1
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Oppewal TR, Jansen ID, Hekelaar J, Mayer C. A Strategy to Select Macrocyclic Peptides Featuring Asymmetric Molecular Scaffolds as Cyclization Units by Phage Display. J Am Chem Soc 2022; 144:3644-3652. [PMID: 35171585 PMCID: PMC8895403 DOI: 10.1021/jacs.1c12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macrocyclic peptides (MPs) have positioned themselves as a privileged class of compounds for the discovery of therapeutics and development of chemical probes. Aided by the development of powerful selection strategies, high-affinity binders against biomolecular targets can readily be elicited from massive, genetically encoded libraries by affinity selection. For example, in phage display, MPs are accessed on the surface of whole bacteriophages via disulfide formation, the use of (symmetric) crosslinkers, or the incorporation of non-canonical amino acids. To facilitate a straightforward cyclization of linear precursors with asymmetric molecular scaffolds, which are often found at the core of naturally occurring MPs, we report an efficient two-step strategy to access MPs via the programmed modification of a unique cysteine residue and an N-terminal amine. We demonstrate that this approach yields MPs featuring asymmetric cyclization units from both synthetic peptides and when linear precursors are appended onto a phage-coat protein. Finally, we showcase that our cyclization strategy is compatible with traditional phage-display protocols and enables the selection of MP binders against a model target protein from naïve libraries. By enabling the incorporation of non-peptidic moieties that (1) can serve as cyclization units, (2) provide interactions for binding, and/or (3) tailor pharmacological properties, our head-to-side-chain cyclization strategy provides access to a currently under-explored chemical space for the development of chemical probes and therapeutics.
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Affiliation(s)
- Titia Rixt Oppewal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Ivar D Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Johan Hekelaar
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, Groningen 9474 AG, The Netherlands
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2
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Gu Y, Iannuzzelli JA, Fasan R. MOrPH-PhD: A Phage Display System for the Functional Selection of Genetically Encoded Macrocyclic Peptides. Methods Mol Biol 2022; 2371:261-286. [PMID: 34596853 PMCID: PMC8493807 DOI: 10.1007/978-1-0716-1689-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for targeting biomolecules with high affinity and selectivity, making methods for the diversification and functional selection of these macrocycles highly valuable for drug discovery purposes. We recently reported a novel phage display platform (called MOrPH-PhD) for the creation and functional exploration of combinatorial libraries of genetically encoded cyclic peptides. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive non-canonical amino acid is integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. Using this system, it is possible to rapidly generate and screen large libraries of phage-displayed macrocyclic peptides (up to 108 to 1010 members) in order to identify high-affinity binders of a target protein of interest. Herein, we describe step-by-step protocols for the production of MOrPH-PhD libraries, the screening of these libraries against an immobilized protein target, and the isolation and characterization of functional macrocyclic peptides from these genetically encoded libraries.
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Affiliation(s)
- Yu Gu
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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3
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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4
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Shah SS, Casanova N, Antuono G, Sabatino D. Polyamide Backbone Modified Cell Targeting and Penetrating Peptides in Cancer Detection and Treatment. Front Chem 2020; 8:218. [PMID: 32296681 PMCID: PMC7136562 DOI: 10.3389/fchem.2020.00218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Cell penetrating and targeting peptides (CPPs and CTPs) encompass an important class of biochemically active peptides owning the capabilities of targeting and translocating within selected cell types. As such, they have been widely used in the delivery of imaging and therapeutic agents for the diagnosis and treatment of various diseases, especially in cancer. Despite their potential utility, first generation CTPs and CPPs based on the native peptide sequences are limited by poor biological and pharmacological properties, thereby restricting their efficacy. Therefore, medicinal chemistry approaches have been designed and developed to construct related peptidomimetics. Of specific interest herein, are the design applications which modify the polyamide backbone of lead CTPs and CPPs. These modifications aim to improve the biochemical characteristics of the native peptide sequence in order to enhance its diagnostic and therapeutic capabilities. This review will focus on a selected set of cell penetrating and targeting peptides and their related peptidomimetics whose polyamide backbone has been modified in order to improve their applications in cancer detection and treatment.
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Affiliation(s)
- Sunil S Shah
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Nelson Casanova
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - Gina Antuono
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ, United States
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5
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Wang XS, Chen PC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang D, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage‐Displayed Cyclic‐Peptide Library. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - J. Trae Hampton
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Jeffery M. Tharp
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Catrina A. Reed
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Sukant K. Das
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Duen‐Shian Wang
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Hamed S. Hayatshahi
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Yang Shen
- Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843-3218 USA
| | - Jin Liu
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Wenshe Ray Liu
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
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6
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Wang XS, Chen PHC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl 2019; 58:15904-15909. [PMID: 31398275 PMCID: PMC6803038 DOI: 10.1002/anie.201908713] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 11/10/2022]
Abstract
Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.
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Affiliation(s)
- Xiaoshan Shayna Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Peng-Hsun Chase Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - J Trae Hampton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Catrina A Reed
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Sukant K Das
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3218, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
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7
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Abstract
Artificial macrocycles recently became popular as a novel research field in drug discovery. As opposed to their natural twins, artificial macrocycles promise to have better control on synthesizability and control over their physicochemical properties resulting in druglike properties. Very few synthetic methods allow for the convergent, fast but diverse access to large macrocycles chemical space. One synthetic technology to access artificial macrocycles with potential biological activity, multicomponent reactions, is reviewed here, with a focus on our own work. We believe that synthetic chemists have to acquaint themselves more with structure and activity to leverage the design aspect of their daily work.
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Affiliation(s)
- Eman M M Abdelraheem
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands,
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Shabnam Shaabani
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands,
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands,
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8
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Abdelraheem EMM, Khaksar S, Dömling A. Concise Synthesis of Macrocycles by Multicomponent Reactions. SYNTHESIS-STUTTGART 2018; 50:1027-1038. [PMID: 31439965 PMCID: PMC6706064 DOI: 10.1055/s-0036-1590946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A short reaction pathway was devised to synthesize a library of artificial 18-27-membered macrocycles. The five-step reaction sequence involves ring opening of a cyclic anhydride with a diamine, esterification, coupling with an amino acid isocyanide, saponification, and, finally, macro-ring closure using an Ugi or, alternatively, a Passerini multicomponent reaction. Three out of the five steps allow for the versatile introduction of linker elements, side chains, and substituents with aromatic, heteroaromatic, and aliphatic character. The versatile pathway is described for 15 different target macrocycles on a mmol scale. Artificial macrocycles have recently become of great interest due to their potential to bind to difficult post-genomic targets.
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Affiliation(s)
- Eman M. M. Abdelraheem
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Chemistry Department, Faculty of Science, Sohag University, Sohag, 82524, Egypt
| | - Samad Khaksar
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Chemistry Department, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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9
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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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10
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Hosseini AS, Wang W, Haeffner F, Gao J. Metal-Assisted Folding of Prolinomycin Allows Facile Design of Functional Peptides. Chembiochem 2017; 18:479-482. [PMID: 28042934 DOI: 10.1002/cbic.201600667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Indexed: 11/07/2022]
Abstract
Cyclic peptides have been proposed as privileged scaffolds that might mimic the folding and function of natural proteins. However, simple cyclic peptides typically cannot fold into well-defined structures. Herein, we describe a foldable cyclic peptide scaffold on which functional side chains can be displayed for targeted recognition of biomolecules. The foldable scaffold is based on prolinomycin, a proline-rich analogue of valinomycin. We report synthetic mutants of prolinomycin that retain the metal-assisted folding behavior under physiological conditions. The predictable structure formation of prolinomycin makes it a powerful platform to enable the development of synthetic receptors for biomolecules of interest. We demonstrate the potential of this scaffold by creating prolinomycin mutants that selectively bind anionic vesicles and bacterial cells.
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Affiliation(s)
- Azade S Hosseini
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Wenjian Wang
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Fredrik Haeffner
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, MA, 02467, USA
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11
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Tavassoli A. SICLOPPS cyclic peptide libraries in drug discovery. Curr Opin Chem Biol 2017; 38:30-35. [PMID: 28258013 DOI: 10.1016/j.cbpa.2017.02.016] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/06/2017] [Accepted: 02/16/2017] [Indexed: 01/08/2023]
Abstract
Cyclic peptide libraries have demonstrated significant potential when employed against challenging targets such as protein-protein interactions. While a variety of methods for library generation exist, genetically encoded libraries hold several advantages over their chemically synthesized counterparts; they are more readily accessible and allow straightforward hit deconvolution. One method for the intracellular generation of such libraries is split-intein circular ligation of peptides and proteins (SICLOPPS). Here we detail and discuss the deployment of SICLOPPS libraries for the identification of cyclic peptide inhibitors of a variety of targets.
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Affiliation(s)
- Ali Tavassoli
- Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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12
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13
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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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14
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Kalhor-Monfared S, Jafari MR, Patterson JT, Kitov PI, Dwyer JJ, Nuss JM, Derda R. Rapid biocompatible macrocyclization of peptides with decafluoro-diphenylsulfone. Chem Sci 2016; 7:3785-3790. [PMID: 30155020 PMCID: PMC6013815 DOI: 10.1039/c5sc03856a] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/19/2016] [Indexed: 01/20/2023] Open
Abstract
In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents via aromatic nucleophilic substitution (SNAr) with perfluoroarenes (fAr).
In this manuscript, we describe modification of Cys-residues in peptides and proteins in aqueous solvents via aromatic nucleophilic substitution (SNAr) with perfluoroarenes (fAr). Biocompatibility of this reaction makes it attractive for derivatization of proteins and peptide libraries comprised of 20 natural amino acids. Measurement of the reaction rates for fAr derivatives by 19F NMR with a model thiol donor (β-mercaptoethanol) in aqueous buffers identified decafluoro-diphenylsulfone (DFS) as the most reactive SNAr electrophile. Reaction of DFS with thiol nucleophiles is >100 000 faster than analogous reaction of perfluorobenzene; this increase in reactivity enables application of DFS at low concentrations in aqueous solutions compatible with biomolecules and protein complexes irreversibly degraded by organic solvents (e.g., bacteriophages). DFS forms macrocycles when reacted with peptides of the general structure Xn–Cys–Xm–Cys–Xl, where X is any amino acid and m = 1–15. It formed cyclic peptides with 6 peptide hormones—oxytocin, urotensin II, salmon calcitonin, melanin-concentrating hormone, somatostatin-14, and atrial natriuretic factor (1–28) as well as peptides displayed on M13 phage. Rates up to 180 M–1 s–1 make this reaction one of the fastest Cys-modifications to-date. Long-term stability of macrocycles derived from DFS and their stability toward oxidation further supports DFS as a promising method for modification of peptide-based ligands, cyclization of genetically-encoded peptide libraries, and discovery of bioactive macrocyclic peptides.
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Affiliation(s)
- S Kalhor-Monfared
- Department of Chemistry , University of Alberta , Edmonton , AB T6G 2G2 , Canada .
| | - M R Jafari
- Department of Chemistry , University of Alberta , Edmonton , AB T6G 2G2 , Canada .
| | - J T Patterson
- Ferring Research Institute , San Diego , California 92121 , USA
| | - P I Kitov
- Department of Chemistry , University of Alberta , Edmonton , AB T6G 2G2 , Canada .
| | - J J Dwyer
- Ferring Research Institute , San Diego , California 92121 , USA
| | - J M Nuss
- Ferring Research Institute , San Diego , California 92121 , USA
| | - R Derda
- Department of Chemistry , University of Alberta , Edmonton , AB T6G 2G2 , Canada .
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15
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Review cyclic peptides on a merry-go-round; towards drug design. Biopolymers 2015; 104:453-61. [DOI: 10.1002/bip.22669] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/14/2015] [Accepted: 05/04/2015] [Indexed: 01/15/2023]
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16
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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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17
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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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18
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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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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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20
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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
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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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21
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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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22
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Lennard KR, Tavassoli A. Peptides Come Round: Using SICLOPPS Libraries for Early Stage Drug Discovery. Chemistry 2014; 20:10608-14. [DOI: 10.1002/chem.201403117] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Indexed: 11/06/2022]
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23
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Zhang C, Dai P, Spokoyny AM, Pentelute BL. Enzyme-catalyzed macrocyclization of long unprotected peptides. Org Lett 2014; 16:3652-5. [PMID: 25002256 PMCID: PMC4372082 DOI: 10.1021/ol501609y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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A glutathione S-transferase (GST) catalyzed macrocyclization
reaction for peptides up to 40 amino acids in length is reported.
GST catalyzes the selective SNAr reaction between an N-terminal glutathione (GSH, γ-Glu-Cys-Gly) tag and
a C-terminal perfluoroaryl-modified cysteine on the
same polypeptide chain. Cyclic peptides ranging from 9 to 24 residues
were quantitatively produced within 2 h in aqueous pH = 8 buffer at
room temperature. The reaction was highly selective for cyclization
at the GSH tag, enabling the combination of GST-catalyzed ligation
with native chemical ligation to generate a large 40-residue peptide
macrocycle.
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Affiliation(s)
- Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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24
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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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25
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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: 64] [Impact Index Per Article: 6.4] [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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26
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Ngo TH, Berndt H, Wilsdorf M, Lentz D, Reissig HU. Linear and cyclic hybrids of alternating thiophene-amino acid units: synthesis and effects of chirality on conformation and molecular packing. Chemistry 2013; 19:15155-65. [PMID: 24105938 DOI: 10.1002/chem.201302143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Indexed: 12/21/2022]
Abstract
The dipeptide isostere 5-aminothiophene carboxylic acid has been combined with L-phenylalanine moieties to provide linear and cyclic hybrid oligopeptides. A suitable protecting group strategy and appropriate coupling methods have been developed to guarantee a high degree of enantiopurity of the resulting amides. Cyclic tetraamides have been efficiently obtained by macrocyclization of the linear derivatives. In the case of racemized cyclization precursors, two diastereomeric macrocycles (S,S/R,R and meso) have been isolated. Their crystal structures show clear effects of the stereogenic centers on the ring conformations and molecular packing.
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Affiliation(s)
- Thien H Ngo
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin (Germany), Fax: (+49) 30-838-55367 http://www.bcp.fu-berlin.de/chemie/oc/reissig
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27
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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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