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Singh R, Chandley P, Rohatgi S. Recent Advances in the Development of Monoclonal Antibodies and Next-Generation Antibodies. Immunohorizons 2023; 7:886-897. [PMID: 38149884 PMCID: PMC10759153 DOI: 10.4049/immunohorizons.2300102] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023] Open
Abstract
mAbs are highly indispensable tools for diagnostic, prophylactic, and therapeutic applications. The first technique, hybridoma technology, was based on fusion of B lymphocytes with myeloma cells, which resulted in generation of single mAbs against a specific Ag. Along with hybridoma technology, several novel and alternative methods have been developed to improve mAb generation, ranging from electrofusion to the discovery of completely novel technologies such as B cell immortalization; phage, yeast, bacterial, ribosome, and mammalian display systems; DNA/RNA encoded Abs; single B cell technology; transgenic animals; and artificial intelligence/machine learning. This commentary outlines the evolution, methodology, advantages, and limitations of various mAb production techniques. Furthermore, with the advent of next-generation Ab technologies such as single-chain variable fragments, nanobodies, bispecific Abs, Fc-engineered Abs, Ab biosimilars, Ab mimetics, and Ab-drug conjugates, the healthcare and pharmaceutical sectors have become resourceful to develop highly specific mAb treatments against various diseases such as cancer and autoimmune and infectious diseases.
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Affiliation(s)
- Rohit Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Pankaj Chandley
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Soma Rohatgi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
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2
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David L, Shpigel E, Levin I, Moshe S, Zimmerman L, Dadon-Simanowitz S, Shemer B, Levkovich SA, Larush L, Magdassi S, Belkin S. Performance upgrade of a microbial explosives' sensor strain by screening a high throughput saturation library of a transcriptional regulator. Comput Struct Biotechnol J 2023; 21:4252-4260. [PMID: 37701016 PMCID: PMC10493890 DOI: 10.1016/j.csbj.2023.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
We present a methodology for a high-throughput screening (HTS) of transcription factor libraries, based on bacterial cells and GFP fluorescence. The method is demonstrated on the Escherichia coli LysR-type transcriptional regulator YhaJ, a key element in 2,4-dinitrotuluene (DNT) detection by bacterial explosives' sensor strains. Enhancing the performance characteristics of the YhaJ transcription factor is essential for future standoff detection of buried landmines. However, conventional directed evolution methods for modifying YhaJ are limited in scope, due to the vast sequence space and the absence of efficient screening methods to select optimal transcription factor mutants. To overcome this limitation, we have constructed a focused saturation library of ca. 6.4 × 107 yhaJ variants, and have screened over 70 % of its sequence space using fluorescence-activated cell sorting (FACS). Through this screening process, we have identified YhaJ mutants exhibiting superior fluorescence responses to DNT, which were then effectively transformed into a bioluminescence-based DNT detection system. The best modified DNT reporter strain demonstrated a 7-fold lower DNT detection threshold, a 45-fold increased signal intensity, and a 40 % shorter response time compared to the parental bioreporter. The FACS-based HTS approach presented here may hold a potential for future molecular enhancement of other sensing and catalytic bioreactions.
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Affiliation(s)
- Lidor David
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | - Etai Shpigel
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Itay Levin
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | - Shaked Moshe
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Lior Zimmerman
- Enzymit Ltd. 3 Pinhas Sapir St., Ness Ziona 7403626, Israel
| | | | - Benjamin Shemer
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Shon A. Levkovich
- George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liraz Larush
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Shlomo Magdassi
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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3
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Lu CW, Ho HC, Yao CL, Tseng TY, Kao CM, Chen SC. Bioremediation potential of cadmium by recombinant Escherichia coli surface expressing metallothionein MTT5 from Tetrahymenathermophila. CHEMOSPHERE 2023; 310:136850. [PMID: 36243083 DOI: 10.1016/j.chemosphere.2022.136850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Cadmium (Cd) is a common heavy metal contaminant in industrial wastewater that causes many diseases in humans. Metallothionein (MT), a cysteine-rich metal-binding protein, is well known in chelate-heavy metals. In this study, we expressed MTT5 of Tetrahymena thermophila fused with Lpp-OmpA in the outer membrane of Escherichia coli to determine its ability to accumulate and adsorb Cd. Our results revealed that our recombinant E. coli had a 4.9-fold greater Cd adsorption compared to wild E. coli. Adsorption isothermic analysis demonstrated that the adsorption behavior for Cd in our recombinant bacteria was better fitted into the Freundlich isotherm model than Langmuir isotherm model. Fourier-transform infrared spectroscopy indicated that phosphate and organic phosphate groups were involved in the interaction between Cd and the bacterial surface. Using quantitative reverse transcription polymerase chain reaction, we further showed that the expression of metal-resistance genes (dnaK and clpB) was downregulated due to surface MTT5 protected our recombinant bacteria from Cd2+ adsorption. Furthermore, we showed that our recombinant bacteria could adsorb Cd from the contaminated wastewater containing other metals and were suggested to be applied in the field study.
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Affiliation(s)
- Che-Wei Lu
- Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan
| | - Hsin-Cheng Ho
- Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan
| | - Chao-Ling Yao
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tsung-Yu Tseng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan.
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.
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4
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Hsieh FL, Chang TH. Antibody Display Technology (ADbody) to Present Challenging and Unstable Target Proteins on Antibodies. Methods Mol Biol 2023; 2681:373-382. [PMID: 37405659 DOI: 10.1007/978-1-0716-3279-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Antibodies are the major components of adaptive immunity for the recognition of diverse antigens. Six complementarity-determining regions (CDRs) from each heavy chain and light chain present the antigen-binding site, which determines the antigen-binding specificity. Here, we describe the detailed method of a novel display technology termed antibody display technology (ADbody) (Hsieh and Chang, bioRxiv, 2021), based on the novel structure of human antibodies from malaria-endemic regions of Africa (Hsieh and Higgins, eLife 6:e27311, 2017). The principle of ADbody is to insert proteins of interest (POI) into the heavy-chain CDR3 while still retaining the biological function of POI on the antibody. In this chapter, we described how to use the ADbody method to display challenging and unstable POI on the antibody in mammalian cells. Collectively, this method is designed to provide an alternative outside the current display systems and to generate novel synthetic antibodies.
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Affiliation(s)
- Fu-Lien Hsieh
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Tao-Hsin Chang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
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5
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Mahdavi SZB, Oroojalian F, Eyvazi S, Hejazi M, Baradaran B, Pouladi N, Tohidkia MR, Mokhtarzadeh A, Muyldermans S. An overview on display systems (phage, bacterial, and yeast display) for production of anticancer antibodies; advantages and disadvantages. Int J Biol Macromol 2022; 208:421-442. [PMID: 35339499 DOI: 10.1016/j.ijbiomac.2022.03.113] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Antibodies as ideal therapeutic and diagnostic molecules are among the top-selling drugs providing considerable efficacy in disease treatment, especially in cancer therapy. Limitations of the hybridoma technology as routine antibody generation method in conjunction with numerous developments in molecular biology led to the development of alternative approaches for the streamlined identification of most effective antibodies. In this regard, display selection technologies such as phage display, bacterial display, and yeast display have been widely promoted over the past three decades as ideal alternatives to traditional methods. The display of antibodies on phages is probably the most widespread of these methods, although surface display on bacteria or yeast have been employed successfully, as well. These methods using various sizes of combinatorial antibody libraries and different selection strategies possessing benefits in screening potency, generating, and isolation of high affinity antibodies with low risk of immunogenicity. Knowing the basics of each method assists in the design and retrieval process of antibodies suitable for different diseases, including cancer. In this review, we aim to outline the basics of each library construction and its display method, screening and selection steps. The advantages and disadvantages in comparison to alternative methods, and their applications in antibody engineering will be explained. Finally, we will review approved or non-approved therapeutic antibodies developed by employing these methods, which may serve as therapeutic antibodies in cancer therapy.
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Affiliation(s)
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran; Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Shirin Eyvazi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Biotechnology Research Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Maryam Hejazi
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Pouladi
- Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mohammad Reza Tohidkia
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Serge Muyldermans
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, China..
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6
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Ma C, Jiang C, Zhao D, Li S, Li R, Li L. Development in Detection Methods for the Expression of Surface-Displayed Proteins. Front Microbiol 2022; 13:899578. [PMID: 35558116 PMCID: PMC9085562 DOI: 10.3389/fmicb.2022.899578] [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: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/29/2022] Open
Abstract
Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. A protein of interest is selected as the template and expressed on a molecular display platform such as a bacteriophage for engineering. Initially, the surface-displayed protein template needs to be checked against the desired target via ELISA to examine whether the functions of the displayed template remain intact. The ELISA signal is subject to the protein-target binding affinity. A low-affinity results in a weak ELISA signal which makes it difficult to determine whether the weak signal is because of low affinity or because of poor expression of the protein. Using a methyllysine-binding chromodomain protein Cbx1 that weakly binds to the histone H3K9me3 peptide, we developed and compared three different approaches to increase the signal-to-background ratio of ELISA measurements. We observed that the specific peptide-binding signal was enhanced by increasing the Cbx1 phage concentration on the ELISA plate. The introduction of previously known gain-of-function mutations to the Cbx1 protein significantly increased the ELISA signals. Moreover, we demonstrated that the H3K9me3-specific binding signal was enhanced by fusing Cbx1 with a high-affinity phosphotyrosine-binding protein and by coating the ELISA plate with a mixture of H3K9me3 and phosphotyrosine peptides. This approach also worked with binding to a lower affinity momomethyllysine peptide H3K9me1. These approaches may help improve ELISA experiments when dealing with low-affinity ligand-protein interactions.
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Affiliation(s)
- Chenglong Ma
- College of Life Sciences, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chunyang Jiang
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Dongping Zhao
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Shuhao Li
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Ronggui Li
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Lei Li
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
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7
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Kenny SE, Antaw F, Locke WJ, Howard CB, Korbie D, Trau M. Next-Generation Molecular Discovery: From Bottom-Up In Vivo and In Vitro Approaches to In Silico Top-Down Approaches for Therapeutics Neogenesis. Life (Basel) 2022; 12:life12030363. [PMID: 35330114 PMCID: PMC8950575 DOI: 10.3390/life12030363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 12/02/2022] Open
Abstract
Protein and drug engineering comprises a major part of the medical and research industries, and yet approaches to discovering and understanding therapeutic molecular interactions in biological systems rely on trial and error. The general approach to molecular discovery involves screening large libraries of compounds, proteins, or antibodies, or in vivo antibody generation, which could be considered “bottom-up” approaches to therapeutic discovery. In these bottom-up approaches, a minimal amount is known about the therapeutics at the start of the process, but through meticulous and exhaustive laboratory work, the molecule is characterised in detail. In contrast, the advent of “big data” and access to extensive online databases and machine learning technologies offers promising new avenues to understanding molecular interactions. Artificial intelligence (AI) now has the potential to predict protein structure at an unprecedented accuracy using only the genetic sequence. This predictive approach to characterising molecular structure—when accompanied by high-quality experimental data for model training—has the capacity to invert the process of molecular discovery and characterisation. The process has potential to be transformed into a top-down approach, where new molecules can be designed directly based on the structure of a target and the desired function, rather than performing screening of large libraries of molecular variants. This paper will provide a brief evaluation of bottom-up approaches to discovering and characterising biological molecules and will discuss recent advances towards developing top-down approaches and the prospects of this.
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Affiliation(s)
- Sophie E. Kenny
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Fiach Antaw
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Warwick J. Locke
- Molecular Diagnostic Solutions, Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Building 101, Clunies Ross Street, Canberra, ACT 2601, Australia;
| | - Christopher B. Howard
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
- Correspondence: (D.K.); (M.T.)
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner of College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia; (S.E.K.); (F.A.); (C.B.H.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (D.K.); (M.T.)
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8
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Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022; 30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
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9
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Taw MN, Li M, Kim D, Rocco MA, Waraho-Zhmayev D, DeLisa MP. Engineering a Supersecreting Strain of Escherichia coli by Directed Coevolution of the Multiprotein Tat Translocation Machinery. ACS Synth Biol 2021; 10:2947-2958. [PMID: 34757717 DOI: 10.1021/acssynbio.1c00183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli remains one of the preferred hosts for biotechnological protein production due to its robust growth in culture and ease of genetic manipulation. It is often desirable to export recombinant proteins into the periplasmic space for reasons related to proper disulfide bond formation, prevention of aggregation and proteolytic degradation, and ease of purification. One such system for expressing heterologous secreted proteins is the twin-arginine translocation (Tat) pathway, which has the unique advantage of delivering correctly folded proteins into the periplasm. However, transit times for proteins through the Tat translocase, comprised of the TatABC proteins, are much longer than for passage through the SecYEG pore, the translocase associated with the more widely utilized Sec pathway. To date, a high protein flux through the Tat pathway has yet to be demonstrated. To address this shortcoming, we employed a directed coevolution strategy to isolate mutant Tat translocases for their ability to deliver higher quantities of heterologous proteins into the periplasm. Three supersecreting translocases were selected that each exported a panel of recombinant proteins at levels that were significantly greater than those observed for wild-type TatABC or SecYEG translocases. Interestingly, all three of the evolved Tat translocases exhibited quality control suppression, suggesting that increased translocation flux was gained by relaxation of substrate proofreading. Overall, our discovery of more efficient translocase variants paves the way for the use of the Tat system as a powerful complement to the Sec pathway for secreted production of both commodity and high value-added proteins.
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Affiliation(s)
- May N. Taw
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Daniel Kim
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Mark A. Rocco
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Dujduan Waraho-Zhmayev
- Biological Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Matthew P. DeLisa
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Cornell Institute of Biotechnology, Cornell University, 130 Biotechnology Building, Ithaca, New York 14853, United States
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10
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Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters. Microorganisms 2021; 9:2277. [PMID: 34835403 PMCID: PMC8620850 DOI: 10.3390/microorganisms9112277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Dental Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Angela M. DeMarco
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
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11
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Sfragano PS, Moro G, Polo F, Palchetti I. The Role of Peptides in the Design of Electrochemical Biosensors for Clinical Diagnostics. BIOSENSORS-BASEL 2021; 11:bios11080246. [PMID: 34436048 PMCID: PMC8391273 DOI: 10.3390/bios11080246] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 12/31/2022]
Abstract
Peptides represent a promising class of biorecognition elements that can be coupled to electrochemical transducers. The benefits lie mainly in their stability and selectivity toward a target analyte. Furthermore, they can be synthesized rather easily and modified with specific functional groups, thus making them suitable for the development of novel architectures for biosensing platforms, as well as alternative labelling tools. Peptides have also been proposed as antibiofouling agents. Indeed, biofouling caused by the accumulation of biomolecules on electrode surfaces is one of the major issues and challenges to be addressed in the practical application of electrochemical biosensors. In this review, we summarise trends from the last three years in the design and development of electrochemical biosensors using synthetic peptides. The different roles of peptides in the design of electrochemical biosensors are described. The main procedures of selection and synthesis are discussed. Selected applications in clinical diagnostics are also described.
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Affiliation(s)
- Patrick Severin Sfragano
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy;
| | - Giulia Moro
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (G.M.); (F.P.)
| | - Federico Polo
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; (G.M.); (F.P.)
| | - Ilaria Palchetti
- Department of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy;
- Correspondence:
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12
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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Sivaccumar J, Sandomenico A, Vitagliano L, Ruvo M. Monoclonal Antibodies: A Prospective and Retrospective View. Curr Med Chem 2021; 28:435-471. [PMID: 32072887 DOI: 10.2174/0929867327666200219142231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Monoclonal Antibodies (mAbs) represent one of the most important classes of biotherapeutic agents. They are used to cure many diseases, including cancer, autoimmune diseases, cardiovascular diseases, angiogenesis-related diseases and, more recently also haemophilia. They can be highly varied in terms of format, source, and specificity to improve efficacy and to obtain more targeted applications. This can be achieved by leaving substantially unchanged the basic structural components for paratope clustering. OBJECTIVES The objective was to trace the most relevant findings that have deserved prestigious awards over the years, to report the most important clinical applications and to emphasize their latest emerging therapeutic trends. RESULTS We report the most relevant milestones and new technologies adopted for antibody development. Recent efforts in generating new engineered antibody-based formats are briefly reviewed. The most important antibody-based molecules that are (or are going to be) used for pharmacological practice have been collected in useful tables. CONCLUSION The topics here discussed prove the undisputed role of mAbs as innovative biopharmaceuticals molecules and as vital components of targeted pharmacological therapies.
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Affiliation(s)
- Jwala Sivaccumar
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Annamaria Sandomenico
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
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14
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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15
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Stimple SD, Smith MD, Tessier PM. Directed evolution methods for overcoming trade-offs between protein activity and stability. AIChE J 2020; 66. [PMID: 32719568 DOI: 10.1002/aic.16814] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Engineered proteins are being widely developed and employed in applications ranging from enzyme catalysts to therapeutic antibodies. Directed evolution, an iterative experimental process composed of mutagenesis and library screening, is a powerful technique for enhancing existing protein activities and generating entirely new ones not observed in nature. However, the process of accumulating mutations for enhanced protein activity requires chemical and structural changes that are often destabilizing, and low protein stability is a significant barrier to achieving large enhancements in activity during multiple rounds of directed evolution. Here we highlight advances in understanding the origins of protein activity/stability trade-offs for two important classes of proteins (enzymes and antibodies) as well as innovative experimental and computational methods for overcoming such trade-offs. These advances hold great potential for improving the generation of highly active and stable proteins that are needed to address key challenges related to human health, energy and the environment.
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Affiliation(s)
- Samuel D. Stimple
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Matthew D. Smith
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
| | - Peter M. Tessier
- Department of Pharmaceutical Sciences Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Chemical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
- Department of Biomedical Engineering Biointerfaces Institute, University of Michigan Ann Arbor Michigan
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16
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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17
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Linciano S, Pluda S, Bacchin A, Angelini A. Molecular evolution of peptides by yeast surface display technology. MEDCHEMCOMM 2019; 10:1569-1580. [PMID: 31803399 PMCID: PMC6836575 DOI: 10.1039/c9md00252a] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
Genetically encoded peptides possess unique properties, such as a small molecular weight and ease of synthesis and modification, that make them suitable to a large variety of applications. However, despite these favorable qualities, naturally occurring peptides are often limited by intrinsic weak binding affinities, poor selectivity and low stability that ultimately restrain their final use. To overcome these limitations, a large variety of in vitro display methodologies have been developed over the past few decades to evolve genetically encoded peptide molecules with superior properties. Phage display, mRNA display, ribosome display, bacteria display, and yeast display are among the most commonly used methods to engineer peptides. While most of these in vitro methodologies have already been described in detail elsewhere, this review describes solely the yeast surface display technology and its valuable use for the evolution of a wide range of peptide formats.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
| | - Stefano Pluda
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
- Fidia Farmaceutici S.p.A , Via Ponte della Fabbrica 3/A , Abano Terme 35031 , Italy
| | - Arianna Bacchin
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems , Ca' Foscari University of Venice , Via Torino 155 , Venezia Mestre 30172 , Italy
- European Centre for Living Technology (ECLT) , Ca' Bottacin, Dorsoduro 3911, Calle Crosera , Venice 30123 , Italy .
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18
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Almagro JC, Pedraza-Escalona M, Arrieta HI, Pérez-Tapia SM. Phage Display Libraries for Antibody Therapeutic Discovery and Development. Antibodies (Basel) 2019; 8:antib8030044. [PMID: 31544850 PMCID: PMC6784186 DOI: 10.3390/antib8030044] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 01/24/2023] Open
Abstract
Phage display technology has played a key role in the remarkable progress of discovering and optimizing antibodies for diverse applications, particularly antibody-based drugs. This technology was initially developed by George Smith in the mid-1980s and applied by John McCafferty and Gregory Winter to antibody engineering at the beginning of 1990s. Here, we compare nine phage display antibody libraries published in the last decade, which represent the state of the art in the discovery and development of therapeutic antibodies using phage display. We first discuss the quality of the libraries and the diverse types of antibody repertoires used as substrates to build the libraries, i.e., naïve, synthetic, and semisynthetic. Second, we review the performance of the libraries in terms of the number of positive clones per panning, hit rate, affinity, and developability of the selected antibodies. Finally, we highlight current opportunities and challenges pertaining to phage display platforms and related display technologies.
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Affiliation(s)
- Juan C Almagro
- GlobalBio, Inc., 320, Cambridge, MA 02138, USA.
- UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico.
| | - Martha Pedraza-Escalona
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Hugo Iván Arrieta
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Sonia Mayra Pérez-Tapia
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
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19
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Farahavar G, Abolmaali SS, Gholijani N, Nejatollahi F. Antibody-guided nanomedicines as novel breakthrough therapeutic, diagnostic and theranostic tools. Biomater Sci 2019; 7:4000-4016. [PMID: 31355391 DOI: 10.1039/c9bm00931k] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in nanotechnology, such as the development of various types of nanoparticles and hybrid nanomaterials, have revolutionized nanomedicine. The small size, customizable surface, enhanced solubility, and multi-functionality endow the nanoparticles with an ability to interact with complex cellular and biological functions in new ways. Furthermore, these systems can deliver drugs to specific tissues and provide a targeted therapy. For this purpose, different categories of molecules, particularly antibodies, have been used as ligands. Antibody-conjugated nanomaterials can significantly enhance the efficiency of nanomedicines, especially in the field of cancer. This review is focused on three major medical applications of antibody-conjugated nanomaterials, namely, therapeutic, diagnostic and theranostic applications. To provide comprehensive information on the topic and an overview of these hybrid nanomaterials for biomedical applications, a brief summary of nanomaterials and antibodies is given. Moreover, the review has depicted the potential applications of antibody-conjugated nanomaterials in different fields and their capabilities to empower nanomedicine, particularly in relation to the treatment and detection of malignancies.
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Affiliation(s)
- Ghazal Farahavar
- Pharmaceutical Nanotechnology Department, Shiraz University of Medical Sciences, Shiraz 71345, Iran.
| | - Samira Sadat Abolmaali
- Pharmaceutical Nanotechnology Department and Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz 71345, Iran.
| | - Nasser Gholijani
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Foroogh Nejatollahi
- Shiraz HIV/AIDS research center, Institute of health, Shiraz University of Medical Sciences, Shiraz, Iran.
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20
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Kwok HS, Vargas-Rodriguez O, Melnikov SV, Söll D. Engineered Aminoacyl-tRNA Synthetases with Improved Selectivity toward Noncanonical Amino Acids. ACS Chem Biol 2019; 14:603-612. [PMID: 30933556 DOI: 10.1021/acschembio.9b00088] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A wide range of noncanonical amino acids (ncAAs) can be incorporated into proteins in living cells by using engineered aminoacyl-tRNA synthetase/tRNA pairs. However, most engineered tRNA synthetases are polyspecific; that is, they can recognize multiple rather than one ncAA. Polyspecificity of engineered tRNA synthetases imposes a limit to the use of genetic code expansion because it prevents specific incorporation of a desired ncAA when multiple ncAAs are present in the growth media. In this study, we employed directed evolution to improve substrate selectivity of polyspecific tRNA synthetases by developing substrate-selective readouts for flow-cytometry-based screening with the simultaneous presence of multiple ncAAs. We applied this method to improve the selectivity of two commonly used tRNA synthetases, p-cyano-l-phenylalanyl aminoacyl-tRNA synthetase ( pCNFRS) and Nε-acetyl-lysyl aminoacyl-tRNA synthetase (AcKRS), with broad specificity. Evolved pCNFRS and AcKRS variants exhibit significantly improved selectivity for ncAAs p-azido-l-phenylalanine ( pAzF) and m-iodo-l-phenylalanine ( mIF), respectively. To demonstrate the utility of our approach, we used the newly evolved tRNA synthetase variant to produce highly pure proteins containing the ncAA mIF, in the presence of multiple ncAAs present in the growth media. In summary, our new approach opens up a new avenue for engineering the next generation of tRNA synthetases with improved selectivity toward a desired ncAA.
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Affiliation(s)
- Hui Si Kwok
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sergey V. Melnikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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21
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Directed Evolution of Cellobiose Dehydrogenase on the Surface of Yeast Cells Using Resazurin-Based Fluorescent Assay. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9071413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cellobiose dehydrogenase (CDH) from Phanerochaete chrysosporium can be used in lactobionic acid production, biosensor for lactose, biofuel cells, lignocellulose degradation, and wound-healing applications. To make it a better biocatalyst, CDH with higher activity in an immobilized form is desirable. For this purpose, CDH was expressed for the first time on the surface of S. cerevisiae EBY100 cells in an active form as a triple mutant tmCDH (D20N, A64T, V592M) and evolved further for higher activity using resazurin-based fluorescent assay. In order to decrease blank reaction of resazurin with yeast cells and to have linear correlation between enzyme activity on the cell surface and fluorescence signal, the assay was optimized with respect to resazurin concentration (0.1 mM), substrate concentration (10 mM lactose and 0.08 mM cellobiose), and pH (6.0). Using optimized assay an error prone PCR gene library of tmCDH was screened. Two mutants with 5 (H5) and 7 mutations (H9) were found having two times higher activity than the parent tmCDH enzyme that already had improved activity compared to wild type CDH whose activity could not be detected on the surface of yeast cells.
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22
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Kylilis N, Riangrungroj P, Lai HE, Salema V, Fernández LÁ, Stan GBV, Freemont PS, Polizzi KM. Whole-Cell Biosensor with Tunable Limit of Detection Enables Low-Cost Agglutination Assays for Medical Diagnostic Applications. ACS Sens 2019; 4:370-378. [PMID: 30623662 DOI: 10.1021/acssensors.8b01163] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Whole-cell biosensors can form the basis of affordable, easy-to-use diagnostic tests that can be readily deployed for point-of-care (POC) testing, but to date the detection of analytes such as proteins that cannot easily diffuse across the cell membrane has been challenging. Here we developed a novel biosensing platform based on cell agglutination using an E. coli whole-cell biosensor surface-displaying nanobodies which bind selectively to a target protein analyte. As a proof-of-concept, we show the feasibility of this design to detect a model analyte at nanomolar concentrations. Moreover, we show that the design architecture is flexible by building assays optimized to detect a range of model analyte concentrations using straightforward design rules and a mathematical model. Finally, we re-engineer our whole-cell biosensor for the detection of a medically relevant biomarker by the display of two different nanobodies against human fibrinogen and demonstrate a detection limit as low as 10 pM in diluted human plasma. Overall, we demonstrate that our agglutination technology fulfills the requirement of POC testing by combining low-cost nanobody production, customizable detection range and low detection limits. This technology has the potential to produce affordable diagnostics for field-testing in the developing world, emergency or disaster relief sites, as well as routine medical testing and personalized medicine.
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Affiliation(s)
- Nicolas Kylilis
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pinpunya Riangrungroj
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hung-En Lai
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Valencio Salema
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Cantoblanco UAM, 28049 Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Cantoblanco UAM, 28049 Madrid, Spain
| | - Guy-Bart V. Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Paul S. Freemont
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen M. Polizzi
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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23
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Nakatani H, Kanie J, Hori K. On‐fiber display of a functional peptide at sites distant from the cell surface using a long bacterionanofiber of a trimeric autotransporter adhesin. Biotechnol Bioeng 2018; 116:239-249. [DOI: 10.1002/bit.26857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/20/2018] [Accepted: 10/30/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Hajime Nakatani
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
| | - Junichi Kanie
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
| | - Katsutoshi Hori
- Department of Biomolecular EngineeringGraduate School of Engineering, Nagoya University, Furo‐cho, Chikusa‐kuNagoya Japan
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24
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Hu FJ, Volk AL, Persson H, Säll A, Borrebaeck C, Uhlen M, Rockberg J. Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders. N Biotechnol 2018; 45:80-88. [DOI: 10.1016/j.nbt.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/28/2017] [Accepted: 07/31/2017] [Indexed: 10/19/2022]
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25
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Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie 2018; 154:132-155. [PMID: 30193856 DOI: 10.1016/j.biochi.2018.09.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/02/2018] [Indexed: 12/14/2022]
Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is an efficient method used to isolate high-affinity single stranded oligonucleotides from a large random sequence pool. These SELEX-derived oligonucleotides named aptamer, can be selected against a broad spectrum of target molecules including proteins, cells, microorganisms and chemical compounds. Like antibodies, aptamers have a great potential in interacting with and binding to their targets through structural recognition and are therefore called "chemical antibodies". However, aptamers offer advantages over antibodies including smaller size, better tissue penetration, higher thermal stability, lower immunogenicity, easier production, lower cost of synthesis and facilitated conjugation or modification with different functional moieties. Thus, aptamers represent an attractive substitution for protein antibodies in the fields of biomarker discovery, diagnosis, imaging and targeted therapy. Enormous interest in aptamer technology triggered the development of SELEX that has underwent numerous modifications since its introduction in 1990. This review will discuss the recent advances in SELEX methods and their advantages and limitations. Aptamer applications are also briefly outlined in this review.
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Affiliation(s)
- Payam Bayat
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahim Nosrati
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Khedri
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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26
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Abstract
Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.
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27
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Kim D, Ku S. Bacillus Cellulase Molecular Cloning, Expression, and Surface Display on the Outer Membrane of Escherichia coli. Molecules 2018; 23:E503. [PMID: 29495265 PMCID: PMC6017809 DOI: 10.3390/molecules23020503] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/18/2022] Open
Abstract
One of the main challenges of using recombinant enzymes is that they are derived from genetically-modified microorganisms commonly located in the intracellular region. The use of these recombinant enzymes for commercial purposes requires the additional processes of cell disruption and purification, which may result in enzyme loss, denaturation, and increased total production cost. In this study, the cellulase gene of Bacillus licheniformis ATCC 14580 was cloned, over-expressed, and surface displayed in recombinant Escherichia coli using an ice-nucleation protein (INP). INP, an outer membrane-bound protein from Pseudomonas syringae, was utilized as an anchor linker, which was cloned with a foreign cellulase gene into the pET21a vector to develop a surface display system on the outer membrane of E. coli. The resulting strain successfully revealed cellulase on the host cell surface. The over-expressed INP-cellulase fusion protein was confirmed via staining assay for determining the extracellular cellulase and Western blotting method for the molecular weight (MW) of cellulase, which was estimated to be around 61.7 kDa. Cell fractionation and localization tests demonstrated that the INP-cellulase fusion protein was mostly present in the supernatant (47.5%) and outer membrane (19.4%), while the wild-type strain intracellularly retained enzymes within cytosol (>61%), indicating that the INP gene directed the cellulase expression on the bacteria cell surface. Further studies of the optimal enzyme activity were observed at 60 °C and pH 7.0, and at least 75% of maximal enzyme activity was preserved at 70 °C.
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Affiliation(s)
- Daehwan Kim
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN 47907, USA.
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Seockmo Ku
- Fermentation Science Program, School of Agribusiness and Agriscience, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
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28
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Almagro JC, Daniels-Wells TR, Perez-Tapia SM, Penichet ML. Progress and Challenges in the Design and Clinical Development of Antibodies for Cancer Therapy. Front Immunol 2018; 8:1751. [PMID: 29379493 PMCID: PMC5770808 DOI: 10.3389/fimmu.2017.01751] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/24/2017] [Indexed: 11/14/2022] Open
Abstract
The remarkable progress in engineering and clinical development of therapeutic antibodies in the last 40 years, after the seminal work by Köhler and Milstein, has led to the approval by the United States Food and Drug Administration (FDA) of 21 antibodies for cancer immunotherapy. We review here these approved antibodies, with emphasis on the methods used for their discovery, engineering, and optimization for therapeutic settings. These methods include antibody engineering via chimerization and humanization of non-human antibodies, as well as selection and further optimization of fully human antibodies isolated from human antibody phage-displayed libraries and immunization of transgenic mice capable of generating human antibodies. These technology platforms have progressively led to the development of therapeutic antibodies with higher human content and, thus, less immunogenicity. We also discuss the genetic engineering approaches that have allowed isotype switching and Fc modifications to modulate effector functions and bioavailability (half-life), which together with the technologies for engineering the Fv fragment, have been pivotal in generating more efficacious and better tolerated therapeutic antibodies to treat cancer.
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Affiliation(s)
| | - Tracy R Daniels-Wells
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Manuel L Penichet
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, United States.,The Molecular Biology Institute, University of California, Los Angeles, CA, United States.,UCLA AIDS Institute, Los Angeles, CA, United States
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Sarkes DA, Jahnke JP, Stratis-Cullum DN. Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates. J Vis Exp 2017. [PMID: 29286465 PMCID: PMC5755526 DOI: 10.3791/56061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Biopanning bacterial display libraries is a proven technique for peptide affinity reagent discovery for recognition of both biotic and abiotic targets. Peptide affinity reagents can be used for similar applications to antibodies, including sensing and therapeutics, but are more robust and able to perform in more extreme environments. Specific enrichment of peptide capture agents to a protein target of interest is enhanced using semi-automated sorting methods which improve binding and wash steps and therefore decrease the occurrence of false positive binders. A semi-automated sorting method is described herein for use with a commercial automated magnetic-activated cell sorting device with an unconstrained bacterial display sorting library expressing random 15-mer peptides. With slight modifications, these methods are extendable to other automated devices, other sorting libraries, and other organisms. A primary goal of this work is to provide a comprehensive methodology and expound the thought process applied in analyzing and minimizing the resulting pool of candidates. These techniques include analysis of on-cell binding using fluorescence-activated cell sorting (FACS), to assess affinity and specificity during sorting and in comparing individual candidates, and the analysis of peptide sequences to identify trends and consensus sequences for understanding and potentially improving the affinity to and specificity for the target of interest.
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Affiliation(s)
- Deborah A Sarkes
- Sensors and Electron Devices Directorate, US Army Research Laboratory;
| | - Justin P Jahnke
- Sensors and Electron Devices Directorate, US Army Research Laboratory
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Jeiranikhameneh M, Razavi MR, Irani S, Siadat SD, Oloomi M. Designing novel construction for cell surface display of protein E on Escherichia coli using non-classical pathway based on Lpp-OmpA. AMB Express 2017; 7:53. [PMID: 28247289 PMCID: PMC5331024 DOI: 10.1186/s13568-017-0350-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/20/2017] [Indexed: 01/30/2023] Open
Abstract
Today, transference of recombinant protein on the outer surface of bacteria is deemed as a valuable process for various applications in biotechnology including preparation of vaccines. In this study, Lpp-OmpA structure was used to present outer membrane protein E of Haemophilus influenzae on E. coli outer membrane. Also, a structure was designed according to Lpp-OmpA based on non-classical secretion pathway using bioinformatics software such as MEMSAT-SVM, ScrotumP and SignalP where it lacked any signal peptide at its N-terminal. Potential of this structure in the presentation of protein E on the surface of E. coli through non-classical pathway was indicated by western blotting, SDS page and fluorescent microscopy techniques, similarly its effectiveness was compared with Lpp-OmpA system. The results of the current study showed that the new structure had higher efficiency than Lpp-OmpA, and it could transport protein E on outer membrane well. This study is the first report in the presentation of H. influenzae PE onto the surface of E. coli by Lpp-OmpA, and the structure originated from Lpp-OmpA, according to the non-classical secretion pathway. Our results suggest that non-classical secretion pathway may be exploited as a new secretory pathway on the outer surface of the cell for recombinant proteins.
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31
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Redesigning of Microbial Cell Surface and Its Application to Whole-Cell Biocatalysis and Biosensors. Appl Biochem Biotechnol 2017; 185:396-418. [PMID: 29168153 DOI: 10.1007/s12010-017-2662-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Microbial cell surface display technology can redesign cell surfaces with functional proteins and peptides to endow cells some unique features. Foreign peptides or proteins are transported out of cells and immobilized on cell surface by fusing with anchoring proteins, which is an effective solution to avoid substance transfer limitation, enzyme purification, and enzyme instability. As the most frequently used prokaryotic and eukaryotic protein surface display system, bacterial and yeast surface display systems have been widely applied in vaccine, biocatalysis, biosensor, bioadsorption, and polypeptide library screening. In this review of bacterial and yeast surface display systems, different cell surface display mechanisms and their applications in biocatalysis as well as biosensors are described with their strengths and shortcomings. In addition to single enzyme display systems, multi-enzyme co-display systems are presented here. Finally, future developments based on our and other previous reports are discussed.
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Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N-terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high-affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen-binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD ).
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Affiliation(s)
- Valencio Salema
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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33
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Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R. Advances in molecular engineering of carbohydrate-binding modules. Proteins 2017; 85:1602-1617. [PMID: 28547780 DOI: 10.1002/prot.25327] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Silvia Moreno-Mendieta
- CONACYT, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
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Lim S, Glasgow JE, Interrante MF, Storm EM, Cochran JR. Dual display of proteins on the yeast cell surface simplifies quantification of binding interactions and enzymatic bioconjugation reactions. Biotechnol J 2017; 12:10.1002/biot.201600696. [PMID: 28299901 PMCID: PMC5708543 DOI: 10.1002/biot.201600696] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 11/12/2022]
Abstract
Yeast surface display, a well-established technology for protein analysis and engineering, involves expressing a protein of interest as a genetic fusion to either the N- or C-terminus of the yeast Aga2p mating protein. Historically, yeast-displayed protein variants are flanked by peptide epitope tags that enable flow cytometric measurement of construct expression using fluorescent primary or secondary antibodies. Here, we built upon this technology to develop a new yeast display strategy that comprises fusion of two different proteins to Aga2p, one to the N-terminus and one to the C-terminus. This approach allows an antibody fragment, ligand, or receptor to be directly coupled to expression of a fluorescent protein readout, eliminating the need for antibody-staining of epitope tags to quantify yeast protein expression levels. We show that this system simplifies quantification of protein-protein binding interactions measured on the yeast cell surface. Moreover, we show that this system facilitates co-expression of a bioconjugation enzyme and its corresponding peptide substrate on the same Aga2p construct, enabling enzyme expression and catalytic activity to be measured on the surface of yeast.
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Affiliation(s)
- Sungwon Lim
- Dept. of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA
| | - Jeff E. Glasgow
- Dept. of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA
- Joint Initiative for Metrology in Biology, Stanford, CA, USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA
| | | | - Erica M. Storm
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Jennifer R. Cochran
- Dept. of Bioengineering, Schools of Engineering and Medicine, Stanford University, Stanford, CA, USA
- Dept. of Chemical Engineering, School of Engineering, Stanford University, Stanford, CA, USA
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Chen L, Mulchandani A, Ge X. Spore-displayed enzyme cascade with tunable stoichiometry. Biotechnol Prog 2017; 33:383-389. [PMID: 27977916 DOI: 10.1002/btpr.2416] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/02/2016] [Indexed: 12/18/2022]
Abstract
Taking the advantages of inert and stable nature of endospores, we developed a biocatalysis platform for multiple enzyme immobilization on Bacillus subtilis spore surface. Among B. subtilis outer coat proteins, CotG mediated a high expression level of Clostridium thermocellum cohesin (CtCoh) with a functional display capability of ∼104 molecules per spore of xylose reductase-C. thermocellum dockerin fusion protein (XR-CtDoc). By co-immobilization of phosphite dehydrogenase (PTDH) on spore surface via Ruminococcus flavefaciens cohesin-dockerin modules, regeneration of NADPH was achieved. Both xylose reductase (XR) and PTDH exhibited enhanced stability upon spore surface display. More importantly, by altering the copy numbers of CtCoh and RfCoh fused with CotG, the molar ratio between immobilized enzymes was adjusted in a controllable manner. Optimization of spore-displayed XR/PTDH stoichiometry resulted in increased yields of xylitol. In conclusion, endospore surface display presents a novel approach for enzyme cascade immobilization with improved stability and tunable stoichiometry. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:383-389, 2017.
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Affiliation(s)
- Long Chen
- Dept. of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521
| | - Ashok Mulchandani
- Dept. of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521
| | - Xin Ge
- Dept. of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521
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37
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Pakulska MM, Miersch S, Shoichet MS. Designer protein delivery: From natural to engineered affinity-controlled release systems. Science 2016; 351:aac4750. [PMID: 26989257 DOI: 10.1126/science.aac4750] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploiting binding affinities between molecules is an established practice in many fields, including biochemical separations, diagnostics, and drug development; however, using these affinities to control biomolecule release is a more recent strategy. Affinity-controlled release takes advantage of the reversible nature of noncovalent interactions between a therapeutic protein and a binding partner to slow the diffusive release of the protein from a vehicle. This process, in contrast to degradation-controlled sustained-release formulations such as poly(lactic-co-glycolic acid) microspheres, is controlled through the strength of the binding interaction, the binding kinetics, and the concentration of binding partners. In the context of affinity-controlled release--and specifically the discovery or design of binding partners--we review advances in in vitro selection and directed evolution of proteins, peptides, and oligonucleotides (aptamers), aided by computational design.
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Affiliation(s)
- Malgosia M Pakulska
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shane Miersch
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders. Sci Rep 2016; 6:22575. [PMID: 26940078 PMCID: PMC4778045 DOI: 10.1038/srep22575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 11/08/2022] Open
Abstract
Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution.
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39
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Emerging therapeutic delivery capabilities and challenges utilizing enzyme/protein packaged bacterial vesicles. Ther Deliv 2015; 6:873-87. [PMID: 26228777 DOI: 10.4155/tde.15.40] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nanoparticle-based therapeutics are poised to play a critical role in treating disease. These complex multifunctional drug delivery vehicles provide for the passive and active targeted delivery of numerous small molecule, peptide and protein-derived pharmaceuticals. This article will first discuss some of the current state of the art nanoparticle classes (dendrimers, lipid-based, polymeric and inorganic), highlighting benefits/drawbacks associated with their implementation. We will then discuss an emerging class of nanoparticle therapeutics, bacterial outer membrane vesicles, that can provide many of the nanoparticle benefits while simplifying assembly. Through molecular biology techniques; outer membrane vesicle hijacking potentially allows for stringent control over nanoparticle production allowing for targeted protein packaged nanoparticles to be fully synthesized by bacteria.
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40
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Bao S, Yu S, Guo X, Zhang F, Sun Y, Tan L, Duan Y, Lu F, Qiu X, Ding C. Construction of a cell-surface display system based on the N-terminal domain of ice nucleation protein and its application in identification of mycoplasma
adhesion proteins. J Appl Microbiol 2015; 119:236-44. [DOI: 10.1111/jam.12824] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
Affiliation(s)
- S. Bao
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - S. Yu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - X. Guo
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - F. Zhang
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Sun
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - L. Tan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - Y. Duan
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - F. Lu
- College of Veterinary Medicine; Gansu Agricultural University; Lanzhou China
| | - X. Qiu
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
| | - C. Ding
- Shanghai Veterinary Research Institute; Chinese Academy of Agricultural Sciences; Shanghai China
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Piñero-Lambea C, Bodelón G, Fernández-Periáñez R, Cuesta AM, Álvarez-Vallina L, Fernández LÁ. Programming controlled adhesion of E. coli to target surfaces, cells, and tumors with synthetic adhesins. ACS Synth Biol 2015; 4:463-73. [PMID: 25045780 PMCID: PMC4410913 DOI: 10.1021/sb500252a] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
In this work we report synthetic
adhesins (SAs) enabling the rational
design of the adhesion properties of E. coli. SAs
have a modular structure comprising a stable β-domain for outer
membrane anchoring and surface-exposed immunoglobulin domains with
high affinity and specificity that can be selected from large repertoires.
SAs are constitutively and stably expressed in an E. coli strain lacking a conserved set of natural adhesins, directing a
robust, fast, and specific adhesion of bacteria to target antigenic
surfaces and cells. We demonstrate the functionality of SAs in vivo, showing that, compared to wild type E.
coli, lower doses of engineered E. coli are
sufficient to colonize solid tumors expressing an antigen recognized
by the SA. In addition, lower levels of engineered bacteria were found
in non-target tissues. Therefore, SAs provide stable and specific
adhesion capabilities to E. coli against target surfaces
of interest for diverse applications using live bacteria.
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Affiliation(s)
- Carlos Piñero-Lambea
- Department
of Microbial Biotechnology, Centro Nacional de Biotecnología
(CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Gustavo Bodelón
- Department
of Microbial Biotechnology, Centro Nacional de Biotecnología
(CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | | | - Angel M. Cuesta
- Molecular
Immunology Unit, Hospital Universitario Puerta de Hierro, Majadahonda, 28222 Madrid, Spain
| | - Luis Álvarez-Vallina
- Molecular
Immunology Unit, Hospital Universitario Puerta de Hierro, Majadahonda, 28222 Madrid, Spain
| | - Luis Ángel Fernández
- Department
of Microbial Biotechnology, Centro Nacional de Biotecnología
(CNB), Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
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Abstract
The method of displaying recombinant proteins on the surface of Saccharomyces cerevisiae via genetic fusion to an abundant cell wall protein, a technology known as yeast surface display, or simply, yeast display, has become a valuable protein engineering tool for a broad spectrum of biotechnology and biomedical applications. This review focuses on the use of yeast display for engineering protein affinity, stability, and enzymatic activity. Strategies and examples for each protein engineering goal are discussed. Additional applications of yeast display are also briefly presented, including protein epitope mapping, identification of protein-protein interactions, and uses of displayed proteins in industry and medicine.
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Fleetwood F, Andersson KG, Ståhl S, Löfblom J. An engineered autotransporter-based surface expression vector enables efficient display of Affibody molecules on OmpT-negative E. coli as well as protease-mediated secretion in OmpT-positive strains. Microb Cell Fact 2014; 13:179. [PMID: 25547008 PMCID: PMC4304625 DOI: 10.1186/s12934-014-0179-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/09/2014] [Indexed: 12/20/2022] Open
Abstract
Background Cell display technologies (e.g. bacterial display) are attractive in directed evolution as they provide the option to use flow-cytometric cell sorting for selection from combinatorial libraries. The aim of this study was to engineer and investigate an expression vector system with dual functionalities: i) recombinant display of Affibody libraries on Escherichia coli for directed evolution and ii) small scale secreted production of candidate affinity proteins, allowing initial downstream characterizations prior to subcloning. Autotransporters form a class of surface proteins in Gram-negative bacteria that have potential for efficient translocation and tethering of recombinant passenger proteins to the outer membrane. We engineered a bacterial display vector based on the E. coli AIDA-I autotransporter for anchoring to the bacterial surface. Potential advantages of employing autotransporters combined with E. coli as host include: high surface expression level, high transformation frequency, alternative promoter systems available, efficient translocation to the outer membrane and tolerance for large multi-domain passenger proteins. Results The new vector was designed to comprise an expression cassette encoding for an Affibody molecule, three albumin binding domains for monitoring of surface expression levels, an Outer membrane Protease T (OmpT) recognition site for potential protease-mediated secretion of displayed affinity proteins and a histidine-tag for purification. A panel of vectors with different promoters were generated and evaluated, and suitable cultivation conditions were investigated. The results demonstrated a high surface expression level of the different evaluated Affibody molecules, high correlation between target binding and surface expression level, high signal-to-background ratio, efficient secretion and purification of binders in OmpT-positive hosts as well as tight regulation of surface expression for the titratable promoters. Importantly, a mock selection using FACS from a 1:100,000 background yielded around 20,000-fold enrichment in a single round and high viability of the isolated bacteria after sorting. Conclusions The new expression vectors are promising for combinatorial engineering of Affibody molecules and the strategy for small-scale production of soluble recombinant proteins has the potential to increase throughput of the entire discovery process. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0179-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filippa Fleetwood
- Division of Protein technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Ken G Andersson
- Division of Protein technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Stefan Ståhl
- Division of Protein technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - John Löfblom
- Division of Protein technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
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Farajnia S, Ahmadzadeh V, Tanomand A, Veisi K, Khosroshahi SA, Rahbarnia L. Development trends for generation of single-chain antibody fragments. Immunopharmacol Immunotoxicol 2014; 36:297-308. [DOI: 10.3109/08923973.2014.945126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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46
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Ng DT, Sarkar CA. NP-Sticky: A Web Server for Optimizing DNA Ligation with Non-Palindromic Sticky Ends. J Mol Biol 2014; 426:1861-9. [DOI: 10.1016/j.jmb.2014.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/17/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
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Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT. Particle display: a quantitative screening method for generating high-affinity aptamers. Angew Chem Int Ed Engl 2014; 53:4796-801. [PMID: 24644057 DOI: 10.1002/anie.201309334] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/08/2022]
Abstract
We report an aptamer discovery technology that reproducibly yields higher affinity aptamers in fewer rounds compared to conventional selection. Our method (termed particle display) transforms libraries of solution-phase aptamers into "aptamer particles", each displaying many copies of a single sequence on its surface. We then use fluorescence-activated cell sorting (FACS) to individually measure the relative affinities of >10(8) aptamer particles and sort them in a high-throughput manner. Through mathematical analysis, we identified experimental parameters that enable optimal screening, and demonstrate enrichment performance that exceeds the theoretical maximum achievable with conventional selection by many orders of magnitude. We used particle display to obtain high-affinity DNA aptamers for four different protein targets in three rounds, including proteins for which previous DNA aptamer selection efforts have been unsuccessful. We believe particle display offers an extraordinarily efficient mechanism for generating high-quality aptamers in a rapid and economic manner, towards accelerated exploration of the human proteome.
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Affiliation(s)
- Jinpeng Wang
- Department of Mechanical Engineering, Materials and Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106 (USA)
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Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT. Particle Display: A Quantitative Screening Method for Generating High-Affinity Aptamers. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309334] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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49
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Hu FJ, Uhlen M, Rockberg J. Generation of HER2 monoclonal antibodies using epitopes of a rabbit polyclonal antibody. N Biotechnol 2014; 31:35-43. [PMID: 24120493 DOI: 10.1016/j.nbt.2013.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/25/2013] [Accepted: 10/01/2013] [Indexed: 10/26/2022]
Abstract
One of the issues in using polyclonal antibodies is the limited amount of reagent available from an immunisation, leading to batch-to-batch variation and difficulties in obtaining the same antibody performance when the same antigen is re-immunised into several separate animals. This led to the development of hybridoma technology allowing, at least theoretically, for an unlimited production of a specific binder. Nevertheless, polyclonal antibodies are widely used in research and diagnostics and there exists a need for robust methods to convert a polyclonal antibody with good binding performance into a renewable monoclonal with identical or similar binding specificity. Here we have used precise information regarding the functional recognition sequence (epitope) of a rabbit polyclonal antibody with attractive binding characteristics as the basis for generation of a renewable mouse monoclonal antibody. First, the original protein fragment antigen was used for immunisation and generation of mouse hybridoma, without obtaining binders to the same epitope region. Instead a peptide designed using the functional epitope and structural information was synthesised and used for hybridoma production. Several of the monoclonal antibodies generated were found to have similar binding characteristics to those of the original polyclonal antibody. These monoclonal antibodies detected native HER2 on cell lines and were also able to stain HER2 in immunohistochemistry using xenografted mice, as well as human normal and cancer tissues.
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Affiliation(s)
- Francis Jingxin Hu
- School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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Ngundi MM, Kulagina NV, Anderson GP, Taitt CR. Nonantibody-based recognition: alternative molecules for detection of pathogens. Expert Rev Proteomics 2014; 3:511-24. [PMID: 17078765 DOI: 10.1586/14789450.3.5.511] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Immunoassays have been well established for many years as the cornerstone of detection technologies. These assays are sensitive, selective and, in general, highly resistant to interference from complex sample matrices when compared with nucleic acid-based tests. However, both antibody- and nucleic acid-based detection systems require a priori knowledge of the target and development of specific reagents; multiplexed assays can become increasingly problematic when attempting to detect a plethora of different targets, the identities of which are unknown. In an effort to circumvent many of the limitations inherent in these conventional assays, other recognition reagents are being explored as alternatives, or indeed as adjuncts, to antibodies for pathogen and toxin detection. This article will review a number of different recognition systems ranging in complexity from small molecules, such as nucleic-acid aptamers, carbohydrates and peptides, to systems as highly complicated as whole cells and organisms. All of these alternative systems have tremendous potential to achieve superior sensitivity, selectivity, and stability, but are also subject to their own limitations, which are also discussed. In short, while in its infancy, this field holds great promise for the development of rapid, fieldable assays that are highly complementary to existing antibody- and nucleic acid-based technologies.
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Affiliation(s)
- Miriam M Ngundi
- US Food and Drug Administration, N29 RM418 HFM-434 8800 Rockville Pike, Bethesda, MD 20892, USA.
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