1
|
Arras P, Zimmermann J, Lipinski B, Valldorf B, Evers A, Elter D, Krah S, Doerner A, Guarnera E, Siegmund V, Kolmar H, Pekar L, Zielonka S. Bovine ultralong CDR-H3 derived knob paratopes elicit potent TNF-α neutralization and enable the generation of novel adalimumab-based antibody architectures with augmented features. Biol Chem 2024; 405:461-470. [PMID: 38373142 DOI: 10.1515/hsz-2023-0370] [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: 12/14/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
In this work we have generated cattle-derived chimeric ultralong CDR-H3 antibodies targeting tumor necrosis factor α (TNF-α) via immunization and yeast surface display. We identified one particular ultralong CDR-H3 paratope that potently neutralized TNF-α. Interestingly, grafting of the knob architecture onto a peripheral loop of the CH3 domain of the Fc part of an IgG1 resulted in the generation of a TNF-α neutralizing Fc (Fcknob) that did not show any potency loss compared with the parental chimeric IgG format. Eventually, grafting this knob onto the CH3 region of adalimumab enabled the engineering of a novel TNF-α targeting antibody architecture displaying augmented TNF-α inhibition.
Collapse
Affiliation(s)
- Paul Arras
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
- Biomolecular Immunotherapy, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
- Targeted mRNA Delivery, Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Jasmin Zimmermann
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Britta Lipinski
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
- Biomolecular Immunotherapy, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Bernhard Valldorf
- Targeted mRNA Delivery, Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Desislava Elter
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Enrico Guarnera
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply & Characterization, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Harald Kolmar
- Applied Biochemistry, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
- Biomolecular Immunotherapy, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| |
Collapse
|
2
|
Zhao G, Richaud AD, Williamson RT, Feig M, Roche SP. De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics. ACS Chem Biol 2024; 19:1583-1592. [PMID: 38916527 PMCID: PMC11299430 DOI: 10.1021/acschembio.4c00236] [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] [Indexed: 06/26/2024]
Abstract
The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and noncanonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone β-hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue, highly conserved across CDR-H3 sequences, was found to extend the kinked base of these β-bulges through a combination of stabilizing intramolecular hydrogen bond and CH/π interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that β-bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics.
Collapse
Affiliation(s)
- Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Alexis D. Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - R. Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28409, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Stéphane P. Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, United States
| |
Collapse
|
3
|
Clarke JD, Douangamath A, Mikolajek H, Bonnet-Di Placido M, Ren J, Fry EE, Stuart DI, Hammond JA, Owens RJ. The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies. Acta Crystallogr F Struct Biol Commun 2024; 80:154-163. [PMID: 38958188 PMCID: PMC11229553 DOI: 10.1107/s2053230x2400606x] [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: 03/11/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024] Open
Abstract
The third complementary-determining regions of the heavy-chain (CDR3H) variable regions (VH) of some cattle antibodies are highly extended, consisting of 48 or more residues. These `ultralong' CDR3Hs form β-ribbon stalks that protrude from the surface of the antibody with a disulfide cross-linked knob region at their apex that dominates antigen interactions over the other CDR loops. The structure of the Fab fragment of a naturally paired bovine ultralong antibody (D08), identified by single B-cell sequencing, has been determined to 1.6 Å resolution. By swapping the D08 native light chain with that of an unrelated antigen-unknown ultralong antibody, it is shown that interactions between the CDR3s of the variable domains potentially affect the fine positioning of the ultralong CDR3H; however, comparison with other crystallographic structures shows that crystalline packing is also a major contributor. It is concluded that, on balance, the exact positioning of ultralong CDR3H loops is most likely to be due to the constraints of crystal packing.
Collapse
Affiliation(s)
- John D. Clarke
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
- ImmunogeneticsThe Pirbright InstituteAsh RoadPirbrightWokingGU24 0NFUnited Kingdom
| | - Alice Douangamath
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
| | - Halina Mikolajek
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
- CrystallographyThe Research Complex at HarwellHarwell Science and Innovation CampusDidcotOX11 0FAUnited Kingdom
| | | | - Jingshan Ren
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
| | - Elizabeth E. Fry
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
| | - Dave I. Stuart
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Macromolecular CrystallographyDiamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0DEUnited Kingdom
| | - John A. Hammond
- ImmunogeneticsThe Pirbright InstituteAsh RoadPirbrightWokingGU24 0NFUnited Kingdom
| | - Raymond J. Owens
- The Division of Structural BiologyUniversity of OxfordRoosevelt DriveOxfordOX3 7BNUnited Kingdom
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, DidcotOX11 0QX, United Kingdom
| |
Collapse
|
4
|
Trommer J, Lesniowski F, Buchner J, Svilenov HL. Specific features of a scaffolding antibody light chain. Protein Sci 2024; 33:e4990. [PMID: 38607241 PMCID: PMC11010950 DOI: 10.1002/pro.4990] [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: 01/28/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
The antigen-binding sites in conventional antibodies are formed by hypervariable complementarity-determining regions (CDRs) from both heavy chains (HCs) and light chains (LCs). A deviation from this paradigm is found in a subset of bovine antibodies that bind antigens via an ultra-long CDR. The HCs bearing ultra-long CDRs pair with a restricted set of highly conserved LCs that convey stability to the antibody. Despite the importance of these LCs, their specific features remained unknown. Here, we show that the conserved bovine LC found in antibodies with ultra-long CDRs exhibits a distinct combination of favorable physicochemical properties such as good secretion from mammalian cells, strong dimerization, high stability, and resistance to aggregation. These physicochemical traits of the LCs arise from a combination of the specific sequences in the germline CDRs and a lambda LC framework. In addition to understanding the molecular architecture of antibodies with ultra-long CDRs, our findings reveal fundamental insights into LC characteristics that can guide the design of antibodies with improved properties.
Collapse
Affiliation(s)
- Johanna Trommer
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Florian Lesniowski
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Johannes Buchner
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Hristo L. Svilenov
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
- Present address:
Faculty of Pharmaceutical SciencesGhent UniversityOttergemsesteenweg 460Ghent9000Belgium
| |
Collapse
|
5
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
6
|
David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
Collapse
Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Adams R, Joyce C, Kuravskiy M, Harrison K, Ahdash Z, Balmforth M, Chia K, Marceddu C, Coates M, Snowden J, Goursaud E, Ménochet K, van den Elsen J, Payne RJ, Lawson ADG, Scott-Tucker A, Macpherson A. Serum albumin binding knob domains engineered within a V H framework III bispecific antibody format and as chimeric peptides. Front Immunol 2023; 14:1170357. [PMID: 37251411 PMCID: PMC10213618 DOI: 10.3389/fimmu.2023.1170357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Background Serum albumin binding is an established mechanism to extend the serum half-life of antibody fragments and peptides. The cysteine rich knob domains, isolated from bovine antibody ultralong CDRH3, are the smallest single chain antibody fragments described to date and versatile tools for protein engineering. Methods Here, we used phage display of bovine immune material to derive knob domains against human and rodent serum albumins. These were used to engineer bispecific Fab fragments, by using the framework III loop as a site for knob domain insertion. Results By this route, neutralisation of the canonical antigen (TNFα) was retained but extended pharmacokinetics in-vivo were achieved through albumin binding. Structural characterisation revealed correct folding of the knob domain and identified broadly common but non-cross-reactive epitopes. Additionally, we show that these albumin binding knob domains can be chemically synthesised to achieve dual IL-17A neutralisation and albumin binding in a single chemical entity. Conclusions This study enables antibody and chemical engineering from bovine immune material, via an accessible discovery platform.
Collapse
Affiliation(s)
- Ralph Adams
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | - Callum Joyce
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | - Zainab Ahdash
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Kelda Chia
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | - Matthew Coates
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | - James Snowden
- Early Solutions, UCB Biopharma UK, Slough, United Kingdom
| | | | | | | | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, Australia
| | | | | | | |
Collapse
|
9
|
Passon M, De Smedt S, Svilenov HL. Principles of antibodies with ultralong complementarity-determining regions and picobodies. Biotechnol Adv 2023; 64:108120. [PMID: 36764335 DOI: 10.1016/j.biotechadv.2023.108120] [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: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
In contrast to other species, cattle possess exceptional antibodies with ultra-long complementarity-determining regions (ulCDRs) that can consist of 40-70 amino acids. The bovine ulCDR is folded into a stalk and a disulfide-rich knob domain. The binding to the antigen is via the 3-6 kDa knob. There exists an immense sequence and structural diversity in the knob that enables binding to different antigens. Here we summarize the current knowledge of the ulCDR structure and provide an overview of the approaches to discover ulCDRs against novel antigens. Furthermore, we outline protein engineering approaches inspired by the natural ulCDRs. Finally, we discuss the enormous potential of using isolated bovine knobs, also named picobodies, as the smallest antigen-binding domains derived from natural antibodies.
Collapse
Affiliation(s)
- Marcel Passon
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - Stefaan De Smedt
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium
| | - Hristo L Svilenov
- Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Gent, Belgium.
| |
Collapse
|
10
|
Burke MJ, Scott JNF, Minshull TC, Gao Z, Manfield I, Savic S, Stockley PG, Calabrese AN, Boyes J. A bovine antibody possessing an ultralong complementarity-determining region CDRH3 targets a highly conserved epitope in sarbecovirus spike proteins. J Biol Chem 2022; 298:102624. [PMID: 36272646 PMCID: PMC9678781 DOI: 10.1016/j.jbc.2022.102624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Broadly neutralizing antibodies have huge potential as novel antiviral therapeutics due to their ability to recognize highly conserved epitopes that are seldom mutated in viral variants. A subset of bovine antibodies possess an ultralong complementarity-determining region (CDR)H3 that is highly adept at recognizing such conserved epitopes, but their reactivity against Sarbecovirus Spike proteins has not been explored previously. Here, we use a SARS-naïve library to isolate a broadly reactive bovine CDRH3 that binds the receptor-binding domain of SARS-CoV, SARS-CoV-2, and all SARS-CoV-2 variants. We show further that it neutralizes viruses pseudo-typed with SARS-CoV Spike, but this is not by competition with angiotensin-converting enzyme 2 (ACE2) binding. Instead, using differential hydrogen-deuterium exchange mass spectrometry, we demonstrate that it recognizes the major site of vulnerability of Sarbecoviruses. This glycan-shielded cryptic epitope becomes available only transiently via interdomain movements of the Spike protein such that antibody binding triggers destruction of the prefusion complex. This proof of principle study demonstrates the power of in vitro expressed bovine antibodies with ultralong CDRH3s for the isolation of novel, broadly reactive tools to combat emerging pathogens and to identify key epitopes for vaccine development.
Collapse
Affiliation(s)
- Matthew J Burke
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - James N F Scott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Thomas C Minshull
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Zeqian Gao
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Iain Manfield
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sinisa Savic
- National Institute for Health Research, Leeds Biomedical Research Centre and Leeds Institute of Rheumatic and Musculoskeletal Medicine, Wellcome Trust Brenner Building, St James's University Hospital, Leeds, United Kingdom
| | - Peter G Stockley
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Antonio N Calabrese
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
| |
Collapse
|