1
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Wills R, Adebomi V, Raj M. Site-Selective Peptide Macrocyclization. Chembiochem 2020; 22:52-62. [PMID: 32794268 DOI: 10.1002/cbic.202000398] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Cyclized peptides have seen a rise in popularity in the pharmaceutical industry as drug molecules. As such, new macrocyclization methodologies have become abundant in the last several decades. However, efficient methods of cyclization without the formation of side products remain a great challenge. Herein, we review cyclization approaches that focus on site-selective chemistry. Site selectivity in macrocyclization decreases the generation of side products, leading to a greater yield of the desired peptide macrocycles. We will also take an in-depth look at the new exclusively intramolecular N-terminal site-selective CyClick strategy for the synthesis of cyclic peptides. The CyClick method uses imine formation between an aldehyde and the N terminus. The imine is then trapped by a nucleophilic attack from the second amidic nitrogen in an irreversible site-selective fashion.
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Affiliation(s)
- Rachel Wills
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
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2
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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3
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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4
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Streefkerk DE, Schmidt M, Ippel JH, Hackeng TM, Nuijens T, Timmerman P, van Maarseveen JH. Synthesis of Constrained Tetracyclic Peptides by Consecutive CEPS, CLIPS, and Oxime Ligation. Org Lett 2019; 21:2095-2100. [PMID: 30912446 PMCID: PMC6456872 DOI: 10.1021/acs.orglett.9b00378] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
In Nature, multicyclic
peptides constitute a versatile molecule
class with various biological functions. For their pharmaceutical
exploitation, chemical methodologies that enable selective consecutive
macrocyclizations are required. We disclose a combination of enzymatic
macrocyclization, CLIPS alkylation, and oxime ligation to prepare
tetracyclic peptides. Five new small molecular scaffolds and differently
sized model peptides featuring noncanonical amino acids were synthesized.
Enzymatic macrocyclization, followed by one-pot scaffold-assisted
cyclizations, yielded 21 tetracyclic peptides in a facile and robust
manner.
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Affiliation(s)
- Dieuwertje E Streefkerk
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands
| | - Marcel Schmidt
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands.,EnzyPep B.V. , Urmonderbaan 22 , 6167 RD Geleen , The Netherlands
| | - Johannes H Ippel
- Department of Biochemistry (CARIM) , University of Maastricht , Universiteitssingel 50, 6229 ER Maastricht , The Netherlands
| | - Tilman M Hackeng
- Department of Biochemistry (CARIM) , University of Maastricht , Universiteitssingel 50, 6229 ER Maastricht , The Netherlands
| | - Timo Nuijens
- EnzyPep B.V. , Urmonderbaan 22 , 6167 RD Geleen , The Netherlands
| | - Peter Timmerman
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands.,Pepscan Therapeutics , Zuidersluisweg 2 , 8243 RC Lelystad , The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam , The Netherlands
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5
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Abstract
Our understanding of the complex molecular processes of living organisms at the molecular level is growing exponentially. This knowledge, together with a powerful arsenal of tools for manipulating the structures of macromolecules, is allowing chemists to to harness and reprogram the cellular machinery in ways previously unimaged. Here we review one example in which the genetic code itself has been expanded with new building blocks that allow us to probe and manipulate the structures and functions of proteins with unprecedented precision.
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Affiliation(s)
- Douglas D. Young
- Department of Chemistry, College of William & Mary,
P.O. Box 8795, Williamsburg, VA 23187 (USA)
| | - Peter G. Schultz
- Department of Chemistry, The Scripps Research Institute,
La Jolla, CA 92037 (USA),
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6
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Abstract
Many biologically active peptides found in nature exhibit a bicyclic structure wherein a head-to-tail cyclic backbone is further constrained by an intramolecular linkage connecting two side chains of the peptide. Accordingly, methods to access macrocyclic peptides sharing this overall topology could be of significant value toward the discovery of new functional entities and bioactive compounds. With this goal in mind, we recently developed a strategy for enabling the biosynthesis of thioether-bridged bicyclic peptides in living bacterial cells. This method involves a split intein-catalyzed head-to-tail cyclization of a ribosomally produced precursor peptide, combined with inter-sidechain cross-linking through a genetically encoded cysteine-reactive amino acid. This approach can be applied to direct the formation of structurally diverse bicyclic peptides with high efficiency and selectivity in living Escherichia coli cells and provides a platform for the generation of combinatorial libraries of genetically encoded bicyclic peptides for screening purposes.
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7
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Taylor RD, Rey-Carrizo M, Passioura T, Suga H. Identification of nonstandard macrocyclic peptide ligands through display screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:17-23. [PMID: 29249238 DOI: 10.1016/j.ddtec.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022]
Abstract
Techniques facilitating the synthesis and screening of very high diversity nonstandard macrocyclic peptide libraries have led to such compounds receiving increasing attention as potential drug candidates. Specifically, approaches which allow the use of non-proteinogenic amino acids are proving to be particularly effective, since they expand the accessible chemical space of the starting library and thus allow the identification of compounds with structural similarity to known drugs. This review focuses on mRNA display screening platforms for drug discovery and their combined use with genetic code reprogramming to identify novel macrocyclic peptides with high affinities for disease-related targets of interest.
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Affiliation(s)
- Rhys Dylan Taylor
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Matias Rey-Carrizo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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8
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Frost JR, Wu Z, Lam YC, Owens AE, Fasan R. Side-chain-to-tail cyclization of ribosomally derived peptides promoted by aryl and alkyl amino-functionalized unnatural amino acids. Org Biomol Chem 2016; 14:5803-12. [PMID: 27064594 PMCID: PMC4909536 DOI: 10.1039/c6ob00192k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A strategy for the production of side-chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Two genetically encodable unnatural amino acids, bearing either an aryl or alkyl amino group, were investigated for their efficiency toward promoting the formation of medium to large-sized peptide macrocycles via intein-mediated side-chain-to-C-terminus cyclization. While only partial cyclization was observed with precursor proteins containing para-amino-phenylalanine, efficient peptide macrocyclization could be achieved using O-2-aminoethyl-tyrosine as the reactive moiety. Conveniently, the latter was generated upon quantitative, post-translational reduction of the azido-containing counterpart, O-2-azidoethyl-tyrosine, directly in E. coli cells. This methodology could be successfully applied for the production of a 12 mer cyclic peptide with enhanced binding affinity for the model target protein streptavidin as compared to the acyclic counterpart (KD: 5.1 μM vs. 22.4 μM), thus demonstrating its utility toward the creation and investigation of novel, functional macrocyclic peptides.
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Affiliation(s)
- John R Frost
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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9
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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10
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Palei S, Mootz HD. Cyclic Peptides Made by Linking Synthetic and Genetically Encoded Fragments. Chembiochem 2016; 17:378-82. [DOI: 10.1002/cbic.201500673] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Shubhendu Palei
- International Graduate School of Chemistry (GSC-MS); Institute of Biochemistry; University of Muenster; Wilhelm-Klemm-Strasse 2 48149 Münster Germany
| | - Henning D. Mootz
- International Graduate School of Chemistry (GSC-MS); Institute of Biochemistry; University of Muenster; Wilhelm-Klemm-Strasse 2 48149 Münster Germany
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11
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Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Aminothiol Unnatural Amino Acids. ACS Chem Biol 2015; 10:1805-16. [PMID: 25933125 DOI: 10.1021/acschembio.5b00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A versatile method for orchestrating the formation of side chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low-micromolar streptavidin binder (KD = 1.1 μM) from a library of cyclic peptides produced in Escherichia coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles.
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Affiliation(s)
- John R. Frost
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Nicholas T. Jacob
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Louis J. Papa
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Andrew E. Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
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12
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Martí-Centelles V, Pandey MD, Burguete MI, Luis SV. Macrocyclization Reactions: The Importance of Conformational, Configurational, and Template-Induced Preorganization. Chem Rev 2015; 115:8736-834. [DOI: 10.1021/acs.chemrev.5b00056] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Mrituanjay D. Pandey
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - M. Isabel Burguete
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Santiago V. Luis
- Departament de Química
Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
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13
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Lau YH, Wu Y, de Andrade P, Galloway WRJD, Spring DR. A two-component 'double-click' approach to peptide stapling. Nat Protoc 2015; 10:585-94. [PMID: 25763835 DOI: 10.1038/nprot.2015.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptide cyclization is a useful strategy for the stabilization of short flexible peptides into well-defined bioactive conformations, thereby enhancing their ability to interact with proteins and other important biomolecules. We present an optimized procedure for the stabilization of linear diazido peptides in an α-helical conformation upon reaction with dialkynyl linkers under Cu(I) catalysis. As this procedure generates side chain-cyclized peptides bearing a bis-triazole linkage, it is referred to as 'double-click' stapling. Double-click stapling can enhance the binding affinity, proteolytic stability and cellular activity of a peptide inhibitor. A distinguishing feature of double-click stapling is the efficiency with which peptides bearing different staple linkages can be synthesized, thus allowing for modular control over peptide bioactivity. This protocol describes the double-click reaction between a 1,3-dialkynylbenzene linker and peptides that contain azidoornithine. Subsequent peptide purification and confirmation steps are also described. The entire double-click stapling protocol can be completed in ∼48 h, including two overnight lyophilization steps.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | - Yuteng Wu
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
| | | | | | - David R Spring
- University Chemical Laboratory, University of Cambridge, Cambridge, UK
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14
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Smith JM, Fasan R. Synthesis of macrocyclic organo-peptide hybrids from ribosomal polypeptide precursors via CuAAC-/hydrazide-mediated cyclization. Methods Mol Biol 2015; 1248:23-38. [PMID: 25616323 PMCID: PMC4481324 DOI: 10.1007/978-1-4939-2020-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Macrocyclic peptides have attracted increasing attention as a potential new source of chemical probes and therapeutics. In particular, their conformationally restricted structure combined with a high degree of functional and stereochemical complexity makes them promising scaffolds for targeting biomolecules with high affinity and selectivity. The exploration of this structural class relies on the availability of efficient and versatile methods for the generation of large and diversified libraries of macrocyclic peptide-based molecules. To this end, we have developed a methodology for the synthesis of hybrid organo-peptide macrocycles via the cyclization of ribosomally derived polypeptide sequences with non-peptidic organic linkers. This strategy relies on the chemoselective and bioorthogonal ligation of azide/hydrazide-based "synthetic precursors" with intein-fused polypeptides harboring a side-chain alkyne functionality. This macrocyclization approach was found to proceed with high efficiency across a range of different target peptide sequences spanning 4-12 residues as well as across multiple mono- and diaryl-based synthetic precursors. This versatility combined with the possibility to integrate non-proteinogenic scaffolds into genetically encoded peptide sequences makes this methodology of particularly high value toward the creation and screening of highly diverse libraries of peptide-based macrocycles.
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15
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Yudin AK. Macrocycles: lessons from the distant past, recent developments, and future directions. Chem Sci 2015; 6:30-49. [PMID: 28553456 PMCID: PMC5424464 DOI: 10.1039/c4sc03089c] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/01/2014] [Indexed: 12/20/2022] Open
Abstract
A noticeable increase in molecular complexity of drug targets has created an unmet need in the therapeutic agents that are larger than traditional small molecules. Macrocycles, which are cyclic compounds comprising 12 atoms or more, are now recognized as molecules that "are up to the task" to interrogate extended protein interfaces. However, because macrocycles (particularly the ones based on peptides) are equipped with large polar surface areas, achieving cellular permeability and bioavailability is anything but straightforward. While one might consider this to be the Achilles' heel of this class of compounds, the synthetic community continues to develop creative approaches toward the synthesis of macrocycles and their site-selective modification. This perspective provides an overview of both mechanistic and structural issues that bear on macrocycles as a unique class of molecules. The reader is offered a historical foray into some of the classic studies that have resulted in the current renaissance of macrocycles. In addition, an attempt is made to overview the more recent developments that give hope that macrocycles might indeed turn into a useful therapeutic modality.
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Affiliation(s)
- Andrei K Yudin
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada . ; Blog: http://www.amphoteros.com
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16
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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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17
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Bionda N, Cryan AL, Fasan R. Bioinspired strategy for the ribosomal synthesis of thioether-bridged macrocyclic peptides in bacteria. ACS Chem Biol 2014; 9:2008-13. [PMID: 25079213 PMCID: PMC4168796 DOI: 10.1021/cb500311k] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Inspired
by the biosynthetic logic of lanthipeptide natural products,
a new methodology was developed to direct the ribosomal synthesis
of macrocyclic peptides constrained by an intramolecular thioether
bond. As a first step, a robust and versatile strategy was implemented
to enable the cyclization of ribosomally derived peptide sequences
via a chemoselective reaction between a genetically encoded cysteine
and a cysteine-reactive unnatural amino acid (O-(2-bromoethyl)-tyrosine).
Combination of this approach with intein-catalyzed protein splicing
furnished an efficient route to achieve the spontaneous, post-translational
formation of structurally diverse macrocyclic peptides in bacterial
cells. The present peptide cyclization strategy was also found to
be amenable to integration with split intein-mediated circular ligation,
resulting in the intracellular synthesis of conformationally constrained
peptides featuring a bicyclic architecture.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Abby L. Cryan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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18
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Hilinski GJ, Kim YW, Hong J, Kutchukian PS, Crenshaw CM, Berkovitch SS, Chang A, Ham S, Verdine GL. Stitched α-helical peptides via bis ring-closing metathesis. J Am Chem Soc 2014; 136:12314-22. [PMID: 25105213 DOI: 10.1021/ja505141j] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Conformationally stabilized α-helical peptides are capable of inhibiting disease-relevant intracellular or extracellular protein-protein interactions in vivo. We have previously reported that the employment of ring-closing metathesis to introduce a single all-hydrocarbon staple along one face of an α-helical peptide greatly increases α-helical content, binding affinity to a target protein, cell penetration through active transport, and resistance to proteolytic degradation. In an effort to improve upon this technology for stabilizing a peptide in a bioactive α-helical conformation, we report the discovery of an efficient and selective bis ring-closing metathesis reaction leading to peptides bearing multiple contiguous staples connected by a central spiro ring junction. Circular dichroism spectroscopy, NMR, and computational analyses have been used to investigate the conformation of these "stitched" peptides, which are shown to exhibit remarkable thermal stabilities. Likewise, trypsin proteolysis assays confirm the achievement of a structural rigidity unmatched by peptides bearing a single staple. Furthermore, fluorescence-activated cell sorting (FACS) and confocal microscopy assays demonstrate that stitched peptides display superior cell penetrating ability compared to their stapled counterparts, suggesting that this technology may be useful not only in the context of enhancing the drug-like properties of α-helical peptides but also in producing potent agents for the intracellular delivery of proteins and oligonucleotides.
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Affiliation(s)
- Gerard J Hilinski
- Department of Chemistry and Chemical Biology and Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, Massachusetts 02138, United States
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19
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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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20
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Lau YH, de Andrade P, Sköld N, McKenzie GJ, Venkitaraman AR, Verma C, Lane DP, Spring DR. Investigating peptide sequence variations for 'double-click' stapled p53 peptides. Org Biomol Chem 2014; 12:4074-7. [PMID: 24817343 DOI: 10.1039/c4ob00742e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Stapling peptides for inhibiting the p53/MDM2 interaction is a promising strategy for developing anti-cancer therapeutic leads. We evaluate double-click stapled peptides formed from p53-based diazidopeptides with different staple positions and azido amino acid side-chain lengths, determining the impact of these variations on MDM2 binding and cellular activity. We also demonstrate a K24R mutation, necessary for cellular activity in hydrocarbon-stapled p53 peptides, is not required for analogous 'double-click' peptides.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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21
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Smith JM, Frost JR, Fasan R. Designer macrocyclic organo-peptide hybrids inhibit the interaction between p53 and HDM2/X by accommodating a functional α-helix. Chem Commun (Camb) 2014; 50:5027-30. [PMID: 24710524 DOI: 10.1039/c4cc01199f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the design of side-chain-to-tail linked organo-peptide hybrids incorporating an α-helical protein-binding motif. Using this strategy, macrocyclic inhibitors of the p53:HDM2 interaction displaying dual specificity against the HDMX homolog as well as increased proteolytic stability could be obtained.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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22
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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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23
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Zou Y, Spokoyny AM, Zhang C, Simon MD, Yu H, Lin YS, Pentelute BL. Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides. Org Biomol Chem 2014; 12:566-73. [PMID: 24310320 PMCID: PMC3935340 DOI: 10.1039/c3ob42168f] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we describe a general synthetic platform for side-chain macrocyclization of an unprotected peptide library based on the SNAr reaction between cysteine thiolates and a new generation of highly reactive perfluoroaromatic small molecule linkers. This strategy enabled us to simultaneously "scan" two cysteine residues positioned from i, i + 1 to i, i + 14 sites in a polypeptide, producing 98 macrocyclic products from reactions of 14 peptides with 7 linkers. A complementary reverse strategy was developed; cysteine residues within the polypeptide were first modified with non-bridging perfluoroaryl moieties and then commercially available dithiol linkers were used for macrocyclization. The highly convergent, site-independent, and modular nature of these two strategies coupled with the unique chemoselectivity of a SNAr transformation allows for the rapid diversity-oriented synthesis of hybrid macrocyclic peptide libraries with varied chemical and structural complexities.
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Affiliation(s)
- Yekui Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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24
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Lau YH, de Andrade P, Quah ST, Rossmann M, Laraia L, Sköld N, Sum TJ, Rowling PJE, Joseph TL, Verma C, Hyvönen M, Itzhaki LS, Venkitaraman AR, Brown CJ, Lane DP, Spring DR. Functionalised staple linkages for modulating the cellular activity of stapled peptides. Chem Sci 2014. [DOI: 10.1039/c4sc00045e] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A divergent synthetic strategy for generating helical p53 peptides bearing functionalised staple linkages, allowing for efficient optimisation of cellular activity.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | | | | | - Maxim Rossmann
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA, UK
| | - Luca Laraia
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
- MRC Cancer Unit
- Hutchison/MRC Research Centre
| | - Niklas Sköld
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | - Tze Jing Sum
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | | | | | - Chandra Verma
- Bioinformatics Institute (A*STAR)
- , Singapore 138671
- Department of Biological Sciences
- National University of Singapore (NUS)
- Singapore 117543
| | - Marko Hyvönen
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA, UK
| | - Laura S. Itzhaki
- Department of Pharmacology
- University of Cambridge
- Cambridge CB2 1PD, UK
| | | | | | | | - David R. Spring
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
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25
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Martí-Centelles V, Burguete MI, Cativiela C, Luis SV. The Role of the Amino Acid-Derived Side Chain in the Preorganization of C2-Symmetric Pseudopeptides: Effect on SN2 Macrocyclization Reactions. J Org Chem 2013; 79:559-70. [DOI: 10.1021/jo4022309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vicente Martí-Centelles
- Departamento
de Química Inorgánica y Orgánica, ESTCE, Universitat Jaume I, E-12071 Castellón, Spain
- Departamento
de Química Orgánica, Instituto de Síntesis Química
y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, E-50009 Zaragoza, Spain
| | - M. Isabel Burguete
- Departamento
de Química Inorgánica y Orgánica, ESTCE, Universitat Jaume I, E-12071 Castellón, Spain
| | - Carlos Cativiela
- Departamento
de Química Orgánica, Instituto de Síntesis Química
y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, E-50009 Zaragoza, Spain
| | - Santiago V. Luis
- Departamento
de Química Inorgánica y Orgánica, ESTCE, Universitat Jaume I, E-12071 Castellón, Spain
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26
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Frost JR, Smith JM, Fasan R. Design, synthesis, and diversification of ribosomally derived peptide macrocycles. Curr Opin Struct Biol 2013; 23:571-80. [PMID: 23856642 DOI: 10.1016/j.sbi.2013.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/19/2013] [Accepted: 06/20/2013] [Indexed: 10/26/2022]
Abstract
Ring topologies are widespread structural motifs among biologically active peptides found in nature. The recurrence of this motif is linked to the inherent advantages resulting from backbone cyclization, which include increased resistance against proteolytic degradation, improved cell permeability, and tighter and more specific interaction with the respective biomolecular target. Inspired by these natural product topologies, a number of groups have recently focused on developing methodologies that hinge upon the chemical elaboration of ribosomally derived polypeptides toward the synthesis and diversification of macrocyclic peptide structures. In this review, we highlight recent advances in this emerging new area and discuss the opportunities created by these methods toward the discovery of new functional entities.
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Affiliation(s)
- John R Frost
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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27
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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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