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Kojima K, Konishi H, Momosaki K, Komatani Y, Katsuyama A, Nakagawa K, Kanamitsu K, Yakushiji F, Fujiya M, Ichikawa S. Synthesis and biological evaluation of echinomycin analogues as potential colon cancer agent. Sci Rep 2024; 14:7628. [PMID: 38561454 PMCID: PMC10985088 DOI: 10.1038/s41598-024-58196-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Colorectal cancer is the third most commonly diagnosed cancer and the second leading cause of cancer-related death, thus a novel chemotherapeutic agent for colon cancer therapy is needed. In this study, analogues of echinomycin, a cyclic peptide natural product with potent toxicity to several human cancer cell lines, were synthesized, and their biological activities against human colon cancer cells were investigated. Analogue 3 as well as 1 inhibit HIF-1α-mediated transcription. Notably, transcriptome analysis indicated that the cell cycle and its regulation were involved in the effects on cells treated with 3. Analogue 3 exhibited superior in vivo efficacy to echinomycin without significant toxicity in mouse xenograft model. The low dose of 3 needed to be efficacious in vivo is also noteworthy and our data suggest that 3 is an attractive and potentially novel agent for the treatment of colon cancer.
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Affiliation(s)
- Keita Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Hiroaki Konishi
- Department of Gastroenterology and Advanced Medical Sciences, Asahikawa Medical University, 2-1-1-1, Midorigaoka, Asahikawa, Hokkaido, 078-8510, Japan
| | - Kyoka Momosaki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuya Komatani
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Sapporo, 060-0812, Japan
| | - Koji Nakagawa
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido, 061-0293, Japan
| | - Kayoko Kanamitsu
- Lead Exploration Unit, Drug Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Sapporo, 060-0812, Japan
| | - Mikihiro Fujiya
- Department of Gastroenterology and Advanced Medical Sciences, Asahikawa Medical University, 2-1-1-1, Midorigaoka, Asahikawa, Hokkaido, 078-8510, Japan
- Division of Gastroenterology, Department of Internal Medicine, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, Sapporo, 060-0812, Japan.
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2
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Lopatniuk M, Riedel F, Wildfeuer J, Stierhof M, Dahlem C, Kiemer AK, Luzhetskyy A. Development of a Streptomyces-based system for facile thioholgamide library generation and analysis. Metab Eng 2023; 78:48-60. [PMID: 37142115 DOI: 10.1016/j.ymben.2023.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/06/2023]
Abstract
Derivatizing natural products (NPs) is essential in structure-activity relationship (SAR) studies, compound optimization, and drug development. Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent one of the major classes of natural products. Thioholgamide represents thioamitide - a recently emerged family of RiPPs with unique structures and great potential in anticancer drug development. Although the method for generating the RiPP library by codon substitutions in the precursor peptide gene is straightforward, the techniques to perform RiPP derivatization in Actinobacteria remain limited and time-consuming. Here, we report a facile system for producing a library of randomized thioholgamide derivatives utilizing an optimized Streptomyces host. This technique enabled us to access all possible amino acid substitutions of the thioholgamide molecule, one position at a time. Out of 152 potential derivatives, 85 were successfully detected, revealing the impact of amino acid substitutions on thioholgamide post-translational modifications (PTMs). Moreover, new PTMs were observed among thioholgamide derivatives: thiazoline heterocycles, which have not yet been reported for thioamitides, and S-methylmethionine, which is very rare in nature. The obtained library was subsequently used for thioholgamide SAR studies and stability assays.
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Affiliation(s)
- Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Florian Riedel
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Julia Wildfeuer
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Marc Stierhof
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, Campus C2.3, 66123, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.
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3
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Komatani Y, Momosaki K, Katsuyama A, Yamamoto K, Kaguchi R, Ichikawa S. Solid-Phase Total Synthesis of Sandramycin and Its Analogues. Org Lett 2023; 25:543-548. [PMID: 36652724 DOI: 10.1021/acs.orglett.2c04327] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solid-phase total synthesis of sandramycin (1), which is a C2-symmetric cyclic decadepsipeptide natural product, and its analogues is described. On-resin ester formation and [5+5] peptide coupling allowed the preparation of a range of desymmetrized analogues. An amino acid residue that would not hamper the biological activity of 1 was successfully identified, and probe molecules and dimeric analogues were prepared on the basis of the result of the structure-activity relationship study.
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Affiliation(s)
- Yuya Komatani
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kyoka Momosaki
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Rintaro Kaguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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4
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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5
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Long F, Cheung CY, Whitman WB, Cook GM, Ronimus RS. Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors. Access Microbiol 2021; 3:000244. [PMID: 34595395 PMCID: PMC8479958 DOI: 10.1099/acmi.0.000244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.
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Affiliation(s)
- Feng Long
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Present address: Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, USA
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ron S Ronimus
- Rumen Microbiology, AgResearch Ltd., Palmerston North, New Zealand
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6
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Shi X, Huang L, Song K, Zhao G, Liu Y, Lv L, Du Y. Enzymatic Tailoring in Luzopeptin Biosynthesis Involves Cytochrome P450‐Mediated Carbon–Nitrogen Bond Desaturation for Hydrazone Formation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
| | - Liming Huang
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Kaihui Song
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
| | - Yu Liu
- College of Life Sciences Zhejiang University 310058 Hangzhou China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
| | - Yi‐Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital Zhejiang University School of Medicine 310058 Hangzhou China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases The First Affiliated Hospital Zhejiang University 310003 Hangzhou China
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7
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Shi X, Huang L, Song K, Zhao G, Liu Y, Lv L, Du YL. Enzymatic Tailoring in Luzopeptin Biosynthesis Involves Cytochrome P450-Mediated Carbon-Nitrogen Bond Desaturation for Hydrazone Formation. Angew Chem Int Ed Engl 2021; 60:19821-19828. [PMID: 34180113 DOI: 10.1002/anie.202105312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Indexed: 01/15/2023]
Abstract
Luzopeptins and related decadepsipeptides are bisintercalator nonribosomal peptides featuring rare acyl-substituted tetrahydropyridazine-3-carboxylic acid (Thp) subunits that are critical to their biological activities. Herein, we reconstitute the biosynthetic tailoring pathway in luzopeptin A biosynthesis through in vivo genetic and in vitro biochemical approaches. Significantly, we revealed a multitasking cytochrome P450 enzyme that catalyzes four consecutive oxidations including the highly unusual carbon-nitrogen bond desaturation, forming the hydrazone-bearing 4-OH-Thp residues. Moreover, we identified a membrane-bound acyltransferase that likely mediates the subsequent O-acetylation extracellularly, as a potential self-protective strategy for the producer strain. Further genome mining of novel decadepsipeptides and an associated P450 enzyme have provided mechanistic insights into the P450-mediated carbon-nitrogen bond desaturation. Our results not only reveal the molecular basis of pharmacophore formation in bisintercalator decadepsipeptides, but also expand the catalytic versatility of P450 family enzymes.
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Affiliation(s)
- Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Liming Huang
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Kaihui Song
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yu Liu
- College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
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8
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Dahiya R, Dahiya S, Kumar P, Kumar RV, Dahiya S, Kumar S, Saharan R, Basu P, Mitra A, Sharma A, Kashaw SK, Patel JK. Structural and biological aspects of natural bridged macrobicyclic peptides from marine resources. Arch Pharm (Weinheim) 2021; 354:e2100034. [PMID: 33913195 DOI: 10.1002/ardp.202100034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 12/29/2022]
Abstract
Among peptide-based drugs, naturally occurring bicyclic compounds have been established as molecules with unique therapeutic potential. The diverse pharmacological activities associated with bicyclic peptides from marine tunicates, sponges, and bacteria render them suitable to be employed as effective surrogate between complex and small therapeutic moieties. Bicyclic peptides possess greater conformational rigidity and higher metabolic stability as compared with linear and monocyclic peptides. The antibody-like affinity and specificity of bicyclic peptides enable their binding to the challenging drug targets. Bridged macrobicyclic peptides from natural marine resources represent an underexplored class of molecules that provides promising platforms for drug development owing to their biocompatibility, similarity, and chemical diversity to proteins. The present review explores major marine-derived bicyclic peptides including disulfide-bridged, histidinotyrosine-bridged, or histidinoalanine-bridged macrobicyclic peptides along with their structural characteristics, synthesis, structure-activity relationship, and bioproperties.The comparison of these macrobicyclic congeners with linear/monocyclic peptides along with their therapeutic potential are also briefly discussed.
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Affiliation(s)
- Rajiv Dahiya
- Laboratory of Peptide Research and Development, School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Sunita Dahiya
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico, USA
| | - Priyank Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, Marshall B. Ketchum University, Fullerton, California, USA
| | - Radhika V Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, American University of Health Sciences, Signal Hill, California, USA
| | - Saurabh Dahiya
- Department of Quality Assurance, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Suresh Kumar
- Department of Pharmaceutical Chemistry, Bharat Institute of Pharmacy, Pehladpur, Babain, Kurukshetra, Haryana, India
| | - Renu Saharan
- Department of Pharmaceutics, M. M. College of Pharmacy, Maharishi Markandeshwar Deemed to be University, Ambala, Haryana, India
| | - Paramita Basu
- Department of Pharmaceutical & Biomedical Sciences, Touro College of Pharmacy, New York, USA
| | - Arindam Mitra
- Department of Microbiology, School of Life Science and Biotechnology, Adamas University, Barasat, West Bengal, India
| | - Ajay Sharma
- Department of Pharmacognosy and Phytochemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Sushil K Kashaw
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, Madhya Pradesh, India
| | - Jayvadan K Patel
- Department of Pharmaceutics, Nootan Pharmacy College, Faculty of Pharmacy, Sankalchand Patel University, Visnagar, Mehsana, Gujarat, India
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9
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Kojima K, Yakushiji F, Katsuyama A, Ichikawa S. Total Synthesis of Echinomycin and Its Analogues. Org Lett 2020; 22:4217-4221. [DOI: 10.1021/acs.orglett.0c01268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Keita Kojima
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6,
Kita-ku, Sapporo 060-0812, Sapporo, Japan
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10
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Exploitation of Potentially New Antibiotics from Mangrove Actinobacteria in Maowei Sea by Combination of Multiple Discovery Strategies. Antibiotics (Basel) 2019; 8:antibiotics8040236. [PMID: 31783564 PMCID: PMC6963217 DOI: 10.3390/antibiotics8040236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Rediscovery of known antibiotics from actinobacteria, especially Streptomyces, has become a bottleneck issue. Nowadays, more specific identification and dereplication could be acquired by a combination of modern analytic techniques with various databases. In this study, 261 actinobacterial strains were isolated from 8 mangrove soil samples by culture-dependent method. A total of 83 strains were selected to evaluate antibacterial activities and mechanisms by disc diffusion method and a unique double fluorescent protein reporter system (pDualrep2), respectively. Thirty-two strains exhibited antagonistic activity against at least one of the “ESKAPE” pathogens. Four Streptomyces strains (B475, B486, B353, and B98) showed strong inhibitory activity against Gram-positive bacteria and induced DNA damage SOS response. One Micromonospora strain (B704) exhibited inhibitory activity against several pathogens and induced attenuation-based translational inhibitors reporter. Seven members of quinoxaline-type antibiotics including quinomycin A, quinomycin monosulfoxide, and other five putative new analogues were found from the culture broth of strain B475 by a combination of anti-MRSA guide, HPTLC, HPLC-UV, and UPLC-UV-HRESIMS/MS analysis, Chemspider searching, and MS/MS-based molecular networking analysis. In conclusion, this study not only demonstrated that mangrove is a rich source of actinobacteria with the potentially new antibiotics but showed rapid dereplication of known antibiotics in the early stage can improve efficiency for the discovery of new antibiotics.
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11
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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12
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Ratnayake AS, Chang LP, Tumey LN, Loganzo F, Chemler JA, Wagenaar M, Musto S, Li F, Janso JE, Ballard TE, Rago B, Steele GL, Ding W, Feng X, Hosselet C, Buklan V, Lucas J, Koehn FE, O'Donnell CJ, Graziani EI. Natural Product Bis-Intercalator Depsipeptides as a New Class of Payloads for Antibody-Drug Conjugates. Bioconjug Chem 2018; 30:200-209. [PMID: 30543418 DOI: 10.1021/acs.bioconjchem.8b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A potent class of DNA-damaging agents, natural product bis-intercalator depsipeptides (NPBIDs), was evaluated as ultrapotent payloads for use in antibody-drug conjugates (ADCs). Detailed investigation of potency (both in cells and via biophysical characterization of DNA binding), chemical tractability, and in vitro and in vivo stability of the compounds in this class eliminated a number of potential candidates, greatly reducing the complexity and resources required for conjugate preparation and evaluation. This effort yielded a potent, stable, and efficacious ADC, PF-06888667, consisting of the bis-intercalator, SW-163D, conjugated via an N-acetyl-lysine-valine-citrulline- p-aminobenzyl alcohol- N, N-dimethylethylenediamine (AcLysValCit-PABC-DMAE) linker to an engineered variant of the anti-Her2 mAb, trastuzumab, catalyzed by transglutaminase.
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Affiliation(s)
- Anokha S Ratnayake
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Li-Ping Chang
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - L Nathan Tumey
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Frank Loganzo
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Joseph A Chemler
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Melissa Wagenaar
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Sylvia Musto
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Fengping Li
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Jeffrey E Janso
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - T Eric Ballard
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Brian Rago
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Greg L Steele
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - WeiDong Ding
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Xidong Feng
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christine Hosselet
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Vlad Buklan
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Judy Lucas
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Frank E Koehn
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christopher J O'Donnell
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Edmund I Graziani
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
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13
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Tenconi E, Rigali S. Self-resistance mechanisms to DNA-damaging antitumor antibiotics in actinobacteria. Curr Opin Microbiol 2018; 45:100-108. [PMID: 29642052 DOI: 10.1016/j.mib.2018.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/08/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022]
Abstract
Streptomyces and few other Actinobacteria naturally produce compounds currently used in chemotherapy for being cytotoxic against various types of tumor cells by damaging the DNA structure and/or inhibiting DNA functions. DNA-damaging antitumor antibiotics belong to different classes of natural compounds that are structurally unrelated such as anthracyclines, bleomycins, enediynes, mitomycins, and prodiginines. By targeting a ubiquitous molecule and housekeeping functions, these compounds are also cytotoxic to their producer. How DNA-damaging antitumor antibiotics producing actinobacteria avoid suicide is the theme of the current review which illustrates the different strategies developed for self-resistance such as toxin sequestration, efflux, modification, destruction, target repair/protection, or stochastic activity. Finally, the observed spatio-temporal correlation between cell death, morphogenesis, and prodiginine production in S. coelicolor suggests a new physiological role for these molecules, that, together with their self-resistance mechanisms, would function as new types of toxin-antitoxin systems recruited in programmed cell death processes of the producer.
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Affiliation(s)
- Elodie Tenconi
- InBioS - Center for Protein Engineering, Université de liège, Institut de Chimie B64, B-4000 Liège, Belgium
| | - Sébastien Rigali
- InBioS - Center for Protein Engineering, Université de liège, Institut de Chimie B64, B-4000 Liège, Belgium.
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14
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Park YS, Shin WS, Kim CS, Ahn CM, Qi XF, Kim SK. Molecular and cellular toxicological profiling of DNA bis-intercalator, quinoxaline compounds: echinomycin as the versatile lead. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0002-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Mori S, Garzan A, Tsodikov OV, Garneau-Tsodikova S. Deciphering Nature’s Intricate Way of N,S-Dimethylating l-Cysteine: Sequential Action of Two Bifunctional Adenylation Domains. Biochemistry 2017; 56:6087-6097. [DOI: 10.1021/acs.biochem.7b00980] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shogo Mori
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Atefeh Garzan
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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16
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Sahoo MK, Jaiswal G, Rana J, Balaraman E. Organo-Photoredox Catalyzed Oxidative Dehydrogenation of N-Heterocycles. Chemistry 2017; 23:14167-14172. [PMID: 28805268 DOI: 10.1002/chem.201703642] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Indexed: 02/03/2023]
Abstract
We report here for the first time the catalytic oxidative dehydrogenation of N-heterocycles by a visible-light organo-photoredox catalyst with low catalyst loading (0.1-1 mol %). The reaction proceeds efficiently under base- and additive-free conditions with ambient air at room temperature. The utility of this benign approach is demonstrated by the synthesis of various pharmaceutically relevant N-heteroarenes such as quinoline, quinoxaline, quinazoline, acridine, and indole.
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Affiliation(s)
- Manoj K Sahoo
- Catalysis Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune -, 411008, India
| | - Garima Jaiswal
- Catalysis Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune -, 411008, India
| | - Jagannath Rana
- Catalysis Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune -, 411008, India
| | - Ekambaram Balaraman
- Catalysis Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune -, 411008, India
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17
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Mori S, Shrestha SK, Fernández J, Álvarez San Millán M, Garzan A, Al-Mestarihi AH, Lombó F, Garneau-Tsodikova S. Activation and Loading of the Starter Unit during Thiocoraline Biosynthesis. Biochemistry 2017; 56:4457-4467. [DOI: 10.1021/acs.biochem.7b00661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shogo Mori
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sanjib K. Shrestha
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Javier Fernández
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - María Álvarez San Millán
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - Atefeh Garzan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Ahmad H. Al-Mestarihi
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Felipe Lombó
- Departamento
de Biología Funcional e Instituto Universitario de Oncología
del Principado de Asturias, Universidad de Oviedo, Oviedo 33006, Spain
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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18
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Helf MJ, Jud A, Piel J. Enzyme from an Uncultivated Sponge Bacterium Catalyzes S-Methylation in a Ribosomal Peptide. Chembiochem 2017; 18:444-450. [DOI: 10.1002/cbic.201600594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Maximilian J. Helf
- Institute of Microbiology; HCI G431; Eidgenössische Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
- Boyce Thompson Institute; Cornell University; 533 Tower Road Ithaca NY 14850 USA
| | - Aurelia Jud
- Institute of Microbiology; HCI G431; Eidgenössische Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Jörn Piel
- Institute of Microbiology; HCI G431; Eidgenössische Technische Hochschule (ETH) Zürich; Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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19
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Hattori K, Koike K, Okuda K, Hirayama T, Ebihara M, Takenaka M, Nagasawa H. Solution-phase synthesis and biological evaluation of triostin A and its analogues. Org Biomol Chem 2016; 14:2090-111. [PMID: 26779679 DOI: 10.1039/c5ob02505b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triostin A is a biosynthetic precursor of echinomycin which is one of the most potent hypoxia inducible factor 1 (HIF-1) inhibitors. An improved solution-phase synthesis of triostin A on a preparative scale has been achieved in 17.5% total yield in 13 steps. New analogues of triostin A with various aromatic chromophores, oxidized intra-peptide disulfide bridges and diastereoisomeric cyclic depsipeptide cores were also successfully synthesized. All analogues had a significant inhibitory effect on HIF-1 transcriptional activation in hypoxia and cytotoxicity on MCF-7 cells, with the exception of the derivatives containing a naphthalene chromophore or a thiosulfonate bridge. For the first time, triostin A, echinomycin and the thiosulfinate analogue of triostin A have been revealed to inhibit not only DNA binding of HIF-1 but also HIF-1α protein accumulation in MCF-7 cells. Furthermore, the thiosulfinate analogue and triostin A exhibited a hypoxia-selective cytotoxicity on MCF-7 cells. The improved solution-phase synthetic procedure described herein will contribute to the development of diverse bicyclic depsipeptide drug candidates with the potential to act as novel anti-cancer agents targeting hypoxic tumor microenvironments.
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Affiliation(s)
- Kozo Hattori
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
| | - Kota Koike
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
| | - Kensuke Okuda
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
| | - Masahiro Ebihara
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu, 501-1193, Japan.
| | - Mei Takenaka
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, 1-25-4 Daigaku-nishi, Gifu, 501-1196, Japan
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20
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Shrestha SK, Garneau-Tsodikova S. Expanding Substrate Promiscuity by Engineering a Novel Adenylating-Methylating NRPS Bifunctional Enzyme. Chembiochem 2016; 17:1328-32. [PMID: 27128382 DOI: 10.1002/cbic.201600234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 12/11/2022]
Abstract
Nonribosomal peptides synthetases (NRPSs), which are multifunctional mega-enzymes producing many biologically active metabolites, are ideal targets for enzyme engineering. NRPS adenylation domains play a critical role in selecting/activating the amino acids to be transferred to downstream NRPS domains in the biosynthesis of natural products. Both monofunctional and bifunctional A domains interrupted with an auxiliary domain are found in nature. Here, we show that a bifunctional interrupted A domain can be uninterrupted by deleting its methyltransferase auxiliary domain portion to make an active monofunctional enzyme. We also demonstrate that a portion of an auxiliary domain with almost no sequence identity to the original auxiliary domain can be insert into naturally interrupted A domain to develop a new active bifunctional A domain with increased substrate profile. This work shows promise for the creation of new interrupted A domains in engineered NRPS enzymes.
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Affiliation(s)
- Sanjib K Shrestha
- Department of Pharmaceutical Sciences, University of Kentucky, BioPharm Complex (Room 423), 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, BioPharm Complex (Room 423), 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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21
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Huang Y, Song Y, Huang M, Fan YR, Tian DN, Zhao QP, Yang XB, Zhang WN. Synthesis, DNA binding, and cytotoxicity activity of bis-naphalenyl compounds with different diamine linkers. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2539-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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22
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Geny S, Moreno PMD, Krzywkowski T, Gissberg O, Andersen NK, Isse AJ, El-Madani AM, Lou C, Pabon YV, Anderson BA, Zaghloul EM, Zain R, Hrdlicka PJ, Jørgensen PT, Nilsson M, Lundin KE, Pedersen EB, Wengel J, Smith CIE. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes. Nucleic Acids Res 2016; 44:2007-19. [PMID: 26857548 PMCID: PMC4797291 DOI: 10.1093/nar/gkw021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson–Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson–Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2′-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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Affiliation(s)
- Sylvain Geny
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden INEB-Instituto de Engenharia Biomedica, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Tomasz Krzywkowski
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Nicolai K Andersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Abdirisaq J Isse
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Amro M El-Madani
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Chenguang Lou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Y Vladimir Pabon
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | | | - Eman M Zaghloul
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | | | - Per T Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Erik B Pedersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
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23
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Zimmerman SC. A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy. Beilstein J Org Chem 2016; 12:125-38. [PMID: 26877815 PMCID: PMC4734311 DOI: 10.3762/bjoc.12.14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/06/2016] [Indexed: 12/02/2022] Open
Abstract
This review summarizes part of the author’s research in the area of supramolecular chemistry, beginning with his early life influences and early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule therapeutic agents for myotonic dystrophy using a rational design approach that heavily relies on principles of supramolecular chemistry. How this work was influenced by that of others in the field and the evolution of each area of research is highlighted with selected examples.
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Affiliation(s)
- Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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24
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Abstract
Cyclic depsipeptides are polypeptides in which one or more amino acid is replaced by a hydroxy acid, resulting in the formation of at least one ester bond in the core ring structure. Many natural cyclic depsipeptides possessing intriguing structural and biological properties, including antitumor, antifungal, antiviral, antibacterial, anthelmintic, and anti-inflammatory activities, have been identified from fungi, plants, and marine organisms. In particular, the potent effects of cyclic depsipeptides on tumor cells have led to a number of clinical trials evaluating their potential as chemotherapeutic agents. Although many of the trials have not achieved the desired results, romidepsin (FK228), a bicyclic depsipeptide that inhibits histone deacetylase, has been shown to have clinical efficacy in patients with refractory cutaneous T-cell lymphoma and has received Food and Drug Administration approval for use in treatment. In this review, we discuss antitumor cyclic depsipeptides that have undergone clinical trials and focus on their structural features, mechanisms, potential applications in chemotherapy, and pharmacokinetic and toxicity data. The results of this study indicate that cyclic depsipeptides could be a rich source of new cancer therapeutics.
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25
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Vippila MR, Ly PK, Cuny GD. Synthesis and Antiproliferative Activity Evaluation of the Disulfide-Containing Cyclic Peptide Thiochondrilline C and Derivatives. JOURNAL OF NATURAL PRODUCTS 2015; 78:2398-2404. [PMID: 26444379 DOI: 10.1021/acs.jnatprod.5b00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Thiochondrilline C (4) was previously isolated from Verrucisispora sp. and reported to have moderate cytotoxicity against human lung adenocarcinoma cells. Herein, we report the synthesis of thiochondrilline C by N-terminal peptide extension, oxidative disulfide bond formation, and heterocycle installation as key steps. Antiproliferative activities for the prepared natural product and several derivatives against the NCI 60 cancer cell line panel are also described. Derivative 22 was identified as a moderately potent antiproliferative agent (50% growth inhibition (GI50) = 0.2-12.2 μM) with leukemia (average GI50 = 1.8 ± 0.1 μM) and colon (average GI50 = 2.4 ± 0.3 μM) cells being most sensitive.
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Affiliation(s)
- Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
| | - Phuong Kim Ly
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
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26
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Hajishaabanha F, Shaabani S, Shaabani A. Synthesis of furan-fused quinoxaline tetracyclic scaffolds via a three-component isocyanide-based reaction. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-2262-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Labby KJ, Watsula SG, Garneau-Tsodikova S. Interrupted adenylation domains: unique bifunctional enzymes involved in nonribosomal peptide biosynthesis. Nat Prod Rep 2015; 32:641-53. [PMID: 25622971 DOI: 10.1039/c4np00120f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonribosomal peptides (NRPs) account for a large portion of drugs and drug leads currently available in the pharmaceutical industry. They are one of two main families of natural products biosynthesized on megaenzyme assembly-lines composed of multiple modules that are, in general, each comprised of three core domains and on occasion of accompanying auxiliary domains. The core adenylation (A) domains are known to delineate the identity of the specific chemical components to be incorporated into the growing NRPs. Previously believed to be inactive, A domains interrupted by auxiliary enzymes have recently been proven to be active and capable of performing two distinct chemical reactions. This highlight summarizes current knowledge on A domains and presents the various interrupted A domains found in a number of nonribosomal peptide synthetase (NRPS) assembly-lines, their predicted or proven dual functions, and their potential for manipulation and engineering for chemoenzymatic synthesis of new pharmaceutical agents with increased potency.
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Affiliation(s)
- Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI 53511, USA
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28
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Sable GA, Lim D. Solid-Phase Synthesis of Triostin A Using a Symmetrical Bis(diphenylmethyl) Linker System. J Org Chem 2015; 80:7486-94. [DOI: 10.1021/acs.joc.5b01055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ganesh A. Sable
- Department
of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Dongyeol Lim
- Department
of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
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Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein PC, Jensen PR. Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species. ACTA ACUST UNITED AC 2015; 22:460-471. [PMID: 25865308 DOI: 10.1016/j.chembiol.2015.03.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/26/2015] [Accepted: 03/10/2015] [Indexed: 12/12/2022]
Abstract
Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.
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Affiliation(s)
- Katherine R Duncan
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Max Crüsemann
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anna Lechner
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Anindita Sarkar
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Li
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Departments of Pharmacology, Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Paul R Jensen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA.
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Camunas-Soler J, Manosas M, Frutos S, Tulla-Puche J, Albericio F, Ritort F. Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline. Nucleic Acids Res 2015; 43:2767-79. [PMID: 25690887 PMCID: PMC4357703 DOI: 10.1093/nar/gkv087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bis-intercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel single-molecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.
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Affiliation(s)
- Joan Camunas-Soler
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Silvia Frutos
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
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31
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Abstract
This review highlights known disulfide-bridged peptide bicycles and the studies on their unique structural and biological features.
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Affiliation(s)
| | - Andrei K. Yudin
- Lash Miller Chemical Laboratories
- University of Toronto
- Toronto
- Canada M5S 3H6
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32
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Al-Mestarihi AH, Villamizar G, Fernández J, Zolova OE, Lombó F, Garneau-Tsodikova S. Adenylation and S-methylation of cysteine by the bifunctional enzyme TioN in thiocoraline biosynthesis. J Am Chem Soc 2014; 136:17350-4. [PMID: 25409494 DOI: 10.1021/ja510489j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The antitumor agent thiocoraline is a nonribosomally biosynthesized bisintercalator natural product, which contains in its peptidic backbone two S-methylated l-cysteine residues. S-Methylation occurs very rarely in nature, and is observed extremely rarely in nonribosomal peptide scaffolds. We have proposed that during thiocoraline biosynthesis, TioN, a stand-alone adenylation domain interrupted by the S-adenosyl-l-methionine binding region of a methyltransferase enzyme, is capable of performing two functions: the adenylation and S-methylation of l-cysteine. Herein, by preparation of knockouts of TioN and its MbtH-like protein partner TioT, we confirmed their role in thiocoraline biosynthesis. We also co-expressed recombinant TioN and TioT and biochemically investigated three potential pathways involving activation, methylation, and loading of l-cysteine onto the TioN partner thiolation domain, TioS(T4). The valuable insights gained into the pathway(s) followed for the production of S-Me-l-Cys-S-TioS(T4) will serve as a guide for the development of novel engineered interrupted adenylation enzymes for combinatorial biosynthesis.
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Affiliation(s)
- Ahmad H Al-Mestarihi
- Department of Pharmaceutical Sciences, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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33
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Bolhuis A, Aldrich-Wright JR. DNA as a target for antimicrobials. Bioorg Chem 2014; 55:51-9. [DOI: 10.1016/j.bioorg.2014.03.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 03/22/2014] [Accepted: 03/24/2014] [Indexed: 11/28/2022]
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Fernández J, Marín L, Alvarez-Alonso R, Redondo S, Carvajal J, Villamizar G, Villar CJ, Lombó F. Biosynthetic modularity rules in the bisintercalator family of antitumor compounds. Mar Drugs 2014; 12:2668-99. [PMID: 24821625 PMCID: PMC4052310 DOI: 10.3390/md12052668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/05/2022] Open
Abstract
Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.
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Affiliation(s)
- Javier Fernández
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Laura Marín
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Raquel Alvarez-Alonso
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Saúl Redondo
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Juan Carvajal
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Germán Villamizar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Claudio J Villar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Felipe Lombó
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
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35
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Katayama K, Okamura T, Sunadome T, Nakagawa K, Takeda H, Shiro M, Matsuda A, Ichikawa S. Synthesis and Biological Evaluation of Quinaldopeptin. J Org Chem 2014; 79:2580-90. [DOI: 10.1021/jo500039d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Katsushi Katayama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takuya Okamura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takuya Sunadome
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Koji Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Hiroshi Takeda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoo Shiro
- Rigaku Corporation, 3-9-12 Matsubara, Akishima, Tokyo 196-0003, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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36
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Ichikawa S, Okamura T, Matsuda A. Total synthesis of quinaldopeptin and its analogues. J Org Chem 2013; 78:12662-70. [PMID: 24236405 DOI: 10.1021/jo402267r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first total synthesis of quinaldopeptin (1) was accomplished. Our approach to the synthesis of 1 includes the solid-phase peptide synthesis of the linear decapeptide 4 followed by macrocyclization and introduction of the quinoline chromophores 2 at a late stage of the synthesis. As for the preparation of 4, a fragment coupling approach was applied considering the C2 symmetrical structure of 1. Chromophore analogues 22 and 23 and desmethyl analogue 27 were also prepared in a manner similar to the synthesis of 1. Synthetic 1 exhibits a strong cytotoxicity with the IC50 value of 3.2 nM. On the other hand, the activity of 23 and 27 was largely reduced.
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Affiliation(s)
- Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University , Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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37
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KtzJ-dependent serine activation and O-methylation by KtzH for kutznerides biosynthesis. J Antibiot (Tokyo) 2013; 67:59-64. [DOI: 10.1038/ja.2013.98] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 08/28/2013] [Accepted: 09/03/2013] [Indexed: 12/11/2022]
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38
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Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. Proc Natl Acad Sci U S A 2013; 110:11797-802. [PMID: 23824289 DOI: 10.1073/pnas.1222159110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Complex microbial ecosystems contain large reservoirs of unexplored biosynthetic diversity. Here we provide an experimental framework and data analysis tool to facilitate the targeted discovery of natural-product biosynthetic gene clusters from the environment. Multiplex sequencing of barcoded PCR amplicons is followed by sequence similarity directed data parsing to identify sequences bearing close resemblance to biosynthetically or biomedically interesting gene clusters. Amplicons are then mapped onto arrayed metagenomic libraries to guide the recovery of targeted gene clusters. When applied to adenylation- and ketosynthase-domain amplicons derived from saturating soil DNA libraries, our analysis pipeline led to the recovery of biosynthetic clusters predicted to encode for previously uncharacterized glycopeptide- and lipopeptide-like antibiotics; thiocoraline-, azinomycin-, and bleomycin-like antitumor agents; and a rapamycin-like immunosuppressant. The utility of the approach is demonstrated by using recovered eDNA sequences to generate glycopeptide derivatives. The experiments described here constitute a systematic interrogation of a soil metagenome for gene clusters capable of encoding naturally occurring derivatives of biomedically relevant natural products. Our results show that previously undetected biosynthetic gene clusters with potential biomedical relevance are very common in the environment. This general process should permit the routine screening of environmental samples for gene clusters capable of encoding the systematic expansion of the structural diversity seen in biomedically relevant families of natural products.
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39
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Tulla-Puche J, Auriemma S, Falciani C, Albericio F. Orthogonal chemistry for the synthesis of thiocoraline-triostin hybrids. Exploring their structure-activity relationship. J Med Chem 2013; 56:5587-600. [PMID: 23746132 DOI: 10.1021/jm4006093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The natural compounds triostin and thiocoraline are potent antitumor agents that act as DNA bisintercalators. From a pharmaceutical point of view, these compounds are highly attractive although they present a low pharmacokinetic profile, in part due to their low solubility. Synthetically, they represent a tour de force because no robust strategies have been developed to access a broad range of these bicyclic (depsi)peptides in a straightforward manner. Here we describe solid-phase strategies to synthesize new bisintercalators, such as thiocoraline-triostin hybrids, as well as analogues bearing soluble tags. Orthogonal protection schemes (up to five from: Fmoc, Boc Alloc, pNZ, o-NBS, and Troc), together with the right concourse of the coupling reagents (HOSu, HOBt, HOAt, Oxyma, EDC, DIPCDI, PyAOP, PyBOP, HATU, COMU), were crucial to establish the synthetic plan. In vitro studies and structure-activity relationships have been shown trends in the structure-activity relationship that will facilitate the design of new bisintercalators.
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Affiliation(s)
- Judit Tulla-Puche
- Institute for Research in Biomedicine Barcelona , Baldiri Reixac 10, 08028 Barcelona, Spain
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40
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Yao QC, Wu DE, Xia M. Synthesis, crystal structure, property research, and DFT calculation of 2,3-diphenylfuro[3,2-b]quinoxaline. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.03.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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41
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He Z, Trinchera P, Adachi S, St Denis JD, Yudin AK. Oxidative geminal functionalization of organoboron compounds. Angew Chem Int Ed Engl 2012; 51:11092-6. [PMID: 23038428 DOI: 10.1002/anie.201206501] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Indexed: 12/20/2022]
Abstract
Excellent tolerance: Stable acylboronates equipped with N-methyliminodiacetyl (MIDA) boryl groups ([B]) were prepared by using a sequence of oxidative manipulations at the boron-bound carbon center (green in scheme). Chemoselective transformations of these acylated organoboron building blocks yielded a range of multifunctionalized boron derivatives and supplied access to valuable borylated heterocycles (see scheme).
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Affiliation(s)
- Zhi He
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St. Toronto, ON, M5S 3H6, Canada
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42
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He Z, Trinchera P, Adachi S, St. Denis JD, Yudin AK. Oxidative Geminal Functionalization of Organoboron Compounds. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206501] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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43
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Rajule R, Bryant VC, Lopez H, Luo X, Natarajan A. Perturbing pro-survival proteins using quinoxaline derivatives: a structure-activity relationship study. Bioorg Med Chem 2012; 20:2227-34. [PMID: 22386982 PMCID: PMC3303926 DOI: 10.1016/j.bmc.2012.02.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/30/2012] [Accepted: 02/07/2012] [Indexed: 01/23/2023]
Abstract
In HeLa cells the combinatorial knockdown of Bcl-xL and Mcl-1 is sufficient to induce spontaneous apoptosis. Quinoxaline derivatives were screened for the induction of Mcl-1 dependent apoptosis using a cell line without functional Bcl-xL. Quinoxaline urea analog 1 h was able to specifically induce apoptosis in an Mcl-1 dependent manner. We demonstrate that even small changes to 1h results in dramatic loss of activity. In addition, 1 h and ABT-737 synergistically inhibit cell growth and induce apoptosis. Our results also suggest that 1h could have therapeutic potential against ABT-737 refractory cancer.
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Affiliation(s)
- Rajkumar Rajule
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198
| | - Vashti C. Bryant
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198
| | - Hernando Lopez
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198
| | - Xu Luo
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198
| | - Amarnath Natarajan
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, Omaha, NE 68198
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198
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44
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Liu Y, Chai Y, Kumar A, Tidwell RR, Boykin DW, Wilson WD. Designed compounds for recognition of 10 base pairs of DNA with two at binding sites. J Am Chem Soc 2012; 134:5290-9. [PMID: 22369366 DOI: 10.1021/ja211628j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Short AT base pair sequences that are separated by a small number of GCs are common in eukaryotic parasite genomes. Cell-permeable compounds that bind effectively and selectively to such sequences present an attractive therapeutic approach. Compounds with linked, one or two amidine-benzimidazole-phenyl (ABP) motifs were designed, synthesized, and evaluated for binding to adjacent AT sites by biosensor-surface plasmon resonance (SPR). A surprising feature of the linked ABP motifs is that a set of six similar compounds has three different minor groove binding modes with the target sequences. Compounds with one ABP bind independently to two separated AT sites. Unexpectedly, compounds with two ABP motifs can bind strongly either as monomers or as cooperative dimers to the full site. The results are supported by mass spectrometry and circular dichroism, and models to explain the different binding modes are presented.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, United States
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45
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Zolova OE, Garneau-Tsodikova S. Importance of the MbtH-like protein TioT for production and activation of the thiocoraline adenylation domain of TioK. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20131c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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46
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Design, synthesis, and biological evaluation of a novel series of bisintercalating DNA-binding piperazine-linked bisanthrapyrazole compounds as anticancer agents. Bioorg Med Chem 2011; 19:7023-32. [PMID: 22041173 DOI: 10.1016/j.bmc.2011.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/23/2011] [Accepted: 10/05/2011] [Indexed: 12/13/2022]
Abstract
A series of bisintercalating DNA binding bisanthrapyrazole compounds containing piperazine linkers were designed by molecular modeling and docking techniques. Because the anthrapyrazoles are not quinones they are unable to be reductively activated like doxorubicin and other anthracyclines and thus they should not be cardiotoxic. The concentration dependent increase in DNA melting temperature was used to determine the strength of DNA binding and the bisintercalation potential of the compounds. Compounds with more than a three-carbon linker that could span four DNA base pairs achieved bisintercalation. All of the bisanthrapyrazoles inhibited human erythroleukemic K562 cell growth in the low to submicromolar concentration range. They also strongly inhibited the decatenation activity of topoisomerase IIα and the relaxation activity of topoisomerase I. However, as measured by their ability to induce double strand breaks in plasmid DNA, the bisanthrapyrazole compounds did not act as topoisomerase IIα poisons. In conclusion, a novel group of bisanthrapyrazole compounds were designed, synthesized, and biologically evaluated as potential anticancer agents.
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47
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Wyche TP, Hou Y, Braun D, Cohen HC, Xiong MP, Bugni TS. First natural analogs of the cytotoxic thiodepsipeptide thiocoraline A from a marine Verrucosispora sp. J Org Chem 2011; 76:6542-7. [PMID: 21736356 DOI: 10.1021/jo200661n] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A marine Verrucosispora sp. isolated from the sponge Chondrilla caribensis f. caribensis was found to produce thiocoraline, a potent cytotoxic compound. Five new analogs of thiocoraline were isolated and represent the first analogs of thiocoraline. 22'-Deoxythiocoraline (2), thiochondrilline C (5), and 12'-sulfoxythiocoraline (6) demonstrated significant cytotoxicity against the A549 human cancer cell line with EC(50) values of 0.13, 2.86, and 1.26 μM, respectively. The analogs provide insight into the SAR and biosynthesis of thiocoraline. The DP4 probability method was used to analyze ab initio NMR calculations to confirm stereochemical assignments.
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Affiliation(s)
- Thomas P Wyche
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, USA
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Mady ASA, Zolova OE, Millán MÁS, Villamizar G, de la Calle F, Lombó F, Garneau-Tsodikova S. Characterization of TioQ, a type II thioesterase from the thiocoraline biosynthetic cluster. MOLECULAR BIOSYSTEMS 2011; 7:1999-2011. [PMID: 21483938 DOI: 10.1039/c1mb05044c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
An antitumor agent thiocoraline is a thiodepsipeptide marine product derived from two Micromonospora sp. strains that inhibits protein synthesis by binding of its key 3-hydroxyquinaldic acid (3HQA) chromophores to duplex DNA. There are at least two potential pathways via which the 3HQA moiety could be biosynthesized from L-Trp. By biochemical characterization and by preparation of knockouts of an adenylation-thiolation enzyme, TioK, and of two type II thioesterases, TioP and TioQ, found in the thiocoraline biosynthetic gene cluster, we gained valuable insight into the pathway followed for the production of 3HQA.
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Affiliation(s)
- Ahmed S A Mady
- University of Michigan, Life Sciences Institute, 210 Washtenaw Ave, Ann Arbor, MI 48109, USA
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