51
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Smith JM, Hill NC, Krasniak PJ, Fasan R. Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation. Org Biomol Chem 2014; 12:1135-42. [PMID: 24395107 DOI: 10.1039/c3ob42222d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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52
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Howell SM, Fiacco SV, Takahashi TT, Jalali-Yazdi F, Millward SW, Hu B, Wang P, Roberts RW. Serum stable natural peptides designed by mRNA display. Sci Rep 2014; 4:6008. [PMID: 25234472 PMCID: PMC4168267 DOI: 10.1038/srep06008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023] Open
Abstract
Peptides constructed with the 20 natural amino acids are generally considered to have little therapeutic potential because they are unstable in the presence of proteases and peptidases. However, proteolysis cleavage can be idiosyncratic, and it is possible that natural analogues of functional sequences exist that are highly resistant to cleavage. Here, we explored this idea in the context of peptides that bind to the signaling protein Gαi1. To do this, we used a two-step in vitro selection process to simultaneously select for protease resistance while retaining function–first by degrading the starting library with protease (chymotrypsin), followed by positive selection for binding via mRNA display. Starting from a pool of functional sequences, these experiments revealed peptides with 100–400 fold increases in protease resistance compared to the parental library. Surprisingly, selection for chymotrypsin resistance also resulted in similarly improved stability in human serum (~100 fold). Mechanistically, the decreases in cleavage results from both a lower rate of cleavage (kcat) and a weaker interaction with the protease (Km). Overall, our results demonstrate that the hydrolytic stability of functional, natural peptide sequences can be improved by two orders of magnitude simply by optimizing the primary sequence.
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Affiliation(s)
- Shannon M Howell
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Stephen V Fiacco
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Farzad Jalali-Yazdi
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles CA, 90089-1211
| | - Steven W Millward
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Biliang Hu
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles CA, 90089-1211
| | - Pin Wang
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles CA, 90089-1211
| | - Richard W Roberts
- 1] Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States [2] Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles CA, 90089-1211
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53
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Bhat A, Roberts LR, Dwyer JJ. Lead discovery and optimization strategies for peptide macrocycles. Eur J Med Chem 2014; 94:471-9. [PMID: 25109255 DOI: 10.1016/j.ejmech.2014.07.083] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
Abstract
Peptide macrocycles represent a chemical space where the best of biological tools can synergize with the best of chemical approaches in the quest for leads against undruggable targets. Peptide macrocycles offer some key advantages in both lead discovery and lead optimization phases of drug discovery when compared to natural product and synthetic macrocycles. In addition, they are uniquely positioned to capitalize on the therapeutic potential of peptides because cyclization can help drive selectivity, potency and overcome the common limitations of metabolic instability of peptides.
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Affiliation(s)
- Abhijit Bhat
- Ipsen Bioscience, Inc. 650 East Kendall Street, Cambridge, MA 02142, USA.
| | - Lee R Roberts
- Pfizer Worldwide Medicinal Chemistry, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
| | - John J Dwyer
- Ferring Research Institute, 4245 Sorrento Valley Blvd., San Diego, CA 92121, USA.
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54
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Lian W, Jiang B, Qian Z, Pei D. Cell-permeable bicyclic peptide inhibitors against intracellular proteins. J Am Chem Soc 2014; 136:9830-3. [PMID: 24972263 PMCID: PMC4227718 DOI: 10.1021/ja503710n] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cyclic peptides have great potential as therapeutic agents and research tools but are generally impermeable to the cell membrane. Fusion of cyclic peptides with a cyclic cell-penetrating peptide produces bicyclic peptides that are cell-permeable and retain the ability to recognize specific intracellular targets. Application of this strategy to protein tyrosine phosphatase 1B and a peptidyl-prolyl cis-trans isomerase (Pin1) isomerase resulted in potent, selective, proteolytically stable, and biologically active inhibitors against the enzymes.
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Affiliation(s)
- Wenlong Lian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Bisheng Jiang
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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55
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Joo SH. Cyclic peptides as therapeutic agents and biochemical tools. Biomol Ther (Seoul) 2014; 20:19-26. [PMID: 24116270 PMCID: PMC3792197 DOI: 10.4062/biomolther.2012.20.1.019] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/28/2011] [Indexed: 01/08/2023] Open
Abstract
There are many cyclic peptides with diverse biological activities, such as antibacterial activity, immunosuppressive activity, and anti-tumor activity, and so on. Encouraged by natural cyclic peptides with biological activity, efforts have been made to develop cyclic peptides with both genetic and synthetic methods. The genetic methods include phage display, intein-based cyclic peptides, and mRNA display. The synthetic methods involve individual synthesis, parallel synthesis, as well as split-and-pool synthesis. Recent development of cyclic peptide library based on split-and-pool synthesis allows on-bead screening, in-solution screening, and microarray screening of cyclic peptides for biological activity. Cyclic peptides will be useful as receptor agonist/antagonist, RNA binding molecule, enzyme inhibitor and so on, and more cyclic peptides will emerge as therapeutic agents and biochemical tools.
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Affiliation(s)
- Sang Hoon Joo
- Laboratory of Biochemistry, College of Pharmacy, Catholic University of Daegu, Gyeongsan 712-702, Republic of Korea
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56
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Abstract
Macrocyclic peptides are an emerging class of therapeutics that can modulate protein-protein interactions. In contrast to the heavily automated high-throughput screening systems traditionally used for the identification of chemically synthesized small-molecule drugs, peptide-based macrocycles can be synthesized by ribosomal translation and identified using in vitro selection techniques, allowing for extremely rapid (hours to days) screening of compound libraries comprising more than 10(13) different species. Furthermore, chemical modification of translated peptides and engineering of the genetic code have greatly expanded the structural diversity of the available peptide libraries. In this review, we discuss the use of these technologies for the identification of bioactive macrocyclic peptides, emphasizing recent developments.
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Affiliation(s)
- Toby Passioura
- Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan; , , ,
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57
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Jafari MR, Deng L, Kitov PI, Ng S, Matochko WL, Tjhung KF, Zeberoff A, Elias A, Klassen JS, Derda R. Discovery of light-responsive ligands through screening of a light-responsive genetically encoded library. ACS Chem Biol 2014; 9:443-50. [PMID: 24195775 DOI: 10.1021/cb4006722] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Light-responsive ligands are useful tools in biochemistry and cell biology because the function of these ligands can be spatially and temporally controlled. Conventional design of such ligands relies on previously available data about the structure of both the ligand and the receptor. In this paper, we describe de novo discovery of light-responsive ligands through screening of a genetically encoded light-responsive library. We ligated a photoresponsive azobenzene core to a random CX7C peptide library displayed on the coat protein of M13 phage. A one-pot alkylation/reduction of the cysteines yielded a photoresponsive library of random heptapeptide macrocycles with over 2 × 10(8) members. We characterized the reaction on-phage and optimized the yield of the modifications in phage libraries. Screening of the library against streptavidin yielded three macrocycles that bind to streptavidin in the dark and cease binding upon irradiation with 370 nm light. All ligands restored their binding properties upon thermal relaxation and could be turned ON and OFF for several cycles. We measured dissociation constants, Kd, by electrospray ionization mass spectrometry (ESI-MS) binding assay. For ligand ACGFERERTCG, the Kd of cis and trans isomers differed by 22-fold; an incomplete isomerization (85%), however, resulted in the apparent difference of 4.5-fold between the dark and the irradiated state. We anticipate that the selection strategy described in this report can be used to find light-responsive ligands for many targets that do not have known natural ligands.
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Affiliation(s)
- Mohammad R. Jafari
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lu Deng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Simon Ng
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wadim L. Matochko
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anthony Zeberoff
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Anastasia Elias
- Department
of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Ratmir Derda
- Department
of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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58
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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59
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mRNA display: from basic principles to macrocycle drug discovery. Drug Discov Today 2013; 19:388-99. [PMID: 24157402 DOI: 10.1016/j.drudis.2013.10.011] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/27/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
We describe a new discovery technology that uses mRNA-display to rapidly synthesize and screen macrocyclic peptide libraries to explore a valuable region of chemical space typified by natural products. This technology allows high-affinity peptidic macrocycles containing modified backbones and unnatural side chains to be readily selected based on target binding. Success stories covering the first examples of these libraries suggest that they could be used for the discovery of intracellular protein-protein interaction inhibitors, highly selective enzyme inhibitors or synthetic replacements for monoclonal antibodies. The review concludes with a look to the future regarding how this technology might be improved with respect to library design for cell permeability and bioavailability.
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60
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Smith JM, Frost JR, Fasan R. Emerging strategies to access peptide macrocycles from genetically encoded polypeptides. J Org Chem 2013; 78:3525-31. [PMID: 23517465 DOI: 10.1021/jo400119s] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Macrocyclic peptides have emerged as attractive molecular scaffolds for the development of chemical probes and therapeutics. In this synopsis, we highlight contemporary strategies to access peptide macrocycles from ribosomally produced polypeptides. Challenges that have been tackled in this area involve orchestrating the desired macrocyclization process in the presence of unprotected polypeptide precursors and expanding the functional space encompassed by these molecules beyond that of canonical amino acid structures. Applications of these methodologies for the discovery of bioactive molecules are also discussed.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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61
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Ito K, Passioura T, Suga H. Technologies for the synthesis of mRNA-encoding libraries and discovery of bioactive natural product-inspired non-traditional macrocyclic peptides. Molecules 2013; 18:3502-28. [PMID: 23507778 PMCID: PMC6270345 DOI: 10.3390/molecules18033502] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 01/04/2023] Open
Abstract
In this review, we discuss emerging technologies for drug discovery, which yields novel molecular scaffolds based on natural product-inspired non-traditional peptides expressed using the translation machinery. Unlike natural products, these technologies allow for constructing mRNA-encoding libraries of macrocyclic peptides containing non-canonical sidechains and N-methyl-modified backbones. The complexity of sequence space in such libraries reaches as high as a trillion (>1012), affording initial hits of high affinity ligands against protein targets. Although this article comprehensively covers several related technologies, we discuss in greater detail the technical development and advantages of the Random non-standard Peptide Integration Discovery (RaPID) system, including the recent identification of inhibitors against various therapeutic targets.
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Affiliation(s)
| | | | - Hiroaki Suga
- Author to whom correspondence should be addressed; E-Mail: ; Tel./Fax: +81-3-5841-8372
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62
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Qian Z, Liu T, Liu YY, Briesewitz R, Barrios AM, Jhiang SM, Pei D. Efficient delivery of cyclic peptides into mammalian cells with short sequence motifs. ACS Chem Biol 2013; 8:423-31. [PMID: 23130658 DOI: 10.1021/cb3005275] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cyclic peptides hold great potential as therapeutic agents and research tools, but their broad application has been limited by poor membrane permeability. Here, we report a potentially general approach for intracellular delivery of cyclic peptides. Short peptide motifs rich in arginine and hydrophobic residues (e.g., FΦRRRR, where Φ is l-2-naphthylalanine), when embedded into small- to medium-sized cyclic peptides (7-13 amino acids), bound to the plasma membrane of mammalian cultured cells and were subsequently internalized by the cells. Confocal microscopy and a newly developed peptide internalization assay demonstrated that cyclic peptides containing these transporter motifs were translocated into the cytoplasm and nucleus at efficiencies 2-5-fold higher than that of nonaarginine (R(9)). Furthermore, incorporation of the FΦRRRR motif into a cyclic peptide containing a phosphocoumaryl aminopropionic acid (pCAP) residue generated a cell permeable, fluorogenic probe for detecting intracellular protein tyrosine phosphatase activities.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and
Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Tao Liu
- Department of Chemistry and
Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
| | - Yu-Yu Liu
- Department of Physiology and
Cell Biology, College of Medicine, The Ohio State University, 1645 Neil Avenue, Columbus, Ohio 43210, United States
| | - Roger Briesewitz
- Department of Pharmacology, College
of Medicine, The Ohio State University,
Columbus, Ohio 43210, United States
| | - Amy M. Barrios
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United
States
| | - Sissy M. Jhiang
- Department of Physiology and
Cell Biology, College of Medicine, The Ohio State University, 1645 Neil Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and
Biochemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus,
Ohio 43210, United States
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63
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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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64
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Frost JR, Vitali F, Jacob NT, Brown MD, Fasan R. Macrocyclization of Organo-Peptide Hybrids through a Dual Bio-orthogonal Ligation: Insights from Structure-Reactivity Studies. Chembiochem 2012. [DOI: 10.1002/cbic.201200579] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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65
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Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM. mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 2012; 110:857-70. [DOI: 10.1002/bit.24760] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
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66
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Iwasaki K, Goto Y, Katoh T, Suga H. Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation. Org Biomol Chem 2012; 10:5783-6. [PMID: 22419118 DOI: 10.1039/c2ob25306b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mode of thioether macrocyclization of peptides containing an N-terminal 2-chloroacetyl group and two or three competing cysteine residues at downstream positions has been extensively studied, leading to a strategy for designated formation of overlapping-bicyclic peptides or dumbbell-type bicyclic peptides.
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Affiliation(s)
- Kazuhiro Iwasaki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
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67
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Hipolito CJ, Suga H. Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems. Curr Opin Chem Biol 2012; 16:196-203. [PMID: 22401851 DOI: 10.1016/j.cbpa.2012.02.014] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/13/2012] [Accepted: 02/14/2012] [Indexed: 11/30/2022]
Abstract
Bioactive natural product peptides have diverse architectures such as non-standard sidechains and a macrocyclic backbone bearing modifications. In vitro translation of peptides bearing these features would provide the research community with a diverse collection of natural product peptide-like molecules with a potential for drug development. The ordinary in vitro translation system, however, is not amenable to the incorporation of non-proteinogenic amino acids or genetic encoding of macrocyclic backbones. To circumvent this problem, flexible tRNA-acylation ribozymes (flexizymes) were combined with a custom-made reconstituted translation system to produce the flexible in vitro translation (FIT) system. The FIT system was integrated with mRNA display to devise an in vitro selection technique, referred to as the random non-standard peptide integrated discovery (RaPID) system. It has recently yielded an N-methylated macrocyclic peptide having high affinity (Kd=0.60 nM) for its target protein, E6AP.
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Affiliation(s)
- Christopher J Hipolito
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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68
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Abstract
The ribosomal synthesis of drug-like peptides containing unnatural amino acids is possible due to the broad substrate specificity of the ribosome. In this protocol, a reconstituted Escherichia coli ribosomal translation system (PURE) is adapted to incorporate unnatural amino acids into mRNA-displayed peptide libraries, which are used in in vitro selection.
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Affiliation(s)
- Zhong Ma
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
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69
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Liu M, Tada S, Ito M, Abe H, Ito Y. In vitro selection of a photo-responsive peptide aptamer using ribosome display. Chem Commun (Camb) 2012; 48:11871-3. [DOI: 10.1039/c2cc36618e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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70
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Touati J, Angelini A, Hinner MJ, Heinis C. Enzymatic cyclisation of peptides with a transglutaminase. Chembiochem 2011; 12:38-42. [PMID: 21154802 DOI: 10.1002/cbic.201000451] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jeremy Touati
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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71
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Post-translational modification of genetically encoded polypeptide libraries. Curr Opin Chem Biol 2011; 15:355-61. [PMID: 21489857 DOI: 10.1016/j.cbpa.2011.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/17/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
The genetic encoding of polypeptides with biological display systems enables the facile generation and screening of very large combinatorial libraries of molecules. By post-translationally modifying the encoded polypeptides, chemically and structurally more diverse molecules beyond linear amino acid polymers can be generated. The first post-translational modification applied to encoded polypeptides, the oxidation of cysteine residues to form disulfide bridges, is a natural one and was used to cyclise short peptides soon after the invention of phage display. Recently a range of non-natural chemical strategies for the post-translational modification of encoded polypeptide repertoires were applied to generate optical biosensors, semisynthetic polypeptides, peptide-drug conjugates, redox-insensitive monocyclic peptides or multicyclic peptides, and these strategies are reviewed in this article.
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72
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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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73
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Terrett NK. Methods for the synthesis of macrocycle libraries for drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e95-e146. [PMID: 24103719 DOI: 10.1016/j.ddtec.2010.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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74
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Yamagishi Y, Ashigai H, Goto Y, Murakami H, Suga H. Ribosomal Synthesis of Cyclic Peptides with a Fluorogenic Oxidative Coupling Reaction. Chembiochem 2009; 10:1469-72. [DOI: 10.1002/cbic.200900021] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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75
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Mizusawa K, Abe K, Sando S, Aoyama Y. Synthesis of puromycin derivatives with backbone-elongated substrates and associated translation inhibitory activities. Bioorg Med Chem 2009; 17:2381-7. [DOI: 10.1016/j.bmc.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/05/2009] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
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76
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Abstract
In vitro genetic approaches are powerful solutions to the protein design problem. mRNA display is an in vitro selection technique enabling the design of peptide and protein ligands ranging from one to over 100 amino acids. Libraries containing more than 10 trillion unique sequences can be synthesized and sieved with exquisite control over binding stringency and specificity.
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Affiliation(s)
- Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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77
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78
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Sako Y, Goto Y, Murakami H, Suga H. Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. ACS Chem Biol 2008; 3:241-9. [PMID: 18338852 DOI: 10.1021/cb800010p] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we report a new enabling technology for the synthesis of peptidase-resistant cyclic peptides by means of genetic code reprogramming involving the flexizyme (a tRNA acylation ribozyme) and PURE (a reconstituted cell-free translation) systems. In this work, we have developed a new nonproteinogenic amino acid bearing a chloroacetyl group in the side chain, which forms a physiologically stable thioether bond by intramolecular reaction with the sulfhydryl group of a Cys residue in the peptide chain upon translation. Significantly, this chemistry takes place spontaneously in situ of the translation solution, giving the corresponding cyclic peptides independent of ring sizes. We have used this method to convert human urotensin II, known as a potent vasoconstrictor, to its analogue containing a thioether bond, showing that this new analogue retains biological activity. Moreover, this peptide exhibits remarkable resistance against peptidases under reducing conditions. Thus, this technology offers a new means to accelerate the discovery of therapeutic peptidic drugs.
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Affiliation(s)
- Yusuke Sako
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo, 113-8656, Japan
| | - Yuki Goto
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
| | - Hiroshi Murakami
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
| | - Hiroaki Suga
- Research Center for Advanced
Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro,
Tokyo, 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo, 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1, Komaba, Meguro, Tokyo, 153-8904, Japan
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79
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Zhang Y, Zhou S, Wavreille AS, DeWille J, Pei D. Cyclic peptidyl inhibitors of Grb2 and tensin SH2 domains identified from combinatorial libraries. ACTA ACUST UNITED AC 2008; 10:247-55. [PMID: 18257540 DOI: 10.1021/cc700185g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides provide attractive lead compounds for drug discovery and excellent molecular probes in biomedical research. In this work, a novel method has been developed for the high-throughput synthesis, screening, and identification of cyclic peptidyl ligands against macromolecular targets. Support-bound cyclic phosphotyrosyl peptide libraries containing randomized amino acid sequences and different ring sizes (theoretical diversity of 3.2 x 10(6)) were synthesized and screened against the SH2 domains of Grb2 and tensin. Potent, selective inhibitors were identified from the libraries and were generally more effective than the corresponding linear peptides. One of the inhibitors selected against the Grb2 SH2 domain inhibited human breast cancer cell growth and disrupted actin filaments. This method should be applicable to the development of cyclic peptidyl inhibitors against other protein domains, enzymes, and receptors.
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Affiliation(s)
- Yanyan Zhang
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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80
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Liu T, Joo SH, Voorhees JL, Brooks CL, Pei D. Synthesis and screening of a cyclic peptide library: discovery of small-molecule ligands against human prolactin receptor. Bioorg Med Chem 2008; 17:1026-33. [PMID: 18234500 DOI: 10.1016/j.bmc.2008.01.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/09/2008] [Accepted: 01/10/2008] [Indexed: 11/18/2022]
Abstract
Prolactin receptor is involved in normal lactation and reproduction; however, excessive prolactin levels can cause various reproductive disorders such as prolactinomas. Small-molecule antagonists against the human prolactin receptor (hPRLr) thus have potential clinical applications and may serve as useful molecular probes in biomedical research. In this work, we synthesized a large, support-bound cyclic peptide library (theoretical diversity of 1.2x10(7)) on 90-microm TentaGel beads and screened it against the extracellular domain of hPRLr. To facilitate hit identification, each TentaGel bead was spatially segregated into outer and inner layers, with a cyclic peptide displayed on the bead surface while the bead interior contained the corresponding linear peptide. The identity of a positive bead was revealed by sequencing the linear encoding peptide within the bead by partial Edman degradation/mass spectrometry. Screening of the library resulted in 20 hits, two of which were selected for further analysis and shown to bind to hPRLr with dissociation constants of 2-3 microM.
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Affiliation(s)
- Tao Liu
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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81
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Ohta A, Murakami H, Higashimura E, Suga H. Synthesis of Polyester by Means of Genetic Code Reprogramming. ACTA ACUST UNITED AC 2007; 14:1315-22. [DOI: 10.1016/j.chembiol.2007.10.015] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 09/11/2007] [Accepted: 10/22/2007] [Indexed: 11/28/2022]
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82
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Hartman MCT, Josephson K, Lin CW, Szostak JW. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2007; 2:e972. [PMID: 17912351 PMCID: PMC1989143 DOI: 10.1371/journal.pone.0000972] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 09/12/2007] [Indexed: 11/23/2022] Open
Abstract
Background The application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. The specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. We have previously shown that over 90 unnatural amino acids can be enzymatically loaded onto tRNA. Methodology/Principal Findings We have now used a competition assay to assess the efficiency of tRNA-aminoacylation of these analogs. We have also used a series of peptide translation assays to measure the efficiency with which these analogs are incorporated into peptides. The translation apparatus tolerates most side chain derivatives, a few α,α disubstituted, N-methyl and α-hydroxy derivatives, but no β-amino acids. We show that over 50 unnatural amino acids can be incorporated into peptides by ribosomal translation. Using a set of analogs that are efficiently charged and translated we were able to prepare individual peptides containing up to 13 different unnatural amino acids. Conclusions/Significance Our results demonstrate that a diverse array of unnatural building blocks can be translationally incorporated into peptides. These building blocks provide new opportunities for in vitro selections with highly modified drug-like peptides.
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Affiliation(s)
- Matthew C. T. Hartman
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kristopher Josephson
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chi-Wang Lin
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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83
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Millward SW, Fiacco S, Austin RJ, Roberts RW. Design of cyclic peptides that bind protein surfaces with antibody-like affinity. ACS Chem Biol 2007; 2:625-34. [PMID: 17894440 PMCID: PMC3747972 DOI: 10.1021/cb7001126] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a pressing need for new molecular tools to target protein surfaces with high affinity and specificity. Here, we describe cyclic messenger RNA display with a trillion-member covalent peptide macrocycle library. Using this library, we have designed a number of high-affinity, redox-insensitive, cyclic peptides that target the signaling protein G alpha i1. In addition to cyclization, our library construction took advantage of an expanded genetic code, utilizing nonsense suppression to insert N-methylphenylalanine as a 21st amino acid. The designed macrocycles exhibit several intriguing features. First, the core motif seen in all of the selected variants is the same and shares an identical context with respect to the macrocyclic scaffold, consistent with the idea that selection simultaneously optimizes both the cyclization chemistry and the structural placement of the binding epitope. Second, detailed characterization of one molecule, cyclic G alpha i binding peptide (cycGiBP), demonstrates substantially enhanced proteolytic stability relative to that of the parent linear molecule. Third and perhaps most important, the cycGiBP peptide binds the target with very high affinity ( K i approximately 2.1 nM), similar to those of many of the best monoclonal antibodies and higher than that of the betagamma heterodimer, an endogenous G alpha i1 ligand. Overall the work provides a general route to design novel, low-molecular-weight, high-affinity ligands that target protein surfaces.
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Affiliation(s)
- Steven W. Millward
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Stephen Fiacco
- Department of Chemistry, Chemical Engineering, and Biology, University of Southern California, 3710 McClintock Avenue, Los Angeles, California 90089-1211
| | - Ryan J. Austin
- Department of Chemistry, Chemical Engineering, and Biology, University of Southern California, 3710 McClintock Avenue, Los Angeles, California 90089-1211
| | - Richard W. Roberts
- Department of Chemistry, Chemical Engineering, and Biology, University of Southern California, 3710 McClintock Avenue, Los Angeles, California 90089-1211
- Corresponding author,
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84
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Fukuda A, Kondo S, Maruyama K, Suzuki K, Hagiwara M. A Pseudo Data Generation Method and a Two-Stage Quantitation Method for Simultaneous Determination Sensor of Nucleotide Derivatives. JOURNAL OF ADVANCED COMPUTATIONAL INTELLIGENCE AND INTELLIGENT INFORMATICS 2007. [DOI: 10.20965/jaciii.2007.p0751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we propose a pseudo data generation method and a two-stage quantitation method for simultaneous determination of nucleotide derivatives sensor that determines concentration of nucleotide derivatives based on sensor response. Conventional sensors are difficult to determine concentration of nucleotide derivatives simultaneously because they have similar structures and they influence each other, so the precision is low. In order to archive high precision and simultaneous determination sensor, this paper proposes a pseudo data generation method and a two-stage quantitation method. To analyze sensor response, we use GRNN (General Regression Neural Network). With this sensor, concentration of nucleotide derivatives is determined simultaneously, easily and fast. It was confirmed by the experiments that proposed methods are effective for determining concentration of nucleotide derivatives.
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