1
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Tang J, Zhang C, Castillo NC, Lalaurie CJ, Gao X, Dalby PA, Kozielski F. Crystal structures and molecular dynamics simulations of a humanised antibody fragment at acidic to basic pH. Sci Rep 2023; 13:16281. [PMID: 37770469 PMCID: PMC10539359 DOI: 10.1038/s41598-023-42698-7] [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: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/30/2023] Open
Abstract
Antibody-fragment (Fab) therapy development has the potential to be accelerated by computational modelling and simulations that predict their target binding, stability, formulation, manufacturability, and the impact of further protein engineering. Such approaches are currently predicated on starting with good crystal structures that closely represent those found under the solution conditions to be simulated. A33 Fab, is an undeveloped immunotherapeutic antibody candidate that was targeted to the human A33 antigen homogeneously expressed in 95% cases of primary and metastatic colorectal cancers. It is now used as a very well characterised testing ground for developing analytics, formulation and protein engineering strategies, and to gain a deeper understanding of mechanisms of destabilisation, representative of the wider therapeutic Fab platform. In this article, we report the structure of A33 Fab in two different crystal forms obtained at acidic and basic pH. The structures overlapped with RMSD of 1.33 Å overall, yet only 0.5 Å and 0.76 Å for the variable- and constant regions alone. While most of the differences were within experimental error, the switch linker between the variable and the constant regions showed some small differences between the two pHs. The two structures then enabled a direct evaluation of the impact of initial crystal structure selection on the outcomes of molecular dynamics simulations under different conditions, and their subsequent use for determining best fit solution structures using previously obtained small-angle x-ray scattering (SAXS) data. The differences in the two structures did not have a major impact on MD simulations regardless of the pH, other than a slight persistence of structure affecting the solvent accessibility of one of the predicted APR regions of A33 Fab. Interestingly, despite being obtained at pH 4 and pH 9, the two crystal structures were more similar to the SAXS solution structures obtained at pH 7, than to those at pH 4 or pH 9. Furthermore, the P65 crystal structure from pH 4 was also a better representation of the solution structures at any other pH, than was the P1 structure obtained at pH 9. Thus, while obtained at different pH, the two crystal structures may represent highly (P65) and lesser (P1) populated species that both exist at pH 7 in solution. These results now lay the foundation for confident MD simulations of A33 Fab that rationalise or predict behaviours in a range of conditions.
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Affiliation(s)
- Jiazhi Tang
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Cheng Zhang
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Nuria Codina Castillo
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Christophe J Lalaurie
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Xin Gao
- Division of Biosciences, Department of Structural and Molecular Biology, UCL, London, WC1E 6BT, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
| | - Frank Kozielski
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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2
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Spanov B, Olaleye O, Mesurado T, Govorukhina N, Jungbauer A, van de Merbel NC, Lingg N, Bischoff R. Pertuzumab Charge Variant Analysis and Complementarity-Determining Region Stability Assessment to Deamidation. Anal Chem 2023; 95:3951-3958. [PMID: 36795375 PMCID: PMC9979147 DOI: 10.1021/acs.analchem.2c03275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Pertuzumab is a monoclonal antibody used for the treatment of HER2-positive breast cancer in combination with trastuzumab. Charge variants of trastuzumab have been extensively described in the literature; however, little is known about the charge heterogeneity of pertuzumab. Here, changes in the ion-exchange profile of pertuzumab were evaluated by pH gradient cation-exchange chromatography after stressing it for up to 3 weeks at physiological and elevated pH and 37 °C. Isolated charge variants arising under stress conditions were characterized by peptide mapping. The results of peptide mapping showed that deamidation in the Fc domain and N-terminal pyroglutamate formation in the heavy chain are the main contributors to charge heterogeneity. The heavy chain CDR2, which is the only CDR containing asparagine residues, was quite resistant to deamidation under stress conditions according to peptide mapping results. Using surface plasmon resonance, it was shown that the affinity of pertuzumab for the HER2 target receptor does not change under stress conditions. Peptide mapping analysis of clinical samples showed an average of 2-3% deamidation in the heavy chain CDR2, 20-25% deamidation in the Fc domain, and 10-15% N-terminal pyroglutamate formation in the heavy chain. These findings suggest that in vitro stress studies are able to predict in vivo modifications.
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Affiliation(s)
- Baubek Spanov
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Oladapo Olaleye
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tomés Mesurado
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Natalia Govorukhina
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alois Jungbauer
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Nico C. van de Merbel
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands,Bioanalytical
Laboratory, ICON, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Nico Lingg
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Rainer Bischoff
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands,
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3
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Hsiao CY, Meng JL, Hong JZ, Ly XH, Lin MH, Chang CY, Nguyen MTT, Cheng TL, Lin WW, Burnouf PA, Al-Qaisi TS, Liu ES, Su YC. Engineering a High-Affinity Anti-Methoxy Poly(ethylene glycol) (mPEG) Antibody for Sensitive Immunosensing of mPEGylated Therapeutics and mPEG Molecules. Bioconjug Chem 2022; 33:2180-2188. [DOI: 10.1021/acs.bioconjchem.2c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chiao-Yu Hsiao
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Jun-Lun Meng
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Jung-Zhe Hong
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Xuan-Huong Ly
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Meng-Hsuan Lin
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Minh-Tram T. Nguyen
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Tian-Lu Cheng
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Wen-Wei Lin
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Pierre-Alain Burnouf
- International Center for Wound Repair and Regeneration (iWRR), National Cheng-Kung University, Tainan 701401, Taiwan
| | - Talal Salem Al-Qaisi
- Department of Medical Laboratory Sciences, Pharmacological and Diagnostic Research Centre, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman 19328, Jordan
| | - En-Shuo Liu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yu-Cheng Su
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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4
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Nguyen MTT, Shih YC, Lin MH, Roffler SR, Hsiao CY, Cheng TL, Lin WW, Lin EC, Jong YJ, Chang CY, Su YC. Structural determination of an antibody that specifically recognizes polyethylene glycol with a terminal methoxy group. Commun Chem 2022; 5:88. [PMID: 35936993 PMCID: PMC9340711 DOI: 10.1038/s42004-022-00709-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Covalent attachment of methoxy poly(ethylene) glycol (mPEG) to therapeutic molecules is widely employed to improve their systemic circulation time and therapeutic efficacy. mPEG, however, can induce anti-PEG antibodies that negatively impact drug therapeutic effects. However, the underlying mechanism for specific binding of antibodies to mPEG remains unclear. Here, we determined the first co-crystal structure of the humanized 15-2b anti-mPEG antibody in complex with mPEG, which possesses a deep pocket in the antigen-binding site to accommodate the mPEG polymer. Structural and mutational analyses revealed that mPEG binds to h15-2b via Van der Waals and hydrogen bond interactions, whereas the methoxy group of mPEG is stabilized in a hydrophobic environment between the VH:VL interface. Replacement of the heavy chain hydrophobic V37 residue with a neutral polar serine or threonine residue offers additional hydrogen bond interactions with methoxyl and hydroxyl groups, resulting in cross-reactivity to mPEG and OH-PEG. Our findings provide insights into understanding mPEG-binding specificity and antigenicity of anti-mPEG antibodies.
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Affiliation(s)
- Minh-Tram T. Nguyen
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Chien Shih
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Meng-Hsuan Lin
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Steve R. Roffler
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chiao-Yu Hsiao
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Tian-Lu Cheng
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Wei Lin
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - En-Chi Lin
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yuh-Jyh Jong
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Departments of Pediatrics and Laboratory Medicine, and Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Cheng Su
- Department of Biological Science and Technology, Center for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biomedical Science and Environmental Biology, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
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5
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Understanding and Modulating Antibody Fine Specificity: Lessons from Combinatorial Biology. Antibodies (Basel) 2022; 11:antib11030048. [PMID: 35892708 PMCID: PMC9326607 DOI: 10.3390/antib11030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
Combinatorial biology methods such as phage and yeast display, suitable for the generation and screening of huge numbers of protein fragments and mutated variants, have been useful when dissecting the molecular details of the interactions between antibodies and their target antigens (mainly those of protein nature). The relevance of these studies goes far beyond the mere description of binding interfaces, as the information obtained has implications for the understanding of the chemistry of antibody–antigen binding reactions and the biological effects of antibodies. Further modification of the interactions through combinatorial methods to manipulate the key properties of antibodies (affinity and fine specificity) can result in the emergence of novel research tools and optimized therapeutics.
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6
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Mittal A, Khattri A, Verma V. Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants. PLoS Pathog 2022; 18:e1010260. [PMID: 35176090 PMCID: PMC8853550 DOI: 10.1371/journal.ppat.1010260] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is continuously evolving, and this poses a major threat to antibody therapies and currently authorized Coronavirus Disease 2019 (COVID-19) vaccines. It is therefore of utmost importance to investigate and predict the putative mutations on the spike protein that confer immune evasion. Antibodies are key components of the human immune system's response to SARS-CoV-2, and the spike protein is a prime target of neutralizing antibodies (nAbs) as it plays critical roles in host cell recognition, fusion, and virus entry. The potency of therapeutic antibodies and vaccines partly depends on how readily the virus can escape neutralization. Recent structural and functional studies have mapped the epitope landscape of nAbs on the spike protein, which illustrates the footprints of several nAbs and the site of escape mutations. In this review, we discuss (1) the emerging SARS-CoV-2 variants; (2) the structural basis for antibody-mediated neutralization of SARS-CoV-2 and nAb classification; and (3) identification of the RBD escape mutations for several antibodies that resist antibody binding and neutralization. These escape maps are a valuable tool to predict SARS-CoV-2 fitness, and in conjunction with the structures of the spike-nAb complex, they can be utilized to facilitate the rational design of escape-resistant antibody therapeutics and vaccines.
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Affiliation(s)
- Anshumali Mittal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Arun Khattri
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Vikash Verma
- Biology Department, University of Massachusetts, Amherst, Massachusetts, United States of America
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7
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Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning. Nat Biomed Eng 2021; 5:600-612. [PMID: 33859386 DOI: 10.1038/s41551-021-00699-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
The optimization of therapeutic antibodies is time-intensive and resource-demanding, largely because of the low-throughput screening of full-length antibodies (approximately 1 × 103 variants) expressed in mammalian cells, which typically results in few optimized leads. Here we show that optimized antibody variants can be identified by predicting antigen specificity via deep learning from a massively diverse space of antibody sequences. To produce data for training deep neural networks, we deep-sequenced libraries of the therapeutic antibody trastuzumab (about 1 × 104 variants), expressed in a mammalian cell line through site-directed mutagenesis via CRISPR-Cas9-mediated homology-directed repair, and screened the libraries for specificity to human epidermal growth factor receptor 2 (HER2). We then used the trained neural networks to screen a computational library of approximately 1 × 108 trastuzumab variants and predict the HER2-specific subset (approximately 1 × 106 variants), which can then be filtered for viscosity, clearance, solubility and immunogenicity to generate thousands of highly optimized lead candidates. Recombinant expression and experimental testing of 30 randomly selected variants from the unfiltered library showed that all 30 retained specificity for HER2. Deep learning may facilitate antibody engineering and optimization.
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8
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Hsiao YC, Chen YJJ, Goldstein LD, Wu J, Lin Z, Schneider K, Chaudhuri S, Antony A, Bajaj Pahuja K, Modrusan Z, Seshasayee D, Seshagiri S, Hötzel I. Restricted epitope specificity determined by variable region germline segment pairing in rodent antibody repertoires. MAbs 2021; 12:1722541. [PMID: 32041466 PMCID: PMC7039645 DOI: 10.1080/19420862.2020.1722541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibodies from B-cell clonal lineages share sequence and structural properties as well as epitope specificity. Clonally unrelated antibodies can similarly share sequence and specificity properties and are said to be convergent. Convergent antibody responses against several antigens have been described in humans and mice and include different classes of shared sequence features. In particular, some antigens and epitopes can induce convergent responses of clonally unrelated antibodies with restricted heavy (VH) and light (VL) chain variable region germline segment usage without similarity in the heavy chain third complementarity-determining region (CDR H3), a critical specificity determinant. Whether these V germline segment-restricted responses reflect a general epitope specificity restriction of antibodies with shared VH/VL pairing is not known. Here, we investigated this question by determining patterns of antigen binding competition between clonally unrelated antigen-specific rat antibodies from paired-chain deep sequencing datasets selected based solely on VH/VL pairing. We found that antibodies with shared VH/VL germline segment pairings but divergent CDR H3 sequences almost invariably have restricted epitope specificity indicated by shared binding competition patterns. This epitope restriction included 82 of 85 clonally unrelated antibodies with 13 different VH/VL pairings binding in 8 epitope groups in 2 antigens. The corollary that antibodies with shared VH/VL pairing and epitope-restricted binding can accommodate widely divergent CDR H3 sequences was confirmed by in vitro selection of variants of anti-human epidermal growth factor receptor 2 antibodies known to mediate critical antigen interactions through CDR H3. Our results show that restricted epitope specificity determined by VH/VL germline segment pairing is a general property of rodent antigen-specific antibodies.
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Affiliation(s)
- Yi-Chun Hsiao
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Ying-Jiun J Chen
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Jia Wu
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, India
| | | | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Isidro Hötzel
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
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9
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van der Kant R, Bauer J, Karow-Zwick AR, Kube S, Garidel P, Blech M, Rousseau F, Schymkowitz J. Adaption of human antibody λ and κ light chain architectures to CDR repertoires. Protein Eng Des Sel 2020; 32:109-127. [PMID: 31535139 PMCID: PMC6908821 DOI: 10.1093/protein/gzz012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/11/2019] [Indexed: 12/16/2022] Open
Abstract
Monoclonal antibodies bind with high specificity to a wide range of diverse antigens, primarily mediated by their hypervariable complementarity determining regions (CDRs). The defined antigen binding loops are supported by the structurally conserved β-sandwich framework of the light chain (LC) and heavy chain (HC) variable regions. The LC genes are encoded by two separate loci, subdividing the entity of antibodies into kappa (LCκ) and lambda (LCλ) isotypes that exhibit distinct sequence and conformational preferences. In this work, a diverse set of techniques were employed including machine learning, force field analysis, statistical coupling analysis and mutual information analysis of a non-redundant antibody structure collection. Thereby, it was revealed how subtle changes between the structures of LCκ and LCλ isotypes increase the diversity of antibodies, extending the predetermined restrictions of the general antibody fold and expanding the diversity of antigen binding. Interestingly, it was found that the characteristic framework scaffolds of κ and λ are stabilized by diverse amino acid clusters that determine the interplay between the respective fold and the embedded CDR loops. In conclusion, this work reveals how antibodies use the remarkable plasticity of the beta-sandwich Ig fold to incorporate a large diversity of CDR loops.
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Affiliation(s)
- Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box, B-3000 Leuven, Belgium
| | - Joschka Bauer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
| | | | - Sebastian Kube
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box, B-3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49 Box, B-3000 Leuven, Belgium
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10
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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11
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Schrade A, Bujotzek A, Spick C, Wagner M, Goerl J, Wezler X, Georges G, Kontermann RE, Brinkmann U. Back-to-Germline (B2G) Procedure for Antibody Devolution. Antibodies (Basel) 2019; 8:antib8030045. [PMID: 31544851 PMCID: PMC6784197 DOI: 10.3390/antib8030045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022] Open
Abstract
Bispecific antibodies (bsAbs) with avidity-enhanced specificity can be used to address target cells with increased specificity, ideally binding efficiently to cells that express two cognate antigens, yet not to cells that express only one of those. Building blocks required to generate such bsAbs are binders that recognize the two antigens with high specificity yet with various (including very low monovalent) affinities. The herein described ‘back-to-germline’ (B2G) procedure defines such derivatives. It converts parent antibodies with high specificity to derivatives that retain specificity but modulate affinity. The approach defines mutations to be introduced into antibody complementarity-determining regions (CDRs) regions without requiring structures of antibody-antigen complexes. Instead, it reverses the B-cell maturation process that increases affinities, with preference on CDR residues with high antigen contact probability. Placing germline residues at those positions generates VH and VL domains and Fv-combinations thereof that retain specificities but are ‘de-matured’ to different degrees. De-maturation influences on-rates and off-rates, and can produce entities with extremely low affinity for which binding can only be detected in bivalent formats. A comparison with alanine replacement in CDRs (so far, the most frequently applied technology) indicates that B2G may be more reliable/predictable without introduction of stickiness or poly-reactivity. The applicability for generating sets of affinity-modulated monospecific variants is exemplarily shown for antibodies that bind CD138, Her2/neu, and EGFR.
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Affiliation(s)
- Anja Schrade
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Christian Spick
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Martina Wagner
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Johannes Goerl
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Xenia Wezler
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Roland E Kontermann
- Institute of Cell Biology & Immunology, Stuttgart University, 70569 Stuttgart, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research (LMR), Roche Innovation Center Munich, 82377 Penzberg, Germany.
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12
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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13
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Chen G, Karauzum H, Long H, Carranza D, Holtsberg FW, Howell KA, Abaandou L, Zhang B, Jarvik N, Ye W, Liao GC, Gross ML, Leung DW, Amarasinghe GK, Aman MJ, Sidhu SS. Potent Neutralization of Staphylococcal Enterotoxin B In Vivo by Antibodies that Block Binding to the T-Cell Receptor. J Mol Biol 2019; 431:4354-4367. [PMID: 30928493 DOI: 10.1016/j.jmb.2019.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 11/15/2022]
Abstract
To develop an antibody (Ab) therapeutic against staphylococcal enterotoxin B (SEB), a potential incapacitating bioterrorism agent and a major cause of food poisoning, we developed a "class T" anti-SEB neutralizing Ab (GC132) targeting an epitope on SEB distinct from that of previously developed "class M" Abs. A systematic engineering approach was applied to affinity-mature Ab GC132 to yield an optimized therapeutic candidate (GC132a) with sub-nanomolar binding affinity. Mapping of the binding interface by hydrogen-deuterium exchange coupled to mass spectrometry revealed that the class T epitope on SEB overlapped with the T-cell receptor binding site, whereas other evidence suggested that the class M epitope overlapped with the binding site for the major histocompatibility complex. In the IgG format, GC132a showed ∼50-fold more potent toxin-neutralizing efficacy than the best class M Ab in vitro, and fully protected mice from lethal challenge in a toxic shock post-exposure model. We also engineered bispecific Abs (bsAbs) that bound tetravalently by utilizing two class M binding sites and two class T binding sites. The bsAbs displayed enhanced toxin neutralization efficacy compared with the respective monospecific Ab subunits as well as a mixture of the two, indicating that enhanced efficacy was due to heterotypic tetravalent binding to two non-overlapping epitopes on SEB. Together, these results suggest that class T anti-SEB Ab GC132a is an excellent candidate for clinical development and for bsAb engineering.
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Affiliation(s)
- Gang Chen
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Hua Long
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Danielle Carranza
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Katie A Howell
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Laura Abaandou
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Bojie Zhang
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Nick Jarvik
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Wei Ye
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Grant C Liao
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA; Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - M Javad Aman
- Integrated Biotherapeutics, Inc., Rockville, MD 20850, USA.
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
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14
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Van Blarcom T, Rossi A, Foletti D, Sundar P, Pitts S, Melton Z, Telman D, Zhao L, Cheung WL, Berka J, Zhai W, Strop P, Pons J, Rajpal A, Chaparro-Riggers J. Epitope Mapping Using Yeast Display and Next Generation Sequencing. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1785:89-118. [PMID: 29714014 DOI: 10.1007/978-1-4939-7841-0_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Monoclonal antibodies are the largest class of therapeutic proteins due in part to their ability to bind an antigen with a high degree of affinity and specificity. A precise determination of their epitope is important for gaining insights into their therapeutic mechanism of action and to help differentiate antibodies that bind the same antigen. Here, we describe a method to precisely and efficiently map the epitopes of multiple antibodies in parallel over the course of just several weeks. This approach is based on a combination of rational library design, yeast surface display, and next generation DNA sequencing and provides quantitative insights into the epitope residues most critical for the antibody-antigen interaction. As an example, we will use this method to map the epitopes of several antibodies that neutralize alpha toxin from Staphylococcus aureus.
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Affiliation(s)
| | - Andrea Rossi
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Davide Foletti
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | | | - Steven Pitts
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | - Zea Melton
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | | | - Lora Zhao
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Wai Ling Cheung
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Princeton University, Princeton, NJ, USA
| | - Jan Berka
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Roche Sequencing Solutions, Pleasanton, CA, USA
| | - Wenwu Zhai
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Pavel Strop
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
| | - Jaume Pons
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Alexo Therapeutics Inc., South San Francisco, CA, USA
| | - Arvind Rajpal
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
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15
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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16
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Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging. PLoS Comput Biol 2017; 13:e1005441. [PMID: 28406988 PMCID: PMC5390981 DOI: 10.1371/journal.pcbi.1005441] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/04/2017] [Indexed: 01/19/2023] Open
Abstract
A high level of HER2 expression in breast cancer correlates with a higher tumor growth rate, high metastatic potential, and a poor long-term patient survival rate. Pertuzumab, a human monoclonal antibody, can reduce the effect of HER2 overexpression by preventing HER2 dimerization. In this study, a combination protocol of molecular dynamics modeling and MM/GBSA binding free energy calculations was applied to design peptides that interact with HER2 based on the HER2/pertuzumab crystal structure. Based on a β hairpin in pertuzumab from Glu46 to Lys65—which plays a key role in interacting with HER2—mutations were carried out in silico to improve the binding free energy of the hairpin that interacts with the Phe256-Lys314 of the HER2 protein. Combined the use of one-bead-one-compound library screening, among all the mutations, a peptide (58F63Y) with the lowest binding free energy was confirmed experimentally to have the highest affinity, and it may be used as a new probe in diagnosing and treating HER2-positive breast cancer. Many therapeutic approaches, including the human monoclonal antibodies trastuzumab and pertuzumab, target the human epidermal growth factor receptor 2 (HER2) of any breast cancer that features HER2 overexpression. Compared to these antibodies, peptides have many advantages, including lower cost, easier synthesis, high affinity, and lower toxicity. Here, we first designed peptides that interact with HER2 protein based on the HER2/pertuzumab crystal structure (PDB entry: 1S78), using a combination protocol of molecular dynamics modeling, molecular mechanics/generalized Born solvent-accessible surface area (MM/GBSA) binding free energy calculations. Then, combined with the peptide library screening, six peptides were selected for further analysis and experimental validations. The results of ex vivo and in vivo experiments confirmed that one peptide (58F63Y) in particular has a strong affinity and high specificity to HER2-overexpressing tumors. This may due to more paired residues and lower binding free energy in peptide 58F63Y and HER2 complex based on free energy decomposition analysis and distances calculation. While both in silico and in vitro screenings point to the same high-affinity peptide, the findings suggest that in silico screening based on calculated binding free energies is rather reliable. Additionally, based on the calculation of binding free energies among mutants, we can reduce the library capacity of one-bead-one-compound screening. In summary, we present a rather simple and rapid means of deriving a peptide with a clear binding site to its target protein.
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17
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Rabinovich E, Heyne M, Bakhman A, Kosloff M, Shifman JM, Papo N. Identifying Residues that Determine SCF Molecular-Level Interactions through a Combination of Experimental and In silico Analyses. J Mol Biol 2016; 429:97-114. [PMID: 27890784 DOI: 10.1016/j.jmb.2016.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/15/2016] [Accepted: 11/22/2016] [Indexed: 11/28/2022]
Abstract
The stem cell factor (SCF)/c-Kit receptor tyrosine kinase complex-with its significant roles in hematopoiesis and angiogenesis-is an attractive target for rational drug design. There is thus a need to map, in detail, the SCF/c-Kit interaction sites and the mechanisms that modulate this interaction. While most residues in the direct SCF/c-Kit binding interface can be identified from the existing crystal structure of the complex, other residues that affect binding through protein unfolding, intermolecular interactions, allosteric or long-distance electrostatic effects cannot be directly inferred. Here, we describe an efficient method for protein-wide epitope mapping using yeast surface display. A library of single SCF mutants that span the SCF sequence was screened for decreased affinity to soluble c-Kit. Sequencing of selected clones allowed the identification of mutations that reduce SCF binding affinity to c-Kit. Moreover, the screening of these SCF clones for binding to a structural antibody helped identify mutations that result in small or large conformational changes in SCF. Computational modeling of the experimentally identified mutations showed that these mutations reduced the binding affinity through one of the three scenarios: through SCF destabilization, through elimination of favorable SCF/c-Kit intermolecular interactions, or through allosteric changes. Eight SCF variants were expressed and purified. Experimentally measured in vitro binding affinities of these mutants to c-Kit confirmed both the yeast surface display selection results and the computational predictions. This study has thus identified the residues crucial for c-Kit/SCF binding and has demonstrated the advantages of using a combination of computational and combinatorial methods for epitope mapping.
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Affiliation(s)
- Eitan Rabinovich
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Heyne
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anna Bakhman
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Mickey Kosloff
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Niv Papo
- Department of Biotechnology Engineering, and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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18
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Gaiotto T, Hufton SE. Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. PLoS One 2016; 11:e0164296. [PMID: 27741319 PMCID: PMC5065140 DOI: 10.1371/journal.pone.0164296] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Cross-neutralising monoclonal antibodies against influenza hemagglutinin (HA) are of considerable interest as both therapeutics and diagnostic tools. We have recently described five different single domain antibodies (nanobodies) which share this cross-neutralising activity and suggest their small size, high stability, and cleft binding properties may present distinct advantages over equivalent conventional antibodies. We have used yeast display in combination with deep mutational scanning to give residue level resolution of positions in the antibody-HA interface which are crucial for binding. In addition, we have mapped positions within HA predicted to have minimal effect on antibody binding when mutated. Our cross-neutralising nanobodies were shown to bind to a highly conserved pocket in the HA2 domain of A(H1N1)pdm09 influenza virus overlapping with the fusion peptide suggesting their mechanism of action is through the inhibition of viral membrane fusion. We also note that the epitope overlaps with that of CR6261 and F10 which are human monoclonal antibodies in clinical development as immunotherapeutics. Although all five nanobodies mapped to the same highly conserved binding pocket we observed differences in the size of the epitope footprint which has implications in comparing the relative genetic barrier each nanobody presents to a rapidly evolving influenza virus. To further refine our epitope map, we have re-created naturally occurring mutations within this HA stem epitope and tested their effect on binding using yeast display. We have shown that a D46N mutation in the HA2 stem domain uniquely interferes with binding of R2b-E8. Further testing of this substitution in the context of full length purified HA from 1918 H1N1 pandemic (Spanish flu), 2009 H1N1 pandemic (swine flu) and highly pathogenic avian influenza H5N1 demonstrated binding which correlated with D46 whereas binding to seasonal H1N1 strains carrying N46 was absent. In addition, our deep sequence analysis predicted that binding to the emerging H1N1 strain (A/Christchurch/16/2010) carrying the HA2-E47K mutation would not affect binding was confirmed experimentally. This demonstrates yeast display, in combination with deep sequencing, may be able to predict antibody reactivity to emerging influenza strains so assisting in the preparation for future influenza pandemics.
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Affiliation(s)
- Tiziano Gaiotto
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
| | - Simon E. Hufton
- Biotherapeutics Group, National Institute for Biological Standards and Control, a centre of the Medicines and Healthcare Products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar, Herts, EN6 3QG, United Kingdom
- * E-mail:
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19
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Augmented Binary Substitution: Single-pass CDR germ-lining and stabilization of therapeutic antibodies. Proc Natl Acad Sci U S A 2015; 112:15354-9. [PMID: 26621728 DOI: 10.1073/pnas.1510944112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Although humanized antibodies have been highly successful in the clinic, all current humanization techniques have potential limitations, such as: reliance on rodent hosts, immunogenicity due to high non-germ-line amino acid content, v-domain destabilization, expression and formulation issues. This study presents a technology that generates stable, soluble, ultrahumanized antibodies via single-step complementarity-determining region (CDR) germ-lining. For three antibodies from three separate key immune host species, binary substitution CDR cassettes were inserted into preferred human frameworks to form libraries in which only the parental or human germ-line destination residue was encoded at each position. The CDR-H3 in each case was also augmented with 1 ± 1 random substitution per clone. Each library was then screened for clones with restored antigen binding capacity. Lead ultrahumanized clones demonstrated high stability, with affinity and specificity equivalent to, or better than, the parental IgG. Critically, this was mainly achieved on germ-line frameworks by simultaneously subtracting up to 19 redundant non-germ-line residues in the CDRs. This process significantly lowered non-germ-line sequence content, minimized immunogenicity risk in the final molecules and provided a heat map for the essential non-germ-line CDR residue content of each antibody. The ABS technology therefore fully optimizes the clinical potential of antibodies from rodents and alternative immune hosts, rendering them indistinguishable from fully human in a simple, single-pass process.
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20
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Frei JC, Kielian M, Lai JR. Comprehensive mapping of functional epitopes on dengue virus glycoprotein E DIII for binding to broadly neutralizing antibodies 4E11 and 4E5A by phage display. Virology 2015; 485:371-82. [PMID: 26339794 DOI: 10.1016/j.virol.2015.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/04/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022]
Abstract
Here we investigated the binding of Dengue virus envelope glycoprotein domain III (DIII) by two broadly neutralizing antibodies (bNAbs), 4E11 and 4E5A. There are four serotypes of Dengue virus (DENV-1 to -4), whose DIII sequences vary by up to 49%. We used combinatorial alanine scanning mutagenesis, a phage display approach, to map functional epitopes (those residues that contribute most significantly to the energetics of antibody-antigen interaction) on these four serotypes. Our results showed that 4E11, which binds strongly to DENV-1, -2, and -3, and moderately to DENV-4, recognized a common conserved core functional epitope involving DIII residues K310, L/I387, L389, and W391. There were also unique recognition features for each serotype, suggesting that 4E11 has flexible recognition requirements. Similar scanning studies for the related bNAb 4E5A, which binds more tightly to DENV-4, identified broader functional epitopes on DENV-1. These results provide useful information for immunogen and therapeutic antibody design.
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Affiliation(s)
- Julia C Frei
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Jonathan R Lai
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States.
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21
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Chen G, Gorelik L, Simon KJ, Pavlenco A, Cheung A, Brickelmaier M, Chen LL, Jin P, Weinreb PH, Sidhu SS. Synthetic antibodies and peptides recognizing progressive multifocal leukoencephalopathy-specific point mutations in polyomavirus JC capsid viral protein 1. MAbs 2015; 7:681-92. [PMID: 25879139 PMCID: PMC4623438 DOI: 10.1080/19420862.2015.1038447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Accepted: 04/01/2015] [Indexed: 10/23/2022] Open
Abstract
Polyomavirus JC (JCV) is the causative agent of progressive multifocal leukoencephalopathy (PML), a rare and frequently fatal brain disease that afflicts a small fraction of the immune-compromised population, including those affected by AIDS and transplantation recipients on immunosuppressive drug therapy. Currently there is no specific therapy for PML. The major capsid viral protein 1 (VP1) involved in binding to sialic acid cell receptors is believed to be a key player in pathogenesis. PML-specific mutations in JCV VP1 sequences present at the binding pocket of sialic acid cell receptors, such as L55F and S269F, abolish sialic acid recognition and might favor PML onset. Early diagnosis of these PML-specific mutations may help identify patients at high risk of PML, thus reducing the risks associated with immunosuppressive therapy. As a first step in the development of such early diagnostic tools, we report identification and characterization of affinity reagents that specifically recognize PML-specific mutations in VP1 variants using phage display technology. We first identified 2 peptides targeting wild type VP1 with moderate specificity. Fine-tuning via selection of biased libraries designed based on 2 parental peptides yielded peptides with different, yet still moderate, bindinspecificities. In contrast, we had great success in identifying synthetic antibodies that recognize one of the PML-specific mutations (L55F) with high specificity from the phage-displayed libraries. These peptides and synthetic antibodies represent potential candidates for developing tailored immune-based assays for PML risk stratification in addition to complementing affinity reagents currently available for the study of PML and JCV.
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Key Words
- BSA, bovine serum albumin
- CDR, complementarity determining region
- CSF, cerebrospinal fluid
- D66H, Asp to His mutation at position 66
- DHFR, dihydrofolate reductase
- ELISA, enzyme linked immunosorbent assay
- HRP, horseradish peroxidase
- IPTG, isopropyl β-D-1-thiogalactopyranoside
- JC virus
- JCV, polyomavirus JC
- L55F, Leu to Phe mutation at position 55
- P8, M13 major coat protein
- PBS, phosphate-buffered saline
- PCR, polymerase chain reaction
- PML, progressive multifocal leukoencephalopathy
- S269F, Ser to Phe mutation at position 269
- TMB, 3,3',5,5'-tetramethylbenzidine
- VLP, virus-like particle
- VP1, major capsid viral protein 1
- WT: type 3 wild type JCV VP1
- phage display
- protein engineering
- synthetic antibody
- virus-like particle
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Affiliation(s)
- Gang Chen
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto, Ontario, Canada
| | | | | | - Alevtina Pavlenco
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto, Ontario, Canada
| | | | | | | | | | | | - Sachdev S Sidhu
- Banting and Best Department of Medical Research; Terrence Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto, Ontario, Canada
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22
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Precise and Efficient Antibody Epitope Determination through Library Design, Yeast Display and Next-Generation Sequencing. J Mol Biol 2015; 427:1513-1534. [DOI: 10.1016/j.jmb.2014.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/17/2014] [Accepted: 09/26/2014] [Indexed: 01/18/2023]
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23
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Fellouse F, Pal G. Methods for the Construction of Phage-Displayed Libraries. ACTA ACUST UNITED AC 2015. [DOI: 10.1201/b18196-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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24
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Robin G, Sato Y, Desplancq D, Rochel N, Weiss E, Martineau P. Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody–Antigen Complexes. J Mol Biol 2014; 426:3729-3743. [DOI: 10.1016/j.jmb.2014.08.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/31/2014] [Accepted: 08/09/2014] [Indexed: 12/28/2022]
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25
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Chen G, Koellhoffer JF, Zak SE, Frei JC, Liu N, Long H, Ye W, Nagar K, Pan G, Chandran K, Dye JM, Sidhu SS, Lai JR. Synthetic antibodies with a human framework that protect mice from lethal Sudan ebolavirus challenge. ACS Chem Biol 2014; 9:2263-73. [PMID: 25140871 PMCID: PMC4201348 DOI: 10.1021/cb5006454] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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The ebolaviruses cause severe and
rapidly progressing hemorrhagic
fever. There are five ebolavirus species; although much is known about
Zaire ebolavirus (EBOV) and its neutralization by antibodies, little
is known about Sudan ebolavirus (SUDV), which is emerging with increasing
frequency. Here we describe monoclonal antibodies containing a human
framework that potently inhibit infection by SUDV and protect mice
from lethal challenge. The murine antibody 16F6, which binds the SUDV
envelope glycoprotein (GP), served as the starting point for design.
Sequence and structural alignment revealed similarities between 16F6
and YADS1, a synthetic antibody with a humanized scaffold. A focused
phage library was constructed and screened to impart 16F6-like recognition
properties onto the YADS1 scaffold. A panel of 17 antibodies were
characterized and found to have a range of neutralization potentials
against a pseudotype virus infection model. Neutralization correlated
with GP binding as determined by ELISA. Two of these clones, E10 and
F4, potently inhibited authentic SUDV and conferred protection and
memory immunity in mice from lethal SUDV challenge. E10 and F4 were
further shown to bind to the same epitope on GP as 16F6 with comparable
affinities. These antibodies represent strong immunotherapeutic candidates
for treatment of SUDV infection.
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Affiliation(s)
- Gang Chen
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
| | | | - Samantha E. Zak
- Virology
Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Maryland 21702, United States
| | | | | | - Hua Long
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
| | - Wei Ye
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
| | - Kaajal Nagar
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
| | - Guohua Pan
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
| | | | - John M. Dye
- Virology
Division, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Maryland 21702, United States
| | - Sachdev S. Sidhu
- Banting
and Best Department of Medical Research, Terrence Donnelly Centre
for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 3E1
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26
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PURE ribosome display and its application in antibody technology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1925-1932. [PMID: 24747149 DOI: 10.1016/j.bbapap.2014.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 11/23/2022]
Abstract
Ribosome display utilizes formation of the mRNA-ribosome-polypeptide ternary complex in a cell-free protein synthesis system to link genotype (mRNA) to phenotype (polypeptide). However, the presence of intrinsic components, such as nucleases in the cell-extract-based cell-free protein synthesis system, reduces the stability of the ternary complex, which would prevent attainment of reliable results. We have developed an efficient and highly controllable ribosome display system using the PURE (Protein synthesis Using Recombinant Elements) system. The mRNA-ribosome-polypeptide ternary complex is highly stable in the PURE system, and the selected mRNA can be easily recovered because activities of nucleases and other inhibitory factors are very low in the PURE system. We have applied the PURE ribosome display to antibody engineering approaches, such as epitope mapping and affinity maturation of antibodies, and obtained results showing that the PURE ribosome display is more efficient than the conventional method. We believe that the PURE ribosome display can contribute to the development of useful antibodies. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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27
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Lee CV, Koenig P, Fuh G. A two-in-one antibody engineered from a humanized interleukin 4 antibody through mutation in heavy chain complementarity-determining regions. MAbs 2014; 6:622-7. [PMID: 24618680 DOI: 10.4161/mabs.28483] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A mono-specific antibody may recruit a second antigen binding specificity, thus converting to a dual-specific Two-in-One antibody through mutation at the light chain complementarity-determining regions (CDRs). It is, however, unknown whether mutation at the heavy chain CDRs may evolve such dual specificity. Herein, we examined the CDRs of a humanized interleukin 4 (IL4) antibody using alanine scanning and structural modeling, designed libraries of mutants in regions that tolerate mutation, and isolated dual specific antibodies harboring mutation at the heavy chain CDRs only. We then affinity improved an IL4/IL5 dual specific antibody to variants with dissociation constants in the low nanomolar range for both antigens. The results demonstrate the full capacity of antibodies to evolve dual binding specificity.
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Affiliation(s)
- Chingwei V Lee
- Department of Antibody Engineering; Genentech Inc.; South San Francisco, CA USA
| | - Patrick Koenig
- Department of Antibody Engineering; Genentech Inc.; South San Francisco, CA USA
| | - Germaine Fuh
- Department of Antibody Engineering; Genentech Inc.; South San Francisco, CA USA
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28
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Mukund S, Shang Y, Clarke HJ, Madjidi A, Corn JE, Kates L, Kolumam G, Chiang V, Luis E, Murray J, Zhang Y, Hötzel I, Koth CM, Allan BB. Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor. J Biol Chem 2013; 288:36168-78. [PMID: 24189067 PMCID: PMC3861664 DOI: 10.1074/jbc.m113.496984] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Elevated glucagon levels and increased hepatic glucagon receptor (GCGR) signaling contribute to hyperglycemia in type 2 diabetes. We have identified a monoclonal antibody that inhibits GCGR, a class B G-protein coupled receptor (GPCR), through a unique allosteric mechanism. Receptor inhibition is mediated by the binding of this antibody to two distinct sites that lie outside of the glucagon binding cleft. One site consists of a patch of residues that are surface-exposed on the face of the extracellular domain (ECD) opposite the ligand-binding cleft, whereas the second binding site consists of residues in the αA helix of the ECD. A docking model suggests that the antibody does not occlude the ligand-binding cleft. We solved the crystal structure of GCGR ECD containing a naturally occurring G40S mutation and found a shift in the register of the αA helix that prevents antibody binding. We also found that alterations in the αA helix impact the normal function of GCGR. We present a model for the allosteric inhibition of GCGR by a monoclonal antibody that may form the basis for the development of allosteric modulators for the treatment of diabetes and other class B GPCR-related diseases.
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29
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Zhang X, Shi X, Xu L, Yuan J, Fang X. Atomic force microscopy study of the effect of HER 2 antibody on EGF mediated ErbB ligand–receptor interaction. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2013; 9:627-35. [DOI: 10.1016/j.nano.2012.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 11/13/2012] [Accepted: 11/25/2012] [Indexed: 01/22/2023]
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30
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Stewart A, Harrison JS, Regula LK, Lai JR. Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment. BMC BIOCHEMISTRY 2013; 14:9. [PMID: 23566198 PMCID: PMC3626704 DOI: 10.1186/1471-2091-14-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/25/2013] [Indexed: 11/10/2022]
Abstract
Background Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464–5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor. Results Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1–3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5. Conclusions Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high-affinity interaction involving an antibody from the VH1-69 germline segment.
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Affiliation(s)
- Alex Stewart
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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31
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Rojas G, Pupo A, Gómez S, Krengel U, Moreno E. Engineering the binding site of an antibody against N-glycolyl GM3: from functional mapping to novel anti-ganglioside specificities. ACS Chem Biol 2013; 8:376-86. [PMID: 23138862 DOI: 10.1021/cb3003754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The structurally related gangliosides N-glycolyl GM3 and N-acetyl GM3 are potential targets for tumor immunotherapy. 14F7 is a monoclonal antibody able to discriminate the tumor-specific antigen N-glycolyl GM3 from the closely related N-acetyl GM3 on the basis of the presence of a single additional hydroxyl group in the former. A combinatorial phage display strategy, based on the screening of a large library followed by refined mutagenesis, allowed a thorough exploration of the binding chemistry of this unique antibody. Three essential features of the heavy chain variable region were identified: two aromatic rings (in positions 33 and 100D) contributing to the binding site architecture and an arginine residue (position 98) critical for recognition. Directed evolution of 14F7 resulted in novel variants that cross-react with the tumor-associated antigen N-acetyl GM3 and display recurrent replacements: the substitution W33Q and the appearance of additional arginine residues at several positions of CDR H1. Successful conversion of such engineered variable regions into whole cross-reactive anti-GM3 immunoglobulins validated our phage-based approach to study and modify the lead antibody 14F7. The resulting family of closely related antibodies offers new tools to study the mechanisms of cell death induced by antibodies targeting gangliosides. In vitro directed evolution was useful to overcome the technical limitations to obtain anti-ganglioside antibodies. The case of 14F7 illustrates the power of combining library screening with focused site-directed randomization for a comprehensive scanning of protein interactions.
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Affiliation(s)
- Gertrudis Rojas
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, PO Box
16040, La Habana CP 11600, Cuba
| | - Amaury Pupo
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, PO Box
16040, La Habana CP 11600, Cuba
| | - Silvia Gómez
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, PO Box
16040, La Habana CP 11600, Cuba
| | - Ute Krengel
- Department of Chemistry, University of Oslo, PO Box 1033 Blindern, NO-0315 Oslo,
Norway
| | - Ernesto Moreno
- Center of Molecular Immunology, Calle 216 esq 15, Atabey, Playa, PO Box
16040, La Habana CP 11600, Cuba
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32
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Tsolis AC, Papandreou NC, Iconomidou VA, Hamodrakas SJ. A consensus method for the prediction of 'aggregation-prone' peptides in globular proteins. PLoS One 2013; 8:e54175. [PMID: 23326595 PMCID: PMC3542318 DOI: 10.1371/journal.pone.0054175] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 12/11/2012] [Indexed: 02/03/2023] Open
Abstract
The purpose of this work was to construct a consensus prediction algorithm of ‘aggregation-prone’ peptides in globular proteins, combining existing tools. This allows comparison of the different algorithms and the production of more objective and accurate results. Eleven (11) individual methods are combined and produce AMYLPRED2, a publicly, freely available web tool to academic users (http://biophysics.biol.uoa.gr/AMYLPRED2), for the consensus prediction of amyloidogenic determinants/‘aggregation-prone’ peptides in proteins, from sequence alone. The performance of AMYLPRED2 indicates that it functions better than individual aggregation-prediction algorithms, as perhaps expected. AMYLPRED2 is a useful tool for identifying amyloid-forming regions in proteins that are associated with several conformational diseases, called amyloidoses, such as Altzheimer's, Parkinson's, prion diseases and type II diabetes. It may also be useful for understanding the properties of protein folding and misfolding and for helping to the control of protein aggregation/solubility in biotechnology (recombinant proteins forming bacterial inclusion bodies) and biotherapeutics (monoclonal antibodies and biopharmaceutical proteins).
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Affiliation(s)
- Antonios C. Tsolis
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
| | - Nikos C. Papandreou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
| | - Vassiliki A. Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
| | - Stavros J. Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
- * E-mail:
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33
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Pershad K, Kay BK. Generating thermal stable variants of protein domains through phage display. Methods 2012; 60:38-45. [PMID: 23276752 DOI: 10.1016/j.ymeth.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES-MC 066, Chicago, IL 60607-7060, USA
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34
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Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning. Biochem Biophys Res Commun 2012; 428:395-400. [PMID: 23103372 DOI: 10.1016/j.bbrc.2012.10.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 10/17/2012] [Indexed: 10/27/2022]
Abstract
Development of protein therapeutics or biosensors often requires in vitro affinity maturation. Here we report a robust affinity engineering strategy using a custom designed library. The strategy consists of two steps beginning with identification of beneficial single amino acid substitutions then combination. A high quality combinatorial library specifically customized to a given binding-interface can be rapidly designed by high-throughput mutational scanning of single substitution libraries. When applied to the optimization of a model antibody Fab fragment, the strategy created a diverse panel of high affinity variants. The most potent variant achieved 2110-fold affinity improvement to an equilibrium dissociation constant (Kd) of 3.45 pM with only 7 amino acid substitutions. The method should facilitate affinity engineering of a wide variety of protein-protein interactions due to its context-dependent library design strategy.
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35
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Traxlmayr MW, Hasenhindl C, Hackl M, Stadlmayr G, Rybka JD, Borth N, Grillari J, Rüker F, Obinger C. Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing. J Mol Biol 2012; 423:397-412. [PMID: 22846908 PMCID: PMC3469823 DOI: 10.1016/j.jmb.2012.07.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/13/2012] [Accepted: 07/18/2012] [Indexed: 12/21/2022]
Abstract
One of the most important but still poorly understood issues in protein chemistry is the relationship between sequence and stability of proteins. Here, we present a method for analyzing the influence of each individual residue on the foldability and stability of an entire protein. A randomly mutated library of the crystallizable fragment of human immunoglobulin G class 1 (IgG1-Fc) was expressed on the surface of yeast, followed by heat incubation at 79 °C and selection of stable variants that still bound to structurally specific ligands. High throughput sequencing allowed comparison of the mutation rate between the starting and selected library pools, enabling the generation of a stability landscape for the entire CH3 domain of human IgG1 at single residue resolution. Its quality was analyzed with respect to (i) the structure of IgG1-Fc, (ii) evolutionarily conserved positions and (iii) in silico calculations of the energy of unfolding of all variants in comparison with the wild-type protein. In addition, this new experimental approach allowed the assignment of functional epitopes of structurally specific ligands used for selection [Fc γ‐receptor I (CD64) and anti-human CH2 domain antibody] to distinct binding regions in the CH2 domain.
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Affiliation(s)
- Michael W Traxlmayr
- Christian Doppler Laboratory for Antibody Engineering, Vienna Institute of BioTechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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36
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Karauzum H, Chen G, Abaandou L, Mahmoudieh M, Boroun AR, Shulenin S, Devi VS, Stavale E, Warfield KL, Zeitlin L, Roy CJ, Sidhu SS, Aman MJ. Synthetic human monoclonal antibodies toward staphylococcal enterotoxin B (SEB) protective against toxic shock syndrome. J Biol Chem 2012; 287:25203-15. [PMID: 22645125 PMCID: PMC3408135 DOI: 10.1074/jbc.m112.364075] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/04/2012] [Indexed: 01/25/2023] Open
Abstract
Staphylococcal enterotoxin B (SEB) is a potent toxin that can cause toxic shock syndrome and act as a lethal and incapacitating agent when used as a bioweapon. There are currently no vaccines or immunotherapeutics available against this toxin. Using phage display technology, human antigen-binding fragments (Fabs) were selected against SEB, and proteins were produced in Escherichia coli cells and characterized for their binding affinity and their toxin neutralizing activity in vitro and in vivo. Highly protective Fabs were converted into full-length IgGs and produced in mammalian cells. Additionally, the production of anti-SEB antibodies was explored in the Nicotiana benthamiana plant expression system. Affinity maturation was performed to produce optimized lead anti-SEB antibody candidates with subnanomolar affinities. IgGs produced in N. benthamiana showed characteristics comparable with those of counterparts produced in mammalian cells. IgGs were tested for their therapeutic efficacy in the mouse toxic shock model using different challenge doses of SEB and a treatment with 200 μg of IgGs 1 h after SEB challenge. The lead candidates displayed full protection from lethal challenge over a wide range of SEB challenge doses. Furthermore, mice that were treated with anti-SEB IgG had significantly lower IFNγ and IL-2 levels in serum compared with mock-treated mice. In summary, these anti-SEB monoclonal antibodies represent excellent therapeutic candidates for further preclinical and clinical development.
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Affiliation(s)
- Hatice Karauzum
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Gang Chen
- the Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Laura Abaandou
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Mahta Mahmoudieh
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Atefeh R. Boroun
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Sergey Shulenin
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - V. Sathya Devi
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | - Eric Stavale
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
| | | | - Larry Zeitlin
- Mapp Biopharmaceutical, San Diego, California 92121, and
| | - Chad J. Roy
- the Tulane National Primate Research Center, Tulane School of Medicine, Covington, Louisiana 70433
| | - Sachdev S. Sidhu
- the Banting and Best Department of Medical Research, Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - M. Javad Aman
- From Integrated Biotherapeutics, Inc., Gaithersburg, Maryland 20878
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37
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Miersch S, Sidhu SS. Synthetic antibodies: concepts, potential and practical considerations. Methods 2012; 57:486-98. [PMID: 22750306 DOI: 10.1016/j.ymeth.2012.06.012] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 06/18/2012] [Accepted: 06/21/2012] [Indexed: 01/08/2023] Open
Abstract
The last 100 years of enquiry into the fundamental basis of humoral immunity has resulted in the identification of antibodies as key molecular sentinels responsible for the in vivo surveillance, neutralization and clearance of foreign substances. Intense efforts aimed at understanding and exploiting their exquisite molecular specificity have positioned antibodies as a cornerstone supporting basic research, diagnostics and therapeutic applications [1]. More recently, efforts have aimed to circumvent the limitations of developing antibodies in animals by developing wholly in vitro techniques for designing antibodies of tailored specificity. This has been realized with the advent of synthetic antibody libraries that possess diversity outside the scope of natural immune repertoires and are thus capable of yielding specificities not otherwise attainable. This review examines the convergence of technologies that have contributed to the development of combinatorial phage-displayed antibody libraries. It further explores the practical concepts that underlie phage display, antibody diversity and the methods used in the generation of and selection from phage-displayed synthetic antibody libraries, highlighting specific applications in which design approaches gave rise to specificities that could not easily be obtained with libraries based upon natural immune repertories.
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Affiliation(s)
- S Miersch
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
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38
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Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. Molecular basis of a million-fold affinity maturation process in a protein-protein interaction. J Mol Biol 2011; 411:321-8. [PMID: 21689661 DOI: 10.1016/j.jmb.2011.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 06/02/2011] [Accepted: 06/04/2011] [Indexed: 11/30/2022]
Abstract
Protein engineering is becoming increasingly important for pharmaceutical applications where controlling the specificity and affinity of engineered proteins is required to create targeted protein therapeutics. Affinity increases of several thousand-fold are now routine for a variety of protein engineering approaches, and the structural and energetic bases of affinity maturation have been investigated in a number of such cases. Previously, a 3-million-fold affinity maturation process was achieved in a protein-protein interaction composed of a variant T-cell receptor fragment and a bacterial superantigen. Here, we present the molecular basis of this affinity increase. Using X-ray crystallography, shotgun reversion/replacement scanning mutagenesis, and computational analysis, we describe, in molecular detail, a process by which extrainterfacial regions of a protein complex can be rationally manipulated to significantly improve protein engineering outcomes.
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Affiliation(s)
- Daniel A Bonsor
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472, USA
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39
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Johnston MA, Søndergaard CR, Nielsen JE. Integrated prediction of the effect of mutations on multiple protein characteristics. Proteins 2011; 79:165-78. [PMID: 21058401 DOI: 10.1002/prot.22870] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Site-directed mutagenesis is routinely used in modern biology to elucidate the functional or biophysical roles of protein residues, and plays an important role in the field of rational protein design. Over the past decade, a number of computational tools have been developed that can predict the effect of point mutations on a protein's biophysical characteristics. However, these programs usually provide predictions for only a single characteristic. Furthermore, online versions of these tools are often impractical to use for examination of large and diverse sets of mutants. We have created a new web application, (http://enzyme.ucd.ie/PEAT_SA), that can simultaneously predict the effect of mutations on stability, ligand affinity and pK(a) values. PEAT-SA also provides an expanded feature-set with respect to other online tools which includes the ability to obtain predictions for multiple mutants in one submission. As a result, researchers who use site-directed mutagenesis can access state-of-the-art protein design methods with a fraction of the effort previously required. The results of benchmarking PEAT-SA on standard test-sets demonstrate that its accuracy for all three prediction types compares well to currently available tools. We illustrate PEAT-SA's potential by using it to investigate the influence of mutations on the activity of Subtilisin BPN'. This example demonstrates how the ability to obtain a wide range of information from one source, that can be combined to obtain deeper insight into the influence of mutations, makes PEAT-SA a valuable service to both experimental and computational biologists.
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Affiliation(s)
- Michael A Johnston
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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40
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Bonsor DA, Sundberg EJ. Dissecting protein-protein interactions using directed evolution. Biochemistry 2011; 50:2394-402. [PMID: 21332192 DOI: 10.1021/bi102019c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions are essential for life. They are responsible for most cellular functions and when they go awry often lead to disease. Proteins are inherently complex. They are flexible macromolecules whose constituent amino acid components act in combinatorial and networked ways when they engage one another in binding interactions. It is just this complexity that allows them to conduct such a broad array of biological functions. Despite decades of intense study of the molecular basis of protein-protein interactions, key gaps in our understanding remain, hindering our ability to accurately predict the specificities and affinities of their interactions. Until recently, most protein-protein investigations have been probed experimentally at the single-amino acid level, making them, by definition, incapable of capturing the combinatorial nature of, and networked communications between, the numerous residues within and outside of the protein-protein interface. This aspect of protein-protein interactions, however, is emerging as a major driving force for protein affinity and specificity. Understanding a combinatorial process necessarily requires a combinatorial experimental tool. Much like the organisms in which they reside, proteins naturally evolve over time, through a combinatorial process of mutagenesis and selection, to functionally associate. Elucidating the process by which proteins have evolved may be one of the keys to deciphering the molecular rules that govern their interactions with one another. Directed evolution is a technique performed in the laboratory that mimics natural evolution on a tractable time scale that has been utilized widely to engineer proteins with novel capabilities, including altered binding properties. In this review, we discuss directed evolution as an emerging tool for dissecting protein-protein interactions.
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Affiliation(s)
- Daniel A Bonsor
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, Massachusetts 02472, United States
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Da Silva GF, Harrison JS, Lai JR. Contribution of light chain residues to high affinity binding in an HIV-1 antibody explored by combinatorial scanning mutagenesis. Biochemistry 2010; 49:5464-72. [PMID: 20518570 DOI: 10.1021/bi100293q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed analysis of factors governing high affinity antibody-antigen interactions yields important insight into molecular recognition and facilitates the design of functional antibody libraries. Here we describe comprehensive mutagenesis of the light chain complementarity determining regions (CDRs) of HIV-1 antibody D5 (which binds its target, "5-Helix", with a reported K(D) of 50 pM). Combinatorial scanning mutagenesis libraries were prepared in which CDR residues on the D5 light chain were varied among WT side chain identity or alanine. Selection of these libraries against 5-Helix and then sequence analysis of the resulting population were used to quantify energetic consequences of mutation from wild-type to alanine (DeltaDeltaG(Ala-WT)) at each position. This analysis revealed several hotspot residues (DeltaDeltaG(Ala-WT) >or= 1 kcal/mol) that formed combining site features critical to the affinity of the interaction. Tolerance of D5 light chain residues to alternative mutations was explored with a second library. We found that light chain residues located at the center and at the periphery of the D5 combining site contribute to shape complementarity and electrostatic characteristics. Thus, the affinity of D5 for 5-Helix arises from extended interactions involving both the heavy and light chains of D5. These results provide significant insight for future antibody engineering efforts.
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Affiliation(s)
- Gustavo F Da Silva
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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42
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Wilkinson IC, Hall CJ, Veverka V, Shi JY, Muskett FW, Stephens PE, Taylor RJ, Henry AJ, Carr MD. High resolution NMR-based model for the structure of a scFv-IL-1beta complex: potential for NMR as a key tool in therapeutic antibody design and development. J Biol Chem 2009; 284:31928-35. [PMID: 19776018 DOI: 10.1074/jbc.m109.025304] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Monoclonal antibodies have recently started to deliver on their promise as highly specific and active drugs; however, a more effective, knowledge-based approach to the selection, design, and optimization of potential therapeutic antibodies is currently limited by the surprising lack of detailed structural information for complexes formed with target proteins. Here we show that complexes formed with minimal antigen binding single chain variable fragments (scFv) reliably reflect all the features of the binding interface present in larger Fab fragments, which are commonly used as therapeutics, and report the development of a robust, reliable, and relatively rapid approach to the determination of high resolution models for scFv-target protein complexes. This NMR spectroscopy-based approach combines experimental determination of the interaction surfaces and relative orientations of the scFv and target protein, with NMR restraint-driven, semiflexible docking of the proteins to produce a reliable and highly informative model of the complex. Experience with scFvs and Fabs targeted at a number of secreted regulatory proteins suggests that the approach will be applicable to many therapeutic antibodies targeted at proteins, and its application is illustrated for a potential therapeutic antibody targeted at the cytokine IL-1beta. The detailed structural information that can be obtained by this approach has the potential to have a major impact on the rational design and development of an increasingly important class of biological pharmaceuticals.
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Affiliation(s)
- Ian C Wilkinson
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
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43
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Lee EF, Fedorova A, Zobel K, Boyle MJ, Yang H, Perugini MA, Colman PM, Huang DCS, Deshayes K, Fairlie WD. Novel Bcl-2 homology-3 domain-like sequences identified from screening randomized peptide libraries for inhibitors of the pro-survival Bcl-2 proteins. J Biol Chem 2009; 284:31315-26. [PMID: 19748896 DOI: 10.1074/jbc.m109.048009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interactions between Bcl-2 homology-3 (BH3)-only proteins and their pro-survival Bcl-2 family binding partners initiate the intrinsic apoptosis pathway. These interactions are mediated by a short helical motif, the BH3 domain, on the BH3-only protein, which inserts into a hydrophobic groove on the pro-survival molecule. To identify novel peptidic ligands that bind Mcl-1, a pro-survival protein relative of Bcl-2, both human and mouse Mcl-1 were screened against large randomized phage-displayed peptide libraries. We identified a number of 16-mer peptides with sub-micromolar affinity that were highly selective for Mcl-1, as well as being somewhat selective for the species of Mcl-1 (human or mouse) against which the library was panned. Interestingly, these sequences all strongly resembled natural BH3 domain sequences. By switching residues within the best of the human Mcl-1-binding sequences, or extending beyond the core sequence identified, we were able to alter the pro-survival protein interaction profile of this peptide such that it now bound all members tightly and was a potent killer when introduced into cells. Introduction of an amide lock constraint within this sequence also increased its helicity and binding to pro-survival proteins. These data provide new insights into the determinants of BH3 domain:pro-survival protein affinity and selectivity.
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Affiliation(s)
- Erinna F Lee
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, Victoria 3052, Australia
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44
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Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS. Rapid Evolution of Functional Complexity in a Domain Family. Sci Signal 2009; 2:ra50. [DOI: 10.1126/scisignal.2000416] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Improving antibody binding affinity and specificity for therapeutic development. Methods Mol Biol 2009; 525:353-76, xiii. [PMID: 19252851 DOI: 10.1007/978-1-59745-554-1_19] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Affinity maturation is an important part of the therapeutic antibody development process as in vivo activity often requires high binding affinity. Here, we describe a targeted approach for affinity improvement of therapeutic antibodies. Sets of CDR residues that are solvent accessible and relatively diverse in natural antibodies are targeted for diversification. Degenerate oligonucleotides are used to generate combinatorial phage-displayed antibody libraries with varying degree of diversity at randomized positions from which high-affinity antibodies can be selected. An advantage of using antibodies for therapy is their exquisite target specificity, which enables selective antigen binding and reduces off-target effects. However, it can be useful, and often it is necessary, to generate cross-reactive antibodies binding to not only the human antigen but also the corresponding non-human primate or rodent orthologs. Such cross-reactive antibodies can be used to validate the therapeutic targeting and examine the safety profile in preclinical animal models before committing to a costly development track. We show how affinity improvement and cross-species binding can be achieved in a one-step process.
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46
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Abstract
One of the more useful tags for a protein in biochemical experiments is biotin, because of its femtomolar dissociation constant with streptavidin or avidin. Robust methodologies have been developed for other the in vivo addition of a single biotin to recombinant protein or the in vitro enzymatic or chemical addition of biotin to a protein. Such modified proteins can be used in a variety of experiments, such as affinity selection of phage-displayed peptides or antibodies, pull-down of interacting proteins from cell lysates, or displaying proteins on arrays. We present three complementary approaches for biotinylating proteins in vivo in Escherichia coli or in vitro using chemical or enzymatical reactions all of which can be scaled up to tag large numbers of proteins in parallel.
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Schmiedel J, Blaukat A, Li S, Knoechel T, Ferguson KM. Matuzumab binding to EGFR prevents the conformational rearrangement required for dimerization. Cancer Cell 2008; 13:365-73. [PMID: 18394559 PMCID: PMC2725356 DOI: 10.1016/j.ccr.2008.02.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/21/2008] [Accepted: 02/27/2008] [Indexed: 01/07/2023]
Abstract
An increasing number of therapeutic antibodies targeting tumors that express the epidermal growth factor receptor (EGFR) are in clinical use or late stages of clinical development. Here we investigate the molecular basis for inhibition of EGFR activation by the therapeutic antibody matuzumab (EMD72000). We describe the X-ray crystal structure of the Fab fragment of matuzumab (Fab72000) in complex with isolated domain III from the extracellular region of EGFR. Fab72000 interacts with an epitope on EGFR that is distinct from the ligand-binding region on domain III and from the cetuximab/Erbitux epitope. Matuzumab blocks ligand-induced receptor activation indirectly by sterically preventing the domain rearrangement and local conformational changes that must occur for high-affinity ligand binding and receptor dimerization.
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Affiliation(s)
- Judith Schmiedel
- Dept. Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- NCE Lead Discovery Technologies, Merck Serono Research, Merck KGaA, Darmstadt, Germany
| | - Andree Blaukat
- TA Oncology, Merck Serono Research, Merck KGaA, Darmstadt, Germany
| | - Shiqing Li
- Dept. Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Thorsten Knoechel
- NCE Lead Discovery Technologies, Merck Serono Research, Merck KGaA, Darmstadt, Germany
- Address correspondence to either author: Kathryn M. Ferguson, Dept. Physiology, University of Pennsylvania School of Medicine, B400 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104-6085, U.S.A, Phone: (215) 573-1207, Fax: (215) 573-5851, E-mail: . Thorsten Knoechel, NCE Lead Discovery Technologies, Merck Serono Research, Merck KGaA, Frankfurter Strasse 250, D-64293, Darmstadt, Germany., Phone: +49 6151 72 2751, Fax: +49 6151 72 91 2751, E-mail:
| | - Kathryn M. Ferguson
- Dept. Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- Address correspondence to either author: Kathryn M. Ferguson, Dept. Physiology, University of Pennsylvania School of Medicine, B400 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104-6085, U.S.A, Phone: (215) 573-1207, Fax: (215) 573-5851, E-mail: . Thorsten Knoechel, NCE Lead Discovery Technologies, Merck Serono Research, Merck KGaA, Frankfurter Strasse 250, D-64293, Darmstadt, Germany., Phone: +49 6151 72 2751, Fax: +49 6151 72 91 2751, E-mail:
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48
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Birtalan S, Zhang Y, Fellouse FA, Shao L, Schaefer G, Sidhu SS. The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J Mol Biol 2008; 377:1518-28. [PMID: 18336836 DOI: 10.1016/j.jmb.2008.01.093] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 01/28/2008] [Accepted: 01/31/2008] [Indexed: 11/24/2022]
Abstract
Synthetic antibody libraries with restricted chemical diversity were used to explore the intrinsic contributions of four amino acids (Tyr, Ser, Gly and Arg) to the affinity and specificity of antigen recognition. There was no correlation between nonspecific binding and the content of Tyr, Ser or Gly in the antigen-binding site, and in fact, the most specific antibodies were those with the highest Tyr content. In contrast, Arg content was clearly correlated with increased nonspecific binding. We combined Tyr, Ser and Gly to generate highly specific synthetic antibodies with affinities in the subnanomolar range, showing that the high abundance of Tyr, Ser and Gly in natural antibody germ line sequences reflects the intrinsic capacity of these residues to work together to mediate antigen recognition. Despite being a major functional contributor to co-evolved protein-protein interfaces, we find that Arg does not contribute generally to the affinity of naïve antigen-binding sites and is detrimental to specificity. Again, this is consistent with studies of natural antibodies, which have shown that nonspecific, self-reactive antibodies are rich in Arg and other positively charged residues. Our findings suggest that the principles governing naïve molecular recognition differ from those governing co-evolved interactions. Analogous studies can be designed to explore the roles of the other amino acids in molecular recognition. Results of such studies should illuminate the basic principles underlying natural protein-protein interactions and should aid the design of synthetic binding proteins with functions beyond the scope of natural proteins.
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Affiliation(s)
- Sara Birtalan
- Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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49
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Fox RJ, Huisman GW. Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. Trends Biotechnol 2008; 26:132-8. [PMID: 18222559 DOI: 10.1016/j.tibtech.2007.12.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2007] [Revised: 11/30/2007] [Accepted: 12/05/2007] [Indexed: 12/29/2022]
Abstract
Directed evolution is a powerful tool for the creation of commercially useful enzymes, particularly those approaches that are based on in vitro recombination methods, such as DNA shuffling. Although these types of search algorithms are extraordinarily efficient compared with purely random methods, they do not explicitly represent or interrogate the genotype-phenotype relationship and are essentially blind in nature. Recently, however, researchers have begun to apply multivariate statistical techniques to model protein sequence-function relationships and guide the evolutionary process by rapidly identifying beneficial diversity for recombination. In conjunction with state-of-the-art library generation methods, the statistical approach to sequence optimization is now being used routinely to create enzymes efficiently for industrial applications.
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Affiliation(s)
- Richard J Fox
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA.
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50
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Runyon ST, Zhang Y, Appleton BA, Sazinsky SL, Wu P, Pan B, Wiesmann C, Skelton NJ, Sidhu SS. Structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3. Protein Sci 2007; 16:2454-71. [PMID: 17962403 PMCID: PMC2211686 DOI: 10.1110/ps.073049407] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2007] [Revised: 07/20/2007] [Accepted: 07/27/2007] [Indexed: 10/22/2022]
Abstract
High-temperature requirement A (HtrA) and its homologs contain a serine protease domain followed by one or two PDZ domains. Bacterial HtrA proteins and the mitochondrial protein HtrA2/Omi maintain cell function by acting as both molecular chaperones and proteases to manage misfolded proteins. The biological roles of the mammalian family members HtrA1 and HtrA3 are less clear. We report a detailed structural and functional analysis of the PDZ domains of human HtrA1 and HtrA3 using peptide libraries and affinity assays to define specificity, structural studies to view the molecular details of ligand recognition, and alanine scanning mutagenesis to investigate the energetic contributions of individual residues to ligand binding. In common with HtrA2/Omi, we show that the PDZ domains of HtrA1 and HtrA3 recognize hydrophobic polypeptides, and while C-terminal sequences are preferred, internal sequences are also recognized. However, the details of the interactions differ, as different domains rely on interactions with different residues within the ligand to achieve high affinity binding. The results suggest that mammalian HtrA PDZ domains interact with a broad range of hydrophobic binding partners. This promiscuous specificity resembles that of bacterial HtrA family members and suggests a similar function for recognizing misfolded polypeptides with exposed hydrophobic sequences. Our results support a common activation mechanism for the HtrA family, whereby hydrophobic peptides bind to the PDZ domain and induce conformational changes that activate the protease. Such a mechanism is well suited to proteases evolved for the recognition and degradation of misfolded proteins.
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Affiliation(s)
- Steven T Runyon
- Department of Medicinal Chemistry, Genetech, Inc., South San Francisco, CA 94080, USA
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