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Small bioactive molecules designed to be probes as baits “fishing out” cellular targets: finding the fish in the proteome sea. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Dactylospongia elegans—A Promising Drug Source: Metabolites, Bioactivities, Biosynthesis, Synthesis, and Structural-Activity Relationship. Mar Drugs 2022; 20:md20040221. [PMID: 35447894 PMCID: PMC9033123 DOI: 10.3390/md20040221] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Marine environment has been identified as a huge reservoir of novel biometabolites that are beneficial for medical treatments, as well as improving human health and well-being. Sponges have been highlighted as one of the most interesting phyla as new metabolites producers. Dactylospongia elegans Thiele (Thorectidae) is a wealth pool of various classes of sesquiterpenes, including hydroquinones, quinones, and tetronic acid derivatives. These metabolites possessed a wide array of potent bioactivities such as antitumor, cytotoxicity, antibacterial, and anti-inflammatory. In the current work, the reported metabolites from D. elegans have been reviewed, including their bioactivities, biosynthesis, and synthesis, as well as the structural-activity relationship studies. Reviewing the reported studies revealed that these metabolites could contribute to new drug discovery, however, further mechanistic and in vivo studies of these metabolites are needed.
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Totsuka Y, Yasuno Y, Shinada T. First Synthesis of All-trans-polyprenol with 100 Carbons. CHEM LETT 2019. [DOI: 10.1246/cl.190046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yusuke Totsuka
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
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Ghodke PP, Albertolle ME, Johnson KM, Guengerich FP. Synthesis and Characterization of Site-Specific O 6 -Alkylguanine DNA-Alkyl Transferase-Oligonucleotide Crosslinks. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2019; 76:e74. [PMID: 30657645 PMCID: PMC6504252 DOI: 10.1002/cpnc.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O6 -Alkylguanine DNA-alkyltransferase (AGT), a DNA repair protein, can form crosslinks with DNA. The AGT-DNA crosslinks are known to be mutagenic when AGT is heterologously expressed in Escherichia coli, as well as in mammalian cells. To understand the biological consequences, reliable access to AGT-oligonucleotide crosslinks is needed. This article describes the synthesis and characterization of site-specific AGT-oligonucleotide crosslinks at the N2-position of deoxyguanosine and N6-position of deoxyadenosine. We developed a post-oligomerization strategy for the synthesis of propargyl-modified oligonucleotides. Copper-catalyzed azide-alkyne cycloaddition was used as a key step to obtain the iodoacetamide-linked oligonucleotides, which serve as good electrophiles for the crosslinking reaction with cysteine-145 of the active site of AGT. Trypsinization of AGT and hydrolysis of oligonucleotides, combined with analysis by liquid chromatography-tandem mass spectrometry, was utilized to confirm the nucleobase-adducted peptides. This method provides a useful strategy for the synthesis and characterization of site-specific DNA-protein crosslinks, which can be further used to understand proteolytic degradation-coupled DNA repair mechanisms. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Matthew E Albertolle
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kevin M Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
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Kotoku N, Ishida R, Matsumoto H, Arai M, Toda K, Setiawan A, Muraoka O, Kobayashi M. Biakamides A-D, Unique Polyketides from a Marine Sponge, Act as Selective Growth Inhibitors of Tumor Cells Adapted to Nutrient Starvation. J Org Chem 2017; 82:1705-1718. [PMID: 28090774 DOI: 10.1021/acs.joc.6b02948] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Biakamides A-D, novel unusually unique polyketides, were isolated from an Indonesian marine sponge (Petrosaspongia sp.) with a constructed bioassay using PANC-1 human pancreatic cancer cells. Through detailed analyses of the one- and two-dimensional NMR spectra of biakamides, planar chemical structures possessing a terminal thiazole, two N-methyl amides, a chloromethylene, and a substituted butyryl moiety were obtained. After elucidation of the configuration of the secondary alcohol moiety in biakamides A and B, the absolute stereostructures of the two secondary methyl groups in biakamides A-D were determined by the asymmetric total syntheses of all possible stereoisomers from the optically pure monoprotected 2,4-dimethyl-1,5-diol. Biakamides A-D showed selective antiproliferative activities against PANC-1 cells cultured under glucose-deficient conditions in a concentration-dependent manner. The primary mode of action of biakamides was found to be inhibition of complex I in the mitochondrial electron transport chain.
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Affiliation(s)
- Naoyuki Kotoku
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
| | - Ryosuke Ishida
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
| | - Hirokazu Matsumoto
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
| | - Kazunari Toda
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
| | - Andi Setiawan
- Department of Chemistry, Faculty of Science, Lampung University , Jl. Prof. Dr. Sumantri Brodjonegoro No. 1, Bandar, Lampung 35145, Indonesia
| | - Osamu Muraoka
- School of Pharmacy, Kindai University , 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Motomasa Kobayashi
- Graduate School of Pharmaceutical Sciences, Osaka University , Yamada-oka 1-6, Suita, Osaka 565-0871, Japan
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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Saxena C. Identification of protein binding partners of small molecules using label-free methods. Expert Opin Drug Discov 2016; 11:1017-25. [DOI: 10.1080/17460441.2016.1227316] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Lee B, Sun W, Lee H, Basavarajappa H, Sulaiman RS, Sishtla K, Fei X, Corson TW, Seo SY. Design, synthesis and biological evaluation of photoaffinity probes of antiangiogenic homoisoflavonoids. Bioorg Med Chem Lett 2016; 26:4277-81. [PMID: 27481561 DOI: 10.1016/j.bmcl.2016.07.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/16/2016] [Accepted: 07/20/2016] [Indexed: 12/26/2022]
Abstract
A naturally occurring homoisoflavonoid, cremastranone (1) inhibited angiogenesis in vitro and in vivo. We developed an analogue SH-11037 (2) which is more potent than cremastranone in human retinal microvascular endothelial cells (HRECs) and blocks neovascularization in animal models. Despite their efficacy, the mechanism of these compounds is not yet fully known. In the course of building on a strong foundation of SAR and creating a novel chemical tool for target identification of homoisoflavonoid-binding proteins, various types of photoaffinity probes were designed and synthesized in which benzophenone and biotin were attached to homoisoflavanonoids using PEG linkers on either the C-3' or C-7 position. Notably, the photoaffinity probes linking on the phenol group of the C-3' position retain excellent activity of inhibiting retinal endothelial cell proliferation with up to 72nM of GI50.
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Affiliation(s)
- Bit Lee
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Wei Sun
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Hyungjun Lee
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Halesha Basavarajappa
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Rania S Sulaiman
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Kamakshi Sishtla
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Xiang Fei
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Timothy W Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Seung-Yong Seo
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea.
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Arai M, Kawachi T, Kotoku N, Nakata C, Kamada H, Tsunoda SI, Tsutsumi Y, Endo H, Inoue M, Sato H, Kobayashi M. Furospinosulin-1, Marine Spongean Furanosesterterpene, Suppresses the Growth of Hypoxia-Adapted Cancer Cells by Binding to Transcriptional Regulators p54(nrb) and LEDGF/p75. Chembiochem 2015; 17:181-9. [PMID: 26561285 DOI: 10.1002/cbic.201500519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/09/2022]
Abstract
Hypoxia-adapted cancer cells in tumors contribute to the pathological progression of cancer. Cancer research has therefore focused on the identification of molecules responsible for hypoxia adaptation in cancer cells, as well as the development of new compounds with action against hypoxia-adapted cancer cells. The marine natural product furospinosulin-1 (1) has displayed hypoxia-selective growth inhibition against cultured cancer cells, and has shown in vivo anti-tumor activity, although its precise mode of action and molecular targets remain unclear. In this study, we found that 1 is selectively effective against hypoxic regions of tumors, and that it directly binds to the transcriptional regulators p54(nrb) and LEDGF/p75, which have not been previously identified as mediators of hypoxia adaptation in cancer cells.
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Affiliation(s)
- Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.
| | - Takashi Kawachi
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan
| | - Naoyuki Kotoku
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan
| | - Chiaki Nakata
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan
| | - Haruhiko Kamada
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.,National Institute of Biomedical Innovation, 7-6-8 Saitoasagi, Ibaraki, Osaka, 567-0085, Japan
| | - Shin-ichi Tsunoda
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.,National Institute of Biomedical Innovation, 7-6-8 Saitoasagi, Ibaraki, Osaka, 567-0085, Japan
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.,National Institute of Biomedical Innovation, 7-6-8 Saitoasagi, Ibaraki, Osaka, 567-0085, Japan
| | - Hiroko Endo
- Osaka Medical Center for Cancer and Cardiovascular Diseases, Higashinari-ku, Osaka, 537-8511, Japan
| | - Masahiro Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.,Osaka Medical Center for Cancer and Cardiovascular Diseases, Higashinari-ku, Osaka, 537-8511, Japan
| | - Hiroki Sato
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan
| | - Motomasa Kobayashi
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka 1-6, Suita, Osaka, 565-0871, Japan.
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Abstract
Photoaffinity labeling (PAL) using a chemical probe to covalently bind its target in response to activation by light has become a frequently used tool in drug discovery for identifying new drug targets and molecular interactions, and for probing the location and structure of binding sites. Methods to identify the specific target proteins of hit molecules from phenotypic screens are highly valuable in early drug discovery. In this review, we summarize the principles of PAL including probe design and experimental techniques for in vitro and live cell investigations. We emphasize the need to optimize and validate probes and highlight examples of the successful application of PAL across multiple disease areas.
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Affiliation(s)
- Ewan Smith
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, London, UK
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, London, UK
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