1
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Machida H, Kanemoto K. N-Terminal-Specific Dual Modification of Peptides through Copper-Catalyzed [3+2] Cycloaddition. Angew Chem Int Ed Engl 2024; 63:e202320012. [PMID: 38282290 DOI: 10.1002/anie.202320012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Site-specific introduction of multiple components into peptides is greatly needed for the preparation of densely functionalized and structurally uniform peptides. In this regard, N-terminal-specific peptide modification is attractive, but it can be difficult due to the presence of highly nucleophilic lysine ϵ-amine. In this work, we developed a method for the N-terminal-specific dual modification of peptides through a three-component [3+2] cycloaddition with aldehydes and maleimides under mild copper catalysis. This approach enables exclusive functionalization at the glycine N-terminus of iminopeptides, regardless of the presence of lysine ϵ-amine, thus affording the cycloadducts in excellent yields. Tolerating a broad range of functional groups and molecules, the present method provides the opportunity to rapidly construct doubly functionalized peptides using readily accessible aldehyde and maleimide modules.
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Affiliation(s)
- Haruka Machida
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Kazuya Kanemoto
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga Bunkyo-ku, Tokyo, 112-8551, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
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2
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Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
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3
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Mendoza A, Bernardino SJ, Dweck MJ, Valencia I, Evans D, Tian H, Lee W, Li Y, Houk KN, Harran PG. Cascade Synthesis of Fluorinated Spiroheterocyclic Scaffolding for Peptidic Macrobicycles. J Am Chem Soc 2023. [PMID: 37441722 DOI: 10.1021/jacs.3c03071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Octafluorocyclopentene (OFCP) engages linear, unprotected peptides in polysubstitution cascades that generate complex fluorinated polycycles. The reactions occur in a single flask at 0-25 °C and require no catalysts or heavy metals. OFCP can directly polycyclize linear sequences using native functionality, or fluorospiroheterocyclic intermediates can be intercepted with exogenous nucleophiles. The latter tactic generates molecular hybrids composed of peptides, sugars, lipids, and heterocyclic components. The platform can create stereoisomers of both single- and double-looped macrocycles. Calculations indicate that the latter can mimic diverse protein surface loops. Subsets of the molecules have low energy conformers that shield the polar surface area through intramolecular hydrogen bonding. A significant fraction of OFCP-derived macrocycles tested show moderate to high passive permeability in parallel artificial membrane permeability assays.
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Affiliation(s)
- Angel Mendoza
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Salvador J Bernardino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Morris J Dweck
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Isabel Valencia
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Alcalá de Henares 28805, Spain
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Haowen Tian
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - William Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yu Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Patrick G Harran
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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4
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Walther R, Westermann LM, Carmali S, Jackson SE, Brötz-Oesterhelt H, Spring DR. Identification of macrocyclic peptides which activate bacterial cylindrical proteases. RSC Med Chem 2023; 14:1186-1191. [PMID: 37360394 PMCID: PMC10285738 DOI: 10.1039/d3md00136a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
The caseinolytic protease complex ClpXP is an important house-keeping enzyme in prokaryotes charged with the removal and degradation of misfolded and aggregated proteins and performing regulatory proteolysis. Dysregulation of its function, particularly by inhibition or allosteric activation of the proteolytic core ClpP, has proven to be a promising strategy to reduce virulence and eradicate persistent bacterial infections. Here, we report a rational drug-design approach to identify macrocyclic peptides which increase proteolysis by ClpP. This work expands the understanding of ClpP dynamics and sheds light on the conformational control exerted by its binding partner, the chaperone ClpX, by means of a chemical approach. The identified macrocyclic peptide ligands may, in the future, serve as a starting point for the development of ClpP activators for antibacterial applications.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Linda M Westermann
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Sheiliza Carmali
- School of Pharmacy, Queen's University Belfast BT9 7BL Belfast UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Dept. of Bioactive Compounds, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence Controlling Microbes to Fight Infections Germany
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road CB2 1EW Cambridge UK
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5
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Frolov AI, Chankeshwara SV, Abdulkarim Z, Ghiandoni GM. pIChemiSt ─ Free Tool for the Calculation of Isoelectric Points of Modified Peptides. J Chem Inf Model 2023; 63:187-196. [PMID: 36573842 PMCID: PMC9832473 DOI: 10.1021/acs.jcim.2c01261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The isoelectric point (pI) is a fundamental physicochemical property of peptides and proteins. It is widely used to steer design away from low solubility and aggregation and guide peptide separation and purification. Experimental measurements of pI can be replaced by calculations knowing the ionizable groups of peptides and their corresponding pKa values. Different pKa sets are published in the literature for natural amino acids, however, they are insufficient to describe synthetically modified peptides, complex peptides of natural origin, and peptides conjugated with structures of other modalities. Noncanonical modifications (nCAAs) are ignored in the conventional sequence-based pI calculations, therefore producing large errors in their pI predictions. In this work, we describe a pI calculation method that uses the chemical structure as an input, automatically identifies ionizable groups of nCAAs and other fragments, and performs pKa predictions for them. The method is validated on a curated set of experimental measures on 29 modified and 119093 natural peptides, providing an improvement of R2 from 0.74 to 0.95 and 0.96 against the conventional sequence-based approach for modified peptides for the two studied pKa prediction tools, ACDlabs and pKaMatcher, correspondingly. The method is available in the form of an open source Python library at https://github.com/AstraZeneca/peptide-tools, which can be integrated into other proprietary and free software packages. We anticipate that the pI calculation tool may facilitate optimization and purification activities across various application domains of peptides, including the development of biopharmaceuticals.
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Affiliation(s)
- Andrey I. Frolov
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D,
AstraZeneca, Gothenburg, Sweden,
| | - Sunay V. Chankeshwara
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism (CVRM), BioPharmaceuticals R&D,
AstraZeneca, Gothenburg, Sweden
| | - Zeyed Abdulkarim
- Early
Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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6
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Elinson MN, Vereshchagin AN, Ryzhkova YE, Karpenko KA, Ryzhkov FV, Egorov MP. Electrocatalytic Cascade Selective Approach to 3-Aryl-2' H,3 H,4 H-Spiro{Furo[2,3- с]Chromene-2,5'-Pyrimidine}-2',4,4',6'(1' H,3' H)Tetraones and Its Automatic Screening Docking Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2149568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- Michail N. Elinson
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Anatoly N. Vereshchagin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Yuliya E. Ryzhkova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kirill A. Karpenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Fedor V. Ryzhkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mikhail P. Egorov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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7
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Li B, Wan Z, Zheng H, Cai S, Tian HW, Tang H, Chu X, He G, Guo DS, Xue XS, Chen G. Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine. J Am Chem Soc 2022; 144:10080-10090. [PMID: 35639413 DOI: 10.1021/jacs.2c04620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.
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Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han-Wen Tian
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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8
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Bell HJ, Malins LR. Peptide macrocyclisation via late-stage reductive amination. Org Biomol Chem 2022; 20:6250-6256. [PMID: 35621075 DOI: 10.1039/d2ob00782g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A two-component reductive amination approach to the synthesis of peptide macrocycles is reported which leverages the inherent reactivity of proteinogenic amine nucleophiles. Unprotected peptides bearing α-amine and side chain amine motifs undergo two-fold reductive amination reactions with 2,6-pyridinedialdehyde linkers in aqueous media to afford macrocyclic peptide products with backbone embedded pyridine motifs. Dialdehyde staples bearing valuable azide and alkyne handles also enable the post-cyclisation modification of peptides using copper-catalysed azide-alkyne cycloaddition (CuAAC) chemistry.
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Affiliation(s)
- Hayden J Bell
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia
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9
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Glavaš M, Gredičak M, Štefanić Z, Jerić I. Synthesis of 14-membered enediyne-embedded macrocycles. Org Biomol Chem 2022; 20:3823-3834. [PMID: 35470844 DOI: 10.1039/d2ob00090c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A concise and practical strategy towards a novel class of 14-membered macrocycles containing an enediyne (Z-3-ene-1,5-diyne) structural unit is described. A highly modular assembly of various precursors via sequential Ugi/Sonogashira reactions allowed the preparation of hybrid enediyne-peptide macrocycles in most cases as single diastereoisomers. Selected macrocyclic compounds showed moderate antiproliferative activity, and can be considered as templates suitable for further diversification in terms of ring size, shape, and stereochemistry.
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Affiliation(s)
- Mladena Glavaš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Matija Gredičak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
| | - Zoran Štefanić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia.
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10
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Zhang X, Zhang C, Jiang B, Gao Y, Xu X, Miao Z. Ligand-Controlled Palladium-Catalyzed Asymmetric [4+3] and [2+3] Annulation Reactions of Spirovinylcyclopropyl Oxindoles with o-Quinone Methides. Org Lett 2022; 24:3097-3101. [PMID: 35436115 DOI: 10.1021/acs.orglett.2c01137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We herein report regiodivergent ligand-controlled palladium-catalyzed asymmetric cycloaddition reactions between spirovinylcyclopropyl oxindoles and o-quinone methides. Specifically, by using the chiral P,P-ligand Segphos (L5), we obtained various spirooxindole-3,4-benzo[b]oxepanes in moderate to good yields with excellent enantioselectivities via [4+3] cycloaddition reactions. In contrast, reactions involving Trost's ligand (L7) showed different regio- and stereoselectivities, affording bispirooxindole heterocyclic compounds in good yields via [2+3] cycloaddition reactions.
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Affiliation(s)
- Xiyuan Zhang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, China
| | - Cong Zhang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bo Jiang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, China
| | - Yanfeng Gao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, China
| | - Xiufang Xu
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhiwei Miao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin 300071, China
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11
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022; 61:e202114328. [PMID: 34978373 PMCID: PMC9303634 DOI: 10.1002/anie.202114328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 01/02/2023]
Abstract
Design and synthesis of pseudo‐natural products (PNPs) through recombination of natural product (NP) fragments in unprecedented arrangements enables the discovery of novel biologically relevant chemical matter. With a view to wider coverage of NP‐inspired chemical and biological space, we describe the combination of this principle with macrocycle formation. PNP‐macrocycles were synthesized efficiently in a stereoselective one‐pot procedure including the 1,3‐dipolar cycloadditions of different dipolarophiles with dimeric cinchona alkaloid‐derived azomethine ylides formed in situ. The 20‐membered bis‐cycloadducts embody 18 stereocenters and an additional fragment‐sized NP‐structure. After further functionalization, a collection of 163 macrocyclic PNPs was obtained. Biological investigation revealed potent inducers of the lipidation of the microtubule associated protein 1 light chain 3 (LC3) protein, which plays a prominent role in various autophagy‐related processes.
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Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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12
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Traboulsi H, Khedr MA, Elgorashe R, Al-Faiyz Y, Negm A. Development of superior antibodies against the S-protein of SARS-Cov-2 using macrocyclic epitopes. ARAB J CHEM 2022; 15:103631. [PMID: 34909055 PMCID: PMC8662835 DOI: 10.1016/j.arabjc.2021.103631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 12/06/2021] [Indexed: 11/29/2022] Open
Abstract
One of the proven methods to prevent and inhibit viral infections is to use antibodies to block the initial Receptor Binding Domain (RBD) of SARS-CoV-2 S protein and avoid its binding with the host cells. Thus, developing these RBD-targeting antibodies would be a promising approach for treating the SARS-CoV-2 infectious disease and stop virus replication. Macrocyclic epitopes constitute closer mimics of the receptor's actual topology and, as such, are expected to be superior epitopes for antibody generation. This work demonstrated the vital effect of the three-dimensional shape of epitopes on the developed antibodies' activity against RBD protein of SARS-CoV-2. The molecular dynamics studies showed the greater stability of the cyclic epitopes in comparison with the linear counterpart, which was reflected in the activity of their produced antibodies. Indeed, the antibodies we developed using macrocyclic epitopes showed superiority with respect to binding to RBD proteins compared to antibodies formed from a linear peptide. The results of the present work constitute a roadmap for developing superior antibodies that could be used to inhibit the activity of the SARS-CoV-2 and prevent its reproduction.
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Affiliation(s)
- Hassan Traboulsi
- Department of Chemistry, College of Science, King Faisal University, P.O Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Mohammed A Khedr
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-AHasa 31982, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, P.O. Box 11795, Cairo, Egypt
| | - Rafea Elgorashe
- Department of Chemistry, College of Science, King Faisal University, P.O Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Yasair Al-Faiyz
- Department of Chemistry, College of Science, King Faisal University, P.O Box 400, Al-Ahsa 31982, Saudi Arabia
| | - Amr Negm
- Department of Chemistry, College of Science, King Faisal University, P.O Box 400, Al-Ahsa 31982, Saudi Arabia
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
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13
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Li J, Lai W, Pang A, Liu L, Ye L, Xiong XF. On-Resin Synthesis of Linear Aryl Thioether Containing Peptides and in-Solution Cyclization via Cysteine S NAr Reaction. Org Lett 2022; 24:1673-1677. [PMID: 35195423 DOI: 10.1021/acs.orglett.2c00234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyclic peptides represent one of the most promising therapeutic agents in drug discovery due to their good affinity and selectivity. Herein, an on-resin synthesis of aryl thioether containing peptides and a concise cyclization strategy via chemoselective cysteine SNAr reaction was developed. The arylation group could be incorporated into a series of amino acids and used for standard SPPS and peptides cyclization. Constructed cyclic peptides showed increased cellular uptakes compared to their linear peptides.
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Affiliation(s)
- Jian Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Weihong Lai
- School of Pharmacy, Guangdong Pharmaceutical University, 510006 Guangzhou, Guangdong, P. R. China
| | - Ao Pang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Lu Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
| | - Lianbao Ye
- School of Pharmacy, Guangdong Pharmaceutical University, 510006 Guangzhou, Guangdong, P. R. China
| | - Xiao-Feng Xiong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006 Guangzhou, Guangdong, P. R. China
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14
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Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles. Molecules 2022; 27:molecules27031012. [PMID: 35164274 PMCID: PMC8839925 DOI: 10.3390/molecules27031012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022] Open
Abstract
Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C–C and C–heteroatom cross-coupling, copper- or ruthenium-catalyzed azide–alkyne cycloaddition, intramolecular SNAr or SN2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.
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15
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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16
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Chu X, Shen L, Li B, Yang P, Du C, Wang X, He G, Messaoudi S, Chen G. Construction of Peptide Macrocycles via Palladium-Catalyzed Multiple S-Arylation: An Effective Strategy to Expand the Structural Diversity of Cross-Linkers. Org Lett 2021; 23:8001-8006. [PMID: 34582221 DOI: 10.1021/acs.orglett.1c03003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A simple and versatile method for macrocyclizing unprotected native peptides with a wide range of easily accessible diiodo and triiodoarene reagents via the palladium-catalyzed multiple S-arylation of cysteine residues is developed. Iodoarenes with different arene and heteroarene cores can be incorporated into peptide macrocycles of varied ring sizes and amino acid compositions with high efficiency and selectivity under mild conditions.
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Affiliation(s)
- Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Linhua Shen
- University Paris-Saclay, CNRS, BioCIS, 92296 Chat̂enay-Malabry, France
| | - Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Peng Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chengzhuo Du
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiaoye Wang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Samir Messaoudi
- University Paris-Saclay, CNRS, BioCIS, 92296 Chat̂enay-Malabry, France
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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17
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Chen XX, Tang Y, Wu M, Zhang YN, Chen K, Zhou Z, Fang GM. Helix-Constrained Peptides Constructed by Head-to-Side Chain Cross-Linking Strategies. Org Lett 2021; 23:7792-7796. [PMID: 34551517 DOI: 10.1021/acs.orglett.1c02820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Facile head-to-side chain cross-linking strategies are developed to generate helix-constrained peptides. In our strategies, a covalent cross-linker is incorporated at N, i+7 or N, i+1 positions to lock the peptide into a helical conformation. The described patterns of head-to-side chain cross-linking will provide new frameworks for constrained helical peptide.
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Affiliation(s)
- Xiao-Xu Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yang Tang
- Center of Minimally Invasive Treatment for Tumor, Department of Medical Ultrasound, Shanghai Tenth People's Hospital; Ultrasound Research and Education Institute, Clinical Research Center for Interventional Medicine, School of Medicine, Tongji University, Shanghai 200072, P. R. China
| | - Meng Wu
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Yan-Ni Zhang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Kai Chen
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Ge-Min Fang
- School of Life Science, Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, P. R. China
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18
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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19
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Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat Commun 2021; 12:3384. [PMID: 34099674 PMCID: PMC8185074 DOI: 10.1038/s41467-021-23609-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
Abstract
Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational "anchor extension" methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC50 values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.
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20
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Xiao JA, Li JL, Cheng XL, Chen K, Peng H, Chen WQ, Su W, Huang YM, Yang H. Enantioselective formal [3+2]-cycloadditions to access spirooxindoles bearing four contiguous stereocenters through synergistic catalysis. Chem Commun (Camb) 2021; 57:4456-4459. [PMID: 33949393 DOI: 10.1039/d0cc07957j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An enantioselective ring-opening formal [3+2]-cycloaddition of spirovinylcyclopropyl oxindoles with enals via synergistic catalysis of palladium(0) and a chiral organocatalyst has been developed, affording spirooxindoles bearing four contiguous stereocenters in good yields with excellent enantioselectivities. The generality and utility of the protocol were also demonstrated through scale-up experiments and synthetic transformation of the resulting cycloadduct.
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Affiliation(s)
- Jun-An Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Jin-Lian Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Xiu-Liang Cheng
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Kai Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China. and State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Hai Peng
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Wen-Qiang Chen
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Wei Su
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Yan-Min Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, P. R. China.
| | - Hua Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.
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21
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Schreiber CL, Zhai C, Smith BD. Chiral figure-eight molecular scaffold for fluorescent probe development. Org Biomol Chem 2021; 19:3213-3219. [PMID: 33885576 PMCID: PMC8075008 DOI: 10.1039/d1ob00306b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted fluorescent molecular probes are useful for cell microscopy, diagnostics, and biological imaging. An emerging discovery paradigm is to screen libraries of fluorescent molecules and identify hit compounds with interesting targeting properties. However, a current limitation with this approach is the lack of fluorescent molecular scaffolds that can produce libraries of probe candidates with three dimensional globular shape, chiral centers, and constrained conformation. This study evaluated a new probe scaffold called squaraine figure-eight (SF8), a self-threaded molecular architecture that is comprised of an encapsulated deep-red fluorescent squaraine dye, surrounding tetralactam macrocycle, and peripheral loops. Easy synthetic variation of the loops produced four chiral isomeric SF8 probes, with the same log P values. Cell microscopy showed that subtle changes in the loop structure led to significant differences in intracellular targeting. Most notably, a comparison of enantiomeric probes revealed a large difference in mitochondrial accumulation, very likely due to differences in affinity for a chiral biomarker within the organelle. A tangible outcome of the research is a probe candidate that can be: (a) developed further as a bright and photostable, deep-red fluorescent probe for mitochondrial imaging, and (b) used as a molecular tool to identify the mitochondrial biomarker for selective targeting. It will be straightforward to expand the SF8 probe chemical space and produce structurally diverse probe libraries with high potential for selective targeting of a wide range of biomarkers.
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Affiliation(s)
- Cynthia L Schreiber
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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22
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A versatile resin for the generation of thioether-bonded head-to-tail cyclized peptides. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
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24
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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25
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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26
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García‐Mingüens E, Caletková O, Berkeš D, Nájera C, Sansano JM. Silver‐Catalyzed Diastereoselective Synthesis of Spirocyclic Pyrrolidine‐Lactones by 1,3‐Dipolar Cycloaddition. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Eduardo García‐Mingüens
- Departamento de Química Orgánica. Facultad de Ciencias Universidad de Alicante 03080 Alicante Spain
- Centro de Innovación en Química Avanzada (ORFEO‐CINQA) Spain
- Instituto de Síntesis Orgánica (ISO) Universidad de Alicante 03080 Alicante Spain
| | - Oľga Caletková
- Department of Organic Chemistry Slovak University of Technology in Bratislava Slovakia
| | - Dušan Berkeš
- Department of Organic Chemistry Slovak University of Technology in Bratislava Slovakia
| | - Carmen Nájera
- Centro de Innovación en Química Avanzada (ORFEO‐CINQA) Spain
| | - José M. Sansano
- Departamento de Química Orgánica. Facultad de Ciencias Universidad de Alicante 03080 Alicante Spain
- Centro de Innovación en Química Avanzada (ORFEO‐CINQA) Spain
- Instituto de Síntesis Orgánica (ISO) Universidad de Alicante 03080 Alicante Spain
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27
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Reguera L, Rivera DG. Macrocyclic Iminopeptides Diversify To Better Target Proteins. ChemMedChem 2020; 15:1111-1112. [DOI: 10.1002/cmdc.202000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Leslie Reguera
- Faculty of ChemistryUniversity of Havana, Zapata y G Havana 10400 Cuba
| | - Daniel G. Rivera
- Faculty of ChemistryUniversity of Havana, Zapata y G Havana 10400 Cuba
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