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Li D, Pucci F, Rooman M. Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks. Int J Mol Sci 2024; 25:5434. [PMID: 38791470 PMCID: PMC11121317 DOI: 10.3390/ijms25105434] [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: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope-epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope-epitope images derived from experimental structures of antibody-antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody-antigen docking poses.
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Affiliation(s)
- Dong Li
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium; (D.L.); (F.P.)
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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2
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Patel R, Verma P, Nagraj AK, Gavade A, Sharma OP, Patil J. Significance of antibody numbering systems in the development of antibody engineering. Hum Antibodies 2023; 31:71-80. [PMID: 38217590 DOI: 10.3233/hab-230014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Immunotherapy has become increasingly popular in recent years for treating a variety of diseases including inflammatory, neurological, oncological, and auto-immune disorders. The significant interest in antibody development is due to the high binding affinity and specificity of an antibody against a specific antigen. Recent advances in antibody engineering have provided a different view on how to engineer antibodies in silico for therapeutic and diagnostic applications. In order to improve the clinical utility of therapeutic antibodies, it is of paramount importance to understand the various molecular properties which impact antigen targeting and its potency. In antibody engineering, antibody numbering (AbN) systems play an important role to identify the complementarity determining regions (CDRs) and the framework regions (FR). Hence, it is crucial to accurately define and understand the CDR, FR and the crucial residues of heavy and light chains that aid in the binding of the antibody to the antigenic site. Detailed understanding of amino acids positions are useful for modifying the binding affinity, specificity, physicochemical features, and half-life of an antibody. In this review, we have summarized the different antibody numbering systems that are widely used in antibody engineering and highlighted their significance. Here, we have systematically explored and mentioned the various tools and servers that harness different AbN systems.
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Affiliation(s)
- Riya Patel
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | - Pratibha Verma
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | | | - Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
| | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, Pune, Maharashtra, India
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3
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Peng HP, Yang AS. Computational Analysis of Antibody Paratopes for Antibody Sequences in Antibody Libraries. Methods Mol Biol 2023; 2552:437-445. [PMID: 36346607 DOI: 10.1007/978-1-0716-2609-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To ensure the functionalities of the antibodies in phage-displayed synthetic antibody libraries, we use computational method to evaluate the designs of the antibody libraries. The computational methodologies developed in our lab for designing antibody library provide rich information on the function of the designed antibody sequences-adequate antibody designs for a specific antigen type should have predicted paratopes for the antigen type. This computational assessment of the designed antibody sequences helps eliminate non-functional designs before proceeding to construct the library designs in the wet lab. As such, only reasonable antibody designs are constructed for antibody discoveries.
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Affiliation(s)
- Hung-Pin Peng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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4
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Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens. Sci Rep 2022; 12:12555. [PMID: 35869245 PMCID: PMC9307644 DOI: 10.1038/s41598-022-16841-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies recognize protein antigens with exquisite specificity in a complex aqueous environment, where interfacial waters are an integral part of the antibody–protein complex interfaces. In this work, we elucidate, with computational analyses, the principles governing the antibodies’ specificity and affinity towards their cognate protein antigens in the presence of explicit interfacial waters. Experimentally, in four model antibody–protein complexes, we compared the contributions of the interaction types in antibody–protein antigen complex interfaces with the antibody variants selected from phage-displayed synthetic antibody libraries. Evidently, the specific interactions involving a subset of aromatic CDR (complementarity determining region) residues largely form the predominant determinant underlying the specificity of the antibody–protein complexes in nature. The interfacial direct/water-mediated hydrogen bonds accompanying the CDR aromatic interactions are optimized locally but contribute little in determining the epitope location. The results provide insights into the phenomenon that natural antibodies with limited sequence and structural variations in an antibody repertoire can recognize seemingly unlimited protein antigens. Our work suggests guidelines in designing functional artificial antibody repertoires with practical applications in developing novel antibody-based therapeutics and diagnostics for treating and preventing human diseases.
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Gutiérrez LJ, Tosso RD, Zarycz MNC, Enriz RD, Baldoni HA. Epitopes mapped onto SARS-CoV-2 receptor-binding motif by five distinct human neutralising antibodies. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Lucas J. Gutiérrez
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Rodrigo D. Tosso
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - M. Natalia C. Zarycz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
| | - Ricardo D. Enriz
- Multidisciplinary Institute of Biological Research (IMIBIO-SL. CONICET), San Luis, Argentina
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
| | - Héctor A. Baldoni
- Faculty of Chemistry, Biochemistry and Pharmacy, National University of San Luis, San Luis, Argentina
- Institute of Applied Mathematics of San Luis (IMASL. CONICET), San Luis, Argentina
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6
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Maruthachalam BV, Barreto K, Hogan D, Kusalik A, Geyer CR. Generation of synthetic antibody fragments with optimal complementarity determining region lengths for Notch-1 recognition. Front Microbiol 2022; 13:931307. [PMID: 35992693 PMCID: PMC9381698 DOI: 10.3389/fmicb.2022.931307] [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: 04/28/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Synthetic antibodies have been engineered against a wide variety of antigens with desirable biophysical, biochemical, and pharmacological properties. Here, we describe the generation and characterization of synthetic antigen-binding fragments (Fabs) against Notch-1. Three single-framework synthetic Fab libraries, named S, F, and modified-F, were screened against the recombinant human Notch-1 extracellular domain using phage display. These libraries were built on a modified trastuzumab framework, containing two or four diversified complementarity-determining regions (CDRs) and different CDR diversity designs. In total, 12 Notch-1 Fabs were generated with 10 different CDRH3 lengths. These Fabs possessed a high affinity for Notch-1 (sub-nM to mid-nM KDapp values) and exhibited different binding profiles (mono-, bi-or tri-specific) toward Notch/Jagged receptors. Importantly, we showed that screening focused diversity libraries, implementing next-generation sequencing approaches, and fine-tuning the CDR length diversity provided improved binding solutions for Notch-1 recognition. These findings have implications for antibody library design and antibody phage display.
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Affiliation(s)
| | - Kris Barreto
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Clarence Ronald Geyer
- Department of Pathology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Clarence Ronald Geyer,
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A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile. Int J Mol Sci 2022; 23:ijms23116255. [PMID: 35682935 PMCID: PMC9181208 DOI: 10.3390/ijms23116255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries.
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8
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Forinová M, Pilipenco A, Víšová I, Lynn NS, Dostálek J, Mašková H, Hönig V, Palus M, Selinger M, Kočová P, Dyčka F, Štěrba J, Houska M, Vrabcová M, Horák P, Anthi J, Tung CP, Yu CM, Chen CY, Huang YC, Tsai PH, Lin SY, Hsu HJ, Yang AS, Dejneka A, Vaisocherová-Lísalová H. Functionalized Terpolymer-Brush-Based Biointerface with Improved Antifouling Properties for Ultra-Sensitive Direct Detection of Virus in Crude Clinical Samples. ACS APPLIED MATERIALS & INTERFACES 2021; 13:60612-60624. [PMID: 34902239 DOI: 10.1021/acsami.1c16930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
New analytical techniques that overcome major drawbacks of current routinely used viral infection diagnosis methods, i.e., the long analysis time and laboriousness of real-time reverse-transcription polymerase chain reaction (qRT-PCR) and the insufficient sensitivity of "antigen tests", are urgently needed in the context of SARS-CoV-2 and other highly contagious viruses. Here, we report on an antifouling terpolymer-brush biointerface that enables the rapid and sensitive detection of SARS-CoV-2 in untreated clinical samples. The developed biointerface carries a tailored composition of zwitterionic and non-ionic moieties and allows for the significant improvement of antifouling capabilities when postmodified with biorecognition elements and exposed to complex media. When deployed on a surface of piezoelectric sensor and postmodified with human-cell-expressed antibodies specific to the nucleocapsid (N) protein of SARS-CoV-2, it made possible the quantitative analysis of untreated samples by a direct detection assay format without the need of additional amplification steps. Natively occurring N-protein-vRNA complexes, usually disrupted during the sample pre-treatment steps, were detected in the untreated clinical samples. This biosensor design improved the bioassay sensitivity to a clinically relevant limit of detection of 1.3 × 104 PFU/mL within a detection time of only 20 min. The high specificity toward N-protein-vRNA complexes was validated both by mass spectrometry and qRT-PCR. The performance characteristics were confirmed by qRT-PCR through a comparative study using a set of clinical nasopharyngeal swab samples. We further demonstrate the extraordinary fouling resistance of this biointerface through exposure to other commonly used crude biological samples (including blood plasma, oropharyngeal, stool, and nasopharyngeal swabs), measured via both the surface plasmon resonance and piezoelectric measurements, which highlights the potential to serve as a generic platform for a wide range of biosensing applications.
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Affiliation(s)
- Michala Forinová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Alina Pilipenco
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Ivana Víšová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - N Scott Lynn
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Jakub Dostálek
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
- Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Hana Mašková
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Václav Hönig
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Pavlína Kočová
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Filip Dyčka
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Jan Štěrba
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Milan Houska
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Markéta Vrabcová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Petr Horák
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Judita Anthi
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Chi-Yung Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Yu-Chuan Huang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Pei-Hsun Tsai
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Szu-Yu Lin
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
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Hsu HJ, Tung CP, Yu CM, Chen CY, Chen HS, Huang YC, Tsai PH, Lin SI, Peng HP, Chiu YK, Tsou YL, Kuo WY, Jian JW, Hung FH, Hsieh CY, Hsiao M, Chuang SSH, Shen CN, Wang YA, Yang AS. Eradicating mesothelin-positive human gastric and pancreatic tumors in xenograft models with optimized anti-mesothelin antibody-drug conjugates from synthetic antibody libraries. Sci Rep 2021; 11:15430. [PMID: 34326410 PMCID: PMC8322431 DOI: 10.1038/s41598-021-94902-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023] Open
Abstract
Mesothelin (MSLN) is an attractive candidate of targeted therapy for several cancers, and hence there are increasing needs to develop MSLN-targeting strategies for cancer therapeutics. Antibody–drug conjugates (ADCs) targeting MSLN have been demonstrated to be a viable strategy in treating MSLN-positive cancers. However, developing antibodies as targeting modules in ADCs for toxic payload delivery to the tumor site but not to normal tissues is not a straightforward task with many potential hurdles. In this work, we established a high throughput engineering platform to develop and optimize anti-MSLN ADCs by characterizing more than 300 scFv CDR-variants and more than 50 IgG CDR-variants of a parent anti-MSLN antibody as candidates for ADCs. The results indicate that only a small portion of the complementarity determining region (CDR) residues are indispensable in the MSLN-specific targeting. Also, the enhancement of the hydrophilicity of the rest of the CDR residues could drastically increase the overall solubility of the optimized anti-MSLN antibodies, and thus substantially improve the efficacies of the ADCs in treating human gastric and pancreatic tumor xenograft models in mice. We demonstrated that the in vivo treatments with the optimized ADCs resulted in almost complete eradication of the xenograft tumors at the treatment endpoints, without detectable off-target toxicity because of the ADCs’ high specificity targeting the cell surface tumor-associated MSLN. The technological platform can be applied to optimize the antibody sequences for more effective targeting modules of ADCs, even when the candidate antibodies are not necessarily feasible for the ADC development due to the antibodies’ inferior solubility or affinity/specificity to the target antigen.
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Affiliation(s)
- Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chi-Yung Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Hong-Sen Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yu-Chuan Huang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Pei-Hsun Tsai
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Su-I Lin
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Hung-Pin Peng
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yi-Kai Chiu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Yueh-Liang Tsou
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Wei-Ying Kuo
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Jhih-Wei Jian
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Fei-Hung Hung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Chiao-Yun Hsieh
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | | | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan
| | | | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang Dist., Taipei, 115, Taiwan.
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10
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Bélanger K, Tanha J. High-efficacy, high-manufacturability human VH domain antibody therapeutics from transgenic sources. Protein Eng Des Sel 2021; 34:6276122. [PMID: 33991089 DOI: 10.1093/protein/gzab012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 11/14/2022] Open
Abstract
Interest in single-domain antibodies (sdAbs) stems from their unique structural/pronounced, hence therapeutically desirable, features. From the outset-as therapeutic modalities-human antibody heavy chain variable domains (VHs) attracted a particular attention compared with 'naturally-occurring' camelid and shark heavy-chain-only antibody variable domains (VHHs and VNARs, respectively) due to their perceived lack of immunogenicity. However, they have not quite lived up to their initial promise as the VH hits, primarily mined from synthetic VH phage display libraries, have too often been plagued with aggregation tendencies, low solubility and low affinity. Largely unexplored, synthetic camelized human VH display libraries appeared to have remediated the aggregation problem, but the low affinity of the VH hits still persisted, requiring undertaking additional, laborious affinity maturation steps to render VHs therapeutically feasible. A wholesome resolution has recently emerged with the development of non-canonical transgenic rodent antibody discovery platforms that appear to facilely and profusely generate high affinity, high solubility and aggregation-resistant human VHs.
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Affiliation(s)
- Kasandra Bélanger
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Jamshid Tanha
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada.,Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
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11
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Brockmann EC, Pyykkö M, Hannula H, Khan K, Lamminmäki U, Huovinen T. Combinatorial mutagenesis with alternative CDR-L1 and -H2 loop lengths contributes to affinity maturation of antibodies. N Biotechnol 2020; 60:173-182. [PMID: 33039698 DOI: 10.1016/j.nbt.2020.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/17/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
Loop length variation in the complementary determining regions (CDRs) 1 and 2 encoded in germline variable antibody genes provides structural diversity in naïve antibody libraries. In synthetic single framework libraries the parental CDR-1 and CDR-2 length is typically unchanged and alternative lengths are provided only at CDR-3 sites. Based on an analysis of the germline repertoire and structure-solved anti-hapten and anti-peptide antibodies, we introduced combinatorial diversity with alternative loop lengths into the CDR-L1, CDR-L3 and CDR-H2 loops of anti-digoxigenin and anti-microcystin-LR single chain Fv fragments (scFvs) sharing human IGKV3-20/IGHV3-23 frameworks. The libraries were phage display selected for folding and affinity, and analysed by single clone screening and deep sequencing. Among microcystin-LR binders the most frequently encountered alternative loop lengths were one amino acid shorter (6 aa) and four amino acids longer (11 aa) CDR-L1 loops leading up to 17- and 28-fold improved affinity, respectively. Among digoxigenin binders, 2 amino acids longer (10 aa) CDR-H2 loops were strongly enriched, but affinity improved anti-digoxigenin scFvs were also encountered with 7 aa CDR-H2 and 11 aa CDR-L1 loops. Despite the fact that CDR-L3 loop length variants were not specifically enriched in selections, one clone with 22-fold improved digoxigenin binding affinity was identified containing a 2 residues longer (10 aa) CDR-L3 loop. Based on our results the IGKV3-20/IGHV3-23 scaffold tolerates loop length variation, particularly in CDR-L1 and CDR-H2 loops, without compromising antibody stability, laying the foundation for developing novel synthetic antibody libraries with loop length combinations not existing in the natural human Ig gene repertoire.
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Affiliation(s)
| | - Mikko Pyykkö
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Heidi Hannula
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland; Current Affiliation: Microelectronics Research Unit, Faculty of Information Technology and Electrical Engineering, University of Oulu, Finland
| | - Kamran Khan
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Urpo Lamminmäki
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland
| | - Tuomas Huovinen
- University of Turku, Department of Biochemistry/Biotechnology, Turku, Finland.
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A panel of anti-influenza virus nucleoprotein antibodies selected from phage-displayed synthetic antibody libraries with rapid diagnostic capability to distinguish diverse influenza virus subtypes. Sci Rep 2020; 10:13318. [PMID: 32770098 PMCID: PMC7414213 DOI: 10.1038/s41598-020-70135-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Immunoassays based on sandwich immuno-complexes of capture and detection antibodies simultaneously binding to the target analytes have been powerful technologies in molecular analyses. Recent developments in single molecule detection technologies enable the detection limit of the sandwich immunoassays approaching femtomolar (10-15 M), driving the needs of developing sensitive and specific antibodies for ever-increasingly broad applications in detecting and quantifying biomarkers. The key components underlying the sandwich immunoassays are antibody-based affinity reagents, for which the conventional sources are mono- or poly-clonal antibodies from immunized animals. The downsides of the animal-based antibodies as affinity reagents arise from the requirement of months of development timespan and limited choices of antibody candidates due to immunodominance of humoral immune responses in animals. Hence, developing animal antibodies capable of distinguishing highly related antigens could be challenging. To overcome the limitation imposed by the animal immune systems, we developed an in vitro methodology based on phage-displayed synthetic antibody libraries for diverse antibodies as affinity reagents against closely related influenza virus nucleoprotein (NP) subtypes, aiming to differentiating avian influenza virus (H5N1) from seasonal influenza viruses (H1N1 and H3N2), for which the NPs are closely related by 90-94% in terms of pairwise amino acid sequence identity. We applied the methodology to attain, within four weeks, a panel of IgGs with distinguishable specificities against a group of representative NPs with pairwise amino acid sequence identities up to more than 90%, and the antibodies derived from the antibody libraries without further affinity refinement had comparable affinity of mouse antibodies to the NPs with the detection limit less than 1 nM of viral NP from lysed virus with sandwich ELISA. The panel of IgGs were capable of rapidly distinguishing infections due to virulent avian influenza virus from infections of seasonal flu, in responding to a probable emergency scenario where avian influenza virus would be transmissible among humans overlapping with the seasonal influenza infections. The results indicate that the in vitro antibody development methodology enables developing diagnostic antibodies that would not otherwise be available from animal-based antibody technologies.
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