1
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Sawant MS, Streu CN, Wu L, Tessier PM. Toward Drug-Like Multispecific Antibodies by Design. Int J Mol Sci 2020; 21:E7496. [PMID: 33053650 PMCID: PMC7589779 DOI: 10.3390/ijms21207496] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The success of antibody therapeutics is strongly influenced by their multifunctional nature that couples antigen recognition mediated by their variable regions with effector functions and half-life extension mediated by a subset of their constant regions. Nevertheless, the monospecific IgG format is not optimal for many therapeutic applications, and this has led to the design of a vast number of unique multispecific antibody formats that enable targeting of multiple antigens or multiple epitopes on the same antigen. Despite the diversity of these formats, a common challenge in generating multispecific antibodies is that they display suboptimal physical and chemical properties relative to conventional IgGs and are more difficult to develop into therapeutics. Here we review advances in the design and engineering of multispecific antibodies with drug-like properties, including favorable stability, solubility, viscosity, specificity and pharmacokinetic properties. We also highlight emerging experimental and computational methods for improving the next generation of multispecific antibodies, as well as their constituent antibody fragments, with natural IgG-like properties. Finally, we identify several outstanding challenges that need to be addressed to increase the success of multispecific antibodies in the clinic.
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Affiliation(s)
- Manali S. Sawant
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Craig N. Streu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemistry, Albion College, Albion, MI 49224, USA
| | - Lina Wu
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; (M.S.S.); (C.N.S.)
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Sankaran S, de Ruiter M, Cornelissen JJLM, Jonkheijm P. Supramolecular Surface Immobilization of Knottin Derivatives for Dynamic Display of High Affinity Binders. Bioconjug Chem 2015; 26:1972-80. [PMID: 26270829 DOI: 10.1021/acs.bioconjchem.5b00419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Knottins are known as a robust and versatile class of miniprotein scaffolds for the presentation of high-affinity binding peptides; however, to date their application in biomaterials, biological coatings, and surface applications have not been explored. We have developed a strategy to recombinantly synthesize a β-trypsin inhibitory knottin with supramolecular guest tags that enable it to adhere to self-assembled monolayers of the supramolecular host cucurbit[8]uril (CB[8]). We have described a strategy to easily express knottins in E. coli by conjugating them to a fluorescent protein after which they are cleaved and purified. Knottin constructs that varied in the number and position of the supramolecular tag at either the N- or C-termini or at both ends have been verified for their trypsin inhibitory function and CB[8]-binding properties in solution and on surfaces. All of the knottin constructs showed strong inhibition of trypsin with inhibition constants between 10 and 30 nM. Using microscale thermophoresis, we determined that the supramolecular guest tags on the knottins bind CB[8] with a Kd of ∼6 μM in solution. At the surface, strong divalent binding has been determined with a Kd of 0.75 μM in the case of the knottin with two supramolecular guest tags, whereas only weak monovalent binding occurred when only one guest tag was present. We also show successful supramolecular surface immobilization of the knottin using CB[8] and prove that they can be used to immobilize β-trypsin at the surface.
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Affiliation(s)
- Shrikrishnan Sankaran
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
| | | | | | - Pascal Jonkheijm
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7500 AE Enschede, The Netherlands
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3
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Sun H, Wu GM, Chen YY, Tian Y, Yue YH, Zhang GL. Expression, production, and renaturation of a functional single-chain variable antibody fragment (scFv) against human ICAM-1. ACTA ACUST UNITED AC 2014; 47:540-7. [PMID: 24919171 PMCID: PMC4123832 DOI: 10.1590/1414-431x20143276] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 02/27/2014] [Indexed: 11/22/2022]
Abstract
Intercellular adhesion molecule-1 (ICAM-1) is an important factor in the progression
of inflammatory responses in vivo. To develop a new
anti-inflammatory drug to block the biological activity of ICAM-1, we produced a
monoclonal antibody (Ka=4.19×10−8 M) against human
ICAM-1. The anti-ICAM-1 single-chain variable antibody fragment (scFv) was expressed
at a high level as inclusion bodies in Escherichia coli. We refolded
the scFv (Ka=2.35×10−7 M) by ion-exchange chromatography,
dialysis, and dilution. The results showed that column chromatography refolding by
high-performance Q Sepharose had remarkable advantages over conventional dilution and
dialysis methods. Furthermore, the anti-ICAM-1 scFv yield of about 60 mg/L was higher
with this method. The purity of the final product was greater than 90%, as shown by
denaturing gel electrophoresis. Enzyme-linked immunosorbent assay, cell culture, and
animal experiments were used to assess the immunological properties and biological
activities of the renatured scFv.
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Affiliation(s)
- H Sun
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - G M Wu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Y Y Chen
- Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Y Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Y H Yue
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - G L Zhang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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4
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Hsu HJ, Lee KH, Jian JW, Chang HJ, Yu CM, Lee YC, Chen IC, Peng HP, Wu CY, Huang YF, Shao CY, Chiu KP, Yang AS. Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments. Structure 2013; 22:22-34. [PMID: 24268647 DOI: 10.1016/j.str.2013.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/03/2013] [Accepted: 10/01/2013] [Indexed: 01/21/2023]
Abstract
Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and assessing the consequences of all the variations. In this work, groups of β strand residues of model antibody variable domains were randomized with saturated mutagenesis and the functional variants were selected for high-throughput sequencing and high-throughput thermal stability measurements. The results show that the sequence preferences of the intradomain hydrophobic core residues are strikingly flexible among hydrophobic residues, implying that these residues are coupled indirectly with antigen binding through energetic stabilization of the protein structures. By contrast, the interdomain interface residues are directly coupled with antigen binding. The interdomain interface should be treated as an integral part of the antigen-binding site.
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Affiliation(s)
- Hung-Ju Hsu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Kuo Hao Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Science, National Taiwan University, Taipei 106, Taiwan; Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program at Academia Sinica, Taipei 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chih Yuan Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Yun Shao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Kuo Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
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5
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Chang HJ, Jian JW, Hsu HJ, Lee YC, Chen HS, You JJ, Hou SC, Shao CY, Chen YJ, Chiu KP, Peng HP, Lee KH, Yang AS. Loop-sequence features and stability determinants in antibody variable domains by high-throughput experiments. Structure 2013; 22:9-21. [PMID: 24268648 DOI: 10.1016/j.str.2013.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/11/2013] [Accepted: 10/12/2013] [Indexed: 12/24/2022]
Abstract
Protein loops are frequently considered as critical determinants in protein structure and function. Recent advances in high-throughput methods for DNA sequencing and thermal stability measurement have enabled effective exploration of sequence-structure-function relationships in local protein regions. Using these data-intensive technologies, we investigated the sequence-structure-function relationships of six complementarity-determining regions (CDRs) and ten non-CDR loops in the variable domains of a model vascular endothelial growth factor (VEGF)-binding single-chain antibody variable fragment (scFv) whose sequence had been optimized via a consensus-sequence approach. The results show that only a handful of residues involving long-range tertiary interactions distant from the antigen-binding site are strongly coupled with antigen binding. This implies that the loops are passive regions in protein folding; the essential sequences of these regions are dictated by conserved tertiary interactions and the consensus local loop-sequence features contribute little to protein stability and function.
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Affiliation(s)
- Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hong-Sen Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Jhong-Jhe You
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Shin-Chen Hou
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Yun Shao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Zoology, College of Life Sciences, National Taiwan University, Taipei 106, Taiwan
| | - Yen-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Kuo Hao Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
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6
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Fukunaga A, Tsumoto K. Improving the affinity of an antibody for its antigen via long-range electrostatic interactions. Protein Eng Des Sel 2013; 26:773-80. [DOI: 10.1093/protein/gzt053] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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7
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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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8
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Weatherill EE, Cain KL, Heywood SP, Compson JE, Heads JT, Adams R, Humphreys DP. Towards a universal disulphide stabilised single chain Fv format: importance of interchain disulphide bond location and vL-vH orientation. Protein Eng Des Sel 2012; 25:321-9. [PMID: 22586154 DOI: 10.1093/protein/gzs021] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Engineered introduction of interface interchain disulphide bonds is perceived to be a simple method to increase the stability of single chain Fv (scFv). Six disulphide bond locations have been cited within the literature but the potential for the broad use of each has not been examined. Five of these disulphide bond locations were introduced into one scFv in order to compare their relative effects on expression, thermal stability, percent monomer formation and retention of antigen binding. The disulphide bond position vH44-vL100 was observed to enable the most favourable balance of biophysical properties. The vH44-vL100 disulphide bond was introduced into five additional scFv in both vL-vH and vH-vL orientations in order to investigate its general applicability. Data are presented to show the relative influence of scFv sequence, v-region organisation and interchain disulphide bond on expression yield, thermal stability and percent monomer. Introduction of the vH44-vL100 disulphide bond typically resulted in no or little increase in thermal stability and no change in percent monomer but did confer the benefit of permanently fixing monomer:dimer ratios during purification and analysis.
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Affiliation(s)
- Eve E Weatherill
- Protein Expression and Purification Group, UCB, Slough, Berkshire SL1 3WE, England
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9
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Antibody phage display libraries: contributions to oncology. Int J Mol Sci 2012; 13:5420-5440. [PMID: 22754305 PMCID: PMC3382779 DOI: 10.3390/ijms13055420] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/05/2012] [Accepted: 04/24/2012] [Indexed: 12/16/2022] Open
Abstract
Since the advent of phage display technology, dating back to 1985, antibody libraries displayed on filamentous phage surfaces have been used to identify specific binders for many different purposes, including the recognition of tumors. Phage display represents a high-throughput technique for screening billions of random fusion antibodies against virtually any target on the surface or inside cancer cells, or even soluble markers found in patient serum. Many phage display derived binders targeting important tumor markers have been identified. Selection directed to tumoral cells’ surfaces lead to the identification of unknown tumoral markers. Also the improvement of methods that require smaller amounts of cells has opened the possibility to use this approach on patient samples. Robust techniques combining an antibody library displayed on the phage surface and protein microarray allowed the identification of auto antibodies recognized by patient sera. Many Ab molecules directly or indirectly targeting angiogenesis have been identified, and one of them, ramucirumab, has been tested in 27 phase I–III clinical trials in a broad array of cancers. Examples of such antibodies will be discussed here with emphasis on those used as probes for molecular imaging and other clinical trials.
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10
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Yu CM, Peng HP, Chen IC, Lee YC, Chen JB, Tsai KC, Chen CT, Chang JY, Yang EW, Hsu PC, Jian JW, Hsu HJ, Chang HJ, Hsu WL, Huang KF, Ma AC, Yang AS. Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface. PLoS One 2012; 7:e33340. [PMID: 22457753 PMCID: PMC3310866 DOI: 10.1371/journal.pone.0033340] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 02/14/2012] [Indexed: 12/01/2022] Open
Abstract
Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes.
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Affiliation(s)
- Chung-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Ing-Chien Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jun-Bo Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Department of Computer Science, National Tsing-Hua University, Hsinchu, Taiwan
| | | | - Ching-Tai Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Systems Biology, National Chiao-Tung University, Hsinchu, Taiwan
- Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Jeng-Yih Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Ei-Wen Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
| | - Po-Chiang Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Life Sciences, National Defense University, Taipei, Taiwan
| | - Hung-Ju Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Sciences, Academia Sinica, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Alex Che Ma
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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11
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Lee YC, Chen IC, Yu CM, Huang YJ, Hsu HJ, Yang AS. Effects of signal sequence on phage-displayed disulfide-stabilized single chain antibody variable fragment (sc-dsFv) libraries. Biochem Biophys Res Commun 2011; 411:348-353. [PMID: 21741355 DOI: 10.1016/j.bbrc.2011.06.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 06/22/2011] [Indexed: 05/31/2023]
Abstract
Phage-displayed single chain variable fragment (scFv) libraries are powerful tools in antibody engineering. Disulfide-stabilized scFv (sc-dsFv) with an interface disulfide bond is structure-wise more stable than the corresponding scFv. A set of recently discovered signal sequences replacing the wild type (pelB) signal peptidase cleavage site in the c-region has been shown to be effective in rescuing the expression of sc-dsFv libraries on the phage surface. However, the effects of the other regions of the signal sequence on the expression of the sc-dsFv libraries and on the formation of the interface disulfide bond in the phage-displayed sc-dsFv have not been clear. In this work, selected novel signal sequence variants in the h-region were shown to be equally effective in promoting sc-dsFv library expression on the phage surface; the expression level and complexity of the sc-dsFv libraries were comparable to the corresponding scFv libraries produced with the wild-type (pelB) signal sequence. The interface disulfide bond in the phage-displayed sc-dsFv was proven to form to a large extent in the library variant ensemble generated with signal sequence variants in both the h-region and the c-region. The sc-dsFv engineering platform established in this work can be applied to many of the known scFv molecules which are in need of a more stable version for the applications under harsh conditions or for longer shelf-life.
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Affiliation(s)
- Yu-Ching Lee
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC
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12
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Wang T, Duan Y. Probing the stability-limiting regions of an antibody single-chain variable fragment: a molecular dynamics simulation study. Protein Eng Des Sel 2011; 24:649-57. [PMID: 21729946 DOI: 10.1093/protein/gzr029] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antibody single-chain variable fragments (scFvs) offer particular advantages over the full-size antibodies, including easy expression, efficient local concentration and fast body clearance. However, scFvs typically show low thermal stability that limits their biomedical and biotechnological applications. In this study, we examined the thermal stability of the human and murine vascular endothelial growth factor antibody scFv fragment by molecular dynamics simulations. A consistent observation was the dissociation of the light-chain (VL) and heavy-chain (VH) domains and loss of the native structures of both domains in the simulations at the elevated temperatures. The stability-limiting structural elements in the protein were revealed from the detailed analyses on the native contacts. We found that dissociation of the VL-VH domains was the first event leading to the unfolding of the native structure of the protein and the disruption of the VL-VH interface was largely due to the break of the interfacial hydrophobic and aromatic interactions while the hydrogen-bonding interaction between Gln38 in VL and Gln39 in VH remained. Within the β-barrel structure of the VL and VH domains, β-strands β6, β2 and β11 appeared to be the least stable. In addition, we found that the VH domain was more thermally resistant than the VL domain. Based on these findings, we discussed potential strategies to improve the stability of this therapeutically important scFv fragment.
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Affiliation(s)
- Ting Wang
- Department of Applied Science, University of California, Davis, CA 95616-8816, USA
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13
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Ding G, Chen X, Zhu J, Cao B. Identification of two aberrant transcripts derived from a hybridoma with amplification of functional immunoglobulin variable genes. Cell Mol Immunol 2010; 7:349-54. [PMID: 20657605 DOI: 10.1038/cmi.2010.33] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Murine monoclonal antibodies (mAbs) are widely used but have limitations if administered in humans. The use of chimeric or humanized mAbs can reduce immunogenicity. The first step in producing such mAbs is to clone murine variable genes from a hybridoma, but it is possible to amplify both functional and aberrant variable genes, as they coexist in the hybridoma. During the development of a murine-human chimeric antibody, we have cloned from a hybridoma the functional heavy chain variable region (V(H)) and light chain variable region (V(L)) genes of a mAb that blocks the binding of anthrax lethal factor to protective antigen. In this study, we report the detection of two aberrant transcripts from a hybridoma produced using myeloma cell line OUR-1, the development of a method to distinguish between the functional and abundant aberrant V(L) transcripts, and the origins of these aberrant genes. The aberrant V(L) gene is derived from OUR-1 cells, while the aberrant V(H) gene might derive from antibody repertoires in B cells or from gene rearrangement in the hybridoma cells. The aberrant V(H) and V(L) genes in this study may facilitate discrimination between the functional and aberrant variable genes from hybridoma cells.
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Affiliation(s)
- Guipeng Ding
- Department of Pathology, Nanjing Medical University, Nanjing, China
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Chen IC, Yu CM, Lee YC, Huang YJ, Hsu HJ, Yang AS. Signal sequence as a determinant in expressing disulfide-stabilized single chain antibody variable fragments (sc-dsFv) against human VEGF. MOLECULAR BIOSYSTEMS 2010; 6:1307-15. [PMID: 20424732 DOI: 10.1039/b921106c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Phage-displayed single chain variable fragment (scFv) libraries have been powerful tools in antibody engineering. But the scFv structures are frequently unstable due to the dissociation of the dimeric interface between the two variable domains. One solution is the sc-dsFv construct, where the single chain variable domain fragment is stabilized with an additional interface disulfide bond, leading to stable and homogeneous dimeric interface for the sc-dsFv structure. However, the phagemid system that is capable of effective expression for both sc-dsFv-pIII fusion proteins on phage surface and secreted non-fusion sc-dsFv in bacterial culture medium has not been demonstrated. In this work, a biological combinatorial approach was applied to optimize the signal sequence N-terminal to the sc-dsFv-pIII fusion protein encoded in a phagemid. The optimized sc-dsFv phage display systems were compatible with both the phage-based directed evolution procedure and the high throughput screening of the soluble sc-dsFv. The utility of the phagemid systems was demonstrated in generating anti-VEGF sc-dsFv with VEGF-binding affinity one order of magnitude higher than the corresponding scFv, due only to the interface disulfide bond in the sc-dsFv. Moreover, the protein stability of the sc-dsFv construct was unmatched by the corresponding scFv. These advantages of the sc-dsFv were gained through the interface disulfide bond of the sc-dsFv and the novel signal sequence in the phagemid.
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Affiliation(s)
- Ing-Chien Chen
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2 Taipei, 115 Taiwan, ROC
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