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McConnell SA, Casadevall A. Immunoglobulin constant regions provide stabilization to the paratope and enforce epitope specificity. J Biol Chem 2024; 300:107397. [PMID: 38763332 PMCID: PMC11215335 DOI: 10.1016/j.jbc.2024.107397] [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: 04/11/2024] [Accepted: 05/09/2024] [Indexed: 05/21/2024] Open
Abstract
Constant domains in antibody molecules at the level of the Fab (CH1 and CL) have long been considered to be simple scaffolding elements that physically separate the paratope-defining variable (V) region from the effector function-mediating constant (C) regions. However, due to recent findings that C domains of different isotypes can modulate the fine specificity encoded in the V region, elucidating the role of C domains in shaping the paratope and influencing specificity is a critical area of interest. To dissect the relative contributions of each C domain to this phenomenon, we generated antibody fragments with different C regions omitted, using a set of antibodies targeting capsular polysaccharides from the fungal pathogen, Cryptococcus neoformans. Antigen specificity mapping and functional activity measurements revealed that V region-only antibody fragments exhibited poly-specificity to antigenic variants and extended to recognition of self-antigens, while measurable hydrolytic activity of the capsule was greatly attenuated. To better understand the mechanistic origins of the remarkable loss of specificity that accompanies the removal of C domains from identical paratopes, we performed molecular dynamics simulations which revealed increased paratope plasticity in the scFv relative to the corresponding Fab. Together, our results provide insight into how the remarkable specificity of immunoglobulins is governed and maintained at the level of the Fab through the enforcement of structural restrictions on the paratope by CH1 domains.
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Affiliation(s)
- Scott A McConnell
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
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2
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Rizk SS, Moustafa DM, ElBanna SA, Nour El-Din HT, Attia AS. Nanobodies in the fight against infectious diseases: repurposing nature's tiny weapons. World J Microbiol Biotechnol 2024; 40:209. [PMID: 38771414 PMCID: PMC11108896 DOI: 10.1007/s11274-024-03990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
Nanobodies are the smallest known antigen-binding molecules to date. Their small size, good tissue penetration, high stability and solubility, ease of expression, refolding ability, and negligible immunogenicity in the human body have granted them excellence over conventional antibodies. Those exceptional attributes of nanobodies make them promising candidates for various applications in biotechnology, medicine, protein engineering, structural biology, food, and agriculture. This review presents an overview of their structure, development methods, advantages, possible challenges, and applications with special emphasis on infectious diseases-related ones. A showcase of how nanobodies can be harnessed for applications including neutralization of viruses and combating antibiotic-resistant bacteria is detailed. Overall, the impact of nanobodies in vaccine design, rapid diagnostics, and targeted therapies, besides exploring their role in deciphering microbial structures and virulence mechanisms are highlighted. Indeed, nanobodies are reshaping the future of infectious disease prevention and treatment.
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Affiliation(s)
- Soha S Rizk
- Microbiology and Immunology Postgraduate Program, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Dina M Moustafa
- Department of Medical Sciences, Faculty of Dentistry, The British University in Egypt, El Sherouk City, Cairo, 11837, Egypt
| | - Shahira A ElBanna
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Hanzada T Nour El-Din
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Ahmed S Attia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
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3
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Eirich P, Nesterov P, Shityakov S, Skorb EV, Sander B, Broscheit J, Dandekar T, Jones NG, Engstler M. The release of host-derived antibodies bound to the variant surface glycoprotein (VSG) of Trypanosoma brucei cannot be explained by pH-dependent conformational changes of the VSG dimer. OPEN RESEARCH EUROPE 2024; 4:87. [PMID: 38903703 PMCID: PMC11187536 DOI: 10.12688/openreseurope.16783.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 06/22/2024]
Abstract
Background Trypanosoma brucei is a protozoan parasite that evades the mammalian host's adaptive immune response by antigenic variation of the highly immunogenic variant surface glycoprotein (VSG). VSGs form a dense surface coat that is constantly recycled through the endosomal system. Bound antibodies are separated in the endosome from the VSG and destroyed in the lysosome. For VSGs it has been hypothesized that pH-dependent structural changes of the VSG could occur in the more acidic environment of the endosome and hence, facilitate the separation of the antibody from the VSG. Methods We used size exclusion chromatography, where molecules are separated according to their hydrodynamic radius to see if the VSG is present as a homodimer at both pH values. To gain information about the structural integrity of the protein we used circular dichroism spectroscopy by exposing the VSG in solution to a mixture of right- and left-circularly polarized light and analysing the absorbed UV spectra. Evaluation of protein stability and molecular dynamics simulations at different pH values was performed using different computational methods. Results We show, for an A2-type VSG, that the dimer size is only slightly larger at pH 5.2 than at pH 7.4. Moreover, the dimer was marginally more stable at lower pH due to the higher affinity (ΔG = 353.37 kcal/mol) between the monomers. Due to the larger size, the predicted epitopes were more exposed to the solvent at low pH. Moderate conformational changes (ΔRMSD = 0.35 nm) in VSG were detected between the dimers at pH 5.2 and pH 7.4 in molecular dynamics simulations, and no significant differences in the protein secondary structure were observed by circular dichroism spectroscopy. Conclusions Thus, the dissociation of anti-VSG-antibodies in endosomes cannot be explained by changes in pH.
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Affiliation(s)
- Patrick Eirich
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Pavel Nesterov
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
| | - Sergey Shityakov
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
- Department of Bioinformatics, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
| | - Bodo Sander
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Jens Broscheit
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Nicola G. Jones
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Markus Engstler
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
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4
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Yanakieva D, Vollmer L, Evers A, Siegmund V, Arras P, Pekar L, Doerner A, Valldorf B, Kolmar H, Zielonka S, Krah S. Cattle-derived knob paratopes grafted onto peripheral loops of the IgG1 Fc region enable the generation of a novel symmetric bispecific antibody format. Front Immunol 2023; 14:1238313. [PMID: 37942319 PMCID: PMC10628450 DOI: 10.3389/fimmu.2023.1238313] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
In this work we present a novel symmetric bispecific antibody format based on engraftments of cattle-derived knob paratopes onto peripheral loops of the IgG1 Fc region. For this, knob architectures obtained from bovine ultralong CDR-H3 antibodies were inserted into the AB loop or EF loop of the CH3 domain, enabling the introduction of an artificial binding specificity into an IgG molecule. We demonstrate that inserted knob domains largely retain their binding affinities, resulting into bispecific antibody derivatives versatile for effector cell redirection. Essentially, generated bispecifics demonstrated adequate biophysical properties and were not compromised in their Fc mediated functionalities such as FcRn or FcγRIIIa binding.
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Affiliation(s)
- Desislava Yanakieva
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lena Vollmer
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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5
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Huang R, Warner Jenkins G, Kim Y, Stanfield RL, Singh A, Martinez-Yamout M, Kroon GJ, Torres JL, Jackson AM, Kelley A, Shaabani N, Zeng B, Bacica M, Chen W, Warner C, Radoicic J, Joh J, Dinali Perera K, Sang H, Kim T, Yao J, Zhao F, Sok D, Burton DR, Allen J, Harriman W, Mwangi W, Chung D, Teijaro JR, Ward AB, Dyson HJ, Wright PE, Wilson IA, Chang KO, McGregor D, Smider VV. The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2303455120. [PMID: 37722054 PMCID: PMC10523490 DOI: 10.1073/pnas.2303455120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/15/2023] [Indexed: 09/20/2023] Open
Abstract
Cows produce antibodies with a disulfide-bonded antigen-binding domain embedded within ultralong heavy chain third complementarity determining regions. This "knob" domain is analogous to natural cysteine-rich peptides such as knottins in that it is small and stable but can accommodate diverse loops and disulfide bonding patterns. We immunized cattle with SARS-CoV-2 spike and found ultralong CDR H3 antibodies that could neutralize several viral variants at picomolar IC50 potencies in vitro and could protect from disease in vivo. The independent CDR H3 peptide knobs were expressed and maintained the properties of the parent antibodies. The knob interaction with SARS-CoV-2 spike was revealed by electron microscopy, X-ray crystallography, NMR spectroscopy, and mass spectrometry and established ultralong CDR H3-derived knobs as the smallest known recombinant independent antigen-binding fragment. Unlike other vertebrate antibody fragments, these knobs are not reliant on the immunoglobulin domain and have potential as a new class of therapeutics.
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Affiliation(s)
- Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA92127
| | | | - Yunjeong Kim
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Amrinder Singh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Maria Martinez-Yamout
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard J. Kroon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Abigail Kelley
- Applied Biomedical Science Institute, San Diego, CA92127
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | | | | | - Wen Chen
- Ligand Pharmaceuticals, San Diego, CA92121
| | | | | | - Joongho Joh
- School of Medicine, Department of Medicine, University of Louisville, Louisville, KY40202
| | - Krishani Dinali Perera
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Huldah Sang
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Tae Kim
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Jianxiu Yao
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Jeff Allen
- Ligand Pharmaceuticals, San Diego, CA92121
| | | | - Waithaka Mwangi
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Donghoon Chung
- School of Medicine, Department of Microbiology and Immunology, University of Louisville, Louisville, KY40202
| | - John R. Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Kyeong-Ok Chang
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | | | - Vaughn V. Smider
- Applied Biomedical Science Institute, San Diego, CA92127
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
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6
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Sharma P, Joshi RV, Pritchard R, Xu K, Eicher MA. Therapeutic Antibodies in Medicine. Molecules 2023; 28:6438. [PMID: 37764213 PMCID: PMC10535987 DOI: 10.3390/molecules28186438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/05/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Antibody engineering has developed into a wide-reaching field, impacting a multitude of industries, most notably healthcare and diagnostics. The seminal work on developing the first monoclonal antibody four decades ago has witnessed exponential growth in the last 10-15 years, where regulators have approved monoclonal antibodies as therapeutics and for several diagnostic applications, including the remarkable attention it garnered during the pandemic. In recent years, antibodies have become the fastest-growing class of biological drugs approved for the treatment of a wide range of diseases, from cancer to autoimmune conditions. This review discusses the field of therapeutic antibodies as it stands today. It summarizes and outlines the clinical relevance and application of therapeutic antibodies in treating a landscape of diseases in different disciplines of medicine. It discusses the nomenclature, various approaches to antibody therapies, and the evolution of antibody therapeutics. It also discusses the risk profile and adverse immune reactions associated with the antibodies and sheds light on future applications and perspectives in antibody drug discovery.
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Affiliation(s)
- Prerna Sharma
- Geisinger Commonwealth School of Medicine, Scranton, PA 18509, USA
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7
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Ott JA, Mitchell C, Sheppard M, Deiss TC, Horton JMC, Haakenson JK, Huang R, Kelley AR, Davis BW, Derr JN, Smider VV, Criscitiello MF. Evolution of immunogenetic components encoding ultralong CDR H3. Immunogenetics 2023; 75:323-339. [PMID: 37084012 PMCID: PMC10119515 DOI: 10.1007/s00251-023-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christian Mitchell
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Morgan Sheppard
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Thad C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J M Cody Horton
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Brian W Davis
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James N Derr
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, 77807, USA.
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8
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Huan T, Guan B, Li H, Tu X, Zhang C, Tang B. Principles and current clinical landscape of NK cell engaging bispecific antibody against cancer. Hum Vaccin Immunother 2023; 19:2256904. [PMID: 37772505 PMCID: PMC10543353 DOI: 10.1080/21645515.2023.2256904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
Monoclonal antibody-based targeted therapies have greatly improved treatment options for patients by binding to the innate immune system. However, the long-term efficacy of such antibodies is limited by mechanisms of drug resistance. Over the last 50 years, with advances in protein engineering technology, more and more bispecific antibody (bsAb) platforms have been engineered to meet diverse clinical needs. Bispecific NK cell engagers (BiKEs) or tri-specific NK cell engagers (TriKEs) allow for direct targeting of immune cells to tumors, and therefore resistance and serious adverse effects are greatly reduced. Many preclinical and clinical trials are currently underway, depicting the promise of antibody-based natural killer cell engager therapeutics. In this review, we compile worldwide efforts to explore the involvement of NK cells in bispecific antibodies. With a particular emphasis on lessons learned, we focus on preclinical and clinical studies in malignancies and discuss the reasons for the limited success of NK-cell engagers against solid tumors, offering plausible new ideas for curing some advanced cancers shortly.
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Affiliation(s)
- Tian Huan
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Bugao Guan
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
| | - Hongbo Li
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
| | - Xiu Tu
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
| | - Chi Zhang
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
| | - Bin Tang
- Department of General Surgery, Jinhu County People’s Hospital, Huaian, Jiangsu, China
- Department of Central Laboratory, Jinhu County People’s Hospital, Huaian, Jiangsu, China
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9
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Hurley K, Cao M, Huang H, Wang Y. Targeted Alpha Therapy (TAT) with Single-Domain Antibodies (Nanobodies). Cancers (Basel) 2023; 15:3493. [PMID: 37444603 DOI: 10.3390/cancers15133493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The persistent threat of cancer necessitates the development of improved and more efficient therapeutic strategies that limit damage to healthy tissues. Targeted alpha therapy (TαT), a novel form of radioimmuno-therapy (RIT), utilizes a targeting vehicle, commonly antibodies, to deliver high-energy, but short-range, alpha-emitting particles specifically to cancer cells, thereby reducing toxicity to surrounding normal tissues. Although full-length antibodies are often employed as targeting vehicles for TαT, their high molecular weight and the presence of an Fc-region lead to a long blood half-life, increased bone marrow toxicity, and accumulation in other tissues such as the kidney, liver, and spleen. The discovery of single-domain antibodies (sdAbs), or nanobodies, naturally occurring in camelids and sharks, has introduced a novel antigen-specific vehicle for molecular imaging and TαT. Given that nanobodies are the smallest naturally occurring antigen-binding fragments, they exhibit shorter relative blood half-lives, enhanced tumor uptake, and equivalent or superior binding affinity and specificity. Nanobody technology could provide a viable solution for the off-target toxicity observed with full-length antibody-based TαT. Notably, the pharmacokinetic properties of nanobodies align better with the decay characteristics of many short-lived α-emitting radionuclides. This review aims to encapsulate recent advancements in the use of nanobodies as a vehicle for TαT.
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Affiliation(s)
- Kate Hurley
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Meiyun Cao
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
| | - Haiming Huang
- Research Center, Forlong Biotechnology Inc., Suzhou 215004, China
| | - Yi Wang
- Radiobiology and Health, Canadian Nuclear Laboratories, Chalk River, ON K0J 1J0, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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10
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Sioud M, Olberg A. Antibody Surface Profiling Identifies Glycoforms in Multiple Myeloma as Targets for Immunotherapy: From Antibody Derivatives to Mimetic Peptides for Killing Tumor Cells. Cancers (Basel) 2023; 15:cancers15071934. [PMID: 37046595 PMCID: PMC10093763 DOI: 10.3390/cancers15071934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/15/2023] [Accepted: 03/18/2023] [Indexed: 04/14/2023] Open
Abstract
Despite therapeutic advances in recent years, there are still unmet medical needs for patients with multiple myeloma (MM). Hence, new therapeutic strategies are needed. Using phage display for screening a large repertoire of single chain variable fragments (scFvs), we isolated several candidates that recognize a heavily sulfated MM-specific glycoform of the surface antigen syndecan-1 (CD138). One of the engineered scFv-Fc antibodies, named MM1, activated NK cells and induced antibody-dependent cellular cytotoxicity against MM cells. Analysis of the binding specificity by competitive binding assays with various glycan ligands identified N-sulfation of glucosamine units as essential for binding. Additionally, site-directed mutagenesis revealed that the amino acids arginine and histidine in the complementarily determining regions (CDRs) 2 and 3 of the heavy chain are important for binding. Based on this observation, a heavy-chain antibody, known as a nanobody, and a peptide mimicking the CDR loop sequences were designed. Both variants exhibited high affinity and specificity to MM cells as compared to blood lymphocytes. Specific killing of MM cells was achieved by conjugating the CDR2/3 mimic peptide to a pro-apoptotic peptide (KLAKLAK)2. In a co-culture model, the fusion peptide killed MM cells, while leaving normal peripheral blood mononuclear cells unaffected. Collectively, the development of antibodies and peptides that detect tumor-specific glycoforms of therapeutic targets holds promise for improving targeted therapies and tumor imaging.
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Affiliation(s)
- Mouldy Sioud
- Department of Cancer Immunology, Division of Cancer Medicine, Oslo University Hospital-Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
| | - Anniken Olberg
- Department of Cancer Immunology, Division of Cancer Medicine, Oslo University Hospital-Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
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11
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Abstract
The immune systems protect vertebrates from foreign molecules or antigens, and antibodies are important mediators of this system. The sequences and structural features of antibodies vary depending on species. Many of antibodies from vertebrates, including camelids, have both heavy and light chain variable domains, but camelids also have antibodies that lack the light chains. In antibodies that lack light chains, the C-terminal variable region is called the VHH domain. Antibodies recognize antigens through six complementarity-determining regions (CDRs). The third CDR of the heavy chain (CDR-H3) is at the center of the antigen-binding site and is diverse in terms of sequence and structure. Due to the importance of antibodies in basic science as well as in medical applications, there have been many studies of CDR-H3s of antibodies that possess both light and heavy chains. However, nature of CDR-H3s of single-domain VHH antibodies is less well studied. In this chapter, we describe current knowledge of sequence-structure-function correlations of single-domain VHH antibodies with emphasis on CDR-H3. Based on the 370 crystal structures in the Protein Data Bank, we also attempt structural classification of CDR-H3 in single-domain VHH antibodies and discuss lessons learned from the ever-increasing number of the structures.
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Affiliation(s)
- Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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12
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Banik SSR, Kushnir N, Doranz BJ, Chambers R. Breaking barriers in antibody discovery: harnessing divergent species for accessing difficult and conserved drug targets. MAbs 2023; 15:2273018. [PMID: 38050985 DOI: 10.1080/19420862.2023.2273018] [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: 05/31/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023] Open
Abstract
To exploit highly conserved and difficult drug targets, including multipass membrane proteins, monoclonal antibody discovery efforts increasingly rely on the advantages offered by divergent species such as rabbits, camelids, and chickens. Here, we provide an overview of antibody discovery technologies, analyze gaps in therapeutic antibodies that stem from the historic use of mice, and examine opportunities to exploit previously inaccessible targets through discovery now possible in alternate species. We summarize the clinical development of antibodies raised from divergent species, discussing how these animals enable robust immune responses against highly conserved binding sites and yield antibodies capable of penetrating functional pockets via long HCDR3 regions. We also discuss the value of pan-reactive molecules often produced by these hosts, and how these antibodies can be tested in accessible animal models, offering a faster path to clinical development.
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13
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Hambach J, Fumey W, Stähler T, Gebhardt AJ, Adam G, Weisel K, Koch-Nolte F, Bannas P. Half-Life Extended Nanobody-Based CD38-Specific Bispecific Killercell Engagers Induce Killing of Multiple Myeloma Cells. Front Immunol 2022; 13:838406. [PMID: 35651607 PMCID: PMC9150782 DOI: 10.3389/fimmu.2022.838406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/19/2022] [Indexed: 01/14/2023] Open
Abstract
CD38 is a target for immunotherapy of multiple myeloma. Llama-derived CD38-specific nanobodies allow easy reformatting into mono-, bi- and multispecific proteins. To evaluate the utility of nanobodies for constructing CD38-specific nanobody-based killer cell engagers (nano-BiKEs), we generated half-life extended nano-BiKEs (HLE-nano-BiKEs) by fusing a CD38-specific nanobody to a CD16-specific nanobody for binding to the Fc-receptor on NK cells and further to an albumin-specific nanobody to extend the half-life in vivo. HLE-nano-BiKEs targeting three different epitopes (E1, E2, E3) of CD38 were expressed in transiently transfected HEK-6E cells. We verified specific and simultaneous binding to CD38 on myeloma cells, CD16 on NK cells, and to albumin. We tested the capacity of these HLE-nano-BiKEs to mediate cytotoxicity against CD38-expressing multiple myeloma cell lines and primary myeloma cells from human bone marrow biopsies in bioluminescence and flowcytometry assays with NK92 cells as effector cells. The results revealed specific time- and dose-dependent cytolysis of CD38+ myeloma cell lines and effective depletion of CD38-expressing multiple myeloma cells from primary human bone marrow samples. Our results demonstrate the efficacy of CD38-specific HLE-nano-BiKEs in vitro and ex vivo, warranting further preclinical evaluation in vivo of their therapeutic potential for the treatment of multiple myeloma.
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Affiliation(s)
- Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - William Fumey
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Stähler
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Josephine Gebhardt
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gerhard Adam
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Weisel
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Bannas
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- *Correspondence: Peter Bannas,
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14
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Sirupurapu V, Safonova Y, Pevzner P. Gene prediction in the immunoglobulin loci. Genome Res 2022; 32:1152-1169. [PMID: 35545447 DOI: 10.1101/gr.276676.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
The V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) is critical for studies of the adaptive immune system. However, since the standard gene finding algorithms are not suitable for predicting IG genes, they have been semi-manually annotated in very few species. We developed the IGDetective algorithm for predicting IG genes and applied it to species with the assembled IG loci. IGDetective generated the first large collection of IG genes across many species and enabled their evolutionary analysis, including the analysis of the "bat IG diversity" hypothesis. This analysis revealed extremely conserved V genes in evolutionary distant species indicating that these genes may be subjected to the same selective pressure, e.g., pressure driven by common pathogens. IGDetective also revealed extremely diverged V genes and a new family of evolutionary conserved V genes in bats with unusual noncanonical cysteines. Moreover, in difference from all other previously reported antibodies, these cysteines are located within complementarity-determining regions. Since cysteines form disulfide bonds, we hypothesize that these cysteine-rich V genes might generate antibodies with noncanonical conformations and could potentially form a unique part of the immune repertoire in bats. We also analyzed the diversity landscape of the recombination signal sequences and revealed their features that trigger the high/low usage of the IG genes.
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15
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Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Res 2022; 32:791-804. [PMID: 35361626 PMCID: PMC8997358 DOI: 10.1101/gr.276027.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 02/28/2022] [Indexed: 11/24/2022]
Abstract
An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold the key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated data set, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.
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Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sung Bong Shin
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
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16
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Yu J, Guo Y, Gu Y, Li F, Song H, Nian R, Fan X, Liu W. Targeting and neutralizing human epididymis protein 4 by novel nanobodies to suppress ovarian cancer cells and attenuate cisplatin resistance. Int J Biol Macromol 2022; 199:298-306. [PMID: 35016970 DOI: 10.1016/j.ijbiomac.2022.01.015] [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: 12/08/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 11/05/2022]
Abstract
Human epididymis protein 4 (HE4) is a glycoprotein secreted by epithelial ovarian cancer (EOC) cells and is a novel and specific biomarker for diagnosing and prognosing EOC. Previous studies have shown that overexpression of HE4 is correlated with EOC tumorigenesis and chemoresistance. However, less has been reported regarding the direct effect of the secreted HE4 protein as an autocrine factor in EOC cells. Here, we investigated the molecular mechanism of the secretory form of HE4 on the growth of EOC cells by applying nanobodies with a targeted interaction of free HE4. Three anti-HE4 nanobodies were selected from an immune library by phage display. HE4 secreted by serum-free cultured OVCAR3 cells increased and was effectively neutralized by anti-HE4 nanobodies, which inhibited cell viability. Treatment with the anti-HE4 nanobody 1G8 decreased Bcl-2 expression and increased BAX, cleaved PARP, and p53 levels, resulting in apoptosis of OVCAR3 cells. Moreover, 1G8 significantly improved the cisplatin response of OVCAR3 cells. Our data suggest that secretory HE4 played a novel pro-survival autocrine role and was a target of the anti-HE4 nanobody to improve the therapeutic effects of cisplatin-based chemotherapy.
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Affiliation(s)
- Jianli Yu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Yang Guo
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
| | - Yi Gu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Fei Li
- Shenzhen Innova Nanobodi Co., Ltd., No. 1301 Guanguang Road, Shenzhen 518110, China
| | - Haipeng Song
- Shenzhen Innova Nanobodi Co., Ltd., No. 1301 Guanguang Road, Shenzhen 518110, China
| | - Rui Nian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China
| | - Xiying Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China.
| | - Wenshuai Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao 266101, China.
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17
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Warimwe GM, Francis MJ, Bowden TA, Thumbi SM, Charleston B. Using cross-species vaccination approaches to counter emerging infectious diseases. Nat Rev Immunol 2021; 21:815-822. [PMID: 34140665 PMCID: PMC8211312 DOI: 10.1038/s41577-021-00567-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 02/08/2023]
Abstract
Since the initial use of vaccination in the eighteenth century, our understanding of human and animal immunology has greatly advanced and a wide range of vaccine technologies and delivery systems have been developed. The COVID-19 pandemic response leveraged these innovations to enable rapid development of candidate vaccines within weeks of the viral genetic sequence being made available. The development of vaccines to tackle emerging infectious diseases is a priority for the World Health Organization and other global entities. More than 70% of emerging infectious diseases are acquired from animals, with some causing illness and death in both humans and the respective animal host. Yet the study of critical host-pathogen interactions and the underlying immune mechanisms to inform the development of vaccines for their control is traditionally done in medical and veterinary immunology 'silos'. In this Perspective, we highlight a 'One Health vaccinology' approach and discuss some key areas of synergy in human and veterinary vaccinology that could be exploited to accelerate the development of effective vaccines against these shared health threats.
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Affiliation(s)
- George M Warimwe
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- The Pirbright Institute, Woking, UK.
| | | | - Thomas A Bowden
- Wellcome Centre for Human Genetics, Division of Structural Biology, University of Oxford, Oxford, UK
| | - Samuel M Thumbi
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
- Center for Epidemiological Modelling and Analysis, Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
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18
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Mechanistic principles of an ultra-long bovine CDR reveal strategies for antibody design. Nat Commun 2021; 12:6737. [PMID: 34795299 PMCID: PMC8602281 DOI: 10.1038/s41467-021-27103-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 11/03/2021] [Indexed: 11/08/2022] Open
Abstract
Antibodies bind antigens via flexible loops called complementarity-determining regions (CDRs). These are usually 6-20 residues long. However, some bovine antibodies have ultra-long CDRs comprising more than 50 residues organized in a stalk and a disulfide-rich knob. The design features of this structural unit and its influence on antibody stability remained enigmatic. Here, we show that the stalk length is critical for the folding and stability of antibodies with an ultra-long CDR and that the disulfide bonds in the knob do not contribute to stability; they are important for organizing the antigen-binding knob structure. The bovine ultra-long CDR can be integrated into human antibody scaffolds. Furthermore, mini-domains from de novo design can be reformatted as ultra-long CDRs to create unique antibody-based proteins neutralizing SARS-CoV-2 and the Alpha variant of concern with high efficiency. Our findings reveal basic design principles of antibody structure and open new avenues for protein engineering.
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19
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Ikeuchi E, Kuroda D, Nakakido M, Murakami A, Tsumoto K. Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain V HH antibodies. Sci Rep 2021; 11:20624. [PMID: 34663870 PMCID: PMC8523659 DOI: 10.1038/s41598-021-98977-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
The high binding affinities and specificities of antibodies have led to their use as drugs and biosensors. Single-domain VHH antibodies exhibit high specificity and affinity but have higher stability and solubility than conventional antibodies as they are single-domain proteins. In this work, based on physicochemical measurements and molecular dynamics (MD) simulations, we have gained insight that will facilitate rational design of single-chain VHH antibodies. We first assessed two homologous VHH antibodies by differential scanning calorimetry (DSC); one had a high (64.8 °C) and the other a low (58.6 °C) melting temperature. We then generated a series of the variants of the low stability antibody and analyzed their thermal stabilities by DSC and characterized their structures through MD simulations. We found that a single mutation that resulted in 8.2 °C improvement in melting temperature resulted in binding affinity an order of magnitude lower than the parent antibody, likely due to a shift of conformational space explored by the single-chain VHH antibody. These results suggest that the delicate balance among conformational stability, binding capability, and conformational space explored by antibodies must be considered in design of fully functional single-chain VHH antibodies.
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Affiliation(s)
- Emina Ikeuchi
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Panasonic Corporation Technology Division, Kyoto, 619-0237, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Akikazu Murakami
- Department of Parasitology and Immunopathoetiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan. .,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan. .,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan. .,Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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20
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Nilvebrant J, Ereño-Orbea J, Gorelik M, Julian MC, Tessier PM, Julien JP, Sidhu SS. Systematic Engineering of Optimized Autonomous Heavy-Chain Variable Domains. J Mol Biol 2021; 433:167241. [PMID: 34508727 DOI: 10.1016/j.jmb.2021.167241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 01/06/2023]
Abstract
Autonomous heavy-chain variable (VH) domains are the smallest functional antibody fragments, and they possess unique features, including small size and convex paratopes, which provide enhanced targeting of concave epitopes that are difficult to access with larger conventional antibodies. However, human VH domains have evolved to fold and function with a light chain partner, and alone, they typically suffer from low stability and high aggregation propensity. Development of autonomous human VH domains, in which aggregation propensity is reduced without compromising antigen recognition, has proven challenging. Here, we used an autonomous human VH domain as a scaffold to construct phage-displayed synthetic libraries in which aspartate was systematically incorporated at different paratope positions. In selections, the library yielded many anti-EphA1 receptor VH domains, which were characterized in detail. Structural analyses of a parental anti-EphA1 VH domain and an improved variant provided insights into the effects of aspartate and other substitutions on preventing aggregation while retaining function. Our naïve libraries and in vitro selection procedures offer a systematic approach to generating highly functional autonomous human VH domains that resist aggregation and could be used for basic research and biomedical applications.
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Affiliation(s)
- Johan Nilvebrant
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute and Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Maryna Gorelik
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Mark C Julian
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Departments of Chemical Engineering, Pharmaceutical Sciences, and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute and Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
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21
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Akiba H, Tamura H, Caaveiro JMM, Tsumoto K. Epitope-dependent thermodynamic signature of single-domain antibodies against hen egg lysozyme. J Biochem 2021; 170:623-629. [PMID: 34519785 DOI: 10.1093/jb/mvab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/10/2021] [Indexed: 11/14/2022] Open
Abstract
A substantial body of work has been carried out describing the structural features of the complex between single-domain antibodies (VHHs) and antigens, and the preeminence for epitopes located at concave surfaces of the antigen. However, the thermodynamic basis of binding is far less clear. Here, we have analyzed the energetic profiles of five VHHs binding to the catalytic cleft as well as a non-cleft epitope of hen egg lysozyme. Various binding energetic profiles with distinctive enthalpic/entropic contributions and structural distribution of critical residues were found in the five antibodies analyzed. Collectively, we suggest that from an energetic point of view the binding mechanism is influenced by the shape of the epitope. This information may be beneficial for the design of tailored epitopes for VHHs and their practical use.
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Affiliation(s)
- Hiroki Akiba
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroko Tamura
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113- 8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113- 8656, Japan.,Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8629, Japan
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22
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A CDR-based approach to generate covalent inhibitory antibody for human rhinovirus protease. Bioorg Med Chem 2021; 42:116219. [PMID: 34077853 DOI: 10.1016/j.bmc.2021.116219] [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: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/21/2022]
Abstract
Covalent target modulation with small molecules has been emerging as a promising strategy for drug discovery. However, covalent inhibitory antibody remains unexplored due to the lack of efficient strategies to engineer antibody with desired bioactivity. Herein, we developed an intracellular selection method to generate covalent inhibitory antibody against human rhinovirus 14 (HRV14) 3C protease through unnatural amino acid mutagenesis along the heavy chain complementarity-determining region 3 (CDR-H3). A library of antibody mutants was thus constructed and screened in vivo through co-expression with the target protease. Using this screening strategy, six covalent antibodies with proximity-enabled bioactivity were identified, which were shown to covalently target HRV14-3C protease with high inhibitory potency and exquisite selectivity. Compared to structure-based rational design, this library-based screening method provides a simple and efficient way for the discovery and engineering of covalent antibody for enzyme inhibition.
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23
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Prabakaran P, Chowdhury PS. Landscape of Non-canonical Cysteines in Human V H Repertoire Revealed by Immunogenetic Analysis. Cell Rep 2021; 31:107831. [PMID: 32610132 PMCID: PMC7326410 DOI: 10.1016/j.celrep.2020.107831] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Human antibody repertoire data captured through next-generation sequencing (NGS) has enabled deeper insights into B cell immunogenetics and paratope diversity. By analyzing large public NGS datasets, we map the landscape of non-canonical cysteines in human variable heavy-chain domains (VHs) at the repertoire level. We identify remarkable usage of non-canonical cysteines within the heavy-chain complementarity-determining region 3 (CDR-H3) and other CDRs and framework regions. Furthermore, our study reveals the diversity and location of non-canonical cysteines and their associated motifs in human VHs, which are reminiscent of and more complex than those found in other non-human species such as chicken, camel, llama, shark, and cow. These results explain how non-canonical cysteines strategically occur in the human antibodyome to expand its paratope space. This study will guide the design of human antibodies harboring disulfide-stabilized long CDR-H3s to access difficult-to-target epitopes and influence a paradigm shift in developability involving non-canonical cysteines. NGS-based non-canonical cysteine landscape in human VHs 1 to 8 non-canonical cysteines and up to 30% in long CDR-H3s An array of potential disulfide motifs adds paratope diversity Non-canonical cysteines in human VHs are reminiscent of lower animals
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24
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Abstract
Unique, functional, homodimeric heavy chain-only antibodies, devoid of light chains, are circulating in the blood of Camelidae. These antibodies recognize their cognate antigen via one single domain, known as VHH or Nanobody. This serendipitous discovery made three decades ago has stimulated a growing number of researchers to generate highly specific Nanobodies against a myriad of targets. The small size, strict monomeric state, robustness, and easy tailoring of these Nanobodies have inspired many groups to design innovative Nanobody-based multi-domain constructs to explore novel applications. As such, Nanobodies have been employed as an exquisite research tool in structural, cell, and developmental biology. Furthermore, Nanobodies have demonstrated their benefit for more sensitive diagnostic tests. Finally, several Nanobody-based constructs have been designed to develop new therapeutic products.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, 1050 Brussels, Belgium; .,Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian 116023, Liaoning, People's Republic of China
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25
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Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput Biol 2020; 16:e1007837. [PMID: 32339161 PMCID: PMC7295240 DOI: 10.1371/journal.pcbi.1007837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/15/2020] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
Immunoglobulin genes are formed through V(D)J recombination, which joins the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics focuses on finding alleles of germline genes across various patients. Although reconstruction of V and J genes is a well-studied problem, the more challenging task of reconstructing D genes remained open until the IgScout algorithm was developed in 2019. In this work, we address limitations of IgScout by developing a probabilistic MINING-D algorithm for D gene reconstruction, apply it to hundreds of immunosequencing datasets from multiple species, and validate the newly inferred D genes by analyzing diverse whole genome sequencing datasets and haplotyping heterozygous V genes. Antibodies provide specific binding to an enormous range of antigens and represent a key component of the adaptive immune system. Immunosequencing has emerged as a method of choice for generating millions of reads that sample antibody repertoires and provides insights into monitoring immune response to disease and vaccination. Most of the previous immunogenomics studies rely on the reference germline genes in the immunoglobulin locus rather than the germline genes in a specific patient. This approach is deficient since the set of known germline genes is incomplete (particularly for non-European humans and non-human species) and contains alleles that resulted from sequencing and annotation errors. The problem of de novo inference of diversity (D) genes from immunosequencing data remained open until the IgScout algorithm was developed in 2019. We address limitations of IgScout by developing a probabilistic MINING-D algorithm for D gene reconstruction and infer multiple D genes across multiple species that are not present in standard databases.
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Affiliation(s)
- Vinnu Bhardwaj
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
| | - Massimo Franceschetti
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
| | - Ramesh Rao
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
- Qualcomm Institute, University of California San Diego, San Diego, California, United States of America
| | - Pavel A. Pevzner
- Computer Science and Engineering Department, University of California San Diego, San Diego, California, United States of America
- * E-mail:
| | - Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, San Diego, California, United States of America
- Center for Information Theory and Applications, University of California San Diego, San Diego, California, United States of America
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26
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Burke MJ, Stockley PG, Boyes J. Broadly Neutralizing Bovine Antibodies: Highly Effective New Tools against Evasive Pathogens? Viruses 2020; 12:v12040473. [PMID: 32331321 PMCID: PMC7232318 DOI: 10.3390/v12040473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Potent antibody-mediated neutralization is critical for an organism to combat the vast array of pathogens it will face during its lifetime. Due to the potential genetic diversity of some viruses, such as HIV-1 and influenza, standard neutralizing antibodies are often ineffective or easily evaded as their targets are masked or rapidly mutated. This has thwarted efforts to both prevent and treat HIV-1 infections and means that entirely new formulations are required to vaccinate against influenza each year. However, some rare antibodies isolated from infected individuals confer broad and potent neutralization. A subset of these broadly neutralizing antibodies possesses a long complementarity-determining 3 region of the immunoglobulin heavy chain (CDR H3). This feature generates unique antigen binding site configurations that can engage conserved but otherwise inaccessible epitope targets thus neutralizing many viral variants. Remarkably, ultralong CDR H3s are a common feature of the cow antibody repertoire and are encoded by a single variable, diversity, joining (VDJ) recombination that is extensively diversified prior to antigen exposure. Recently, it was shown that cows rapidly generate a broadly neutralizing response upon exposure to HIV-1 and this is primarily mediated by these novel ultralong antibody types. This review summarises the current knowledge of these unusual CDR H3 structures and discusses their known and potential future uses.
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Affiliation(s)
- Matthew J. Burke
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
| | - Peter G. Stockley
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Correspondence:
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27
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Development of sandwich chemiluminescent immunoassay based on an anti-staphylococcal enterotoxin B Nanobody–Alkaline phosphatase fusion protein for detection of staphylococcal enterotoxin B. Anal Chim Acta 2020; 1108:28-36. [DOI: 10.1016/j.aca.2020.01.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023]
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28
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Ching KH, Berg K, Morales J, Pedersen D, Harriman WD, Abdiche YN, Leighton PA. Expression of human lambda expands the repertoire of OmniChickens. PLoS One 2020; 15:e0228164. [PMID: 31995598 PMCID: PMC6988971 DOI: 10.1371/journal.pone.0228164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the approved monoclonal antibodies used in the clinic were initially discovered in mice. However, many targets of therapeutic interest are highly conserved proteins that do not elicit a robust immune response in mice. There is a need for non-mammalian antibody discovery platforms which would allow researchers to access epitopes that are not recognized in mammalian hosts. Recently, we introduced the OmniChicken®, a transgenic animal carrying human VH3-23 and VK3-15 at its immunoglobulin loci. Here, we describe a new version of the OmniChicken which carries VH3-23 and either VL1-44 or VL3-19 at its heavy and light chain loci, respectively. The Vλ-expressing birds showed normal B and T populations in the periphery. A panel of monoclonal antibodies demonstrated comparable epitope coverage of a model antigen compared to both wild-type and Vκ-expressing OmniChickens. Kinetic analysis identified binders in the picomolar range. The Vλ-expressing bird increases the antibody diversity available in the OmniChicken platform, further enabling discovery of therapeutic leads.
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Affiliation(s)
- Kathryn H. Ching
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Kimberley Berg
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Jacqueline Morales
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Darlene Pedersen
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - William D. Harriman
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | | | - Philip A. Leighton
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
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29
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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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30
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Sun Y, Huang T, Hammarström L, Zhao Y. The Immunoglobulins: New Insights, Implications, and Applications. Annu Rev Anim Biosci 2019; 8:145-169. [PMID: 31846352 DOI: 10.1146/annurev-animal-021419-083720] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immunoglobulins (Igs), as one of the hallmarks of adaptive immunity, first arose approximately 500 million years ago with the emergence of jawed vertebrates. Two events stand out in the evolutionary history of Igs from cartilaginous fish to mammals: (a) the diversification of Ig heavy chain (IgH) genes, resulting in Ig isotypes or subclasses associated with novel functions, and (b) the diversification of genetic and structural strategies, leading to the creation of the antibody repertoire we know today. This review first gives an overview of the IgH isotypes identified in jawed vertebrates to date and then highlights the implications or applications of five new recent discoveries arising from comparative studies of Igs derived from different vertebrate species.
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Affiliation(s)
- Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, Shandong, People's Republic of China;
| | - Tian Huang
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Sciences, Henan University, Kaifeng 475004, Henan, People's Republic of China;
| | - Lennart Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Department of Laboratory Medicine, Karolinska Institutet at Karolinska Hospital Huddinge, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
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31
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Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep 2019; 9:15481. [PMID: 31664051 PMCID: PMC6820745 DOI: 10.1038/s41598-019-50722-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/10/2019] [Indexed: 01/06/2023] Open
Abstract
Single-domain antibodies (VHHs or nanobodies), developed from heavy chain-only antibodies of camelids, are gaining attention as next-generation therapeutic agents. Despite their small size, the high affinity and specificity displayed by VHHs for antigen molecules rival those of IgGs. How such small antibodies achieve that level of performance? Structural studies have revealed that VHHs tend to recognize concave surfaces of their antigens with high shape-complementarity. However, the energetic contribution of individual residues located at the binding interface has not been addressed in detail, obscuring the actual mechanism by which VHHs target the concave surfaces of proteins. Herein, we show that a VHH specific for hen egg lysozyme, D3-L11, not only displayed the characteristic binding of VHHs to a concave region of the surface of the antigen, but also exhibited a distribution of energetic hot-spots like those of IgGs and conventional protein-protein complexes. The highly preorganized and energetically compact interface of D3-L11 recognizes the concave epitope with high shape complementarity by the classical lock-and-key mechanism. Our results shed light on the fundamental basis by which a particular VHH accommodate to the concave surface of an antigens with high affinity in a specific manner, enriching the mechanistic landscape of VHHs.
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32
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Haakenson JK, Deiss TC, Warner GF, Mwangi W, Criscitiello MF, Smider VV. A Broad Role for Cysteines in Bovine Antibody Diversity. Immunohorizons 2019; 3:478-487. [PMID: 31619454 PMCID: PMC7366855 DOI: 10.4049/immunohorizons.1900058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/29/2019] [Indexed: 01/26/2023] Open
Abstract
Ab diversity in most vertebrates results from the assortment of amino acid side chains on CDR loops formed through V(D)J recombination. Cows (Bos taurus) have a low combinatorial diversity potential because of a small number of highly homologous V, D, and J gene segments. Despite this, a subset of the Ab repertoire (~10%) contains exceptionally long CDR H chain (HC) 3 (H3) regions with a rich diversity of cysteines and disulfide-bonded loops that diversify through a single V-D-J recombination event followed by massive somatic hypermutation. However, the much larger portion of the repertoire, encoding shorter CDR H3s, has not been examined in detail. Analysis of germline gene segments reveals noncanonical cysteines in the HC V regions and significant cysteine content in the HC D regions. Deep sequencing analysis of naturally occurring shorter CDR H3 (<40 aa) Ab genes shows that HC V and HC D regions preferentially combine to form a functional gene with an even number of total cysteines in the final V region, suggesting that disulfide bonds contribute to diversity not only in ultralong CDR H3 bovine Abs but in shorter CDR H3 bovine Abs as well. In addition to germline “hard-coded” cysteines, the bovine Ab repertoire can produce additional cysteine codons through somatic hypermutation, further diversifying the repertoire. Given the limited combinatorial diversity at the bovine Ig loci, this helps to explain how diversity is created in shorter CDR H3 Abs and potentially provides novel structural paratopes in bovine Ab combining sites.
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Affiliation(s)
- Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA 92127.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Thaddeus C Deiss
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843; and
| | - Gabrielle F Warner
- Applied Biomedical Science Institute, San Diego, CA 92127.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Waithaka Mwangi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
| | - Michael F Criscitiello
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843; and
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA 92127; .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
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33
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Storek KM, Chan J, Vij R, Chiang N, Lin Z, Bevers J, Koth CM, Vernes JM, Meng YG, Yin J, Wallweber H, Dalmas O, Shriver S, Tam C, Schneider K, Seshasayee D, Nakamura G, Smith PA, Payandeh J, Koerber JT, Comps-Agrar L, Rutherford ST. Massive antibody discovery used to probe structure-function relationships of the essential outer membrane protein LptD. eLife 2019; 8:46258. [PMID: 31237236 PMCID: PMC6592684 DOI: 10.7554/elife.46258] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/17/2019] [Indexed: 12/17/2022] Open
Abstract
Outer membrane proteins (OMPs) in Gram-negative bacteria dictate permeability of metabolites, antibiotics, and toxins. Elucidating the structure-function relationships governing OMPs within native membrane environments remains challenging. We constructed a diverse library of >3000 monoclonal antibodies to assess the roles of extracellular loops (ECLs) in LptD, an essential OMP that inserts lipopolysaccharide into the outer membrane of Escherichia coli. Epitope binning and mapping experiments with LptD-loop-deletion mutants demonstrated that 7 of the 13 ECLs are targeted by antibodies. Only ECLs inaccessible to antibodies were required for the structure or function of LptD. Our results suggest that antibody-accessible loops evolved to protect key extracellular regions of LptD, but are themselves dispensable. Supporting this hypothesis, no α-LptD antibody interfered with essential functions of LptD. Our experimental workflow enables structure-function studies of OMPs in native cellular environments, provides unexpected insight into LptD, and presents a method to assess the therapeutic potential of antibody targeting. The overuse and misuse of antibiotics has led to the rise of multi-drug resistant bacteria which threaten global public health. Antibiotics interfere with essential processes in bacteria so they are unable to divide or survive, but over time, the microbes have found ways to become immune to the drugs. New antibiotics are now desperately needed. Gram-negative bacteria are wrapped in an outer membrane made of large molecules called lipopolysaccharides. This structure is an extra barrier to molecules (such as drugs) that try to enter the cell, but it could also hold new targets for antibiotics to exploit. A protein called LptD is embedded in the outer membrane, where it inserts new lipopolysaccharides. It is critical for bacteria to grow and survive, and is a relatively new potential target for antibiotic development. The protein has a number of ‘extracellular loops’ that extend into the environment, but their roles in the structure and the activity of LptD are still largely unknown. This is partly due to a lack of tools to investigate these elements. In response, Storek et al. built a library of over 3,000 custom antibodies, which are small Y-shaped proteins that can each recognise a specific portion in one of the extracellular loops and potentially incapacitate LptD. The antibodies were used to target LptD in its native environment, when it is embedded in the bacteria. In parallel, mutant bacteria were created in which the loops were genetically removed one by one to assess their importance for LptD activity. The experiments revealed that although the antibodies could target most extracellular loops, they could not target the few loops that were essential for LptD to work properly. This suggests that antibody-accessible loops are expendable and that these structures could serve to shield other regions of LptD which are critical for survival. The findings will help to prioritise research that develops other approaches to inhibit LptD. Finally, the antibody workflow designed by Storek et al. can serve as a road map to study other membrane proteins in their native cellular environment.
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Affiliation(s)
- Kelly M Storek
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Joyce Chan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Christopher M Koth
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - JianPing Yin
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Heidi Wallweber
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Olivier Dalmas
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - Stephanie Shriver
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc, South San Francisco, United States
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Peter A Smith
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc, South San Francisco, United States
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc, South San Francisco, United States
| | - Laetitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc, South San Francisco, United States
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech, Inc, South San Francisco, United States
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Santos MLD, Quintilio W, Manieri TM, Tsuruta LR, Moro AM. Advances and challenges in therapeutic monoclonal antibodies drug development. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000001007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | - Ana Maria Moro
- Butantan Institute, Brazil; National Institute for Science and Technology, Brazil
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35
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Abstract
Single-domain antibodies (sdAbs), the autonomous variable domains of heavy chain-only antibodies produced naturally by camelid ungulates and cartilaginous fishes, have evolved to bind antigen using only three complementarity-determining region (CDR) loops rather than the six present in conventional VH:VL antibodies. It has been suggested, based on limited evidence, that sdAbs may adopt paratope structures that predispose them to preferential recognition of recessed protein epitopes, but poor or non-recognition of protuberant epitopes and small molecules. Here, we comprehensively surveyed the evidence in support of this hypothesis. We found some support for a global structural difference in the paratope shapes of sdAbs compared with those of conventional antibodies: sdAb paratopes have smaller molecular surface areas and diameters, more commonly have non-canonical CDR1 and CDR2 structures, and have elongated CDR3 length distributions, but have similar amino acid compositions and are no more extended (interatomic distance measured from CDR base to tip) than conventional antibody paratopes. Comparison of X-ray crystal structures of sdAbs and conventional antibodies in complex with cognate antigens showed that sdAbs and conventional antibodies bury similar solvent-exposed surface areas on proteins and form similar types of non-covalent interactions, although these are more concentrated in the compact sdAb paratope. Thus, sdAbs likely have privileged access to distinct antigenic regions on proteins, but only owing to their small molecular size and not to general differences in molecular recognition mechanism. The evidence surrounding the purported inability of sdAbs to bind small molecules was less clear. The available data provide a structural framework for understanding the evolutionary emergence and function of autonomous heavy chain-only antibodies.
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Affiliation(s)
- Kevin A Henry
- a Human Health Therapeutics Research Centre , National Research Council Canada , Ottawa , Ontario , Canada
| | - C Roger MacKenzie
- a Human Health Therapeutics Research Centre , National Research Council Canada , Ottawa , Ontario , Canada.,b School of Environmental Sciences , University of Guelph , Guelph , Ontario , Canada
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36
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Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N-terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high-affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen-binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD ).
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Affiliation(s)
- Valencio Salema
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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Darling TL, Sherwood LJ, Hayhurst A. Intracellular Crosslinking of Filoviral Nucleoproteins with Xintrabodies Restricts Viral Packaging. Front Immunol 2017; 8:1197. [PMID: 29021793 PMCID: PMC5623874 DOI: 10.3389/fimmu.2017.01197] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022] Open
Abstract
Viruses assemble large macromolecular repeat structures that become part of the infectious particles or virions. Ribonucleocapsids (RNCs) of negative strand RNA viruses are a prime example where repetition of nucleoprotein (NP) along the genome creates a core polymeric helical scaffold that accommodates other nucleocapsid proteins including viral polymerase. The RNCs are transported through the cytosol for packaging into virions through association with viral matrix proteins at cell membranes. We hypothesized that RNC would be ideal targets for crosslinkers engineered to promote aberrant protein–protein interactions, thereby blocking their orderly transport and packaging. Previously, we had generated single-domain antibodies (sdAbs) against Filoviruses that have all targeted highly conserved C-terminal regions of NP known to be repetitively exposed along the length of the RNCs of Marburgvirus (MARV) and Ebolavirus (EBOV). Our crosslinker design consisted of dimeric sdAb expressed intracellularly, which we call Xintrabodies (X- for crosslinking). Electron microscopy of purified NP polymers incubated with purified sdAb constructs showed NP aggregation occurred in a genus-specific manner with dimeric and not monomeric sdAb. A virus-like particle (VLP) assay was used for initial evaluation where we found that dimeric sdAb inhibited NP incorporation into VP40-based VLPs whereas monomeric sdAb did not. Inhibition of NP packaging was genus specific. Confocal microscopy revealed dimeric sdAb was diffuse when expressed alone but focused on pools of NP when the two were coexpressed, while monomeric sdAb showed ambivalent partition. Infection of stable Vero cell lines expressing dimeric sdAb specific for either MARV or EBOV NP resulted in smaller plaques and reduced progeny of cognate virus relative to wild-type Vero cells. Though the impact was marginal at later time-points, the collective data suggest that viral replication can be reduced by crosslinking intracellular NP using relatively small amounts of dimeric sdAb to restrict NP packaging. The stoichiometry and ease of application of the approach would likely benefit from transitioning away from intracellular expression of crosslinking sdAb to exogenous delivery of antibody. By retuning sdAb specificity, the approach of crosslinking highly conserved regions of assembly critical proteins may well be applicable to inhibiting replication processes of a broad spectrum of viruses.
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Affiliation(s)
- Tamarand Lee Darling
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States.,Department of Microbiology, Immunology and Molecular Genetics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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38
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Fang T, Van Elssen CHMJ, Duarte JN, Guzman JS, Chahal JS, Ling J, Ploegh HL. Targeted antigen delivery by an anti-class II MHC VHH elicits focused αMUC1(Tn) immunity. Chem Sci 2017; 8:5591-5597. [PMID: 28970938 PMCID: PMC5618788 DOI: 10.1039/c7sc00446j] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/23/2017] [Indexed: 12/21/2022] Open
Abstract
Unusual patterns of glycosylation on the surface of transformed cells contribute to immune modulation and metastasis of malignant tumors. Active immunization against them requires effective antigen presentation, which is complicated by a lack of access to tumor-specific posttranslational modifications through standard genetic approaches and by the low efficiency of passive antigen sampling. We found that antigen targeted to antigen presenting cells via class II MHC products can elicit a robust immune response against MUC1(Tn) bearing a defined tumor-associated glycoform, Tn. The two-component vaccine construct was prepared by sortase-mediated protein ligation of a synthetic MUC1(Tn) fragment to a class II MHC-binding single-domain antibody fragment (VHH7) as targeting moiety. We show that VHH7 targets antigen presenting cells in vivo, and when conjugated to MUC1(Tn) can elicit a strong αMUC1(Tn) immune response in mice. The resulting sera preferentially recognized the MUC1 epitope with the tumor-associated carbohydrate antigen Tn and were capable of killing cancer cells in a complement-mediated cytotoxicity assay. Immunoglobulin isotype analysis and cytokine release assays suggested a favorable Th1 response. A single boost 12 months after primary immunization triggered a recall response of the same quality, suggesting that long-term αMUC1(Tn) memory had been achieved.
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Affiliation(s)
- Tao Fang
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
| | | | - Joao N Duarte
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
| | - Jonathan S Guzman
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
- Department of Biology , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA
| | - Jasdave S Chahal
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
| | - Jingjing Ling
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research , 9 Cambridge Center , Cambridge , MA 02142 , USA .
- Department of Biology , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA
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39
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Stijlemans B, De Baetselier P, Caljon G, Van Den Abbeele J, Van Ginderachter JA, Magez S. Nanobodies As Tools to Understand, Diagnose, and Treat African Trypanosomiasis. Front Immunol 2017; 8:724. [PMID: 28713367 PMCID: PMC5492476 DOI: 10.3389/fimmu.2017.00724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 06/08/2017] [Indexed: 02/04/2023] Open
Abstract
African trypanosomes are strictly extracellular protozoan parasites that cause diseases in humans and livestock and significantly affect the economic development of sub-Saharan Africa. Due to an elaborate and efficient (vector)–parasite–host interplay, required to complete their life cycle/transmission, trypanosomes have evolved efficient immune escape mechanisms that manipulate the entire host immune response. So far, not a single field applicable vaccine exists, and chemotherapy is the only strategy available to treat the disease. Current therapies, however, exhibit high drug toxicity and an increased drug resistance is being reported. In addition, diagnosis is often hampered due to the inadequacy of current diagnostic procedures. In the context of tackling the shortcomings of current treatment and diagnostic approaches, nanobodies (Nbs, derived from the heavy chain-only antibodies of camels and llamas) might represent unmet advantages compared to conventional tools. Indeed, the combination of their small size, high stability, high affinity, and specificity for their target and tailorability represents a unique advantage, which is reflected by their broad use in basic and clinical research to date. In this article, we will review and discuss (i) diagnostic and therapeutic applications of Nbs that are being evaluated in the context of African trypanosomiasis, (ii) summarize new strategies that are being developed to optimize their potency for advancing their use, and (iii) document on unexpected properties of Nbs, such as inherent trypanolytic activities, that besides opening new therapeutic avenues, might offer new insight in hidden biological activities of conventional antibodies.
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Affiliation(s)
- Benoit Stijlemans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Patrick De Baetselier
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp (UA), Antwerp, Belgium
| | - Jan Van Den Abbeele
- Unit of Veterinary Protozoology, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp (ITM), Antwerp, Belgium
| | - Jo A Van Ginderachter
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
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40
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Martin C, Moors SLC, Danielsen M, Betti C, Fabris C, Sejer Pedersen D, Pardon E, Peyressatre M, Fehér K, Martins JC, Mosolff Mathiesen J, Morris MC, Devoogdt N, Caveliers V, De Proft F, Steyaert J, Ballet S. Rational Design of Nanobody80 Loop Peptidomimetics: Towards Biased β 2 Adrenergic Receptor Ligands. Chemistry 2017; 23:9632-9640. [PMID: 28449310 DOI: 10.1002/chem.201701321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Indexed: 01/10/2023]
Abstract
G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been reported. Nb80, in particular, is able to bind the intracellular G protein binding site of β2 AR and stabilize the receptor in an active conformation. Within Nb80, the complementarity-determining region 3 (CDR3) is responsible for most of the binding interactions. Hence, we hypothesized that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial inhibition of cAMP production.
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Affiliation(s)
- Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Mia Danielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cecilia Betti
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Cecilia Fabris
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Els Pardon
- Structural Biology Brussels, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Marion Peyressatre
- Institut des Biomolécules Max Mousseron-IBMM-CNRS-UMR 5247, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Krisztina Fehér
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Gent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Gent, Belgium
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - May C Morris
- Institut des Biomolécules Max Mousseron-IBMM-CNRS-UMR 5247, Faculté de Pharmacie, Université de Montpellier, Montpellier, France
| | - Nick Devoogdt
- In Vivo Cellular and Molecular Imaging lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Vicky Caveliers
- In Vivo Cellular and Molecular Imaging lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
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41
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Ahani R, Roohvand F, Cohan RA, Etemadzadeh MH, Mohajel N, Behdani M, Shahosseini Z, Madani N, Azadmanesh K. Sindbis Virus-Pseudotyped Lentiviral Vectors Carrying VEGFR2-Specific Nanobody for Potential Transductional Targeting of Tumor Vasculature. Mol Biotechnol 2017; 58:738-747. [PMID: 27647452 DOI: 10.1007/s12033-016-9973-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction of selectivity/specificity into viral-based gene delivery systems, such as lentiviral vectors (LVs), is crucial in their systemic administration for cancer gene therapy. The pivotal role of tumor-associated endothelial cells (TAECs) in tumor angiogenesis and overexpression of vascular endothelial growth factor receptor-2 (VEGFR2 or KDR) in TAECs makes them a potent target in cancer treatment. Herein, we report the development of VEGFR2-targeted LVs pseudotyped with chimeric sindbis virus E2 glycoprotein (cSVE2s). For this purpose, either sequence of a VEGFR2-specific nanobody or its natural ligand (VEGF121) was inserted into the binding site of sindbis virus E2 glycoprotein. In silico modeling data suggested that the inserted targeting motifs were exposed in the context of cSVE2s. Western blot analysis of LVs indicated the incorporation of cSVE2s into viral particles. Capture ELISA demonstrated the specificity/functionality of the incorporated cSVE2s. Transduction of 293/KDR (expressing VEGFR2) or 293T cells (negative control) by constructed LVs followed by fluorescent microscopy and flow cytometric analyses indicated selective transduction of 293/KDR cells (30 %) by both targeting motifs compared to 293T control cells (1-2 %). These results implied similar targeting properties of VEGFR2-specific nanobody compared to the VEGF121 and indicated the potential for transductional targeting of tumor vasculature by the nanobody displaying LVs.
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Affiliation(s)
- Roshank Ahani
- Department of Virology, Pasteur Institute of Iran, 69 Pasteur Avenue, Kargar Avenue, Tehran, 1316943551, Iran
| | - Farzin Roohvand
- Department of Virology, Pasteur Institute of Iran, 69 Pasteur Avenue, Kargar Avenue, Tehran, 1316943551, Iran.
| | - Reza Ahangari Cohan
- New Technologies Research Group, Department of Pilot Nanobiotechnology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Nasir Mohajel
- Department of Virology, Pasteur Institute of Iran, 69 Pasteur Avenue, Kargar Avenue, Tehran, 1316943551, Iran
| | - Mahdi Behdani
- Biotechnology Research Center, Venom & Biotherapeutics Molecules Lab, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Shahosseini
- Department of Virology, Pasteur Institute of Iran, 69 Pasteur Avenue, Kargar Avenue, Tehran, 1316943551, Iran
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Kayhan Azadmanesh
- Department of Virology, Pasteur Institute of Iran, 69 Pasteur Avenue, Kargar Avenue, Tehran, 1316943551, Iran.
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42
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Veugelen S, Dewilde M, De Strooper B, Chávez-Gutiérrez L. Screening and Characterization Strategies for Nanobodies Targeting Membrane Proteins. Methods Enzymol 2016; 584:59-97. [PMID: 28065273 DOI: 10.1016/bs.mie.2016.10.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The study of membrane protein function and structure requires their successful detection, expression, solubilization, and/or reconstitution, which poses a challenging task and relies on the availability of suitable tools. Several research groups have successfully applied Nanobodies in the purification, as well as the functional and structural characterization of membrane proteins. Nanobodies are small, single-chain antibody fragments originating from camelids presenting on average a longer CDR3 which enables them to bind in cavities and clefts (such as active and allosteric sites). Notably, Nanobodies generally bind conformational epitopes making them very interesting tools to stabilize, dissect, and characterize specific protein conformations. In the clinic, several Nanobodies are under evaluation either as potential drug candidates or as diagnostic tools. In recent years, we have successfully generated high-affinity, conformation-sensitive anti-γ-secretase Nanobodies. γ-Secretase is a multimeric membrane protease involved in processing of the amyloid precursor protein with high clinical relevance as mutations in its catalytic subunit (Presenilin) cause early-onset Alzheimer's disease. Advancing our knowledge on the mechanisms governing γ-secretase intramembrane proteolysis through various strategies may lead to novel therapeutic avenues for Alzheimer's disease. In this chapter, we present the strategies we have developed and applied for the screening and characterization of anti-γ-secretase Nanobodies. These protocols could be of help in the generation of Nanobodies targeting other membrane proteins.
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Affiliation(s)
- S Veugelen
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - M Dewilde
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - B De Strooper
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium; UCL Institute of Neurology, London, United Kingdom
| | - L Chávez-Gutiérrez
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium.
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43
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Könning D, Zielonka S, Grzeschik J, Empting M, Valldorf B, Krah S, Schröter C, Sellmann C, Hock B, Kolmar H. Camelid and shark single domain antibodies: structural features and therapeutic potential. Curr Opin Struct Biol 2016; 45:10-16. [PMID: 27865111 DOI: 10.1016/j.sbi.2016.10.019] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022]
Abstract
In addition to canonical antibodies composed of heavy and light chains, the adaptive immune systems of camelids and cartilaginous fish comprise heavy-chain only isotypes (HcAb) devoid of light chains, where antigen-binding is mediated exclusively by one variable domain. Due to their inherent favorable attributes, such as high affinity and specificity for their cognate antigen, extraordinary stability, small size and, most importantly, the possibility to complement classical antibodies in terms of 'drugable' target-space, HcAb-derived entities evolved as promising candidates for biomedical applications of which many have already proven to be successful in early stage clinical trials.
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Affiliation(s)
- Doreen Könning
- 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
| | - Julius Grzeschik
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Department Drug Design and Optimization, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
| | - Bernhard Valldorf
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany
| | - Christian Schröter
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany
| | - Carolin Sellmann
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany
| | - Björn Hock
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293 Darmstadt, Germany.
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany.
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44
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Vadnais ML, Smider VV. Bos taurus ultralong CDR H3 antibodies. Curr Opin Struct Biol 2016; 38:62-7. [PMID: 27295423 PMCID: PMC6667352 DOI: 10.1016/j.sbi.2016.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/14/2016] [Accepted: 05/18/2016] [Indexed: 02/03/2023]
Abstract
Cow antibodies are unusual in having an exceptionally long third complementarity determining region of the heavy chain (CDR H3). These CDR H3s have a multitude of cysteines and form a distinct domain characterized by a β-ribbon 'stalk' and disulfide bonded 'knob'. Cows appear to utilize somatic hypermutation of a single VDJ rearrangement to produce an astounding variety of distinct CDR H3 sequences with different disulfide bonding patterns within the knob. Thus, cows may be unique amongst vertebrates in evolving an antibody system with both a different scaffold for binding antigen as well as an unusual diversity creating process.
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Affiliation(s)
- Melissa L Vadnais
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, United States
| | - Vaughn V Smider
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, United States.
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45
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Nilvebrant J, Tessier PM, Sidhu SS. Engineered Autonomous Human Variable Domains. Curr Pharm Des 2016; 22:6527-6537. [PMID: 27655414 PMCID: PMC5326600 DOI: 10.2174/1381612822666160921143011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The complex multi-chain architecture of antibodies has spurred interest in smaller derivatives that retain specificity but can be more easily produced in bacteria. Domain antibodies consisting of single variable domains are the smallest antibody fragments and have been shown to possess enhanced ability to target epitopes that are difficult to access using multidomain antibodies. However, in contrast to natural camelid antibody domains, human variable domains typically suffer from low stability and high propensity to aggregate. METHODS This review summarizes strategies to improve the biophysical properties of heavy chain variable domains from human antibodies with an emphasis on aggregation resistance. Several protein engineering approaches have targeted antibody frameworks and complementarity determining regions to stabilize the native state and prevent aggregation of the denatured state. CONCLUSION Recent findings enable the construction of highly diverse libraries enriched in aggregation-resistant variants that are expected to provide binders to diverse antigens. Engineered domain antibodies possess unique advantages in expression, epitope preference and flexibility of formatting over conventional immunoreagents and are a promising class of antibody fragments for biomedical development.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Peter M. Tessier
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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