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Thomas B, Chockalingam K, Chen Z. Methods for Engineering Binders to Multi-Pass Membrane Proteins. Bioengineering (Basel) 2023; 10:1351. [PMID: 38135942 PMCID: PMC10741020 DOI: 10.3390/bioengineering10121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/11/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Numerous potential drug targets, including G-protein-coupled receptors and ion channel proteins, reside on the cell surface as multi-pass membrane proteins. Unfortunately, despite advances in engineering technologies, engineering biologics against multi-pass membrane proteins remains a formidable task. In this review, we focus on the different methods used to prepare/present multi-pass transmembrane proteins for engineering target-specific biologics such as antibodies, nanobodies and synthetic scaffold proteins. The engineered biologics exhibit high specificity and affinity, and have broad applications as therapeutics, probes for cell staining and chaperones for promoting protein crystallization. We primarily cover publications on this topic from the past 10 years, with a focus on the different formats of multi-pass transmembrane proteins. Finally, the remaining challenges facing this field and new technologies developed to overcome a number of obstacles are discussed.
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Affiliation(s)
- Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
| | - Zhilei Chen
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77845, USA;
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA;
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2
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Amir A, Taussig D, Bitton A, Nahary L, Vaisman-Mentesh A, Benhar I, Wine Y. Antibody Isolation from Human Synthetic Libraries of Single-Chain Antibodies and Analysis Using NGS. Methods Mol Biol 2023; 2702:347-372. [PMID: 37679629 DOI: 10.1007/978-1-0716-3381-6_18] [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: 09/09/2023]
Abstract
Antibody libraries came into existence 30 years ago when the accumulating sequence data of immunoglobulin genes and the advent of PCR technology made it possible to clone antibody gene repertoires. Phage display (most common) and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. As other antibody discovery tools, phage display is not an off-the-shelf technology and not offered as a kit but rather requires experience and expertise for making it indeed very useful.Next-generation sequencing (NGS) coupled with bioinformatics is a powerful tool for analyzing large amount of DNA sequence output of the panning. Here, we demonstrate how NGS analysis of phage biopanning (phage-Seq) of complex antibody libraries can facilitate the antibody discovery process and provide insights regarding the biopanning process (see Fig. 1).
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Affiliation(s)
- Adi Amir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Limor Nahary
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Itai Benhar
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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3
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Philpott D, Gomis S, Wang H, Atwal R, Kelil A, Sack T, Morningstar B, Burnie C, Sargent EH, Angers S, Sidhu S, Kelley SO. Rapid On-Cell Selection of High-Performance Human Antibodies. ACS CENTRAL SCIENCE 2022; 8:102-109. [PMID: 35106377 PMCID: PMC8796304 DOI: 10.1021/acscentsci.1c01205] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 06/14/2023]
Abstract
Phage display is a critical tool for developing antibodies. However, existing approaches require many time-consuming rounds of biopanning and screening of potential candidates due to a high rate of failure during validation. Herein, we present a rapid on-cell phage display platform which recapitulates the complex in vivo binding environment to produce high-performance human antibodies in a short amount of time. Selection is performed in a highly stringent heterogeneous mixture of cells to quickly remove nonspecific binders. A microfluidic platform then separates antigen-presenting cells with high throughput and specificity. An unsupervised machine learning algorithm analyzes sequences of phage from all pools to identify the structural trends that contribute to affinity and proposes ideal candidates for validation. In a proof-of-concept screen against human Frizzled-7, a key ligand in the Wnt signaling pathway, antibodies with picomolar affinity were discovered in two rounds of selection that outperformed current gold-standard reagents. This approach, termed μCellect, is low cost, high throughput, and compatible with a wide variety of cell types, enabling widespread adoption for antibody development.
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Affiliation(s)
- David
N. Philpott
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Surath Gomis
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Hansen Wang
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Randy Atwal
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Abdellali Kelil
- Donnelly
Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Tanja Sack
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Brandon Morningstar
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Chris Burnie
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Edward H. Sargent
- Edward
S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Stephane Angers
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Sachdev Sidhu
- Donnelly
Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Shana O. Kelley
- Department
of Pharmaceutical Sciences, University of
Toronto, Toronto, Ontario M5S 3M2, Canada
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4
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Antibody Isolation From a Human Synthetic Combinatorial and Other Libraries of Single-Chain Antibodies. Methods Mol Biol 2018; 1701:349-363. [PMID: 29116515 DOI: 10.1007/978-1-4939-7447-4_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibody libraries came into existence 25 years ago when the accumulating sequence data of immunoglobulin genes and the advent of the PCR technology made it possible to clone antibody gene repertoires. Phage display (most common) and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. "Synthetic" or "semisynthetic" libraries are from naive-non-immunized source and considered to be a source for many different targets, including self-antigens.As other antibody discovery tools, phage display is not an off-the-shelf technology and not offered as a kit but rather requires experience and expertise for making it indeed very useful. Here we present application notes that expand the usefulness of antibody phage display as a very versatile and robust antibody discovery tool.
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5
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Miura T, Nagamune T, Kawahara M. Ligand-inducible dimeric antibody for selecting antibodies against a membrane protein based on mammalian cell proliferation. Biotechnol Bioeng 2015; 113:1113-23. [DOI: 10.1002/bit.25858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/23/2015] [Accepted: 10/13/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Tomohiro Miura
- Department of Bioengineering; Graduate School of Engineering, The University of Tokyo; Tokyo Japan
| | - Teruyuki Nagamune
- Department of Bioengineering; Graduate School of Engineering, The University of Tokyo; Tokyo Japan
- Department of Chemistry and Biotechnology; Graduate School of Engineering, The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku; Tokyo 113-8656 Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology; Graduate School of Engineering, The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku; Tokyo 113-8656 Japan
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