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Iqbal Z, Sadaf S. Forty Years of Directed Evolution and its Continuously Evolving Technology Toolbox - A Review of the Patent Landscape. Biotechnol Bioeng 2021; 119:693-724. [PMID: 34923625 DOI: 10.1002/bit.28009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022]
Abstract
Generating functional protein variants with novel or improved characteristics has been a goal of the biotechnology industry and life sciences, for decades. Rational design and directed evolution are two major pathways to achieve the desired ends. Whilst rational protein design approach has made substantial progress, the idea of using a method based on cycles of mutagenesis and natural selection to develop novel binding proteins, enzymes and structures has attracted great attention. Laboratory evolution of proteins/enzymes requires new tools and analytical approaches to create genetic diversity and identifying variants with desired traits. In this pursuit, construction of sufficiently large libraries of target molecules to search for improved variants and the need for new protocols to alter the properties of target molecules has been a continuing challenge in the directed evolution experiments. This review will discuss the in vivo and in vitro gene diversification tools, library screening or selection approaches, and artificial intelligence/machine-learning-based strategies to mutagenesis developed in the last forty years to accelerate the natural process of evolution in creating new functional protein variants, optimization of microbial strains and transformation of enzymes into industrial machines. Analyzing patent position over these techniques and mechanisms also constitutes an integral and distinctive part of this review. The aim is to provide an up-to-date resource/technology toolbox for research-based and pharmaceutical companies to discover the boundaries of competitor's intellectual property (IP) portfolio, their freedom-to-operate in the relevant IP landscape, and the need for patent due diligence analysis to rule out whether use of a particular patented mutagenesis method, library screening/selection technique falls outside the safe harbor of experimental use exemption. While so doing, we have referred to some recent cases that emphasize the significance of selecting a suitable gene diversification strategy in directed evolution experiments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zarina Iqbal
- PakPat World Intellectual Property Protection Services, Lahore, 54000, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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Cho JH, Ha NR, Koh SH, Yoon MY. Design of a PKCδ-specific small peptide as a theragnostic agent for glioblastoma. Anal Biochem 2015; 496:63-70. [PMID: 26739937 DOI: 10.1016/j.ab.2015.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 12/16/2022]
Abstract
Glioblastoma is an aggressive malignant brain tumor that starts in the brain or spine and frequently recurs after anticancer treatment. The development of an accurate diagnostic system combined with effective cancer therapy is essential to improve prognosis of glioma patients. Peptides, produced from phage display, are attractive biomolecules for glioma treatment because of their biostability, nontoxicity, and small size. In this study, we employed phage display methodology to screen for peptides that specifically recognize the target PKCδ as a novel biomarker for glioma. The phage library screening yielded four different peptides displayed on phages with a 20- to 200-pM Kd value for the recombinant PKCδ catalytic domain. Among these four phage peptides, we selected one to synthesize and tagged it with fluorescein isothiocyanate (FITC) based on the sequence of the PKCδ-binding phage clone. The synthetic peptide showed a relative binding affinity for antibody and localization in the U373 glioma cell. The kinase activity of PKCδ was inhibited by FITC-labeled peptide with an IC50 of 1.4 μM in vitro. Consequently, the peptide found in this study might be a promising therapeutic agent against malignant brain tumor.
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Affiliation(s)
- Jun-Haeng Cho
- Department of Chemistry and Institute for Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Na-Reum Ha
- Department of Chemistry and Institute for Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Seong-Ho Koh
- Department of Neurology, Hanyang University, Seoul 133-791, South Korea
| | - Moon-Young Yoon
- Department of Chemistry and Institute for Natural Sciences, Hanyang University, Seoul 133-791, South Korea.
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Ma C, Li C, Jiang D, Gao X, Han J, Xu N, Wu Q, Nie G, Chen W, Lin F, Hou Y. Screening of a specific peptide binding to esophageal squamous carcinoma cells from phage displayed peptide library. Mol Cell Probes 2015; 29:182-9. [PMID: 25886968 DOI: 10.1016/j.mcp.2015.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/04/2015] [Accepted: 04/06/2015] [Indexed: 01/22/2023]
Abstract
To select a specifically binding peptide for imaging detection of human esophageal squamous cell carcinoma (ESCC), a phage-displayed 12-mer peptide library was used to screen the peptide that bind to ESCC cells specifically. After four rounds of bio-panning, the phage recovery rate gradually increased, and specific phage clones were effectively enriched. The 60 randomly selected phage clones were tested using cellular enzyme-linked immunosorbent assay (ELISA), and 41 phage clones were identified as positive clones with the over 2.10 ratio of absorbance higher than other clones, IRP and PBS controls. From the sequencing results of the positive clones, 14 peptide sequences were obtained and ESCP9 consensus sequence was identified as the peptide with best affinity to ESCC cells via competitive inhibition, fluorescence microscopy, and flow cytometry. The results indicate that the peptide ESCP9 can bind to ESCC cells specifically and sensitively, and it is a potential candidate to be developed as an useful molecule to the imaging detection and targeting therapy for ESCC.
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Affiliation(s)
- Caixia Ma
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Chunyan Li
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | | | - Xiaojie Gao
- College of Life and Geography Science, Qinghai Normal University, Xining, Qinghai 810008, China
| | - Juanjuan Han
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Nan Xu
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Qiong Wu
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
| | - Guochao Nie
- Center of Medical Nanomaterial, Yulin Normal College, Yulin, Guangxi 537000, China
| | - Wei Chen
- Department of Physics and the SAVANT Center, The University of Texas at Arlington, Arlington, TX 76019, USA
| | - Fenghuei Lin
- Institute of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Yingchun Hou
- Co-Innovation Center for Qinba Region's Sustainable Development, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.
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Lee KJ, Lee JH, Chung HK, Choi J, Park J, Park SS, Ju EJ, Park J, Shin SH, Park HJ, Ko EJ, Suh N, Kim I, Hwang JJ, Song SY, Jeong SY, Choi EK. Novel peptides functionally targeting in vivo human lung cancer discovered by in vivo peptide displayed phage screening. Amino Acids 2014; 47:281-9. [DOI: 10.1007/s00726-014-1852-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
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Xiao H, Bao Z, Zhao H. High Throughput Screening and Selection Methods for Directed Enzyme Evolution. Ind Eng Chem Res 2014; 54:4011-4020. [PMID: 26074668 PMCID: PMC4461044 DOI: 10.1021/ie503060a] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 02/08/2023]
Abstract
Successful
evolutionary enzyme engineering requires a high throughput
screening or selection method, which considerably increases the chance
of obtaining desired properties and reduces the time and cost. In
this review, a series of high throughput screening and selection methods
are illustrated with significant and recent examples. These high throughput
strategies are also discussed with an emphasis on compatibility with
phenotypic analysis during directed enzyme evolution. Lastly, certain
limitations of current methods, as well as future developments, are
briefly summarized.
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Affiliation(s)
- Han Xiao
- Department of Chemical and Biomolecular Engineering, Department of Biochemistry, and Departments of Chemistry and Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Zehua Bao
- Department of Chemical and Biomolecular Engineering, Department of Biochemistry, and Departments of Chemistry and Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Department of Biochemistry, and Departments of Chemistry and Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Cheung CS, Lui JC, Baron J. Identification of chondrocyte-binding peptides by phage display. J Orthop Res 2013; 31:1053-8. [PMID: 23440926 PMCID: PMC4803314 DOI: 10.1002/jor.22325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/23/2013] [Indexed: 02/04/2023]
Abstract
As an initial step toward targeting cartilage tissue for potential therapeutic applications, we sought cartilage-binding peptides using phage display, a powerful technology for selection of peptides that bind to molecules of interest. A library of phage displaying random 12-amino acid peptides was iteratively incubated with cultured chondrocytes to select phage that bind cartilage. The resulting phage clones demonstrated increased affinity to chondrocytes by ELISA, when compared to a wild-type, insertless phage. Furthermore, the selected phage showed little preferential binding to other cell types, including primary skin fibroblast, myocyte and hepatocyte cultures, suggesting a tissue-specific interaction. Immunohistochemical staining revealed that the selected phage bound chondrocytes themselves and the surrounding extracellular matrix. FITC-tagged peptides were synthesized based on the sequence of cartilage-binding phage clones. These peptides, but not a random peptide, bound cultured chondrocytes, and extracelluar matrix. In conclusion, using phage display, we identified peptide sequences that specifically target chondrocytes. We anticipate that such peptides may be coupled to therapeutic molecules to provide targeted treatment for cartilage disorders.
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Affiliation(s)
- Crystal S.F. Cheung
- Developmental Endocrinology Branch, Program in Developmental Endocrinology and Genetics; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda; Maryland
| | - Julian C. Lui
- Developmental Endocrinology Branch, Program in Developmental Endocrinology and Genetics; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda; Maryland
| | - Jeffrey Baron
- Developmental Endocrinology Branch, Program in Developmental Endocrinology and Genetics; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda; Maryland
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Lamichhane TN, Abeydeera ND, Duc ACE, Cunningham PR, Chow CS. Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. Molecules 2011; 16:1211-39. [PMID: 21278676 PMCID: PMC6259748 DOI: 10.3390/molecules16021211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 01/13/2023] Open
Abstract
Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.
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Affiliation(s)
- Tek N. Lamichhane
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | | | | | - Philip R. Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Christine S. Chow
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel: +1-313-577-2594; Fax: +1-313-577-8822
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