWCNTs-COOH) via P-C bonding behaved with a satisfactory stability and good catalytic performance for the ferricyanide/ferrocyanide probe, while the small-sized Nb showed good compatibility with the functionalized BP and also had less influence on electron transfer than monoclonal antibody (mAb). Expectedly, the as-prepared immunosensing interface was very sensitive to AFB1 detection by differential pulse voltammetry (DPV) in a redox probe system. Under optimized conditions, a linear range from 1.0 pM to 5.0 nM and an ultralow detection limit of 0.27 pM were obtained. Additionally, the fabricated immunosensor exhibited satisfactory stability, specificity, and reproducibility. The strategy proposed here provides a more reliable reference for label-free sensing of small molecules in food samples.
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Affiliation(s)
- Xue Zhang
- Research Center of Mycotoxin, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, People's Republic of China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables/Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits &Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Xiaoning Liao
- Research Center of Mycotoxin, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, People's Republic of China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables/Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits &Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Yongfa Wu
- Research Center of Mycotoxin, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, People's Republic of China
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables/Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits &Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Wanming Xiong
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits & Vegetables/Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruits &Vegetables in Jiangxi Province, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Juan Du
- Key Lab for Agro-Product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Zhui Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, Jiangxi, China
| | - Wuying Yang
- Key Lab for Agro-Product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Dan Wang
- Research Center of Mycotoxin, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, People's Republic of China.
- Key Lab for Agro-Product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
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20
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Pekar L, Klewinghaus D, Arras P, Carrara SC, Harwardt J, Krah S, Yanakieva D, Toleikis L, Smider VV, Kolmar H, Zielonka S. Milking the Cow: Cattle-Derived Chimeric Ultralong CDR-H3 Antibodies and Their Engineered CDR-H3-Only Knobbody Counterparts Targeting Epidermal Growth Factor Receptor Elicit Potent NK Cell-Mediated Cytotoxicity. Front Immunol 2021; 12:742418. [PMID: 34759924 PMCID: PMC8573386 DOI: 10.3389/fimmu.2021.742418] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/04/2021] [Indexed: 01/11/2023] Open
Abstract
In this work, we have generated epidermal growth factor receptor (EGFR)-specific cattle-derived ultralong CDR-H3 antibodies by combining cattle immunization with yeast surface display. After immunization, ultralong CDR-H3 regions were specifically amplified and grafted onto an IGHV1-7 scaffold by homologous recombination to facilitate Fab display. Antigen-specific clones were readily obtained by fluorescence-activated cell sorting (FACS) and reformatted as chimeric antibodies. Binning experiments revealed epitope targeting of domains I, II, and IV of EGFR with none of the generated binders competing with Cetuximab, Matuzumab, or EGF for binding to EGFR. Cattle-derived chimeric antibodies were potent in inducing antibody-dependent cell-mediated cytotoxicity (ADCC) against EGFR-overexpressing tumor cells with potencies (EC50 killing) in the picomolar range. Moreover, most of the antibodies were able to significantly inhibit EGFR-mediated downstream signaling. Furthermore, we demonstrate that a minor fraction of CDR-H3 knobs derived from generated antibodies was capable of independently functioning as a paratope facilitating EGFR binding when grafted onto the Fc part of human IgG1. Besides slightly to moderately diminished capacities, these engineered Knobbodies largely retained main properties of their parental antibodies such as cellular binding and triggering of ADCC. Hence, Knobbodies might emerge as promising tools for biotechnological applications upon further optimization.
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Affiliation(s)
- Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniel Klewinghaus
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Paul Arras
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefania C. Carrara
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julia Harwardt
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Desislava Yanakieva
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Vaughn V. Smider
- The Applied Biomedical Science Institute, San Diego, CA, United States
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
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Pekar L, Busch M, Valldorf B, Hinz SC, Toleikis L, Krah S, Zielonka S. Biophysical and biochemical characterization of a VHH-based IgG-like bi- and trispecific antibody platform. MAbs 2021; 12:1812210. [PMID: 32887531 PMCID: PMC7531565 DOI: 10.1080/19420862.2020.1812210] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Here, we report the characterization of a VHH-derived IgG-like bi- and trispecific antibody platform that essentially relies on the replacement of the VH and VL regions of a conventional antibody by two independently functioning VHH domains. Consequently, a VHH is engrafted onto constant region CH1 while the other VHH-based paratope is engrafted on the constant region of the light chain, Cκ or Cλ, resulting in a tetravalent bispecific IgG-like molecule. Combined with a heavy chain heterodimerization technique, this platform allows facile engineering of bi- and trispecific antibodies with flexible valencies. We demonstrate the general applicability of this generic platform approach and elaborate on the limitations of specific formats.
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Affiliation(s)
- Lukas Pekar
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Busch
- Discovery Pharmacology, Merck KGaA , Darmstadt, Germany
| | - Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA , Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry , Technische Universität Darmstadt, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA , Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA , Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA , Darmstadt, Germany
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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Liu M, Li L, Jin D, Liu Y. Nanobody-A versatile tool for cancer diagnosis and therapeutics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1697. [PMID: 33470555 DOI: 10.1002/wnan.1697] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/19/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022]
Abstract
In spite of the successful use of monoclonal antibodies (mAbs) in clinic for tumor treatment, their applications are still hampered in therapeutic development due to limitations, such as tumor penetration and high cost of manufacture. Nanobody, a single domain antibody that holds the strong antigen targeting and binding capacity, has demonstrated various advantages relative to antibody. Nanobody is considered as a next-generation of antibody-derived tool in the antigen related recognition and modulation. A number of nanobodies have been developed and evaluated in different stages of clinical trials for cancer treatment. Here we summarized the current progress of nanobody in tumor diagnosis and therapeutics, particularly on the conjugation of nanobody with functional moieties. The nanobody conjugation of diagnostic agents, such as radionuclide and optical tracers, can achieve specific tumor imaging. The nanobody-drug conjugates can enhance the therapeutic efficacy of anti-tumor drugs and reduce the adverse effects. The decoration of nanobody on nanodrug delivery systems can further improve the drug targeting to specific tumors. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Manman Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Li Li
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Duo Jin
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Yangzhong Liu
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, China
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Meinke G, Dalda N, Brigham BS, Bohm A. Synthesis of libraries and multi-site mutagenesis using a PCR-derived, dU-containing template. Synth Biol (Oxf) 2021; 6:ysaa030. [PMID: 34239985 PMCID: PMC8260824 DOI: 10.1093/synbio/ysaa030] [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] [Received: 08/14/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 12/03/2022] Open
Abstract
Directed DNA libraries are useful because they focus genetic diversity in the most important regions within a sequence. Ideally, all sequences in such libraries should appear with the same frequency and there should be no significant background from the starting sequence. These properties maximize the number of different sequences that can be screened. Described herein is a method termed SLUPT (Synthesis of Libraries via a dU-containing PCR-derived Template) for generating highly targeted DNA libraries and/or multi-site mutations wherein the altered bases may be widely distributed within a target sequence. This method is highly efficient and modular. Moreover, multiple distinct sites, each with one or more base changes, can be altered in a single reaction. There is very low background from the starting sequence, and SLUPT libraries have similar representation of each base at the positions selected for variation. The SLUPT method utilizes a single-stranded dU-containing DNA template that is made by polymerase chain reaction (PCR). Synthesis of the template in this way is significantly easier than has been described earlier. A series of oligonucleotide primers that are homologous to the template and encode the desired genetic diversity are extended and ligated in a single reaction to form the mutated product sequence or library. After selective inactivation of the template, only the product library is amplified. There are no restrictions on the spacing of the mutagenic primers except that they cannot overlap.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nahide Dalda
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Benjamin S Brigham
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Andrew Bohm
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
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Yu S, Xiong G, Zhao S, Tang Y, Tang H, Wang K, Liu H, Lan K, Bi X, Duan S. Nanobodies targeting immune checkpoint molecules for tumor immunotherapy and immunoimaging (Review). Int J Mol Med 2020; 47:444-454. [PMID: 33416134 PMCID: PMC7797440 DOI: 10.3892/ijmm.2020.4817] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022] Open
Abstract
The immune checkpoint blockade is an effective strategy to enhance the anti-tumor T cell effector activity, thus becoming one of the most promising immunotherapeutic strategies in the history of cancer treatment. Several immune checkpoint inhibitor have been approved by the FDA, such as anti-CTLA-4, anti-PD-1, anti-PD-L1 monoclonal antibodies. Most tumor patients benefitted from these antibodies, but some of the patients did not respond to them. To increase the effectiveness of immunotherapy, including immune checkpoint blockade therapies, miniaturization of antibodies has been introduced. A single-domain antibody, also known as nanobody, is an attractive reagent for immunotherapy and immunoimaging thanks to its unique structural characteristic consisting of a variable region of a single heavy chain antibody. This structure confers to the nanobody a light molecular weight, making it smaller than conventional antibodies, although remaining able to bind to a specific antigen. Therefore, this review summarizes the production of nanobodies targeting immune checkpoint molecules and the application of nanobodies targeting immune checkpoint molecules in immunotherapy and immunoimaging.
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Affiliation(s)
- Sheng Yu
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Gui Xiong
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Shimei Zhao
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Yanbo Tang
- Department of Gastroenterology, The First Affiliated Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545001, P.R. China
| | - Hua Tang
- Department of Clinical Laboratory, The Second Clinical Medical College of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545006, P.R. China
| | - Kaili Wang
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Hongjing Liu
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Ke Lan
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
| | - Xiongjie Bi
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545001, P.R. China
| | - Siliang Duan
- Department of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi Zhuang Autonomous Region 545005, P.R. China
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Mir MA, Mehraj U, Sheikh BA, Hamdani SS. Nanobodies: The "Magic Bullets" in therapeutics, drug delivery and diagnostics. Hum Antibodies 2020; 28:29-51. [PMID: 31322555 DOI: 10.3233/hab-190390] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
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Serum albumin: clinical significance of drug binding and development as drug delivery vehicle. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:193-218. [PMID: 33485484 DOI: 10.1016/bs.apcsb.2020.08.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human serum albumin, the primary transport and reservoir protein in the human circulatory system, interacts with numerous endogenous and exogenous ligands of varying structural characteristics. The mode of binding of drugs to albumin is central to understanding their pharmacokinetic profiles and has a major influence on their in vivo efficacy. Altered drug binding to albumin due to drug-drug interactions or abnormal physiology may result in marked changes in the active drug concentration, thus affecting its pharmacokinetic and pharmacodynamic properties. The propensity of drug-drug interaction to be clinically significant as well as possible exploitation of such interactions for therapeutic purposes is reviewed. Being the major organs of albumin metabolism, any impairment in the liver and kidney functions frequently alter the level of serum albumin, which affects the pharmacokinetic profiles of drugs and may have serious clinical implications. The natural function of serum albumin as a drug carrier is facilitated by its interaction with various cellular receptors. These receptors not only promote the uptake of drugs into cells but are also responsible for the extraordinarily long circulatory half-life of albumin. This property in combination with the presence of multiple ligand binding pockets have led to the emergence of serum albumin as an attractive vehicle for novel drug delivery systems. Here, we provide an overview of various albumin-based drug delivery strategies, classified according to their methods of drug attachment, and highlight their experimental and clinical successes.
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Wang Y, Jiang J, Fotina H, Zhang H, Chen J. Advances in Antibody Preparation Techniques for Immunoassays of Total Aflatoxin in Food. Molecules 2020; 25:molecules25184113. [PMID: 32916811 PMCID: PMC7571119 DOI: 10.3390/molecules25184113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022] Open
Abstract
Aflatoxin (AF) contamination is a major concern in the food and feed industry because of its prevalence and toxicity. Improved aflatoxin detection methods are still needed. Immunoassays are an important method for total aflatoxin (TAF) analysis in food due to its technical advantages such as high specificity, sensitivity, and simplicity, but require high-quality antibodies. Here, we first review the three ways to prepare high-quality antibodies for TAF immunoassay, second, compare the advantages and disadvantages of antigen synthesis methods for B-group and G-group aflatoxins, and third, describe the status of novel genetic engineering antibodies. This review can provide new methods and ideas for the development of TAF immunoassays.
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Affiliation(s)
- Yanan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.W.); (H.Z.); (J.C.)
- Faculty of Veterinary Medicine, Sumy National Agrarian University, 40021 Sumy, Ukraine
| | - Jinqing Jiang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.W.); (H.Z.); (J.C.)
- Correspondence: (J.J.); (H.F.); Tel.: +86-135-2508-3536 (J.J.)
| | - Hanna Fotina
- Faculty of Veterinary Medicine, Sumy National Agrarian University, 40021 Sumy, Ukraine
- Correspondence: (J.J.); (H.F.); Tel.: +86-135-2508-3536 (J.J.)
| | - Haitang Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.W.); (H.Z.); (J.C.)
| | - Junjie Chen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (Y.W.); (H.Z.); (J.C.)
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29
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Lwin TM, Hernot S, Hollandsworth H, Amirfakhri S, Filemoni F, Debie P, Hoffman RM, Bouvet M. Tumor-specific near-infrared nanobody probe rapidly labels tumors in an orthotopic mouse model of pancreatic cancer. Surgery 2020; 168:85-91. [PMID: 32370916 DOI: 10.1016/j.surg.2020.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/07/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Nanobodies, derived from camelid antibodies made of only heavy chains, are the smallest, biologic, antigen-binding fragments (~15kDa) with faster pharmacokinetics and better tumor penetration efficiency than standard antibodies. The present study evaluates the efficacy of a fluorescent, anti-carcinoembryonic antigen (CEA) nanobody for rapid tumor labeling in an orthotopic mouse model of pancreatic cancer. METHODS Anti-CEA or control nanobodies were conjugated with the near-infrared fluorophore IRDye 800CW. Fragments of BxPC-3 (high-CEA expressing) or MiaPACA-2 (low-CEA expressing) human pancreatic cancer cell lines were orthotopically implanted into the pancreatic tail of nude mice. After tumors reached 7 to 10 mm in size, 2 nmol anti-CEA or control nanobody-IRDye800CW were injected intravenously. Mice were imaged at various time points hours post-injection. RESULTS Anti-CEA nanobodies clearly labeled BxPC3 orthotopic pancreatic tumors 3 hours after injection. The signal was present as early as 15 minutes after injection and was robust at 1 to 3 hours after injection with a tumor-to-background ratio of 2.66. In contrast, there was very low accumulation in the low CEA-expressing, MiaPACA2 pancreatic orthotopic tumors. The fluorophore-conjugated nanobody was specific for CEA-expressing tumors, while the control nanobody did not show any tumor-specific signal. Both nanobodies had strong kidney uptake as expected for small-molecule probes. The fluorescence signal was detectable using 2 clinical, Food and Drug Administration-approved, 800 nm imaging devices as well as small animal imaging systems. CONCLUSION This anti-CEA, nanobody-based, fluorescent probe labeled pancreatic orthotopic tumors within 15 minutes of intravenous injection. Fluorescent anti-CEA nanobodies have labeling kinetics that approach the speed of nonspecific dyes such as indocyanine green but with the specificity of antibodies. The use of fluorescently-labeled, intact antibodies leads to a labeling delay of 48 to 96 hours between probe administration and the necessarily delayed time of operation, which can be avoided with nanobodies. The kinetics of a nanobody-based probe makes it a practical agent for same-day, patient administration and fluorescence-guided surgery.
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Affiliation(s)
- Thinzar M Lwin
- Department of Surgery, University of California San Diego, CA
| | - Sophie Hernot
- Laboratory for In vivo Cellular and Molecular Imaging, ICMI-BEFY/MIMA, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hannah Hollandsworth
- Department of Surgery, University of California San Diego, CA; VA San Diego Healthcare System, CA
| | - Siamak Amirfakhri
- Department of Surgery, University of California San Diego, CA; VA San Diego Healthcare System, CA
| | - Filemoni Filemoni
- Department of Surgery, University of California San Diego, CA; VA San Diego Healthcare System, CA
| | - Pieterjan Debie
- Laboratory for In vivo Cellular and Molecular Imaging, ICMI-BEFY/MIMA, Vrije Universiteit Brussel, Brussels, Belgium
| | - Robert M Hoffman
- Department of Surgery, University of California San Diego, CA; VA San Diego Healthcare System, CA; AntiCancer, Inc, San Diego, CA
| | - Michael Bouvet
- Department of Surgery, University of California San Diego, CA; VA San Diego Healthcare System, CA.
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30
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Xia L, Teng Q, Chen Q, Zhang F. Preparation and Characterization of Anti-GPC3 Nanobody Against Hepatocellular Carcinoma. Int J Nanomedicine 2020; 15:2197-2205. [PMID: 32280214 PMCID: PMC7125335 DOI: 10.2147/ijn.s235058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background Glypican-3 (GPC3) is a newly identified target molecule for the early diagnosis of hepatocellular carcinoma (HCC), while targeted inhibition of GPC3 signaling may help to control the proliferation and metastasis of HCC cells. The purpose of this study was to prepare the anti-GPC3 nanobody and to investigate the affinity of the anti-GPC3 nanobodies in vitro and the anticancer effects on hepatocellular carcinoma in vivo. Methods To screen for unknown anti-GPC3 antibodies, we constructed an antibody phage display library. After three rounds of panning, positive phage clones were identified by enzyme-linked immunosorbent assay (ELISA). Further, the nanobody fusion protein was expressed in E. coli BL21 cells and purified by affinity chromatography. Competitive ELISA and flow cytometry were conducted to confirm the affinity of the anti-GPC3 nanobodies in vitro. The antitumor effects of VHHGPC3 were assessed in vivo. Results The results showed that the nanobody VHHGPC3 had specific high-affinity binding to His-GPC3 antigen. Moreover, VHHGPC3 exhibited specific binding to commercial human GPC3 and recognized the surface GPC3 protein of the hepatoma cell line HepG2. Importantly, in vivo study showed that GPC3 nanobody suppresses the growth of HepG2 and improves the survival rate of tumor mice. Discussion In summary, our new anti-GPC3 nanobody suggests a strong application potential for targeted therapy of liver cancer.
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Affiliation(s)
- Lijie Xia
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Qiao Teng
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Qi Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, People's Republic of China
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Cheong WS, Leow CY, Abdul Majeed AB, Leow CH. Diagnostic and therapeutic potential of shark variable new antigen receptor (VNAR) single domain antibody. Int J Biol Macromol 2020; 147:369-375. [PMID: 31926922 PMCID: PMC7112388 DOI: 10.1016/j.ijbiomac.2020.01.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/05/2020] [Accepted: 01/05/2020] [Indexed: 12/29/2022]
Abstract
Conventional monoclonal antibodies (mAbs) have been widely used in research and diagnostic applications due to their high affinity and specificity. However, multiple limitations, such as large size, complex structure and sensitivity to extreme ambient temperature potentially weaken the performance of mAbs in certain applications. To address this problem, the exploration of new antigen binders is extensively required in relation to improve the quality of current diagnostic platforms. In recent years, a new immunoglobulin-based protein, namely variable domain of new antigen receptor (VNAR) was discovered in sharks. Unlike conventional mAbs, several advantages of VNARs, include small size, better thermostability and peculiar paratope structure have attracted interest of researchers to further explore on it. This article aims to first present an overview of the shark VNARs and outline the characteristics as an outstanding new reagent for diagnostic and therapeutic applications.
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Affiliation(s)
- Wei Shien Cheong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | | | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang, Malaysia.
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Yu J, Sun Z, Sun X, Sun X, Wei H, Jia W, Pang M, Zhang L, Deng H. Selection and characterization of a Vibrio parahaemolyticus OmpU antibody by phage display. Microb Pathog 2020; 143:104136. [PMID: 32165333 DOI: 10.1016/j.micpath.2020.104136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is a well-known food-borne human pathogen that can cause a variety of clinical manifestations after the consumption of raw or undercooked seafoods. The crucial roles of Vibrio OmpU in bacterial pathogenesis have been found in recent studies. In the present study, we screened for single domain antibody fragment (sdAb) candidates that bind to V. parahaemolyticus OmpU by using a sdAb phage display library and isolated several positive phage clones. The UAb28, which was one of the positive clones, was shown high enrichment and affinity. The CDRs of UAb28 are speculated to perform the OmpU binding function by molecular docking. The capable of recognizing OmpU was verified by binding and inhibition assays. The UAb28 might be useful in future studies to develop the potential sdAb-based immunotherapeutics against V. parahaemolyticus infection.
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Affiliation(s)
- Junfang Yu
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Zhe Sun
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Xiaoyu Sun
- Department of Pathology, Central Hospital of Zibo, Zibo, 255000, People's Republic of China
| | - Xiaoyue Sun
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Hongmei Wei
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Wenlu Jia
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Mengzhen Pang
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Limei Zhang
- Department of Endocrinology, Central Hospital of Zibo, Zibo, 255000, People's Republic of China.
| | - Hongkuan Deng
- School of Life Sciences, Shandong University of Technology, Zibo, 255000, People's Republic of China.
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Roth L, Krah S, Klemm J, Günther R, Toleikis L, Busch M, Becker S, Zielonka S. Isolation of Antigen-Specific VHH Single-Domain Antibodies by Combining Animal Immunization with Yeast Surface Display. Methods Mol Biol 2020; 2070:173-189. [PMID: 31625096 DOI: 10.1007/978-1-4939-9853-1_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In addition to conventional hetero-tetrameric antibodies, the adaptive immune repertoire of camelids comprises the so-called heavy chain-only antibodies devoid of light chains. Consequently, antigen binding is mediated solely by the variable domain of the heavy chain, referred to as VHH. In recent years, these single-domain moieties emerged as promising tools for biotechnological and biomedical applications. In this chapter, we describe the generation of VHH antibody yeast surface display libraries from immunized Alpacas and Lamas as well as the facile isolation of antigen-specific molecules in a convenient fluorescence-activated cell sorting (FACS)-based selection process.
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Affiliation(s)
- Lukas Roth
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Janina Klemm
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Ralf Günther
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Michael Busch
- Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany.
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34
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Oh J, Warshaviak DT, Mkrtichyan M, Munguia ML, Lin A, Chai F, Pigott C, Kang J, Gallo M, Kamb A. Single variable domains from the T cell receptor β chain function as mono- and bifunctional CARs and TCRs. Sci Rep 2019; 9:17291. [PMID: 31754147 PMCID: PMC6872726 DOI: 10.1038/s41598-019-53756-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/31/2019] [Indexed: 01/21/2023] Open
Abstract
Cell therapy using T cell receptors (TCRs) and chimeric antigen receptors (CARs) represents a new wave of immunotherapies garnering considerable attention and investment. Further progress in this area of medicine depends in part on improving the functional capabilities of the engineered components, while maintaining the overall size of recombinant constructs to ensure their compatibility with existing gene delivery vehicles. We describe a single-variable-domain TCR (svd TCR) that utilizes only the variable domain of the β chain (Vβ). This Vβ module not only works in TCR and CAR formats, but also can be used to create single-chain bispecific CARs and TCRs. Comparison of individual ligand-binding Vβ domains in different formats suggests that the lone Vβ sequence controls the sensitivity and a major part of the specificity of the CAR or TCR construct, regardless of signaling format, in Jurkat and primary T cells.
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Affiliation(s)
- Julyun Oh
- A2 Biotherapeutics, Inc. 30301 Agoura Rd., Agoura Hills, CA, 91301, USA
| | | | | | | | - Abby Lin
- Innovative Targeting Solutions, Inc. 290-2985 Virtual Way, Vancouver, BC, V5M 4X7, Canada
| | - Falene Chai
- Innovative Targeting Solutions, Inc. 290-2985 Virtual Way, Vancouver, BC, V5M 4X7, Canada
| | - Craig Pigott
- Innovative Targeting Solutions, Inc. 290-2985 Virtual Way, Vancouver, BC, V5M 4X7, Canada
| | - Jaspal Kang
- Innovative Targeting Solutions, Inc. 290-2985 Virtual Way, Vancouver, BC, V5M 4X7, Canada
| | - Michael Gallo
- Innovative Targeting Solutions, Inc. 290-2985 Virtual Way, Vancouver, BC, V5M 4X7, Canada
| | - Alexander Kamb
- A2 Biotherapeutics, Inc. 30301 Agoura Rd., Agoura Hills, CA, 91301, USA.
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35
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Farahavar G, Abolmaali SS, Gholijani N, Nejatollahi F. Antibody-guided nanomedicines as novel breakthrough therapeutic, diagnostic and theranostic tools. Biomater Sci 2019; 7:4000-4016. [PMID: 31355391 DOI: 10.1039/c9bm00931k] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in nanotechnology, such as the development of various types of nanoparticles and hybrid nanomaterials, have revolutionized nanomedicine. The small size, customizable surface, enhanced solubility, and multi-functionality endow the nanoparticles with an ability to interact with complex cellular and biological functions in new ways. Furthermore, these systems can deliver drugs to specific tissues and provide a targeted therapy. For this purpose, different categories of molecules, particularly antibodies, have been used as ligands. Antibody-conjugated nanomaterials can significantly enhance the efficiency of nanomedicines, especially in the field of cancer. This review is focused on three major medical applications of antibody-conjugated nanomaterials, namely, therapeutic, diagnostic and theranostic applications. To provide comprehensive information on the topic and an overview of these hybrid nanomaterials for biomedical applications, a brief summary of nanomaterials and antibodies is given. Moreover, the review has depicted the potential applications of antibody-conjugated nanomaterials in different fields and their capabilities to empower nanomedicine, particularly in relation to the treatment and detection of malignancies.
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Affiliation(s)
- Ghazal Farahavar
- Pharmaceutical Nanotechnology Department, Shiraz University of Medical Sciences, Shiraz 71345, Iran.
| | - Samira Sadat Abolmaali
- Pharmaceutical Nanotechnology Department and Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz 71345, Iran.
| | - Nasser Gholijani
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Foroogh Nejatollahi
- Shiraz HIV/AIDS research center, Institute of health, Shiraz University of Medical Sciences, Shiraz, Iran.
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36
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Ulmer N, Ristanovic D, Morbidelli M. Process for Continuous Fab Production by Digestion of IgG. Biotechnol J 2019; 14:e1800677. [PMID: 31169346 DOI: 10.1002/biot.201800677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/21/2019] [Indexed: 11/10/2022]
Abstract
Intensified processing and end-to-end integrated continuous manufacturing are increasingly being considered in bioprocessing as an alternative to the current batch-based technologies. Similar approaches can also be used at later stages of the production chain, such as in the post-translational modifications that are often considered for therapeutic proteins. In this work, a process to intensify the enzymatic digestion of immunoglobulin G (IgG) and the purification of the resulting Fab fragment is developed. The process consists of the integration of a continuous packed-bed reactor into a multicolumn chromatographic process. The integration is realized through the development of a novel multicolumn countercurrent solvent gradient purification (MCSGP) process, which, by adding a third column to the classical two-column MCSGP process, allows for continuous loading and then straight-through processing of the mixture leaving the reactor.
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Affiliation(s)
- Nicole Ulmer
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Dragana Ristanovic
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Massimo Morbidelli
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
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37
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Laursen NS, Friesen RHE, Zhu X, Jongeneelen M, Blokland S, Vermond J, van Eijgen A, Tang C, van Diepen H, Obmolova G, van der Neut Kolfschoten M, Zuijdgeest D, Straetemans R, Hoffman RMB, Nieusma T, Pallesen J, Turner HL, Bernard SM, Ward AB, Luo J, Poon LLM, Tretiakova AP, Wilson JM, Limberis MP, Vogels R, Brandenburg B, Kolkman JA, Wilson IA. Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Science 2018; 362:598-602. [PMID: 30385580 DOI: 10.1126/science.aaq0620] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 09/14/2018] [Indexed: 12/11/2022]
Abstract
Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
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Affiliation(s)
- Nick S Laursen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mandy Jongeneelen
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Sven Blokland
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Jan Vermond
- Janssen Prevention Center, Archimedesweg 6, 2333 CN, Leiden, Netherlands
| | - Alida van Eijgen
- Janssen Prevention Center, Archimedesweg 6, 2333 CN, Leiden, Netherlands
| | - Chan Tang
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Harry van Diepen
- Janssen Prevention Center, Archimedesweg 6, 2333 CN, Leiden, Netherlands
| | - Galina Obmolova
- Janssen Research and Development, Spring House, PA 19002, USA
| | | | - David Zuijdgeest
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Roel Straetemans
- Quantitative Sciences, Janssen Pharmaceutical Companies of Johnson and Johnson, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Ryan M B Hoffman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Travis Nieusma
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steffen M Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jinquan Luo
- Janssen Research and Development, Spring House, PA 19002, USA
| | - Leo L M Poon
- Center of Influenza Research and School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Anna P Tretiakova
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria P Limberis
- Gene Therapy Program, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald Vogels
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Boerries Brandenburg
- Janssen Vaccines and Prevention, Archimedesweg 4-6, 2333 CN, Leiden, Netherlands
| | - Joost A Kolkman
- Janssen Infectious Diseases, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. .,Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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38
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Potential Human Health Applications from Marine Biomedical Research with Elasmobranch Fishes. FISHES 2018. [DOI: 10.3390/fishes3040047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Members of the subclass of fishes collectively known as elasmobranchs (Class Chondrichthyes, Subclass Elasmobranchii) include sharks, skates, rays, guitarfish, and sawfish. Having diverged from the main line of vertebrate evolution some 400 million years ago, these fishes have continued to be successful in our ever-changing oceans. Much of their success must be attributed to their uncanny ability to remain healthy. Based on decades of basic research, some of their secrets may be very close to benefitting man. In this short review, some of the molecular and cellular biological areas that show promise for potential human applications are presented. With a brief background and current status of relevant research, these topics include development of new antibiotics and novel treatments for cancer, macular degeneration, viral pathogens, and Parkinson’s disease; potentially useful genomic information from shark transcriptomes; shark antibody-derived drug delivery systems; and immune cell-derived compounds as potential cancer therapeutic agents.
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39
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Sortaggable liposomes: Evaluation of reaction conditions for single-domain antibody conjugation by Sortase-A and targeting of CD11b+ myeloid cells. Eur J Pharm Biopharm 2018; 133:138-150. [DOI: 10.1016/j.ejpb.2018.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/31/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
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40
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Abstract
Bispecific antibodies have moved from being an academic curiosity with therapeutic promise to reality, with two molecules being currently commercialized (Hemlibra® and Blincyto®) and many more in clinical trials. The success of bispecific antibodies is mainly due to the continuously growing number of mechanisms of actions (MOA) they enable that are not accessible to monoclonal antibodies. One of the earliest MOA of bispecific antibodies and currently the one with the largest number of clinical trials is the redirecting of the cytotoxic activity of T-cells for oncology applications, now extending its use in infective diseases. The use of bispecific antibodies for crossing the blood-brain barrier is another important application because of its potential to advance the therapeutic options for neurological diseases. Another noteworthy application due to its growing trend is enabling a more tissue-specific delivery or activity of antibodies. The different molecular solutions to the initial hurdles that limited the development of bispecific antibodies have led to the current diverse set of bispecific or multispecific antibody formats that can be grouped into three main categories: IgG-like formats, antibody fragment-based formats, or appended IgG formats. The expanded applications of bispecific antibodies come at the price of additional challenges for clinical development. The rising complexity in their structure may increase the risk of immunogenicity and the multiple antigen specificity complicates the selection of relevant species for safety assessment.
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Affiliation(s)
- Bushra Husain
- Protein Chemistry Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Diego Ellerman
- Protein Chemistry Department, Genentech Inc., South San Francisco, CA, 94080, USA.
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41
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Li Q, Miao Z, Luo XG, Zhao J, Song YJ, Li ZY, Zhou H, Zhang TC, Mao LS. Expression and bioactivity analysis of TNF30, a TNFα nanobody, in Escherichia coli. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1480422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Qian Li
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Zhi Miao
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Xue-Gang Luo
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Jian Zhao
- Lidzix Biotechnology Tianjin Co., Ltd, Tianjin, P.R. China
| | - Ya-Jian Song
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Zhong-Yuan Li
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Hao Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Tong-Cun Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Tianjin University of Science and Technology, Ministry of Education, Tianjin, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, P.R. China
| | - Li-Song Mao
- Lidzix Biotechnology Tianjin Co., Ltd, Tianjin, P.R. China
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42
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Förster B, Chung PK, Crobach MJT, Kuijper EJ. Application of Antibody-Mediated Therapy for Treatment and Prevention of Clostridium difficile Infection. Front Microbiol 2018; 9:1382. [PMID: 29988597 PMCID: PMC6027166 DOI: 10.3389/fmicb.2018.01382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/06/2018] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile causes antibiotic- and healthcare-associated diarrhea, which is characterized by a high mortality rate (5–15%) and high recurrence rate of 20% or more. Therapeutic alternatives to antibiotics are urgently needed to improve the overall cure rate. Among these, therapeutic antibodies have shown promising results in clinical studies. Herein, the authors review current monoclonal and polyclonal anti- C. difficile antibodies that have entered the clinical development stage, either for systemic administration or by the oral route. The antibodies can be applied as monotherapy or in combination with standard-of-care to treat an infection with C. difficile or to protect from a recurrence. Bezlotoxumab is the first antibody for secondary prevention of recurrence of C. difficile infection approved by the regulatory agencies in US and Europe. The human monoclonal antibody is administered systemically to patients receiving oral standard-of–care antibiotics. Other antibodies are currently in the clinical pipeline, and some are intended for oral use. They show a good safety profile, high efficacy and low production costs, and can be considered promising therapies of the future. The most promising orally administered drug candidate is a bovine antibody from hyperimmune colostral milk, which is in an advanced clinical development stage. Which antibody will enter the market is dependent on its bioavailability at the site of infection as well as its activity against C. difficile toxins, protection against colonization and possible action on spore formation. The antibody must demonstrate a clear benefit in comparison with other available treatment options to be considered for use by clinicians.
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Affiliation(s)
- Beatrix Förster
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands.,Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Pui Khi Chung
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Monique J T Crobach
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Centre for Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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43
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Allegra A, Innao V, Gerace D, Vaddinelli D, Allegra AG, Musolino C. Nanobodies and Cancer: Current Status and New Perspectives. Cancer Invest 2018; 36:221-237. [DOI: 10.1080/07357907.2018.1458858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Vanessa Innao
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Demetrio Gerace
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Doriana Vaddinelli
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Andrea Gaetano Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Caterina Musolino
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
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44
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Menzel S, Schwarz N, Haag F, Koch-Nolte F. Nanobody-Based Biologics for Modulating Purinergic Signaling in Inflammation and Immunity. Front Pharmacol 2018; 9:266. [PMID: 29636685 PMCID: PMC5880931 DOI: 10.3389/fphar.2018.00266] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/09/2018] [Indexed: 12/18/2022] Open
Abstract
Adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NAD+) are released as danger signals from cells during infection and sterile inflammation. In the extracellular compartment ATP is converted by CD39, CD73, and other ecto-enzymes into metabolites that modulate the activity of T cells and macrophages. While ATP mediates pro-inflammatory signals via P2X7 and other P2 receptors, adenosine triggers anti-inflammatory signaling via the adenosine 2a receptor (Adora2a) and other P1 receptors. The latter also plays a role in maintaining an immunosuppressive tumor microenvironment. NAD+ is converted by CD38, CD203 and other ecto-enzymes to the Ca2+ mobilizing messengers cyclic ADP-ribose and ADP-ribose, and to adenosine. Recent findings on the roles of CD38, CD39, CD73, CD203, P2X7, and Adora2a in inflammation and immunity underscore the potential of these proteins as drug targets. However, available small molecule inhibitors often lack specificity and mediate unwanted off-target toxicity. Nanobodies – single domain antibodies derived from heavy chain antibodies that naturally occur in camelids – display a propensity to bind functional epitopes not accessible to conventional antibodies. Like conventional antibodies, nanobodies and nanobody-based biologics are highly specific and have well-understood, tunable in vivo pharmacodynamics with little if any toxicity. Nanobodies thus represent attractive alternatives to small molecule inhibitors for modulating purinergic signaling in inflammation and immunity. Here we review recent progress made in developing nanobodies against key targets of purinergic signaling.
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Affiliation(s)
- Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicole Schwarz
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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45
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Conic S, Desplancq D, Ferrand A, Fischer V, Heyer V, Reina San Martin B, Pontabry J, Oulad-Abdelghani M, Babu N K, Wright GD, Molina N, Weiss E, Tora L. Imaging of native transcription factors and histone phosphorylation at high resolution in live cells. J Cell Biol 2018; 217:1537-1552. [PMID: 29440513 PMCID: PMC5881509 DOI: 10.1083/jcb.201709153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/16/2023] Open
Abstract
Conic et al. introduce a versatile antibody-based imaging approach to track endogenous nuclear factors in living cells. It allows efficient intracellular delivery of any fluorescent dye–conjugated antibody, or Fab fragment, into a variety of cell types. The dynamics of nuclear targets or posttranslational modifications can be monitored with high precision using confocal and super-resolution microscopy. Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina San Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Pontabry
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epigenetics and Stem Cells, München, Germany
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Kishore Babu N
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Etienne Weiss
- Institut de Recherche de l'ESBS, UMR 7242, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,School of Biological Sciences, Nanyang Technological University, Singapore
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46
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Könning D, Hinz S, Grzeschik J, Schröter C, Krah S, Zielonka S, Kolmar H. Construction of Histidine-Enriched Shark IgNAR Variable Domain Antibody Libraries for the Isolation of pH-Sensitive vNAR Fragments. Methods Mol Biol 2018; 1827:109-127. [PMID: 30196494 DOI: 10.1007/978-1-4939-8648-4_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The adaptive immune system of sharks comprises a heavy chain-only antibody isotype, referred to as immunoglobulin new antigen receptor (IgNAR). Antigen binding in case of IgNAR antibodies is mediated by a single variable domain (vNAR). Due to their inherent beneficial biophysical properties, such as small size and high thermal stability combined with a high specificity and affinity to their target antigens, vNAR domains emerged as promising tools for biotechnological and biomedical applications. Herein, we present detailed protocols for the engineering of pH-sensitivity into IgNAR V domains by constructing histidine-enriched and CDR3-diversified semisynthetic antibody libraries which can then be screened upon using yeast surface display. Protonation or deprotonation of incorporated histidine residues at different pH values results in structural transitions caused by altered electrostatic interactions. These interactions account for an altered binding behavior toward the target antigen. In the following protocol, we describe the generation of a semisynthetic vNAR master library that comprises two histidine residues on average in the 12-residue CDR3 loop. Moreover, once a pH-dependent vNAR population toward the target antigen is identified, this population can further be optimized in terms of affinity and pH sensitivity upon conducting a CDR1-mediated affinity maturation.
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Affiliation(s)
- Doreen Könning
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Steffen Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christian Schröter
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Simon Krah
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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47
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Grzeschik J, Könning D, Hinz SC, Krah S, Schröter C, Empting M, Kolmar H, Zielonka S. Generation of Semi-Synthetic Shark IgNAR Single-Domain Antibody Libraries. Methods Mol Biol 2018; 1701:147-167. [PMID: 29116504 DOI: 10.1007/978-1-4939-7447-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Besides classical antibodies with the composition of heavy and light chains, sharks produce a unique heavy chain only isotype, termed Immunoglobulin New Antigen Receptor (IgNAR), in which antigen binding is solely mediated by a single domain, referred to as vNAR. Owing to their high affinity and specificity combined with their small size and high stability, vNAR domains emerged as promising target-binding scaffolds that can be tailor-made for biotechnological and biomedical applications. Herein, we describe protocols for the construction of semi-synthetic, CDR3-randomized vNAR libraries for the isolation of target-specific antibodies using yeast surface display or phage display as platform technology. Additionally, we provide information for affinity maturation of target-specific molecules through CDR1 diversification and sublibrary establishment.
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Affiliation(s)
- Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Doreen Könning
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany
| | - Simon Krah
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck-Serono, Merck KGaA, Frankfurter Straße 250, D-64293, Darmstadt, Germany
| | - Christian Schröter
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck-Serono, Merck KGaA, Frankfurter Straße 250, D-64293, Darmstadt, Germany
| | - Martin Empting
- Department Drug Design and Optimization, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, Saarbrücken, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany.
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287, Darmstadt, Germany. .,Protein Engineering and Antibody Technologies, Merck-Serono, Merck KGaA, Frankfurter Straße 250, D-64293, Darmstadt, Germany.
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48
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Ubah OC, Steven J, Kovaleva M, Ferguson L, Barelle C, Porter AJR, Barelle CJ. Novel, Anti-hTNF-α Variable New Antigen Receptor Formats with Enhanced Neutralizing Potency and Multifunctionality, Generated for Therapeutic Development. Front Immunol 2017; 8:1780. [PMID: 29312310 PMCID: PMC5743654 DOI: 10.3389/fimmu.2017.01780] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022] Open
Abstract
The management of chronic inflammatory diseases, such as inflammatory bowel disease, psoriasis, and rheumatoid arthritis has significantly improved over the last decade with the clinical availability of anti-TNF-α biologics. Despite this undoubted treatment success, a combination of acquired resistance together with an increased risk of systemic complications, means that a significant number of patients either fail to find a suitable targeted therapy or frustratingly discover that an approach that did work is no longer efficacious. Here, we report the isolation and characterization of a new class of super-neutralizing anti-TNF-α biologics formats, the building blocks of which were originally derived as variable new antigen receptor (VNAR) domains from an immunized nurse shark. These parental small, stable VNAR monomers recognize and neutralize tumor necrosis factor (TNF)-α, in cell-based assays, at nanomolar concentrations. However, the simple, single-chain molecular architecture of VNARs allows for easy and multiple reformatting options. Through reformatting, we achieved a 50,000-fold enhancement in in vitro efficacy with super-neutralizing fusion proteins able to block TNF-α induced cytotoxicity in the 2–5 pM range while retaining other functionality through the addition of fusion proteins known to extend serum half-life in vivo. In an in vitro intestinal epithelial barrier dysfunction efficacy model, the lead VNAR domains, restored barrier function and prevented paracellular flux with comparable efficacy to adalimumab (Humira®). In addition, all multivalent VNAR constructs restored trans-epithelial electrical resistance (TEER) to approximately 94% of the untreated control. Reformatted VNAR domains should be considered as a new class of biologic agents for the treatment of hTNF-α driven diseases; either used systemically with appropriate half-life extension or alternatively where site-specific delivery of small and stable neutralizers may provide improvements to current therapy options.
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Affiliation(s)
| | | | | | | | | | - Andrew J R Porter
- Elasmogen Ltd., Aberdeen, Scotland.,Scottish Biologics Facility, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland
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49
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Xu J, Wu J, Jiang B, He H, Zhang X, Li X, Yang D, Huang X, Sealy JE, Iqbal M, Li Y. Bovine single chain Fv antibody inhibits bovine herpesvirus-1 infectivity by targeting viral glycoprotein D. Appl Microbiol Biotechnol 2017; 101:8331-8344. [PMID: 29063173 DOI: 10.1007/s00253-017-8566-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/20/2023]
Abstract
Glycoprotein D (gD) of bovine herpesvirus-1 (BoHV-1) is essential for attachment and penetration of cells during infection and is a major target for neutralizing antibodies during an adaptive immune response. Currently there are no recombinant antibodies capable of binding gD epitopes for use in treating BoHV-1 infection. In this study, a bovine scFv gene derived from a hybridoma secreting monoclonal antibodies (McAbs) against the amino acid motif MEESKGYEPP of gD was expressed in E. coli. Molecular modeling, western blot and ELISA analysis showed that this scFv had a high affinity for BoHV-1 gD, with a Kd of 161.2 ± 37.58 nM and for whole BoHV-1 virus, with a Kd of 67.44 ± 16.99 nM. In addition, this scFv displayed a high affinity for BoHV-1 antigen in an ELISA and competed with BoHV-1 anti-serum in a competitive ELISA. Immunofluorescence assay (IFA) and laser confocal microscopy showed that this scFv could efficiently bind to and be internalized by BoHV-1 infected Madin-Darby bovine kidney (MDBK) cells. Importantly, this scFv was shown to inhibit BoHV-1 infectivity and to reduce the number of viral plaques by blocking viral attachment to MDBK cells. Our study suggests that this bovine single-chain antibody could be developed for use as a diagnostic and therapeutic agent against BoHV-1 infection in cattle.
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Affiliation(s)
- Jian Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097
| | - Jing Wu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097.,College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, People's Republic of China, 330045
| | - Bo Jiang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097
| | - Houjun He
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, People's Republic of China, 330045
| | - Xixi Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097.,Animal Science and Technology College, Beijing University of Agriculture, Beijing, People's Republic of China, 102206
| | - Xiaoyang Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097.,College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, People's Republic of China, 330045
| | - Dawei Yang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097
| | - Xiufen Huang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097
| | - Joshua E Sealy
- The Pirbright Institute, Ash Rd, Pirbright, Woking, GU24 0NF, UK
| | - Munir Iqbal
- The Pirbright Institute, Ash Rd, Pirbright, Woking, GU24 0NF, UK
| | - Yongqing Li
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, People's Republic of China, 100097.
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50
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Binder U, Skerra A. PASylation®: A versatile technology to extend drug delivery. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.06.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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