1
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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2
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Pirone L, Ripoll-Rozada J, Leone M, Ronca R, Lombardo F, Fiorentino G, Andersen JF, Pereira PJB, Arcà B, Pedone E. Functional analyses yield detailed insight into the mechanism of thrombin inhibition by the antihemostatic salivary protein cE5 from Anopheles gambiae. J Biol Chem 2017; 292:12632-12642. [PMID: 28592490 DOI: 10.1074/jbc.m117.788042] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/23/2017] [Indexed: 11/06/2022] Open
Abstract
Saliva of blood-feeding arthropods carries several antihemostatic compounds whose physiological role is to facilitate successful acquisition of blood. The identification of novel natural anticoagulants and the understanding of their mechanism of action may offer opportunities for designing new antithrombotics disrupting blood clotting. We report here an in-depth structural and functional analysis of the anophelin family member cE5, a salivary protein from the major African malaria vector Anopheles gambiae that specifically, tightly, and quickly binds and inhibits thrombin. Using calorimetry, functional assays, and complementary structural techniques, we show that the central region of the protein, encompassing amino acids Asp-31-Arg-62, is the region mainly responsible for α-thrombin binding and inhibition. As previously reported for the Anopheles albimanus orthologue anophelin, cE5 binds both thrombin exosite I with segment Glu-35-Asp-47 and the catalytic site with the region Pro-49-Arg-56, which includes the highly conserved DPGR tetrapeptide. Moreover, the N-terminal Ala-1-Ser-30 region of cE5 (which includes an RGD tripeptide) and the additional C-terminal serine-rich Asn-63-Glu-82 region (absent in orthologues from anophelines of the New World species A. albimanus and Anopheles darlingi) also played some functionally relevant role. Indeed, we observed decreased thrombin binding and inhibitory properties even when using the central cE5 fragment (Asp-31-Arg-62) alone. In summary, these results shed additional light on the mechanism of thrombin binding and inhibition by this family of salivary anticoagulants from anopheline mosquitoes.
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Affiliation(s)
- Luciano Pirone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Jorge Ripoll-Rozada
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy
| | - Raffaele Ronca
- Department of Biology, Universita' degli Studi di Napoli Federico II, Via Cinthia, 80126 Naples, Italy
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gabriella Fiorentino
- Department of Biology, Universita' degli Studi di Napoli Federico II, Via Cinthia, 80126 Naples, Italy
| | - John F Andersen
- Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland 20852
| | - Pedro José Barbosa Pereira
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Bruno Arcà
- Department of Public Health and Infectious Diseases, Division of Parasitology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy.
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3
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Arcà B, Lombardo F, Struchiner CJ, Ribeiro JMC. Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species. BMC Genomics 2017; 18:153. [PMID: 28193177 PMCID: PMC5307786 DOI: 10.1186/s12864-017-3579-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors. Even though the role of quite a few mosquito salivary proteins has been clarified in the last decade, we still completely ignore the physiological role of many of them as well as the extent of their involvement in the complex interactions taking place between the mosquito vectors, the pathogens they transmit and the vertebrate host. The recent release of the genomes of 16 Anopheles species offered the opportunity to get insights into function and evolution of salivary protein families in anopheline mosquitoes. RESULTS Orthologues of fifty three Anopheles gambiae salivary proteins were retrieved and annotated from 18 additional anopheline species belonging to the three subgenera Cellia, Anopheles, and Nyssorhynchus. Our analysis included 824 full-length salivary proteins from 24 different families and allowed the identification of 79 novel salivary genes and re-annotation of 379 wrong predictions. The comparative, structural and phylogenetic analyses yielded an unprecedented view of the anopheline salivary repertoires and of their evolution over 100 million years of anopheline radiation shedding light on mechanisms and evolutionary forces that contributed shaping the anopheline sialomes. CONCLUSIONS We provide here a comprehensive description, classification and evolutionary overview of the main anopheline salivary protein families and identify two novel candidate markers of human exposure to malaria vectors worldwide. This anopheline sialome catalogue, which is easily accessible as hyperlinked spreadsheet, is expected to be useful to the vector biology community and to improve the capacity to gain a deeper understanding of mosquito salivary proteins facilitating their possible exploitation for epidemiological and/or pathogen-vector-host interaction studies.
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Affiliation(s)
- Bruno Arcà
- Department of Public Health and Infectious Diseases - Division of Parasitology, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Fabrizio Lombardo
- Department of Public Health and Infectious Diseases - Division of Parasitology, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Claudio J Struchiner
- Fundação Oswaldo Cruz, Avenida Brasil, 4365, Rio de Janeiro, Brazil.,Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, 12735 Twinbrook Parkway, Rockville, MD, 20852, USA
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4
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Hacker DE, Almohaini M, Anbazhagan A, Ma Z, Hartman MCT. Peptide and peptide library cyclization via bromomethylbenzene derivatives. Methods Mol Biol 2015; 1248:105-17. [PMID: 25616329 DOI: 10.1007/978-1-4939-2020-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cyclization confers several advantages to peptides, cumulatively serving to make them more drug-like. In this protocol, cyclic peptides are generated via bis-alkylation of cysteine-containing peptides using α,α'-dibromo-m-xylene. The reactions are robust and high yielding. Multiple reaction platforms for the application of this versatile strategy are described herein: the cyclization of solid-phase-synthesized peptides, both in solution and on resin, as well as the cyclization of in vitro translated mRNA-peptide fusion libraries on oligo(dT) resin.
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Affiliation(s)
- David E Hacker
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA, 23298-0037, USA
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5
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Construction and screening of vast libraries of natural product-like macrocyclic peptides using in vitro display technologies. Curr Opin Chem Biol 2015; 24:131-8. [DOI: 10.1016/j.cbpa.2014.11.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/07/2014] [Accepted: 11/14/2014] [Indexed: 11/20/2022]
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6
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Larsen AC, Gillig A, Shah P, Sau SP, Fenton KE, Chaput JC. General approach for characterizing in vitro selected peptides with protein binding affinity. Anal Chem 2014; 86:7219-23. [PMID: 24970615 PMCID: PMC4215864 DOI: 10.1021/ac501614d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
In
vitro selection technologies are important tools for identifying
high affinity peptides to proteins of broad medical and biological
interest. However, the technological advances that have made it possible
to generate long lists of candidate peptides have far outpaced our
ability to characterize the binding properties of individual peptides.
Here, we describe a low cost strategy to rapidly synthesize, purify,
screen, and characterize peptides for high binding affinity. Peptides
are assayed in a 96-well dot blot apparatus using membranes that enable
partitioning of bound and unbound peptide–protein complexes.
We have validated the binding affinity constants produced by this
method using known peptide ligands and applied this process to discover
five new peptides with nanomolar affinity to human α-thrombin.
Given the need for new analytical tools that can accelerate peptide
discovery and characterization, we feel that this approach would be
useful to a wide range of technologies that utilize high affinity
peptides.
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Affiliation(s)
- Andrew C Larsen
- Department of Chemistry and Biochemistry and ‡The Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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7
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Zhao Q, Gao J. Sensitive and selective detection of thrombin by using a cyclic peptide as affinity ligand. Biosens Bioelectron 2014; 63:21-25. [PMID: 25048449 DOI: 10.1016/j.bios.2014.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/23/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
Here we describe a sensitive assay for thrombin by using a high binding-affinity cyclic peptide against thrombin as affinity ligand. The cyclic peptide is immobilized on the magnetic beads or microplates to selectively capture thrombin. The enriched thrombin then catalyzes the cleavage of a substrate of thrombin to a detectable product. The detection of thrombin is finally achieved by measuring the generated product. This assay enables the detection of thrombin at tens fM in 100 µL of sample solution when fluorogenic substrate was applied, while detection limits reached pM level when chromogenic substrate was used. Thrombin in plasma sample can be detected with this assay. This cyclic peptide affinity ligand shows potentials for thrombin analysis in other detection formats.
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Affiliation(s)
- Qiang Zhao
- Research Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| | - Jie Gao
- Research Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
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8
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Abstract
All cellular proteins are derived from preexisting ones by natural selection. Because of the random nature of this process, many potentially useful protein structures never arose or were discarded during evolution. Here, we used a single round of genetic selection in mouse cells to isolate chemically simple, biologically active transmembrane proteins that do not contain any amino acid sequences from preexisting proteins. We screened a retroviral library expressing hundreds of thousands of proteins consisting of hydrophobic amino acids in random order to isolate four 29-aa proteins that induced focus formation in mouse and human fibroblasts and tumors in mice. These proteins share no amino acid sequences with known cellular or viral proteins, and the simplest of them contains only seven different amino acids. They transformed cells by forming a stable complex with the platelet-derived growth factor β receptor transmembrane domain and causing ligand-independent receptor activation. We term this approach de novo selection and suggest that it can be used to generate structures and activities not observed in nature, create prototypes for novel research reagents and therapeutics, and provide insight into cell biology, transmembrane protein-protein interactions, and possibly virus evolution and the origin of life.
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9
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Krall N, Scheuermann J, Neri D. Small Targeted Cytotoxics: Current State and Promises from DNA-Encoded Chemical Libraries. Angew Chem Int Ed Engl 2013; 52:1384-402. [DOI: 10.1002/anie.201204631] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/06/2023]
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10
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Krall N, Scheuermann J, Neri D. Entwicklung zielgerichteter niedermolekularer zytotoxischer Wirkstoffverbindungen mit DNA-codierten chemischen Bibliotheken. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204631] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Uzawa T, Tada S, Wang W, Ito Y. Expansion of the aptamer library from a "natural soup" to an "unnatural soup". Chem Commun (Camb) 2013; 49:1786-95. [PMID: 23283144 DOI: 10.1039/c2cc36348h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of evolving a commonly existing biomolecule into a variety of functional biomolecules has now been realized in the form of aptamers through the development of in vitro selection. In addition to their high affinity and high specificity for the desired targets, aptamers are easily synthesized chemically and can be modified for downstream applications. Although aptamers were originally selected from a library containing only natural components, the past decade has seen a wealth of new aptamers selected from libraries containing unnatural components to provide new aptamer functions artificially. In this review, we highlight this transition (the shift between selection from natural components and selection from unnatural components) and the applications of selected aptamers.
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Affiliation(s)
- Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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12
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Zhao Q, Gao J. An affinity capture involved enzymatic assay for thrombin by using peptide aptamers as affinity ligands on magnetic beads. Chem Commun (Camb) 2013; 49:7720-2. [DOI: 10.1039/c3cc44400g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Valencia CA, Zou J, Liu R. In vitro selection of proteins with desired characteristics using mRNA-display. Methods 2012. [PMID: 23201412 DOI: 10.1016/j.ymeth.2012.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
mRNA-display is an amplification-based, iterative rounds of in vitro protein selection technique that circumvents a number of difficulties associated with yeast two-hybrid and phage display. Because of the covalent linkage between the genotype and the phenotype, mRNA-display provides a powerful means for reading and amplifying a peptide or protein sequence after it has been selected from a library with very high diversity. The purpose of this article is to provide a summary of the field and practical framework of mRNA-display-based selections. We summarize the advantages and limitations of selections using mRNA-display as well as the recent applications, namely, the identification of novel affinity reagents, target-binding partners, and enzyme substrates from synthetic peptide or natural proteome libraries. Practically, we provide a detailed procedure for performing mRNA-display-based selections with the aim of identifying protease substrates and binding partners of a target protein. Furthermore, we describe how to confirm the function of the selected protein sequences by biochemical assays and bioinformatic tools.
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Affiliation(s)
- C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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14
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Schlippe YVG, Hartman MCT, Josephson K, Szostak JW. In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J Am Chem Soc 2012; 134:10469-77. [PMID: 22428867 PMCID: PMC3384292 DOI: 10.1021/ja301017y] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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There is a great demand for the discovery of new therapeutic
molecules
that combine the high specificity and affinity of biologic drugs with
the bioavailability and lower cost of small molecules. Small, natural-product-like
peptides hold great promise in bridging this gap; however, access
to libraries of these compounds has been a limitation. Since ribosomal
peptides may be subjected to in vitro selection techniques,
the generation of extremely large libraries (>1013)
of
highly modified macrocyclic peptides may provide a powerful alternative
for the generation and selection of new useful bioactive molecules.
Moreover, the incorporation of many non-proteinogenic amino acids
into ribosomal peptides in conjunction with macrocyclization should
enhance the drug-like features of these libraries. Here we show that
mRNA-display, a technique that allows the in vitro selection of peptides, can be applied to the evolution of macrocyclic
peptides that contain a majority of unnatural amino acids. We describe
the isolation and characterization of two such unnatural cyclic peptides
that bind the protease thrombin with low nanomolar affinity, and we
show that the unnatural residues in these peptides are essential for
the observed high-affinity binding. We demonstrate that the selected
peptides are tight-binding inhibitors of thrombin, with Kiapp values in the low nanomolar range. The
ability to evolve highly modified macrocyclic peptides in the laboratory
is the first crucial step toward the facile generation of useful molecular
reagents and therapeutic lead molecules that combine the advantageous
features of biologics with those of small-molecule drugs.
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Affiliation(s)
- Yollete V Guillen Schlippe
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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15
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Seelig B. mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries. Nat Protoc 2011; 6:540-52. [DOI: 10.1038/nprot.2011.312] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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16
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Yamaguchi J, Naimuddin M, Biyani M, Sasaki T, Machida M, Kubo T, Funatsu T, Husimi Y, Nemoto N. cDNA display: a novel screening method for functional disulfide-rich peptides by solid-phase synthesis and stabilization of mRNA-protein fusions. Nucleic Acids Res 2009; 37:e108. [PMID: 19528071 PMCID: PMC2760808 DOI: 10.1093/nar/gkp514] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We report a robust display technology for the screening of disulfide-rich peptides, based on cDNA–protein fusions, by developing a novel and versatile puromycin-linker DNA. This linker comprises four major portions: a ‘ligation site’ for T4 RNA ligase, a ‘biotin site’ for solid-phase handling, a ‘reverse transcription primer site’ for the efficient and rapid conversion from an unstable mRNA–protein fusion (mRNA display) to a stable mRNA/cDNA–protein fusion (cDNA display) whose cDNA is covalently linked to its encoded protein and a ‘restriction enzyme site’ for the release of a complex from the solid support. This enables not only stabilizing mRNA–protein fusions but also promoting both protein folding and disulfide shuffling reactions. We evaluated the performance of cDNA display in different model systems and demonstrated an enrichment efficiency of 20-fold per selection round. Selection of a 32-residue random library against interleukin-6 receptor generated novel peptides containing multiple disulfide bonds with a unique linkage for its function. The peptides were found to bind with the target in the low nanomolar range. These results show the suitability of our method for in vitro selections of disulfide-rich proteins and other potential applications.
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Affiliation(s)
- Junichi Yamaguchi
- Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, Saitama Industrial Technology Center, Kawaguchi, Saitama 333-0844, Japan
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17
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Kitamura K, Yoshida C, Kinoshita Y, Kadowaki T, Takahashi Y, Tayama T, Kawakubo T, Naimuddin M, Salimullah M, Nemoto N, Hanada K, Husimi Y, Yamamoto K, Nishigaki K. Development of systemic in vitro evolution and its application to generation of peptide-aptamer-based inhibitors of cathepsin E. J Mol Biol 2008; 387:1186-98. [PMID: 19150354 DOI: 10.1016/j.jmb.2008.12.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 11/16/2008] [Accepted: 12/11/2008] [Indexed: 12/27/2022]
Abstract
Proteases are involved in various biological functions. Thus, inhibition of their activities is scientifically interesting and medically important. However, there is no systematic method established to date to generate endopeptidase inhibitory peptides. Here, we report a general system to identify endopeptidase inhibitory peptides based on the use of in vitro evolution. Using this system, we generated peptides that inhibit cathepsin E (CE) specifically at a submicromolar IC(50). This system generates protease inhibitor peptides utilizing techniques of cDNA display, selection-by-function, Y-ligation-based block shuffling, and others. We further demonstrated the importance and effectiveness of a secondary library for obtaining small-sized and active peptides. CE inhibitory peptides generated by this method were characterized by a small size (8 to 12 aa) and quite different sequences, suggesting that they bind to different sites on CE. Typical CE inhibitory peptide aptamers obtained here (P(i)101; SCGG IIII SCIA) have half an inhibition activity (K(i); 5 nM) of pepstatin A (potent CE inhibitor) without inhibiting cathepsin D (structurally similar to CE). The general applicability of this system suggests that it may be useful to identify inhibitory peptides for various kinds of proteases and that it may therefore contribute to protein science and drug discovery. The peptide binding to a protein is discussed in comparison with the antibody binding to an antigen.
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Affiliation(s)
- Koichiro Kitamura
- Rational Evolutionary Design of Advanced Biomolecules, Saitama (REDS), Saitama Small Enterprise Promotion Corporation, #552, Saitama Industrial Technology Center, 3-12-18 Kami-Aoki, Kawaguchi, Saitama 333-0844, Japan
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18
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Austin RJ, Ja WW, Roberts RW. Evolution of class-specific peptides targeting a hot spot of the Galphas subunit. J Mol Biol 2008; 377:1406-18. [PMID: 18329041 DOI: 10.1016/j.jmb.2008.01.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 12/20/2007] [Accepted: 01/14/2008] [Indexed: 11/16/2022]
Abstract
The four classes of heterotrimeric G-protein alpha subunits act as molecular routers inside cells, gating signals based on a bound guanosine nucleotide (guanosine 5'-triphosphate versus guanosine 5'-diphosphate). Ligands that specifically target individual subunits provide new tools for monitoring and modulating these networks, but are challenging to design due to the high sequence homology and structural plasticity of the Galpha-binding surface. Here we have created an mRNA display library of peptides based on the short Galpha-modulating peptide R6A-1 and selected variants that target a convergent protein-binding surface of Galphas.guanosine 5'-diphosphate. After selection/evolution, the most Galphas-specific peptide, Galphas(s)-binding peptide (GSP), was used to design a second-generation library, resulting in several new affinity- and selectivity-matured peptides denoted as mGSPs. The two-step evolutionary walk from R6A-1 to mGSP-1 resulted in an 8000-fold inversion in binding specificity, altered seven out of nine residues in the starting peptide core, and incorporated both positive and negative design steps. The resulting mGSP-1 peptide shows remarkable selectivity and affinity, exhibiting little or no binding to nine homologous Galpha subunits or human H-Ras, and even discriminates the Galphas splice variant Galphas(l). Selected peptides make specific contacts with the effector-binding region of Galpha, which may explain an interesting bifunctional activity observed in GSP. Overall, our work demonstrates a design of simple, linear, highly specific peptides that target a protein-binding surface of Galphas and argues that mRNA display-based selection/evolution is a powerful route for targeting protein families with high class specificity and state specificity.
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Affiliation(s)
- Ryan J Austin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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19
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Seelig B, Szostak JW. Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 2007; 448:828-31. [PMID: 17700701 PMCID: PMC4476047 DOI: 10.1038/nature06032] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Accepted: 06/19/2007] [Indexed: 11/10/2022]
Abstract
Enzymes are exceptional catalysts that facilitate a wide variety of reactions under mild conditions, achieving high rate-enhancements with excellent chemo-, regio- and stereoselectivities. There is considerable interest in developing new enzymes for the synthesis of chemicals and pharmaceuticals and as tools for molecular biology. Methods have been developed for modifying and improving existing enzymes through screening, selection and directed evolution. However, the design and evolution of truly novel enzymes has relied on extensive knowledge of the mechanism of the reaction. Here we show that genuinely new enzymatic activities can be created de novo without the need for prior mechanistic information by selection from a naive protein library of very high diversity, with product formation as the sole selection criterion. We used messenger RNA display, in which proteins are covalently linked to their encoding mRNA, to select for functional proteins from an in vitro translated protein library of >10(12 )independent sequences without the constraints imposed by any in vivo step. This technique has been used to evolve new peptides and proteins that can bind a specific ligand, from both random-sequence libraries and libraries based on a known protein fold. We now describe the isolation of novel RNA ligases from a library that is based on a zinc finger scaffold, followed by in vitro directed evolution to further optimize these enzymes. The resulting ligases exhibit multiple turnover with rate enhancements of more than two-million-fold.
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Affiliation(s)
- Burckhard Seelig
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology (CCIB), 7215 Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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21
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Abstract
Display technologies are fundamental to the isolation of specific high-affinity binding proteins for diagnostic and therapeutic applications in cancer, neurodegenerative, and infectious diseases as well as autoimmune and inflammatory disorders. Applications extend into the broad field of antibody (Ab) engineering, synthetic enzymes, proteomics, and cell-free protein synthesis. Recently, in vitro display technologies have come to prominence due to the isolation of high-affinity human antibodies by phage display, the development of novel scaffolds for ribosome display, and the discovery of novel protein-protein interactions. In vitro display represents an emerging and innovative technology for the rapid isolation and evolution of high-affinity peptides and proteins. So far, only one clinical drug candidate produced by in vitro display technology has been approved by the FDA for use in humans, but several are in clinical or preclinical testing. This review highlights recent advances in various engineered biopharmaceutical products isolated by in vitro display with a focus on the commercial developments.
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Affiliation(s)
- Achim Rothe
- CSIRO Molecular and Health Technologies, Parkville, Victoria, Australia
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23
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Curtis EA, Bartel DP. New catalytic structures from an existing ribozyme. Nat Struct Mol Biol 2006; 12:994-1000. [PMID: 16228005 DOI: 10.1038/nsmb1003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 09/02/2005] [Indexed: 11/10/2022]
Abstract
Although protein enzymes with new catalytic activities can arise from existing scaffolds, less is known about the origin of ribozymes with new activities. Furthermore, mechanisms by which new macromolecular folds arise are not well characterized for either protein or RNA. Here we investigate how readily ribozymes with new catalytic activities and folds can arise from an existing ribozyme scaffold. Using in vitro selection, we isolated 23 distinct kinase ribozymes from a pool of sequence variants of an aminoacylase parent ribozyme. Analysis of these new kinases showed that ribozymes with new folds and biochemical activities can be found within a short mutational distance of a given ribozyme. However, the probability of finding such ribozymes increases considerably as the mutational distance from the parental ribozyme increases, indicating a need to escape the fold of the parent.
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Affiliation(s)
- Edward A Curtis
- Whitehead Institute for Biomedical Research and Department of Biology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Muranaka N, Hohsaka T, Sisido M. Four-base codon mediated mRNA display to construct peptide libraries that contain multiple nonnatural amino acids. Nucleic Acids Res 2006; 34:e7. [PMID: 16397292 PMCID: PMC1325208 DOI: 10.1093/nar/gnj003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In vitro selection and directed evolution of peptides from mRNA display are powerful strategies to find novel peptide ligands that bind to target biomolecules. In this study, we expanded the mRNA display method to include multiple nonnatural amino acids by introducing three different four-base codons at a randomly selected single position on the mRNA. Another nonnatural amino acid may be introduced by suppressing an amber codon that may appear from a (NNK)n nucleotide sequence on the mRNA. The mRNA display was expressed in an Escherichia coli in vitro translation system in the presence of three types of tRNAs carrying different four-base anticodons and a tRNA carrying an amber anticodon, the tRNAs being chemically aminoacylated with different nonnatural amino acids. The complexity of the starting mRNA-displayed peptide library was estimated to be 1.1 × 1012 molecules. The effectiveness of the four-base codon mediated mRNA display method was demonstrated in the selection of biocytin-containing peptides on streptavidin-coated beads. Moreover, a novel streptavidin-binding nonnatural peptide containing benzoylphenylalanine was obtained from the nonnatural peptide library. The nonnatural peptide library from the four-base codon mediated mRNA display provides much wider functional and structural diversity than conventional peptide libraries that are constituted from 20 naturally occurring amino acids.
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Affiliation(s)
- Norihito Muranaka
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
- School of Materials Science, Japan Advanced Institute of Science and Technology1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- PRESTO, Japan Science and Technology Agency4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- To whom correspondence should be addressed. Tel: +81 761 51 1681; Fax: +81 761 51 1149;
| | - Masahiko Sisido
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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25
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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26
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Hale MB, Nolan GP, Wolkowicz R. Oligonucleotide-directed site-specific integration of high complexity libraries into ssDNA templates. Nucleic Acids Res 2004; 32:e22. [PMID: 14752044 PMCID: PMC373376 DOI: 10.1093/nar/gnh021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an approach that generates an oligomer-based library with minimal need for restriction site modification of sequences in the target vector. The technique has the advantage that it can be applied for generating peptide aptamer libraries at sites within proteins without the need for introducing flanking enzyme sites. As an example we present a phagemid retroviral shuttle vector that can be used to achieve stable expression of the library in mammalian cells for the purpose of screening for peptides with desired biological activity.
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Affiliation(s)
- M B Hale
- Department of Molecular Pharmacology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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27
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Jones D. The clot thickens. Nat Rev Drug Discov 2003. [DOI: 10.1038/nrd1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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