1
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Yu PW, Kao G, Dai Z, Nasertorabi F, Zhang Y. Rational design of humanized antibody inhibitors for cathepsin S. Arch Biochem Biophys 2024; 751:109849. [PMID: 38061628 PMCID: PMC10872949 DOI: 10.1016/j.abb.2023.109849] [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: 08/02/2023] [Revised: 11/10/2023] [Accepted: 12/01/2023] [Indexed: 12/22/2023]
Abstract
Cathepsin S (CTSS) is involved in pathogenesis of many human diseases. Inhibitors blocking its protease activity hold therapeutic potential. In comparison to small-molecule inhibitors, monoclonal antibodies capable of inhibiting CTSS enzymatic activity may possess advantageous pharmacological properties. Here we designed and produced inhibitory antibodies targeting human CTSS by genetically fusing the propeptide of procathepsin S (proCTSS) with antibodies in clinic. The resulting antibody fusions in full-length or fragment antigen-binding format could be stably expressed and potently inhibit CTSS proteolytic activity in high specificity. These fusion antibodies not only demonstrate a new approach for facile synthesis of antibody inhibitors against CTSS, but also represent novel anti-CTSS therapeutic candidates.
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Affiliation(s)
- Po-Wen Yu
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Guoyun Kao
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zhefu Dai
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Fariborz Nasertorabi
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, USC Structure Biology Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA; Research Center for Liver Diseases, University of Southern California, Los Angeles, CA, 90089, USA.
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2
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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: 4] [Impact Index Per Article: 4.0] [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.
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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.
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3
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Tian Z, Yu C, Zhang W, Wu KL, Wang C, Gupta R, Xu Z, Wu L, Chen Y, Zhang XHF, Xiao H. Bone-Specific Enhancement of Antibody Therapy for Breast Cancer Metastasis to Bone. ACS CENTRAL SCIENCE 2022; 8:312-321. [PMID: 35355817 PMCID: PMC8961797 DOI: 10.1021/acscentsci.1c01024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 05/04/2023]
Abstract
Despite the rapid evolution of therapeutic antibodies, their clinical efficacy in the treatment of bone tumors is hampered due to the inadequate pharmacokinetics and poor bone tissue accessibility of these large macromolecules. Here, we show that engineering therapeutic antibodies with bone-homing peptide sequences dramatically enhances their concentrations in the bone metastatic niche, resulting in significantly reduced survival and progression of breast cancer bone metastases. To enhance the bone tumor-targeting ability of engineered antibodies, we introduced varying numbers of bone-homing peptides into permissive sites of the anti-HER2 antibody, trastuzumab. Compared to the unmodified antibody, the engineered antibodies have similar pharmacokinetics and in vitro cytotoxic activity, but exhibit improved bone tumor distribution in vivo. Accordingly, in xenograft models of breast cancer metastasis to bone sites, engineered antibodies with enhanced bone specificity exhibit increased inhibition of both initial bone metastases and secondary multiorgan metastases. Furthermore, this engineering strategy is also applied to prepare bone-targeting antibody-drug conjugates with enhanced therapeutic efficacy. These results demonstrate that adding bone-specific targeting to antibody therapy results in robust bone tumor delivery efficacy. This provides a powerful strategy to overcome the poor accessibility of antibodies to the bone tumors and the consequential resistance to the therapy.
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Affiliation(s)
- Zeru Tian
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Chenfei Yu
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Weijie Zhang
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Kuan-Lin Wu
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Chenhang Wang
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ruchi Gupta
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Zhan Xu
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Ling Wu
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Yuda Chen
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Xiang H.-F. Zhang
- Lester
and Sue Smith Breast Center, Baylor College
of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United
States
| | - Han Xiao
- Department
of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Biosciences, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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4
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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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5
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Therapeutic Antibodies Targeting Potassium Ion Channels. Handb Exp Pharmacol 2021; 267:507-545. [PMID: 33963460 DOI: 10.1007/164_2021_464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monoclonal antibodies combine specificity and high affinity binding with excellent pharmacokinetic properties and are rapidly being developed for a wide range of drug targets including clinically important potassium ion channels. Nonetheless, while therapeutic antibodies come with great promise, K+ channels represent particularly difficult targets for biologics development for a variety of reasons that include their dynamic structures and relatively small extracellular loops, their high degree of sequence conservation (leading to immune tolerance), and their generally low-level expression in vivo. The process is made all the more difficult when large numbers of antibody candidates must be screened for a given target, or when lead candidates fail to cross-react with orthologous channels in animal disease models due to their highly selective binding properties. While the number of antibodies targeting potassium channels in preclinical or clinical development is still modest, significant advances in the areas of protein expression and antibody screening are converging to open the field to an avalanche of new drugs. Here, the opportunities and constraints associated with the discovery of antibodies against K+ channels are discussed, with an emphasis on novel technologies that are opening the field to exciting new possibilities for biologics development.
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6
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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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7
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Animal protein toxins: origins and therapeutic applications. BIOPHYSICS REPORTS 2018; 4:233-242. [PMID: 30533488 PMCID: PMC6245134 DOI: 10.1007/s41048-018-0067-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 07/23/2018] [Indexed: 12/21/2022] Open
Abstract
Venomous animals on the earth have been found to be valuable resources for the development of therapeutics. Enzymatic and non-enzymatic proteins and peptides are the major components of animal venoms, many of which can target various ion channels, receptors, and membrane transporters. Compared to traditional small molecule drugs, natural proteins and peptides exhibit higher specificity and potency to their targets. In this review, we summarize the varieties and characteristics of toxins from a few representative venomous animals, and describe the components and applications of animal toxins as potential drug candidates in the treatment of human diseases, including cancer, neurodegenerative diseases, cardiovascular diseases, neuropathic pain, as well as autoimmune diseases. In the meantime, there are many obstacles to translate new toxin discovery to their clinical applications. The challenges, strategies, and perspectives in the development of the protein toxin-based drugs are discussed as well.
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8
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Du J, Cao Y, Liu Y, Wang Y, Zhang Y, Fu G, Zhang Y, Lu L, Luo X, Kim CH, Schultz PG, Wang F. Engineering Bifunctional Antibodies with Constant Region Fusion Architectures. J Am Chem Soc 2017; 139:18607-18615. [PMID: 29186655 DOI: 10.1021/jacs.7b09641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report a method to generate bifunctional antibodies by grafting full-length proteins into constant region loops of a full-length antibody or an antigen-binding fragment (Fab). The fusion proteins retain the antigen binding activity of the parent antibody but have an additional activity associated with the protein insert. The engineered antibodies have excellent in vitro activity, physiochemical properties, and stability. Among these, a Her2 × CD3 bispecific antibody (BsAb) was constructed by inserting an anti-Her2 single-chain variable fragment (ScFv) into an anti-CD3 Fab. This bispecific antibody efficiently induces targeted cell lysis in the presence of effector cells at as low as sub-picomolar concentrations in vitro. Moreover, the Her2 × CD3 BsAb shows potent in vivo antitumor activity in mouse Her22+ and Her21+ xenograft models. These results demonstrate that insertion of a full-length protein into non-CDR loops of antibodies provides a feasible approach to generate multifunctional antibodies for therapeutic applications.
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Affiliation(s)
- Juanjuan Du
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Cao
- Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yan Liu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yong Zhang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Guangsen Fu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuhan Zhang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Lucy Lu
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Xiaozhou Luo
- Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Chan Hyuk Kim
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G Schultz
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research , 11119 N. Torrey Pines Road, La Jolla, California 92037, United States
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9
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Rational design of a Kv1.3 channel-blocking antibody as a selective immunosuppressant. Proc Natl Acad Sci U S A 2016; 113:11501-11506. [PMID: 27663736 DOI: 10.1073/pnas.1612803113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A variable region fusion strategy was used to generate an immunosuppressive antibody based on a novel "stalk-knob" structural motif in the ultralong complementary-determining region (CDR) of a bovine antibody. The potent Kv1.3 channel inhibitory peptides Moka1-toxin and Vm24-toxin were grafted into different CDRs of the humanized antibodies BVK and Synagis (Syn) using both β-sheet and coiled-coil linkers. Structure-activity relationship efforts led to generation of the fusion protein Syn-Vm24-CDR3L, which demonstrated excellent selectivity and potency against effector human memory T cells (subnanomolar to picomolar EC50 values). This fusion antibody also had significantly improved plasma half-life and serum stability in rodents compared with the parent Vm24 peptide. Finally, this fusion protein showed potent in vivo efficacy in the delayed type hypersensitivity in rats. These results illustrate the utility of antibody CDR fusions as a general and effective strategy to generate long-acting functional antibodies, and may lead to a selective immunosuppressive antibody for the treatment of autoimmune diseases.
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10
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Pasman Y, Soliman C, Ramsland PA, Kaushik AK. Exceptionally long CDR3H of bovine scFv antigenized with BoHV-1 B-epitope generates specific immune response against the targeted epitope. Mol Immunol 2016; 77:113-25. [PMID: 27497190 DOI: 10.1016/j.molimm.2016.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 11/18/2022]
Abstract
We discovered that some bovine antibodies are amongst the largest known to exist due to the presence of an exceptionally long CDR3H (≥49 amino acids) with multiple cysteines that provide a unique knob and stalk structure to the antigen binding site. The large CDR3H size, unlike mouse and human, provides a suitable platform for antigenization with large configurational B-epitopes. Here we report the identification of a B-epitope on the gC envelope protein of bovine herpes virus type-1 (BoHV-1) recognized by a bovine IgG1 antibody. The identified 156 amino acid long gC fragment (gC156) was expressed as a recombinant protein. Subsequently, a functional scFv fragment with a 61 amino-acid long CDR3H (scFv1H12) was expressed such that gC156 was grafted into the CDR3H, replacing the "knob" region (gC156scFv1H12 or Ag-scFv). Importantly, the Ag-scFv could be recognized by a neutralizing antibody fragment (scFv3-18L), which suggests that the engraftment of gC156 into the CDR3H of 1H12 maintained the native conformation of the BoHV-1 B-epitope. A 3D model of gC156 was generated using fold-recognition approaches and this was grafted onto the CDR3H stalk of the 1H12 Fab crystal structure to predict the 3D structure of the Ag-scFv. The grafted antigen in Ag-scFv is predicted to have a compact conformation with the ability to protrude into the solvent. Upon immunization of bovine calves, the antigenized scFv (gC156scFv1H12) induced a higher antibody response as compared to free recombinant gC156. These observations suggest that antigenization of bovine scFv with an exceptionally long CDR3H provides a novel approach to developing the next generation of vaccines against infectious agents that require induction of protective humoral immunity.
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Affiliation(s)
- Yfke Pasman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Caroline Soliman
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Paul A Ramsland
- School of Science, RMIT University, Bundoora, VIC 3083, Australia; Centre for Biomedical Research, Burnet Institute, Melbourne, VIC 3004, Australia; Department of Immunology, Alfred Medical Research and Education Precinct, Monash University, Melbourne, VIC 3004, Australia; Department of Surgery Austin Health, University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Azad K Kaushik
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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11
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Combinatorial antibody libraries: new advances, new immunological insights. Nat Rev Immunol 2016; 16:498-508. [DOI: 10.1038/nri.2016.67] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Stanfield RL, Wilson IA, Smider VV. Conservation and diversity in the ultralong third heavy-chain complementarity-determining region of bovine antibodies. Sci Immunol 2016; 1:aaf7962. [PMID: 27574710 PMCID: PMC5000368 DOI: 10.1126/sciimmunol.aaf7962] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A subset of bovine antibodies have an exceptionally long third heavy-chain complementarity determining region (CDR H3) that is highly variable in sequence and includes multiple cysteines. These long CDR H3s (up to 69 residues) fold into a long stalk atop which sits a knob domain that is located far from the antibody surface. Three new bovine Fab crystal structures have been determined to decipher the conserved and variable features of ultralong CDR H3s that lead to diversity in antigen recognition. Despite high sequence variability, the stalks adopt a conserved β-ribbon structure, while the knob regions share a conserved β-sheet that serves as a scaffold for two connecting loops of variable length and conformation, as well as one conserved disulfide. Variation in patterns and connectivity of the remaining disulfides contribute to the knob structural diversity. The unusual architecture of these ultralong bovine CDR H3s for generating diversity is unique in adaptive immune systems.
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Affiliation(s)
- Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The
Scripps Research Institute, La Jolla, California, 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The
Scripps Research Institute, La Jolla, California, 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research
Institute, La Jolla, California, 92037, USA
| | - Vaughn V. Smider
- Department of Cell and Molecular Biology, The Scripps Research
Institute, La Jolla, California, 92037, USA
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121,
USA
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13
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Muyldermans S, Smider VV. Distinct antibody species: structural differences creating therapeutic opportunities. Curr Opin Immunol 2016; 40:7-13. [PMID: 26922135 PMCID: PMC4884505 DOI: 10.1016/j.coi.2016.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/01/2016] [Accepted: 02/11/2016] [Indexed: 11/27/2022]
Abstract
Antibodies have been a remarkably successful class of molecules for binding a large number of antigens in therapeutic, diagnostic, and research applications. Typical antibodies derived from mouse or human sources use the surface formed by complementarity determining regions (CDRs) on the variable regions of the heavy chain/light chain heterodimer, which typically forms a relatively flat binding surface. Alternative species, particularly camelids and bovines, provide a unique paradigm for antigen recognition through novel domains which form the antigen binding paratope. For camelids, heavy chain antibodies bind antigen with only a single heavy chain variable region, in the absence of light chains. In bovines, ultralong CDR-H3 regions form an independently folding minidomain, which protrudes from the surface of the antibody and is diverse in both its sequence and disulfide patterns. The atypical paratopes of camelids and bovines potentially provide the ability to interact with different epitopes, particularly recessed or concave surfaces, compared to traditional antibodies.
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Affiliation(s)
- Serge Muyldermans
- Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Vaughn V Smider
- Fabrus Inc., Division of Sevion Therapeutics, San Diego, CA 92121, United States; Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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14
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Peng Y, Zeng W, Ye H, Han K, Dharmarajan V, Novick S, Wilson I, Griffin P, Friedman J, Lerner R. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. ACTA ACUST UNITED AC 2015; 22:1134-43. [DOI: 10.1016/j.chembiol.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
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15
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de los Rios M, Criscitiello MF, Smider VV. Structural and genetic diversity in antibody repertoires from diverse species. Curr Opin Struct Biol 2015; 33:27-41. [PMID: 26188469 DOI: 10.1016/j.sbi.2015.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/09/2015] [Accepted: 06/19/2015] [Indexed: 01/01/2023]
Abstract
The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.
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Affiliation(s)
- Miguel de los Rios
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121, United States
| | - Michael F Criscitiello
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Vaughn V Smider
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121, United States; Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
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16
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Liu T, Du J, Luo X, Schultz PG, Wang F. Homogeneously modified immunoglobulin domains for therapeutic application. Curr Opin Chem Biol 2015; 28:66-74. [PMID: 26117722 DOI: 10.1016/j.cbpa.2015.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/02/2015] [Accepted: 06/09/2015] [Indexed: 11/28/2022]
Abstract
The field of therapeutic antibodies has been revolutionized over the past decade, led by the development of novel antibody-modification technologies. Besides the huge success achieved by therapeutic monoclonal antibodies, a diversity of antibody derivatives have emerged with hope to outperform their parental antibodies. Here we review the recent development of methodologies to modify immunoglobulin domains and their therapeutic applications. The innovative genetic and chemical approaches enable novel and controllable modifications on immunoglobulin domains, producing homogeneous therapeutics with new functionalities or enhanced therapeutic profiles. Such therapeutics, including antibody-drug conjugates, bispecific antibodies, and antibody/Fc fusion proteins, have demonstrated great prospects in the treatment of cancer, auto-immune diseases, infectious diseases, and many other disorders.
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Affiliation(s)
- Tao Liu
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States
| | - Juanjuan Du
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States
| | - Xiaozhou Luo
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, United States
| | - Peter G Schultz
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States; Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037, United States.
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Functional human antibody CDR fusions as long-acting therapeutic endocrine agonists. Proc Natl Acad Sci U S A 2015; 112:1356-61. [PMID: 25605877 DOI: 10.1073/pnas.1423668112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
On the basis of the 3D structure of a bovine antibody with a well-folded, ultralong complementarity-determining region (CDR), we have developed a versatile approach for generating human or humanized antibody agonists with excellent pharmacological properties. Using human growth hormone (hGH) and human leptin (hLeptin) as model proteins, we have demonstrated that functional human antibody CDR fusions can be efficiently engineered by grafting the native hormones into different CDRs of the humanized antibody Herceptin. The resulting Herceptin CDR fusion proteins were expressed in good yields in mammalian cells and retain comparable in vitro biological activity to the native hormones. Pharmacological studies in rodents indicated a 20- to 100-fold increase in plasma circulating half-life for these antibody agonists and significantly extended in vivo activities in the GH-deficient rat model and leptin-deficient obese mouse model for the hGH and hLeptin antibody fusions, respectively. These results illustrate the utility of antibody CDR fusions as a general and versatile strategy for generating long-acting protein therapeutics.
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Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational design of a humanized glucagon-like peptide-1 receptor agonist antibody. Angew Chem Int Ed Engl 2014; 54:2126-30. [PMID: 25556336 DOI: 10.1002/anie.201410049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 11/09/2022]
Abstract
Bovine antibody BLV1H12 possesses a unique "stalk-knob" architecture in its ultralong heavy chain CDR3, allowing substitutions of the "knob" domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon-like peptide-1 (GLP-1) receptor agonist antibody by first introducing a coiled-coil "stalk" into CDR3H of the antibody herceptin. Exendin-4 (Ex-4), a GLP-1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex-4 to allow release of the N-terminus of the fused peptide. The resulting clipped herceptin-Ex-4 fusion protein is more potent in vitro in activating GLP-1 receptors than the Ex-4 peptide. The clipped herceptin-Ex-4 has an extended plasma half-life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.
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Affiliation(s)
- Yong Zhang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational Design of a Humanized Glucagon-Like Peptide-1 Receptor Agonist Antibody. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Zhang Y, Liu Y, Wang Y, Schultz PG, Wang F. Rational Design of Humanized Dual-Agonist Antibodies. J Am Chem Soc 2014; 137:38-41. [DOI: 10.1021/ja510519u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yong Zhang
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yan Liu
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G. Schultz
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Feng Wang
- California Institute for Biomedical Research (Calibr), 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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21
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Liu T, Liu Y, Wang Y, Hull M, Schultz PG, Wang F. Rational design of CXCR4 specific antibodies with elongated CDRs. J Am Chem Soc 2014; 136:10557-60. [PMID: 25041362 PMCID: PMC4120998 DOI: 10.1021/ja5042447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 11/29/2022]
Abstract
The bovine antibody (BLV1H12) which has an ultralong heavy chain complementarity determining region 3 (CDRH3) provides a novel scaffold for antibody engineering. By substituting the extended CDRH3 of BLV1H12 with modified CXCR4 binding peptides that adopt a β-hairpin conformation, we generated antibodies specifically targeting the ligand binding pocket of CXCR4 receptor. These engineered antibodies selectively bind to CXCR4 expressing cells with binding affinities in the low nanomolar range. In addition, they inhibit SDF-1-dependent signal transduction and cell migration in a transwell assay. Finally, we also demonstrate that a similar strategy can be applied to other CDRs and show that a CDRH2-peptide fusion binds CXCR4 with a K(d) of 0.9 nM. This work illustrates the versatility of scaffold-based antibody engineering and could greatly expand the antibody functional repertoire in the future.
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Affiliation(s)
- Tao Liu
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yan Liu
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Ying Wang
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Mitchell Hull
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Peter G. Schultz
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Feng Wang
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
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22
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Engineered Bovine Antibodies in the Development of Novel Therapeutics, Immunomodulators and Vaccines. Antibodies (Basel) 2014. [DOI: 10.3390/antib3020205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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23
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An antibody with a variable-region coiled-coil "knob" domain. Angew Chem Int Ed Engl 2014; 53:132-5. [PMID: 24254636 PMCID: PMC3926434 DOI: 10.1002/anie.201307939] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 01/24/2023]
Abstract
The X-ray crystal structure of a bovine antibody (BLV1H12) revealed a unique structure in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent-exposed β-strand "stalk" fused to a disulfide crosslinked "knob" domain. We have substituted an antiparallel heterodimeric coiled-coil motif for the β-strand stalk in this antibody. The resulting antibody (Ab-coil) expresses in mammalian cells and has a stability similar to that of the parent bovine antibody. MS analysis of H-D exchange supports the coiled-coil structure of the substituted peptides. Substitution of the knob-domain of Ab-coil with bovine granulocyte colony-stimulating factor (bGCSF) results in a stably expressed chimeric antibody, which proliferates mouse NFS-60 cells with a potency comparable to that of bGCSF. This work demonstrates the utility of this novel coiled-coil CDR3 motif as a means for generating stable, potent antibody fusion proteins with useful pharmacological properties.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, The Scripps Research Institute 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Devrishi Goswami
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458 (USA)
| | - Danling Wang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92307 (USA)
| | - Tsung-Shing Andrew Wang
- Department of Chemistry, The Scripps Research Institute 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Shiladitya Sen
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 (USA)
| | - Thomas J. Magliery
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210 (USA)
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458 (USA)
| | - Feng Wang
- Department of Chemistry, The Scripps Research Institute 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute 10550 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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Zhang Y, Goswami D, Wang D, Wang TSA, Sen S, Magliery TJ, Griffin PR, Wang F, Schultz PG. An Antibody with a Variable-Region Coiled-Coil “Knob” Domain. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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