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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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A general highly efficient synthesis of biocompatible rhodamine dyes and probes for live-cell multicolor nanoscopy. Nat Commun 2023; 14:1306. [PMID: 36894547 PMCID: PMC9998615 DOI: 10.1038/s41467-023-36913-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
The development of live-cell fluorescence nanoscopy is powered by the availability of suitable fluorescent probes. Rhodamines are among the best fluorophores for labeling intracellular structures. Isomeric tuning is a powerful method for optimizing the biocompatibility of rhodamine-containing probes without affecting their spectral properties. An efficient synthesis pathway for 4-carboxyrhodamines is still lacking. We present a facile protecting-group-free 4-carboxyrhodamines' synthesis based on the nucleophilic addition of lithium dicarboxybenzenide to the corresponding xanthone. This approach drastically reduces the number of synthesis steps, expands the achievable structural diversity, increases overall yields and permits gram-scale synthesis of the dyes. We synthesize a wide range of symmetrical and unsymmetrical 4-carboxyrhodamines covering the whole visible spectrum and target them to multiple structures in living cells - microtubules, DNA, actin, mitochondria, lysosomes, Halo-tagged and SNAP-tagged proteins. The enhanced permeability fluorescent probes operate at submicromolar concentrations, allowing high-contrast STED and confocal microscopy of living cells and tissues.
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3
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Microbial Natural Products with Wound-Healing Properties. Processes (Basel) 2022. [DOI: 10.3390/pr11010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Wound healing continues to pose a challenge in clinical settings. Moreover, wound management must be performed properly and efficiently. Acute wound healing involves multiple cell divisions, a new extracellular matrix, and the process of formation, such as growth factors and cytokines, which are released at the site of the wound to regulate the process. Any changes that disrupt the healing process could cause tissue damage and prolong the healing process. Various factors, such as microbial infection, oxidation, and inflammation, can delay wound healing. In order to counter these problems, utilizing natural products with wound-healing effects has been reported to promote this process. Several natural products have been associated with wound healing, most of which are from medicinal plants. However, secondary microbial metabolites have not been extensively studied for their wound-healing properties. Further, investigations on the wound-healing control of natural microbial products are required due to a lack of studies. This review discussed the in vivo and in vitro research on the wound healing activities of natural microbial products, which may assist in the development of better wound treatments in the future.
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Küllmer F, Vepřek NA, Borowiak M, Nasufović V, Barutzki S, Thorn-Seshold O, Arndt HD, Trauner D. Next Generation Opto-Jasplakinolides Enable Local Remodeling of Actin Networks. Angew Chem Int Ed Engl 2022; 61:e202210220. [PMID: 36048143 PMCID: PMC11256906 DOI: 10.1002/anie.202210220] [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] [Received: 07/13/2022] [Indexed: 11/12/2022]
Abstract
The natural product jasplakinolide is widely used to stabilize F-actin. Based on extensive structure-activity relationship studies, we have developed a new generation of photoswitchable jasplakinolides that feature rationally designed red-shifted azobenzene photoswitches. Our lead compound, nOJ, can be activated with longer wavelengths in the visible range (e.g. 440-475 nm) and rapidly returns to its inactive state through thermal relaxation. nOJ enables the reversible control of F-actin dynamics, as shown through live-cell imaging, cell migration, and cell proliferation assays. Short, local irradiation with blue light resulted in highly localized and reversible actin aggregation with subcellular precision. Our optical tool can be useful in diverse fields to study actin dynamics with excellent spatiotemporal resolution.
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Affiliation(s)
- Florian Küllmer
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Nynke A Vepřek
- New York University, Department of Chemistry, 100 Washington Square East, New York, NY 10003, USA
- Department of Chemistry, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Malgorzata Borowiak
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Veselin Nasufović
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Sebastian Barutzki
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstrasse 5-13, 81377, München, Germany
| | - Hans-Dieter Arndt
- Friedrich-Schiller-Universität (FSU), Institut für Organische Chemie und Makromolekulare Chemie, Humboldtstr. 10, 07743, Jena, Germany
| | - Dirk Trauner
- New York University, Department of Chemistry, 100 Washington Square East, New York, NY 10003, USA
- Department of Chemistry University of Pennsylvania, 231 South 34th St., Philadelphia, PA 19104-6323, USA
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5
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Lv JX, Ding YQ, Huang CM, Guo LL, Fang JL, Jia X, Zhang WH, You S, Qin B. Enzyme- and Chemo-enzyme-Catalyzed Stereodivergent Synthesis. PHARMACEUTICAL FRONTS 2022. [DOI: 10.1055/s-0042-1755556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Multiple stereoisomers can be found when a substance contains chiral carbons in its chemical structure. To obtain the desired stereoisomers, asymmetric synthesis was proposed in the 1970s and developed rapidly at the beginning of this century. Stereodivergent synthesis, an extension of asymmetric synthesis in organic synthesis with the hope to produce all stereoisomers of chiral substances in high conversion and selectivity, enriches the variety of available products and serves as a reference suggestion for the synthesis of their derivatives and other compounds. Since biocatalysis has outstanding advantages of economy, environmental friendliness, high efficiency, and reaction at mild conditions, the biocatalytic reaction is regarded as an efficient strategy to perform stereodivergent synthesis. Thus, in this review, we summarize the stereodivergent synthesis catalyzed by enzymes or chemo-enzymes in cases where a compound contains two or three chiral carbons, i.e., at most four or eight stereoisomers are present. The types of reactions, including reduction of substituent ketones, cyclization reactions, olefin addition, and nonredox transesterification reactions, are also discussed for the understanding of the progress and application of biocatalysis in stereodivergent synthesis.
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Affiliation(s)
- Jia-Xiang Lv
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Ya-Qi Ding
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Chen-Ming Huang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Ling-Ling Guo
- Microbial Research Institute of Liaoning Province, Liaoyang, People's Republic of China
| | - Jia-Li Fang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Xian Jia
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Wen-He Zhang
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Song You
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Bin Qin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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6
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Kim S, Lee CW, Park SY, Asolkar RN, Kim H, Kim GJ, Oh SJ, Kim Y, Lee EY, Oh DC, Yang I, Paik MJ, Choi H, Kim H, Nam SJ, Fenical W. Acremonamide, a Cyclic Pentadepsipeptide with Wound-Healing Properties Isolated from a Marine-Derived Fungus of the Genus Acremonium. JOURNAL OF NATURAL PRODUCTS 2021; 84:2249-2255. [PMID: 34387477 DOI: 10.1021/acs.jnatprod.1c00305] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Acremonamide (1) was isolated from a marine-derived fungus belonging to the genus Acremonium. The chemical structure of 1 was established using MS, UV, and NMR spectroscopic data analyses. Acremonamide (1) was found to contain N-Me-Phe, N-Me-Ala, Val, Phe, and 2-hydroxyisovaleric acid. The absolute configurations of the four aforementioned amino acids were determined through acid hydrolysis followed by the advanced Marfey's method, whereas the absolute configuration of 2-hydroxyisovaleric acid was determined through GC-MS analysis after formation of the O-pentafluoropropionylated derivative of the (-)-menthyl ester of 2-hydroxyisovaleric acid. As an intrinsic biological activity, acremonamide (1) did not exert cytotoxicity to cancer and noncancer cells and increased the migration and invasion. Based on these activities, the wound healing properties of acremonamide (1) were confirmed in vitro and in vivo.
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Affiliation(s)
- Sojeong Kim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Chang Wook Lee
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - So-Yeon Park
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Ratnakar N Asolkar
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, United States
| | - Haerin Kim
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Geum Jin Kim
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Song Jin Oh
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Youngbae Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Eun-Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Inho Yang
- Ocean Science and Technology School, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan-si, Gyeongsangbukdo 38541, Republic of Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, 255 Jungang-ro, Sunchon, Jeonnam 57922, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, California 92093-0204, United States
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7
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Nasufović V, Küllmer F, Bößneck J, Dahse H, Görls H, Bellstedt P, Stallforth P, Arndt H. Total Synthesis and Bioactivity Mapping of Geodiamolide H. Chemistry 2021; 27:11633-11642. [PMID: 34032329 PMCID: PMC8453818 DOI: 10.1002/chem.202100989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Indexed: 01/24/2023]
Abstract
The first total synthesis of the actin-stabilizing marine natural product geodiamolide H was achieved. Solid-phase based peptide assembly paired with scalable stereoselective syntheses of polyketide building blocks and an optimized esterification set the stage for investigating the key ring-closing metathesis. Geodiamolide H and synthetic analogues were characterized for their toxicity and for antiproliferative effects in cellulo, by characterising actin polymerization induction in vitro, and by docking on the F-actin target and property computation in silico, for a better understanding of structure-activity relationships (SAR). A non-natural analogue of geodiamolide H was discovered to be most potent in the series, suggesting significant potential for tool compound design.
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Affiliation(s)
- Veselin Nasufović
- Institut für Organische Chemie und Makromolekulare ChemieFriedrich-Schiller-Universität (FSU)Humboldtstr. 1007743JenaGermany
| | - Florian Küllmer
- Institut für Organische Chemie und Makromolekulare ChemieFriedrich-Schiller-Universität (FSU)Humboldtstr. 1007743JenaGermany
| | - Johanna Bößneck
- Institut für Organische Chemie und Makromolekulare ChemieFriedrich-Schiller-Universität (FSU)Humboldtstr. 1007743JenaGermany
| | - Hans‐Martin Dahse
- Abteilungen Infektionsbiologie und PaläobiotechnologieLeibniz-Institut für Naturstoffforschung – Hans-Knöll-InstitutBeutenbergstr. 11a07745JenaGermany
| | - Helmar Görls
- Institut für Anorganische und Analytische ChemieFriedrich-Schiller-Universität (FSU)Humboldtstr. 807743JenaGermany
| | - Peter Bellstedt
- NMR-PlattformFriedrich-Schiller-Universität (FSU)Humboldtstr. 1007743JenaGermany
| | - Pierre Stallforth
- Abteilungen Infektionsbiologie und PaläobiotechnologieLeibniz-Institut für Naturstoffforschung – Hans-Knöll-InstitutBeutenbergstr. 11a07745JenaGermany
| | - Hans‐Dieter Arndt
- Institut für Organische Chemie und Makromolekulare ChemieFriedrich-Schiller-Universität (FSU)Humboldtstr. 1007743JenaGermany
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8
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Kajetanowicz A, Grela K. Nitro and Other Electron Withdrawing Group Activated Ruthenium Catalysts for Olefin Metathesis Reactions. Angew Chem Int Ed Engl 2021; 60:13738-13756. [PMID: 32808704 PMCID: PMC8246989 DOI: 10.1002/anie.202008150] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Advanced applications of the Nobel Prize winning olefin metathesis reaction require user-friendly and highly universal catalysts. From many successful metathesis catalysts, which belong to the two distinct classes of Schrock and Grubbs-type catalysts, the subclass of chelating-benzylidene ruthenium complexes (so-called Hoveyda-Grubbs catalysts) additionally activated by electron-withdrawing groups (EWGs) provides a highly tunable platform. In the Review, the origin of the EWG-activation concept and selected applications of the resulting catalysts in target-oriented synthesis, medicinal chemistry, as well as in the preparation of fine-chemicals and in materials chemistry is discussed. Based on the examples, some suggestions for end-users regarding minimization of catalyst loading, selectivity control, and general optimization of the olefin metathesis reaction are provided.
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Affiliation(s)
- Anna Kajetanowicz
- Laboratory of Organometallic SynthesisFaculty of ChemistryBiological and Chemical Research CentreUniversity of WarsawŻwirki i Wigury 10102-089WarsawPoland
| | - Karol Grela
- Laboratory of Organometallic SynthesisFaculty of ChemistryBiological and Chemical Research CentreUniversity of WarsawŻwirki i Wigury 10102-089WarsawPoland
- Institute of Organic ChemistryPolish Academy of SciencesKasprzaka 44/5201-224WarsawPoland
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9
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Kajetanowicz A, Grela K. Durch Nitro‐ und andere elektronenziehende Gruppen aktivierte Ruthenium‐Katalysatoren für die Olefinmetathese. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Anna Kajetanowicz
- Labor für Organometall-Synthese Fakultät für Chemie Biological and Chemical Research Centre Universität Warschau Żwirki i Wigury 101 02-089 Warschau Polen
| | - Karol Grela
- Labor für Organometall-Synthese Fakultät für Chemie Biological and Chemical Research Centre Universität Warschau Żwirki i Wigury 101 02-089 Warschau Polen
- Institut für Organische Chemie Polish Academy of Sciences Kasprzaka 44/52 01-224 Warschau Polen
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10
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Pospich S, Küllmer F, Nasufović V, Funk J, Belyy A, Bieling P, Arndt H, Raunser S. Cryo‐EM Resolves Molecular Recognition Of An Optojasp Photoswitch Bound To Actin Filaments In Both Switch States. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Sabrina Pospich
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Florian Küllmer
- Institute of Organic Chemistry and Macromolecular Chemistry Friedrich-Schiller-University Humboldtstr. 10 07743 Jena Germany
| | - Veselin Nasufović
- Institute of Organic Chemistry and Macromolecular Chemistry Friedrich-Schiller-University Humboldtstr. 10 07743 Jena Germany
| | - Johanna Funk
- Department of Systemic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Alexander Belyy
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Peter Bieling
- Department of Systemic Cell Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Hans‐Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry Friedrich-Schiller-University Humboldtstr. 10 07743 Jena Germany
| | - Stefan Raunser
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund Germany
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11
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Pospich S, Küllmer F, Nasufović V, Funk J, Belyy A, Bieling P, Arndt HD, Raunser S. Cryo-EM Resolves Molecular Recognition Of An Optojasp Photoswitch Bound To Actin Filaments In Both Switch States. Angew Chem Int Ed Engl 2021; 60:8678-8682. [PMID: 33449370 PMCID: PMC8048601 DOI: 10.1002/anie.202013193] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Indexed: 12/16/2022]
Abstract
Actin is essential for key processes in all eukaryotic cells. Cellpermeable optojasps provide spatiotemporal control of the actin cytoskeleton, confining toxicity and potentially rendering F-actin druggable by photopharmacology. Here, we report cryo electron microscopy (cryo-EM) structures of both isomeric states of one optojasp bound to actin filaments. The high-resolution structures reveal for the first time the pronounced effects of photoswitching a functionalized azobenzene. By characterizing the optojasp binding site and identifying conformational changes within F-actin that depend on the optojasp isomeric state, we refine determinants for the design of functional F-actin photoswitches.
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Affiliation(s)
- Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Florian Küllmer
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstr. 10, 07743, Jena, Germany
| | - Veselin Nasufović
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstr. 10, 07743, Jena, Germany
| | - Johanna Funk
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Hans-Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-University, Humboldtstr. 10, 07743, Jena, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
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12
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Wu Q, Jing Y, Zhao T, Gao J, Cai M, Xu H, Liu Y, Liang F, Chen J, Wang H. Development of small molecule inhibitor-based fluorescent probes for highly specific super-resolution imaging. NANOSCALE 2020; 12:21591-21598. [PMID: 33094297 DOI: 10.1039/d0nr05188h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To ensure the ultimate high-quality imaging of super-resolution fluorescence microscopy with increasingly high resolution, it is significant to use small specific fluorescent probes. Compared with the common biological fluorescent labeling technology, because of small size, strong specificity, abundance and special binding sites, single-targeted small-molecule inhibitors (SMIs) can link with organic dyes to form small fluorescent probes for various biomolecules. Herein, to confirm the feasibility of the SMI-probes, epidermal growth factor (EGF) receptor (EGFR)-targeted tyrosine kinase inhibitor Gefitinib was selected for modification with the fluorescent dye to form Gefitinib-probe. Then, the labeling superiority of Gefitinib-probe was revealed by comparing the direct stochastic optical reconstruction microscopy (dSTORM) images of EGFR labeled with different probes. Additionally, a high co-localization of fluorescent points from Gefitinib-probe and EGF-probe labeling indicated a high specificity of Gefitinib-probe to EGFR. Finally, higher co-localization of EGFR and HER3 labeled with the probe pair containing Gefitinib-probe than with the antibody-probe pair suggested that Gefitinib-probe with a cytoplasmic binding site benefited dual-color imaging. These results indicate that the SMI-probes are able to serve as versatile labeling tools for high-quality super-resolution imaging.
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Affiliation(s)
- Qiang Wu
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province, College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. of China.
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13
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Belov VN, Stoldt S, Rüttger F, John M, Seikowski J, Schimpfhauser J, Hell SW. Synthesis of Fluorescent Jasplakinolide Analogues for Live-Cell STED Microscopy of Actin. J Org Chem 2020; 85:7267-7275. [PMID: 32418421 PMCID: PMC7281785 DOI: 10.1021/acs.joc.0c00653] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
nanometer thickness of filaments and the dynamic behavior of
actin—a protein playing a crucial role in cellular function
and motility—make it attractive for observation with super-resolution
optical microscopy. We developed the solution-phase synthesis of des-bromo-des-methyl-jasplakinolide-lysine,
used as the “recognition unit” (ligand) for F-actin
in living cells. The first amino acid—Fmoc-O-TIPS-β-tyrosine—was prepared in 78% yield (two steps
in one pot). The new solution-phase synthesis involves 2-phenylisopropyl
protection of the carboxyl group and does not require excesses of
commercially unavailable amino acids. The overall yield of the target
intermediate obtained in nine steps is about 8%. The 2-phenylisopropyl
group can be cleaved from carboxyl with 2–3% (v/v) of TFA in
acetonitrile (0–10 °C), without affecting TIPS protection
of the phenolic hydroxyl in β-tyrosine and N-Boc protection in lysine. Des-bromo-des-methyl-jasplakinolide-lysine
was coupled with red-emitting fluorescent dyes 580CP and 610CP (via 6-aminohexanoate
linker). Actin in living cells was labeled with 580CP and 610CP probes, and the optical resolution measured
as full width at half-maximum of line profiles across actin fibers
was found to be 300–400 nm and 100 nm under confocal and STED
conditions, respectively. The solution-phase synthesis of des-bromo-des-methyl-jasplakinolide-lysine
opens a way to better fluorescent probe perspective for actin imaging.
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Affiliation(s)
- Vladimir N Belov
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry (MPIBPC), Am Fassberg 11, 37077 Göttingen, Germany.,Facility for Synthetic Chemistry, MPIBPC, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Stoldt
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry (MPIBPC), Am Fassberg 11, 37077 Göttingen, Germany
| | - Franziska Rüttger
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Michael John
- Institut für Organische und Biomolekulare Chemie der Georg-August-Universität, Tammannstrasse 2, 37077 Göttingen, Germany
| | - Jan Seikowski
- Facility for Synthetic Chemistry, MPIBPC, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jens Schimpfhauser
- Facility for Synthetic Chemistry, MPIBPC, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan W Hell
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry (MPIBPC), Am Fassberg 11, 37077 Göttingen, Germany
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14
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Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dellsén A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. J Am Chem Soc 2020; 142:4904-4915. [PMID: 32058716 PMCID: PMC7307906 DOI: 10.1021/jacs.0c00269] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
“Hot
loop” protein segments have variable structure
and conformation and contribute crucially to protein–protein
interactions. We describe a new hot loop mimicking modality, termed
PepNats, in which natural product (NP)-inspired structures are incorporated
as conformation-determining and -restricting structural elements into
macrocyclic hot loop-derived peptides. Macrocyclic PepNats representing
hot loops of inducible nitric oxide synthase (iNOS) and human agouti-related
protein (AGRP) were synthesized on solid support employing macrocyclization
by imine formation and subsequent stereoselective 1,3-dipolar cycloaddition
as key steps. PepNats derived from the iNOS DINNN hot loop and the
AGRP RFF hot spot sequence yielded novel and potent ligands of the
SPRY domain-containing SOCS box protein 2 (SPSB2) that binds to iNOS,
and selective ligands for AGRP-binding melanocortin (MC) receptors.
NP-inspired fragment absolute configuration determines the conformation
of the peptide part responsible for binding. These results demonstrate
that combination of NP-inspired scaffolds with peptidic epitopes enables
identification of novel hot loop mimics with conformationally constrained
and biologically relevant structure.
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Affiliation(s)
- Stéphanie M Guéret
- Department of Chemical Biology, AstraZeneca-Max Planck Institute Satellite Unit, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Sasikala Thavam
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Marco Potowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Göran Dahl
- Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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15
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Gerasimaitė R, Seikowski J, Schimpfhauser J, Kostiuk G, Gilat T, D'Este E, Schnorrenberg S, Lukinavičius G. Efflux pump insensitive rhodamine–jasplakinolide conjugates for G- and F-actin imaging in living cells. Org Biomol Chem 2020; 18:2929-2937. [DOI: 10.1039/d0ob00369g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent actin probes made of 6′-carbopyronines and jasplakinolide are insensitive to efflux pumps and stain F- and G-actin efficiently in living cells, allowing high quality 2D and 3D nanoscopy of dynamic actin structures.
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Affiliation(s)
- Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Jan Seikowski
- Facility for Synthetic Chemistry
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Jens Schimpfhauser
- Facility for Synthetic Chemistry
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Georgij Kostiuk
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Tanja Gilat
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Elisa D'Este
- Optical Microscopy Facility
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Sebastian Schnorrenberg
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group
- Department of Nanobiophotonics
- Max Planck Institute for Biophysical Chemistry
- Göttingen
- Germany
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16
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Appavoo SD, Huh S, Diaz DB, Yudin AK. Conformational Control of Macrocycles by Remote Structural Modification. Chem Rev 2019; 119:9724-9752. [DOI: 10.1021/acs.chemrev.8b00742] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Solomon D. Appavoo
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Sungjoon Huh
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Diego B. Diaz
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario, Canada M5S 3H6
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17
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Actin stabilizing compounds show specific biological effects due to their binding mode. Sci Rep 2019; 9:9731. [PMID: 31278311 PMCID: PMC6611809 DOI: 10.1038/s41598-019-46282-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/26/2019] [Indexed: 11/08/2022] Open
Abstract
Actin binding compounds are widely used tools in cell biology. We compare the biological and biochemical effects of miuraenamide A and jasplakinolide, a structurally related prototypic actin stabilizer. Though both compounds have similar effects on cytoskeletal morphology and proliferation, they affect migration and transcription in a distinctive manner, as shown by a transcriptome approach in endothelial cells. In vitro, miuraenamide A acts as an actin nucleating, F-actin polymerizing and stabilizing compound, just like described for jasplakinolide. However, in contrast to jasplakinolide, miuraenamide A competes with cofilin, but not gelsolin or Arp2/3 for binding to F-actin. We propose a binding mode of miuraenamide A, explaining both its similarities and its differences to jasplakinolide. Molecular dynamics simulations suggest that the bromophenol group of miurenamide A interacts with residues Tyr133, Tyr143, and Phe352 of actin. This shifts the D-loop of the neighboring actin, creating tighter packing of the monomers, and occluding the binding site of cofilin. Since relatively small changes in the molecular structure give rise to this selectivity, actin binding compounds surprisingly are promising scaffolds for creating actin binders with specific functionality instead of just "stabilizers".
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18
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Reker D, Bernardes GJL, Rodrigues T. Computational advances in combating colloidal aggregation in drug discovery. Nat Chem 2019; 11:402-418. [PMID: 30988417 DOI: 10.1038/s41557-019-0234-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
Small molecule effectors are essential for drug discovery. Specific molecular recognition, reversible binding and dose-dependency are usually key requirements to ensure utility of a novel chemical entity. However, artefactual frequent-hitter and assay interference compounds may divert lead optimization and screening programmes towards attrition-prone chemical matter. Colloidal aggregates are the prime source of false positive readouts, either through protein sequestration or protein-scaffold mimicry. Nevertheless, assessment of colloidal aggregation remains somewhat overlooked and under-appreciated. In this Review, we discuss the impact of aggregation in drug discovery by analysing select examples from the literature and publicly-available datasets. We also examine and comment on technologies used to experimentally identify these potentially problematic entities. We focus on evidence-based computational filters and machine learning algorithms that may be swiftly deployed to flag chemical matter and mitigate the impact of aggregates in discovery programmes. We highlight the tools that can be used to scrutinize libraries, and identify and eliminate these problematic compounds.
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Affiliation(s)
- Daniel Reker
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,MIT-IBM Watson AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
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19
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Itoh H, Inoue M. Comprehensive Structure–Activity Relationship Studies of Macrocyclic Natural Products Enabled by Their Total Syntheses. Chem Rev 2019; 119:10002-10031. [DOI: 10.1021/acs.chemrev.9b00063] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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Tian Y, Wang J, Liu W, Yuan X, Tang Y, Li J, Chen Y, Zhang W. Stereodivergent total synthesis of Br-nannocystins underpinning the polyketide (10R,11S) configuration as a key determinant of potency. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.12.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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21
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Xu J, Hu L. Asymmetric one-pot synthesis of five- and six-membered lactones via dynamic covalent kinetic resolution: Exploring the regio- and stereoselectivities of lipase. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Lang JH, Lindel T. Synthesis of the polyketide section of seragamide A and related cyclodepsipeptides via Negishi cross coupling. Beilstein J Org Chem 2019; 15:577-583. [PMID: 30873243 PMCID: PMC6404460 DOI: 10.3762/bjoc.15.53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/12/2019] [Indexed: 01/22/2023] Open
Abstract
The synthesis of the polyketide section present in the potently cytotoxic marine cyclodepsipeptide jasplakinolide and related natural products, geodiamolides and seragamides, is reported. The key step is a Negishi cross coupling of (R)-(3-methoxy-2-methyl-3-oxopropyl)zinc(II) bromide and an (E)-iodoalkene that was synthesized via an aluminium ester enolate attack at (R)-propylene oxide. The overall synthesis comprises nine steps with an overall yield of 21%. It proved to be possible to liberate the free 8-hydroxynonenoic acid and to couple it with a protected tripeptide composed of L-alanine, N,O-dimethyl-D-iodotyrosine, and TIPS-protected L-threonine, which occurs as partial structure of seragamide A. The tripeptide section of seragamide A was assembled by solution-phase synthesis and an open-chain analogue of the natural product was obtained.
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Affiliation(s)
- Jan Hendrik Lang
- TU Braunschweig, Institute of Organic Chemistry, Hagenring 30, 38106 Braunschweig, Germany
| | - Thomas Lindel
- TU Braunschweig, Institute of Organic Chemistry, Hagenring 30, 38106 Braunschweig, Germany
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23
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Wang L, Frei MS, Salim A, Johnsson K. Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy. J Am Chem Soc 2019; 141:2770-2781. [PMID: 30550714 DOI: 10.1021/jacs.8b11134] [Citation(s) in RCA: 295] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Super-resolution fluorescence microscopy is a powerful tool to visualize biomolecules and cellular structures at the nanometer scale. Employing these techniques in living cells has opened up the possibility to study dynamic processes with unprecedented spatial and temporal resolution. Different physical approaches to super-resolution microscopy have been introduced over the last years. A bottleneck to apply these approaches for live-cell imaging has become the availability of appropriate fluorescent probes that can be specifically attached to biomolecules. In this Perspective, we discuss the role of small-molecule fluorescent probes for live-cell super-resolution microscopy and the challenges that need to be overcome for their generation. Recent trends in the development of labeling strategies are reviewed together with the required chemical and spectroscopic properties of the probes. Finally, selected examples of the use of small-molecule fluorescent probes in live-cell super-resolution microscopy are given.
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Affiliation(s)
- Lu Wang
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Michelle S Frei
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aleksandar Salim
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Kai Johnsson
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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24
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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25
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Georgess D, Spuul P, Le Clainche C, Le Nihouannen D, Fremaux I, Dakhli T, Delannoy López DM, Deffieux D, Jurdic P, Quideau S, Génot E. Anti-osteoclastic effects of C-glucosidic ellagitannins mediated by actin perturbation. Eur J Cell Biol 2018; 97:533-545. [PMID: 30287085 DOI: 10.1016/j.ejcb.2018.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 08/22/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Actin subunits assemble into actin filaments whose dynamics and three-dimensional architectures are further regulated by a variety of cellular factors to establish the functional actin cytoskeleton. The C-glucosidic ellagitannin vescalagin and its simpler analogue vescalin, affect both the dynamics and the ultrastructure of the actin cytoskeleton by directly binding to F-actin. Herein, we show that in vitro, the two compounds induce the formation of distinct F-actin networks characterized by different superstructures and dynamics. In living mature osteoclasts, highly specialized bone-degrading cells that constantly remodel their cytoskeleton, vescalagin and vescalin alter actin dynamics at podosomes and compromise the integrity of the podosome belt that forms the bone-degrading apparatus. Both compounds target the bone-resorbing activity at concentrations that preserve osteoclastic maturation and survival and with no detectable impact on the behaviour of bone-forming osteoblastic cells. This anti-osteoclastic activity of vescalagin and vescalin reveals the potential of targeting actin dynamics as a new therapeutic opportunity and, in this case, as a plausible approach for the local treatment of osteoporosis.
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Affiliation(s)
- Dan Georgess
- Institut de Génomique Fonctionnelle de Lyon, (ENS-UMR 5242), Université de Lyon, F-69007, Lyon Cedex, France
| | - Pirjo Spuul
- Centre de Recherche Cardio-Thoracique de Bordeaux (INSERM U1045), Université de Bordeaux, F-33076, Bordeaux Cedex, France; Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, 12618, Tallinn, Estonia
| | - Christophe Le Clainche
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette Cedex, France
| | - Damien Le Nihouannen
- Inserm U1026, University of Bordeaux, Tissue Bioengineering, U1026, F-33076 Bordeaux, France
| | - Isabelle Fremaux
- Centre de Recherche Cardio-Thoracique de Bordeaux (INSERM U1045), Université de Bordeaux, F-33076, Bordeaux Cedex, France
| | - Thierry Dakhli
- European Institute of Chemistry and Biology, (UMS 3033/US 001), Université de Bordeaux, 33607 Pessac Cedex, F-33607, France
| | | | - Denis Deffieux
- Institut des Sciences Moléculaires (CNRS-UMR 5255), Université de Bordeaux, Talence Cedex, F-33405, France
| | - Pierre Jurdic
- Institut de Génomique Fonctionnelle de Lyon, (ENS-UMR 5242), Université de Lyon, F-69007, Lyon Cedex, France
| | - Stéphane Quideau
- Institut des Sciences Moléculaires (CNRS-UMR 5255), Université de Bordeaux, Talence Cedex, F-33405, France.
| | - Elisabeth Génot
- Centre de Recherche Cardio-Thoracique de Bordeaux (INSERM U1045), Université de Bordeaux, F-33076, Bordeaux Cedex, France.
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26
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Total synthesis and biological evaluation of nannocystin analogues modified at the polyketide phenyl moiety. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.07.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM. Nat Struct Mol Biol 2018; 25:528-537. [PMID: 29867215 DOI: 10.1038/s41594-018-0074-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/02/2018] [Indexed: 11/08/2022]
Abstract
The function of actin is coupled to the nucleotide bound to its active site. ATP hydrolysis is activated during polymerization; a delay between hydrolysis and inorganic phosphate (Pi) release results in a gradient of ATP, ADP-Pi and ADP along actin filaments (F-actin). Actin-binding proteins can recognize F-actin's nucleotide state, using it as a local 'age' tag. The underlying mechanism is complex and poorly understood. Here we report six high-resolution cryo-EM structures of F-actin from rabbit skeletal muscle in different nucleotide states. The structures reveal that actin polymerization repositions the proposed catalytic base, His161, closer to the γ-phosphate. Nucleotide hydrolysis and Pi release modulate the conformational ensemble at the periphery of the filament, thus resulting in open and closed states, which can be sensed by coronin-1B. The drug-like toxin jasplakinolide locks F-actin in an open state. Our results demonstrate in detail how ATP hydrolysis links to F-actin's conformational dynamics and protein interaction.
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28
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Gandalovičová A, Rosel D, Fernandes M, Veselý P, Heneberg P, Čermák V, Petruželka L, Kumar S, Sanz-Moreno V, Brábek J. Migrastatics-Anti-metastatic and Anti-invasion Drugs: Promises and Challenges. Trends Cancer 2018; 3:391-406. [PMID: 28670628 PMCID: PMC5482322 DOI: 10.1016/j.trecan.2017.04.008] [Citation(s) in RCA: 231] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In solid cancers, invasion and metastasis account for more than 90% of mortality. However, in the current armory of anticancer therapies, a specific category of anti-invasion and antimetastatic drugs is missing. Here, we coin the term ‘migrastatics’ for drugs interfering with all modes of cancer cell invasion and metastasis, to distinguish this class from conventional cytostatic drugs, which are mainly directed against cell proliferation. We define actin polymerization and contractility as target mechanisms for migrastatics, and review candidate migrastatic drugs. Critical assessment of these antimetastatic agents is warranted, because they may define new options for the treatment of solid cancers. Local invasion and metastasis, rather than clonal proliferation, are the dominant features of solid cancer. However, a specific category of anti-invasion and antimetastatic drugs is missing for treatment of solid cancer We propose the term ‘migrastatics’ for drugs interfering with all modes of cancer cell invasiveness and, consequently, with their ability to metastasize (e.g., inhibiting not only local invasion, but also extravasation and metastatic colonization). In solid cancer, drug resistance is the main cause of treatment failure, and is attributed to mutations of the target. Since targeting the cause, although academically desirable, may be futile, a pragmatic and near-term option is to move downstream, to common denominators of cell migration and/or invasion, such as actin polymerization and actomyosin-mediated contractility.
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Affiliation(s)
- Aneta Gandalovičová
- Department of Cell Biology, Charles University, Viničná 7, Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242, Vestec u Prahy, Czech Republic
| | - Daniel Rosel
- Department of Cell Biology, Charles University, Viničná 7, Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242, Vestec u Prahy, Czech Republic
| | | | - Pavel Veselý
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Petr Heneberg
- Charles University, Department of Internal Medicine, Third Faculty of Medicine, Prague, Czech Republic
| | - Vladimír Čermák
- Department of Cell Biology, Charles University, Viničná 7, Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242, Vestec u Prahy, Czech Republic
| | - Luboš Petruželka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Sunil Kumar
- Ayurveda Molecular Modeling, Hyderabad, Telangana, India
| | - Victoria Sanz-Moreno
- Tumor Plasticity Laboratory, Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, UK.
| | - Jan Brábek
- Department of Cell Biology, Charles University, Viničná 7, Prague, Czech Republic; Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Průmyslová 595, 25242, Vestec u Prahy, Czech Republic.
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29
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Tian Y, Xu X, Ding Y, Hao X, Bai Y, Tang Y, Zhang X, Li Q, Yang Z, Zhang W, Chen Y. Synthesis and biological evaluation of nannocystin analogues toward understanding the binding role of the (2R,3S)-Epoxide in nannocystin A. Eur J Med Chem 2018; 150:626-632. [DOI: 10.1016/j.ejmech.2018.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 11/29/2022]
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30
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Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability. Proc Natl Acad Sci U S A 2017; 114:10636-10641. [PMID: 28923924 DOI: 10.1073/pnas.1707506114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During their life cycle, apicomplexan parasites, such as the malaria parasite Plasmodium falciparum, use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and stability are temporally and spatially controlled. In contrast to canonical actin, P. falciparum actin 1 (PfAct1) does not readily polymerize into long, stable filaments. The structural basis of filament instability, which plays a pivotal role in host cell invasion, and thus infectivity, is poorly understood, largely because high-resolution structures of PfAct1 filaments were missing. Here, we report the near-atomic structure of jasplakinolide (JAS)-stabilized PfAct1 filaments determined by electron cryomicroscopy. The general filament architecture is similar to that of mammalian F-actin. The high resolution of the structure allowed us to identify small but important differences at inter- and intrastrand contact sites, explaining the inherent instability of apicomplexan actin filaments. JAS binds at regular intervals inside the filament to three adjacent actin subunits, reinforcing filament stability by hydrophobic interactions. Our study reveals the high-resolution structure of a small molecule bound to F-actin, highlighting the potential of electron cryomicroscopy for structure-based drug design. Furthermore, our work serves as a strong foundation for understanding the structural design and evolution of actin filaments and their function in motility and host cell invasion of apicomplexan parasites.
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31
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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32
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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33
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Wang Y, Bartlett MJ, Denard CA, Hartwig JF, Zhao H. Combining Rh-Catalyzed Diazocoupling and Enzymatic Reduction To Efficiently Synthesize Enantioenriched 2-Substituted Succinate Derivatives. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00254] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yajie Wang
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Mark J. Bartlett
- Department
of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
| | - Carl A. Denard
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California-Berkeley, Berkeley, California 94720, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Departments
of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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34
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Lee J, Torker S, Hoveyda AH. Versatile Homoallylic Boronates by Chemo-, S N 2'-, Diastereo- and Enantioselective Catalytic Sequence of Cu-H Addition to Vinyl-B(pin)/Allylic Substitution. Angew Chem Int Ed Engl 2017; 56:821-826. [PMID: 27996213 PMCID: PMC5267969 DOI: 10.1002/anie.201611444] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 12/31/2022]
Abstract
A highly chemo-, diastereo- and enantioselective catalytic method that efficiently combines a silyl hydride, vinyl-B(pin) (pin=pinacolato) and (E)-1,2-disubstituted allylic phosphates is introduced. Reactions, best promoted by a Cu-based complex with a chiral sulfonate-containing N-heterocyclic carbene, are broadly applicable. Aryl-, heteroaryl-, alkenyl-, alkynyl- and alkyl-substituted allylic phosphates may thus be converted to the corresponding homoallylic boronates and then alcohols (after C-B bond oxidation) in 46-91 % yield and in up to >98 % SN 2':SN 2 ratio, 96:4 diastereomeric ratio and 98:2 enantiomeric ratio. The reasons why an NHC-Cu catalyst is uniquely effective (vs. the corresponding phosphine systems) and the basis for different trends in stereoselectivity are provided with the aid of DFT calculations.
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Affiliation(s)
- Jaehee Lee
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467 (USA)
| | - Sebastian Torker
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467 (USA)
| | - Amir H. Hoveyda
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467 (USA)
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35
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Bebbington MWP. Natural product analogues: towards a blueprint for analogue-focused synthesis. Chem Soc Rev 2017; 46:5059-5109. [DOI: 10.1039/c6cs00842a] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A review of approaches to natural product analogues leads to the suggestion of new methods for the generation of biologically active natural product-like scaffolds.
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36
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Lee J, Torker S, Hoveyda AH. Versatile Homoallylic Boronates by Chemo‐, S
N
2′‐, Diastereo‐ and Enantioselective Catalytic Sequence of Cu−H Addition to Vinyl‐B(pin)/Allylic Substitution. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201611444] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry, Merkert Chemistry Center Boston College Chestnut Hill MA 02467 USA
| | - Sebastian Torker
- Department of Chemistry, Merkert Chemistry Center Boston College Chestnut Hill MA 02467 USA
| | - Amir H. Hoveyda
- Department of Chemistry, Merkert Chemistry Center Boston College Chestnut Hill MA 02467 USA
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37
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Structure-activity relationship study towards non-peptidic positron emission tomography (PET) radiotracer for gastrin releasing peptide receptors: Development of [ 18F] (S)-3-(1H-indol-3-yl)-N-[1-[5-(2-fluoroethoxy)pyridin-2-yl]cyclohexylmethyl]-2-methyl-2-[3-(4-nitrophenyl)ureido]propionamide. Bioorg Med Chem 2016; 25:277-292. [PMID: 27863916 DOI: 10.1016/j.bmc.2016.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/14/2016] [Accepted: 10/27/2016] [Indexed: 11/23/2022]
Abstract
Gastrin-releasing peptide receptors (GRP-Rs, also known as bombesin 2 receptors) are overexpressed in a variety of human cancers, including prostate cancer, and therefore they represent a promising target for in vivo imaging of tumors using positron emission tomography (PET). Structural modifications of the non-peptidic GRP-R antagonist PD-176252 ((S)-1a) led to the identification of the fluorinated analog (S)-3-(1H-indol-3-yl)-N-[1-[5-(2-fluoroethoxy)pyridin-2-yl]cyclohexylmethyl]-2-methyl-2-[3-(4-nitrophenyl)ureido]propionamide ((S)-1m) that showed high affinity and antagonistic properties for GRP-R. This antagonist was stable in rat plasma and towards microsomal oxidative metabolism in vitro. (S)-1m was successfully radiolabeled with fluorine-18 through a conventional radiochemistry procedure. [18F](S)-1m showed high affinity and displaceable interaction for GRP-Rs in PC3 cells in vitro.
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38
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Yang Z, Xu X, Yang CH, Tian Y, Chen X, Lian L, Pan W, Su X, Zhang W, Chen Y. Total Synthesis of Nannocystin A. Org Lett 2016; 18:5768-5770. [DOI: 10.1021/acs.orglett.6b02729] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Zhantao Yang
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
- College
of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, P. R. China
| | - Xiaolong Xu
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Chun-Hua Yang
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
- College
of Chemistry and Chemical Engineering, Anyang Normal University, Anyang 455000, P. R. China
| | - Yunfeng Tian
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Xinyi Chen
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Lihui Lian
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Wenwei Pan
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Xuncheng Su
- State
Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Weicheng Zhang
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
| | - Yue Chen
- State
Key Laboratory of Medicinal Chemical Biology, College of Pharmacy,
and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, P. R. China
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39
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Wu X, Xie F, Ling Z, Tang L, Zhang W. Regio- and Enantioselective Copper-Catalyzed 1,4-Conjugate Addition of Trimethylaluminium to Linear α,β,γ,δ-Unsaturated Alkyl Ketones. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600375] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoting Wu
- School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Road Shanghai 200240 People's Republic of China
| | - Fang Xie
- School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Road Shanghai 200240 People's Republic of China
| | - Zheng Ling
- School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Road Shanghai 200240 People's Republic of China
| | - Liang Tang
- School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Road Shanghai 200240 People's Republic of China
| | - Wanbin Zhang
- School of Chemistry and Chemical Engineering; Shanghai Jiao Tong University; 800 Dongchuan Road Shanghai 200240 People's Republic of China
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40
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Bauer KN, Tee HT, Lieberwirth I, Wurm FR. In-Chain Poly(phosphonate)s via Acyclic Diene Metathesis Polycondensation. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00366] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Kristin N. Bauer
- Max-Planck-Institut
für Polymerforschung, Ackermannweg
10, 55128 Mainz, Germany
| | - Hisaschi T. Tee
- Max-Planck-Institut
für Polymerforschung, Ackermannweg
10, 55128 Mainz, Germany
| | - Ingo Lieberwirth
- Max-Planck-Institut
für Polymerforschung, Ackermannweg
10, 55128 Mainz, Germany
| | - Frederik R. Wurm
- Max-Planck-Institut
für Polymerforschung, Ackermannweg
10, 55128 Mainz, Germany
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41
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Kowada T, Maeda H, Kikuchi K. BODIPY-based probes for the fluorescence imaging of biomolecules in living cells. Chem Soc Rev 2016; 44:4953-72. [PMID: 25801415 DOI: 10.1039/c5cs00030k] [Citation(s) in RCA: 866] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescence imaging techniques have been widely used to visualize biological molecules and phenomena. In particular, several studies on the development of small-molecule fluorescent probes have been carried out, because their fluorescence properties can be easily tuned by synthetic chemical modification. For this reason, various fluorescent probes have been developed for targeting biological components, such as proteins, peptides, amino acids, and ions, to the interior and exterior of cells. In this review, we cover advances in the development of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based fluorescent probes for biological studies over the past decade.
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Affiliation(s)
- Toshiyuki Kowada
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, Japan.
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42
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Notar Francesco I, Cacciuttolo B, Pascu O, Aymonier C, Pucheault M, Antoniotti S. Simple salts of abundant metals (Fe, Bi, and Ti) supported on montmorillonite as efficient and recyclable catalysts for regioselective intramolecular and intermolecular hydroalkoxylation reactions of double bonds and tandem processes. RSC Adv 2016. [DOI: 10.1039/c5ra25176a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Montmorillonites doped with metal cations are efficient and recyclable catalysts for hydroalkoxylation reactions and amenable to flow chemistry.
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Affiliation(s)
- Irene Notar Francesco
- Institut de Chimie de Nice
- UMR 7272 CNRS – Université Nice Sophia Antipolis
- 06108 Nice
- France
| | - Bastien Cacciuttolo
- Institut des Sciences Moléculaires
- UMR 5255 CNRS – Université de Bordeaux
- 33405 Talence Cedex
- France
| | - Oana Pascu
- CNRS, Univ. Bordeaux, ICMCB
- UPR 9048
- F-33608 Pessac
- France
| | | | - Mathieu Pucheault
- Institut des Sciences Moléculaires
- UMR 5255 CNRS – Université de Bordeaux
- 33405 Talence Cedex
- France
| | - Sylvain Antoniotti
- Institut de Chimie de Nice
- UMR 7272 CNRS – Université Nice Sophia Antipolis
- 06108 Nice
- France
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43
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Tetlow DJ, Winder SJ, Aïssa C. The synthesis and biological evaluation of a kabiramide C fragment modified with a WH2 consensus actin-binding motif as a potential disruptor of the actin cytoskeleton. Chem Commun (Camb) 2016; 52:807-10. [DOI: 10.1039/c5cc06081h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite its low affinity for actin monomers, a fragment of kabiramide C disrupts actin filamentsin vitroand in cells.
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44
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Becker D, Kazmaier U. Synthesis and Biological Evaluation of Dichlorinated Chondramide Derivatives. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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45
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Arndt HD, Rizzo S, Nöcker C, Wakchaure VN, Milroy LG, Bieker V, Calderon A, Tran TTN, Brand S, Dehmelt L, Waldmann H. Divergent solid-phase synthesis of natural product-inspired bipartite cyclodepsipeptides: total synthesis of seragamide A. Chemistry 2015; 21:5311-6. [PMID: 25694199 DOI: 10.1002/chem.201500368] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/06/2022]
Abstract
Macrocyclic natural products (NPs) and analogues thereof often show high affinity, selectivity, and metabolic stability, and methods for the synthesis of NP-like macrocycle collections are of major current interest. We report an efficient solid-phase/cyclorelease method for the synthesis of a collection of macrocyclic depsipeptides with bipartite peptide/polyketide structure inspired by the very potent F-actin stabilizing depsipeptides of the jasplakinolide/geodiamolide class. The method includes the assembly of an acyclic precursor chain on a polymeric carrier, terminated by olefins that constitute complementary fragments of the polyketide section and cyclization by means of a relay-ring-closing metathesis (RRCM). The method was validated in the first total synthesis of the actin-stabilizing cyclodepsipeptide seragamide A and the synthesis of a collection of structurally diverse bipartite depsipeptides.
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Affiliation(s)
- Hans-Dieter Arndt
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany), Fax: (+49) 3641948212; Friedrich-Schiller-Universität, Institute of Organic and Macromolecular Chemistry, Humboldtstrasse 10, 07743 Jena (Germany).
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46
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High-Throughput Synthesis of Diverse Compound Collections for Lead Discovery and Optimization. Handb Exp Pharmacol 2015; 232:73-89. [PMID: 26330259 DOI: 10.1007/164_2015_25] [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: 01/01/2023]
Abstract
Small-molecule intervention of protein function is one central dogma of drug discovery. The generation of small-molecule libraries fuels the discovery pipeline at many stages and thereby resembles a key aspect of this endeavor. High-throughput synthesis is a major source for compound libraries utilized in academia and industry, seeking new chemical modulators of pharmacological targets. Here, we discuss the crucial factors of library design strategies from the perspective of synthetic chemistry, giving a brief historic background and a summary of current approaches. Simple measures of success of a high-throughput synthesis such as quantity or diversity have long been discarded and replaced by more integrated measures. Case studies are presented and put into context to highlight the cross-connectivity of the various stages of the drug discovery process.
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47
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Abstract
In this article strategies for the design and synthesis of natural product analogues are summarized and illustrated with some selected examples.
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Affiliation(s)
- Martin E. Maier
- Institut für Organische Chemie
- Eberhard Karls Universität Tübingen
- 72076 Tübingen
- Germany
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48
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Das S, Goswami RK. Stereoselective Total Synthesis of Marine Cyclodepsipeptide Calcaripeptides A–C. J Org Chem 2014; 79:9778-91. [DOI: 10.1021/jo5019798] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sayantan Das
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Rajib Kumar Goswami
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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49
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Unsworth PJ, Leonori D, Aggarwal VK. Stereocontrolled Synthesis of 1,5-Stereogenic Centers through Three-Carbon Homologation of Boronic Esters. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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50
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Unsworth PJ, Leonori D, Aggarwal VK. Stereocontrolled Synthesis of 1,5-Stereogenic Centers through Three-Carbon Homologation of Boronic Esters. Angew Chem Int Ed Engl 2014; 53:9846-50. [DOI: 10.1002/anie.201405700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 12/14/2022]
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