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Ullrich S, Somathilake U, Shang M, Nitsche C. Phage-encoded bismuth bicycles enable instant access to targeted bioactive peptides. Commun Chem 2024; 7:143. [PMID: 38937646 PMCID: PMC11211329 DOI: 10.1038/s42004-024-01232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Genetically encoded libraries play a crucial role in discovering structurally rigid, high-affinity macrocyclic peptide ligands for therapeutic applications. Bicyclic peptides with metal centres like bismuth were recently developed as a new type of constrained peptide with notable affinity, stability and membrane permeability. This study represents the genetic encoding of peptide-bismuth and peptide-arsenic bicycles in phage display. We introduce bismuth tripotassium dicitrate (gastrodenol) as a water-soluble bismuth(III) reagent for phage library modification and in situ bicyclic peptide preparation, eliminating the need for organic co-solvents. Additionally, we explore arsenic(III) as an alternative thiophilic element that is used analogously to our previously introduced bicyclic peptides with a bismuth core. The modification of phage libraries and peptides with these elements is instantaneous and entirely biocompatible, offering an advantage over conventional alkylation-based methods. In a pilot display screening campaign aimed at identifying ligands for the biotin-binding protein streptavidin, we demonstrate the enrichment of bicyclic peptides with dissociation constants two orders of magnitude lower than those of their linear counterparts, underscoring the impact of structural constraint on binding affinity.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Upamali Somathilake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Minghao Shang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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Kobayashi M, Onozawa N, Matsuda K, Wakimoto T. Chemoenzymatic tandem cyclization for the facile synthesis of bicyclic peptides. Commun Chem 2024; 7:67. [PMID: 38548970 PMCID: PMC10978974 DOI: 10.1038/s42004-024-01147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Bicyclic peptides exhibit improved metabolic stabilities and target specificities when compared to their linear or mono-cyclic counterparts; however, efficient and straightforward synthesis remains challenging due to their intricate architectures. Here, we present a highly selective and operationally simple one-pot chemoenzymatic tandem cyclization approach to synthesize bicyclic peptides with small to medium ring sizes. Penicillin-binding protein-type thioesterases (PBP-type TEs) efficiently cyclized azide/alkyne-containing peptides in a head-to-tail manner. Successive copper (I)-catalyzed azide-alkyne cycloaddition generated bicyclic peptides in one-pot, thus omitting the purification of monocyclic intermediates. This chemoenzymatic strategy enabled the facile synthesis of bicyclic peptides bearing hexa-, octa-, and undecapeptidyl head-to-tail cyclic scaffolds.
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Affiliation(s)
- Masakazu Kobayashi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Naho Onozawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
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Voss S, Rademann J, Nitsche C. Peptide–Bismuth Bicycles: In Situ Access to Stable Constrained Peptides with Superior Bioactivity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Saan Voss
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
- Department of Biology, Chemistry and Pharmacy Institute of Pharmacy, Medicinal Chemistry Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy Institute of Pharmacy, Medicinal Chemistry Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Germany
| | - Christoph Nitsche
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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Voss S, Rademann J, Nitsche C. Peptide-Bismuth Bicycles: In Situ Access to Stable Constrained Peptides with Superior Bioactivity. Angew Chem Int Ed Engl 2021; 61:e202113857. [PMID: 34825756 DOI: 10.1002/anie.202113857] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Indexed: 12/12/2022]
Abstract
Constrained peptides are promising next-generation therapeutics. We report here a fundamentally new strategy for the facile generation of bicyclic peptides using linear precursor peptides with three cysteine residues and a non-toxic trivalent bismuth(III) salt. Peptide-bismuth bicycles form instantaneously at physiological pH, are stable in aqueous solution for many weeks, and much more resistant to proteolysis than their linear precursors. The strategy allows the in situ generation of bicyclic ligands for biochemical screening assays. We demonstrate this for two screening campaigns targeting the proteases from Zika and West Nile viruses, revealing a new lead compound that displayed inhibition constants of 23 and 150 nM, respectively. Bicyclic peptides are up to 130 times more active and 19 times more proteolytically stable than their linear analogs without bismuth.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.,Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Zhang Z, Gao R, Hu Q, Peacock H, Peacock DM, Dai S, Shokat KM, Suga H. GTP-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf. ACS CENTRAL SCIENCE 2020; 6:1753-1761. [PMID: 33145412 PMCID: PMC7596874 DOI: 10.1021/acscentsci.0c00514] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Indexed: 05/08/2023]
Abstract
We report the identification of three cyclic peptide ligands of K-Ras(G12D) using an integrated in vitro translation-mRNA display selection platform. These cyclic peptides show preferential binding to the GTP-bound state of K-Ras(G12D) over the GDP-bound state and block Ras-Raf interaction. A co-crystal structure of peptide KD2 with K-Ras(G12D)·GppNHp reveals that this peptide binds in the Switch II groove region with concomitant opening of the Switch II loop and a 40° rotation of the α2 helix, and that a threonine residue (Thr10) on KD2 has direct access to the mutant aspartate (Asp12) on K-Ras. Replacing this threonine with non-natural amino acids afforded peptides with improved potency at inhibiting the interaction between Raf1-RBD and K-Ras(G12D) but not wildtype K-Ras. The union of G12D over wildtype selectivity and GTP state/GDP state selectivity is particularly desirable, considering that oncogenic K-Ras(G12D) exists predominantly in the GTP state in cancer cells, and wildtype K-Ras signaling is important for the maintenance of healthy cells.
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Affiliation(s)
- Ziyang Zhang
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Rong Gao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Qi Hu
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Hayden Peacock
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - D. Matthew Peacock
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Shizhong Dai
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - 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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Sengupta S, Mehta G. Macrocyclization via C-H functionalization: a new paradigm in macrocycle synthesis. Org Biomol Chem 2020; 18:1851-1876. [PMID: 32101232 DOI: 10.1039/c9ob02765c] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The growing emphasis on macrocycles in engaging difficult therapeutic targets such as protein-protein interactions and GPCRs via preferential adaptation of bioactive and cell penetrating conformations has provided impetus to the search for de novo macrocyclization strategies that are efficient, chemically robust and amenable to diversity creation. An emerging macrocyclization paradigm based on the C-H activation logic, of particular promise in the macrocyclization of complex peptides, has added a new dimension to this pursuit, enabling efficacious access to macrocycles of various sizes and topologies with high atom and step economy. Significant achievements in macrocyclization methodologies and their applications in the synthesis of bioactive natural products and drug-like molecules, employing strategic variations of C-H activation are captured in this review. It is expected that this timely account will foster interest in newer ways of macrocycle construction among practitioners of organic synthesis and chemical biology to advance the field.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
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Abstract
The first total synthesis of antiallergic depsipeptide seongsanamide A has been achieved and also the relative and absolute stereochemistry of the natural product has been confirmed.
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Affiliation(s)
- Feipeng Han
- State Key Laboratory of Chemical Oncogenomics
- Peking University Shenzhen Graduate School
- China
| | - Yian Guo
- State Key Laboratory of Chemical Oncogenomics
- Peking University Shenzhen Graduate School
- China
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics
- Peking University Shenzhen Graduate School
- China
- Tsinghua Shenzhen International Graduate School
- Shenzhen
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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Zhang T, Li T, Wu X, Li J. Theoretical Study of Ruthenium(0)-Catalyzed Transfer Hydrogenative Cycloaddition of Cyclohexadiene and Norbornadiene with 1,2-Diols to Form Bridged Carbocycles. J Org Chem 2019; 84:3377-3387. [PMID: 30775919 DOI: 10.1021/acs.joc.8b03276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The recent success of Krische et al. ( Angew. Chem., Int. Ed. 2017 , 56 , 14667 -14671 ) in achieving a ruthenium(0)-catalyzed transfer hydrogenative cycloaddition of 1,2-diols with cyclohexadiene and norbornadiene in excellent yield with exo- and diastereoselectivity represents an exciting development in the synthesis of bridged carbocycles. In the present work, the possible catalytic mechanisms and origin of the exo- and diastereoselectivity for cyclohexadiene and norbornadiene were studied in detail by density functional theory calculations. The theoretical results indicate that the exoselective pathway for the cyclohexadiene substrate proceeds by a novel two-step successive C-C coupling, while the endoselective pathway undergoes the C-C coupling reaction in a conventional concerted manner. The origin of the preferential chemoselectivity of dione-cyclohexadiene C-C coupling over aromatization to benzene was investigated. Aromatization to benzene is unfavorable because of the large distortion energy of the three-membered ring in the transition state of hydrogen migration. From distortion/interaction analysis, for norbornadiene, the distortion energy plays the main role in determining the exoselectivity.
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Affiliation(s)
- Tian Zhang
- Department of Chemistry , Jinan University , Huangpu Road West 601 , Guangzhou , Guangdong 510632 , P. R. China
| | - Ting Li
- Department of Chemistry , Jinan University , Huangpu Road West 601 , Guangzhou , Guangdong 510632 , P. R. China
| | - Xiajun Wu
- Department of Chemistry , Jinan University , Huangpu Road West 601 , Guangzhou , Guangdong 510632 , P. R. China
| | - Juan Li
- Department of Chemistry , Jinan University , Huangpu Road West 601 , Guangzhou , Guangdong 510632 , P. R. China
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