1
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Qi L, Zhang J, Gao Y, Gong P, Liang C, Su Y, Zeng Q, Zhang Y. Peptide-RNA complexation-induced fluorescence "turn on" displacement assay for the recognition of small ligands targeting HIV-1 RNA. J Pharm Anal 2022; 12:923-928. [PMID: 36605574 PMCID: PMC9805967 DOI: 10.1016/j.jpha.2022.07.003] [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: 01/13/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 01/07/2023] Open
Abstract
The regulator of expression of virion (Rev) protein binds specifically to the Rev-responsive element (RRE) RNA in order to regulate the expression of the human immunodeficiency virus (HIV)-1 genes. Fluorescence indicator displacement assays have been used to identify ligands that can inhibit the Rev-RRE interaction; however, the small fluorescence indicators cannot fully replace the Rev peptide or protein. As a result, a single rhodamine B labeled Rev (RB-Rev) model peptide was utilized in this study to develop a direct and efficient Rev-RRE inhibitor screening model. Due to photon-induced electron transfer quenching of the tryptophan residue on the RB fluorophore, the fluorescence of RB in Rev was weakened and could be dramatically reactivated by interaction with RRE RNA in ammonium acetate buffer (approximately six times). The interaction could reduce the electron transfer between tryptophan and RB, and RRE could also increase RB fluorescence. The inhibitor screening model was evaluated using three known positive Rev-RRE inhibitors, namely, proflavin, 6-chloro-9-[3-(2-chloroethylamino)propylamino]-2-methoxyacridine (ICR 191), and neomycin, as well as a negative drug, arginine. With the addition of the positive drugs, the fluorescence of the Rev-RRE decreased, indicating the displacement of RB-Rev. This was confirmed using atomic force microscopy (AFM) and the fluorescence was essentially unaffected by the addition of arginine. The results demonstrated that RB-Rev can be used as a fluorescent probe for recognizing small ligands that target RRE RNA. The Rev-RRE inhibitor screening model offers a novel approach to evaluating and identifying long-acting Rev inhibitors.
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Affiliation(s)
- Liang Qi
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China,Corresponding author.
| | - Jiayun Zhang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Ying Gao
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Pin Gong
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Chengyuan Liang
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yao Su
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Qiao Zeng
- Department of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yafeng Zhang
- Xi'an Institute for Food and Drug Control, Xi'an, 710054, China
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2
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Fernández S, Allegue D, Santamaría J, Ballesteros A. Diastereoselective and Synergistic Gold‐Catalyzed Bispropargylation of Xanthones and Thioxanthones: An Access to Xanthene Derivatives. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Li J, Fan YY, Wen J, Zhang J, Zhang ZQ. Metal-Enhanced Aggregation-Induced Emission Strategy for the HIV-I RNA-Binding Ligand Assay. Anal Chem 2022; 94:4695-4702. [PMID: 35258935 DOI: 10.1021/acs.analchem.1c04889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HIV-Ι trans-activation responsive (TAR) RNA-trans-activator of transcription (Tat) protein complex is crucial for the efficient transcription of the integrated human immunodeficiency virus-I genome and is an established therapeutic target for AIDS diagnosis and treatment. Developing a sensitive strategy for the TAR RNA-binding ligand assay could provide antiviral leads with a radically new mechanism for the treatment of AIDS. Herein, a new TAR RNA-binding ligand assay platform was established using a signal amplification strategy that combines aggregation-induced emission (AIE) with a metal-enhanced fluorescence (MEF) concept. The tetraphenylethylene (TPE) derivative was labeled on the Tat peptide as a fluorescent molecule, while the TAR RNA was immobilized on the surface of the Fe3O4@Au@Ag@SiO2 nanoparticles (NPs) to specifically bind the TPE-Tat peptide. The TPE-Tat peptide was weakly emissive itself while emitting strongly in the NP-TAR-TPE-Tat complex by the AIE and MEF signal amplification effect. It was confirmed by known Tat peptide competitors that this system could be applied to the screening and detection of TAR RNA-binding ligands because they could replace the TPE-Tat peptide from the complex and make the system fluorescence decrease. When this system was adopted to test four candidate ligands, it was found that bisantrene had a favorable TAR RNA-binding ability. The proposed AIE-MEF strategy not only provides a sensitive and reliable method for the TAR RNA-binding ligand assay but also can avoid the influence of ligands on fluorescent detection in the conventional displacement assay.
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Affiliation(s)
- Jun Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yao-Yao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jie Wen
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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4
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NAKATANI K. Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:30-48. [PMID: 35013029 PMCID: PMC8795530 DOI: 10.2183/pjab.98.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.
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Affiliation(s)
- Kazuhiko NAKATANI
- SANKEN, The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
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5
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Das B, Murata A, Nakatani K. A small-molecule fluorescence probe ANP77 for sensing RNA internal loop of C, U and A/CC motifs and their binding molecules. Nucleic Acids Res 2021; 49:8462-8470. [PMID: 34358308 PMCID: PMC8421207 DOI: 10.1093/nar/gkab650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/02/2021] [Accepted: 08/04/2021] [Indexed: 11/12/2022] Open
Abstract
Small-molecules interacting with particular RNAs and modulating their functions are vital tools for RNA-targeting drug discovery. Considering the substantial distribution of the internal loops involving two contiguous cytosines opposite to a single-nucleotide base (Y/CC; Y = C, U or A) within the biologically significant functional RNAs, developing small-molecule probes targeting Y/CC sites should provide profound insight into their functions and roles in biochemical processes. Herein, we report ANP77 as the small-molecule probe for sensing RNA internal loop of Y/CC motifs and molecules binding to the motifs. The Y/CC motifs interact with ANP77 via the formation of a 1:1 complex and quench the fluorescence of ANP77. The flanking sequence-dependent binding to C/CC and U/CC sites was assessed by fluorometric screening, provided the binding heat maps. The quenching phenomena of ANP77 fluorescence was confirmed with intrinsic potential drug target pre-miR-1908. Finally, the binding-dependent fluorescence quenching of ANP77 was utilized in the fluorescence indicator displacement assay to demonstrate the potential of ANP77 as an indicator by using the RNA-binding drugs, risdiplam and branaplam.
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Affiliation(s)
- Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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6
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Furuzono T, Murata A, Okuda S, Mizutani K, Adachi T, Nakatani K. Speeding drug discovery targeting RNAs: An iterative "RNA selection-compounds screening cycle" for exploring RNA-small molecule pairs. Bioorg Med Chem 2021; 36:116070. [PMID: 33773376 DOI: 10.1016/j.bmc.2021.116070] [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: 12/06/2020] [Revised: 01/30/2021] [Accepted: 02/05/2021] [Indexed: 12/30/2022]
Abstract
RNA is an emerging target of next-generation drug development. Recently, new small molecules targeting RNAs were discovered by several pharmaceutical companies. Methods have been reported to identify small molecules targeting a specific RNA sequence and structural motif, however, because of diverse sequence and structural motifs potentially present in the druggable functional RNAs, large sets of structure-activity relationships (SARs) information of small molecule - RNA interactions will be required for the acceleration and efficient startup of the discovery programs toward unprecedented RNA targets. Here we describe our iterative RNA selection and compounds screening to accumulate rich information about small molecules - RNA interaction. The RNAs that selectively bind to the initial molecular target, compound 1 from our in-house chemical library (JT-library), was isolated using in vitro selection technique from a hairpin-structured RNA library mimicking precursor microRNA (pre-miRNA). Then, we engineered pre-let-7f-2 to create its mutant that can bind to compound 1 by embedding the in vitro selected RNA motif for compound 1 in the hairpin loop region. The obtained mutant pre-let-7f-2-loop-mt was used as a target for screening 316 analogs of compound 1. A surface plasmon resonance (SPR) -based screening was performed against pre-let-7f-2-loop-mt-immobilized sensor surface and we obtained four compounds that can bind to the RNA. Among these four compounds, three compounds showed higher affinity to pre-let-7f-2-loop-mt than the parental compound 1, which suggests the feasibility of our strategy for gathering the SAR information on small molecule - RNA interactions. We demonstrated only one cycle of RNA selection and compounds screening in the present study, but can continue this cycle with the selected molecule to gain new RNAs and even new RNA motifs and gather much SAR information with improved accuracy.
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Affiliation(s)
- Tomoko Furuzono
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan; Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco INC., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Satoshi Okuda
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco INC., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kenji Mizutani
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco INC., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco INC., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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7
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Phosphorescent palladium-tetrabenzoporphyrin indicators for immunosensing of small molecules with a novel optical device. Talanta 2020; 224:121927. [PMID: 33379126 DOI: 10.1016/j.talanta.2020.121927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022]
Abstract
Small-molecule detection is important for many applications including clinical diagnostics, drug discovery, environmental screening, and food technology. Current techniques suffer from various limitations including cost, complex sample processing, massive instrumentation, and need for expertise. To overcome these limitations, a new optical immunosensing assay for the detection of small molecules was developed and assessed with the targets estrone (E1) and estradiol (E2). For this purpose, phosphorescent indicators were designed based on the tetrabenzoporphyrin skeleton directly linked to E1 or E2, or attached through a linker, with phosphorescence lifetimes in the range of ~100-~300 μs. The assay is an indicator displacement assay (IDA). The best performances of our optical immunosensor were obtained with the indicators E1-L-Por and E2-L-Por. As they bound to specific polyclonal antibodies, their phosphorescence (τ ~200 μs) was quenched. When an endogenous competitor was added, the indicator was displaced, and the phosphorescence was immediately recovered. These effects were measured with a new optical device, described here, and able to detect picograms of luminescent molecules emitting in the NIR range, simply by measuring phosphorescence decay. This radical switch-off/switch on process demonstrates that E1-L-Por and E2-L-Por are good candidates for in vivo and in vitro immunosensing of E1 and E2. Importantly, the present immunosensing assay can be easily adapted to other small molecules such as other hormones and drugs.
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8
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Ligand-RNA interaction assay based on size-selective fluorescence core-shell nanocomposite. Anal Bioanal Chem 2020; 412:7349-7356. [DOI: 10.1007/s00216-020-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
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9
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Sato Y, Aiba Y, Yajima S, Tanabe T, Higuchi K, Nishizawa S. Strong Binding and Off–On Signaling Functions of Deep‐Red Fluorescent TO‐PRO‐3 for Influenza A Virus RNA Promoter Region. Chembiochem 2019; 20:2752-2756. [DOI: 10.1002/cbic.201900331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Sato
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Yuri Aiba
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Sayaka Yajima
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Takaaki Tanabe
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Kei Higuchi
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
| | - Seiichi Nishizawa
- Department of ChemistryGraduate School of ScienceTohoku University Sendai 980-8578 Japan
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10
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Wicks SL, Hargrove AE. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods 2019; 167:3-14. [PMID: 31051253 DOI: 10.1016/j.ymeth.2019.04.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.
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Affiliation(s)
- Sarah L Wicks
- Duke University, Department of Chemistry, Durham, NC 27705, United States
| | - Amanda E Hargrove
- Duke University, Department of Chemistry, Durham, NC 27705, United States.
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11
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Sato Y, Yajima S, Taguchi A, Baba K, Nakagomi M, Aiba Y, Nishizawa S. Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA. Chem Commun (Camb) 2019; 55:3183-3186. [DOI: 10.1039/c9cc00414a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report that TO-PRO-3 functions as a deep-red fluorescent indicator for the internal loop structure of the bacterial (Escherichia coli) A-site, which enables the assessment of A-site binding capability of various test compounds including blue and even-green-emitting compounds.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Sayaka Yajima
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Akifumi Taguchi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Kyosuke Baba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Mayu Nakagomi
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Yuri Aiba
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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12
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Fluorescent Trimethylated Naphthyridine Derivative with an Aminoalkyl Side Chain as the Tightest Non-aminoglycoside Ligand for the Bacterial A-site RNA. Chemistry 2018; 24:13862-13870. [DOI: 10.1002/chem.201802320] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Indexed: 12/31/2022]
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13
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Yu FC, Lin XR, Liu ZC, Zhang JH, Liu FF, Wu W, Ma YL, Qu WW, Yan SJ, Lin J. Beyond the Antagonism: Self-Labeled Xanthone Inhibitors as Modeled "Two-in-One" Drugs in Cancer Therapy. ACS OMEGA 2017; 2:873-889. [PMID: 30023617 PMCID: PMC6044579 DOI: 10.1021/acsomega.6b00545] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/28/2017] [Indexed: 05/24/2023]
Abstract
Self-labeled inhibitors (SLIs) are promising for creating links, ranging from cancer therapy and metastatic pathways to mechanistic elucidation. In this study, a new category of "two-in-one" fluorescent xanthone inhibitors was developed for the systematic evaluation of anticancer activity and the selective imaging of cytoplasm in vitro. These xanthone inhibitors presented high fluorescent brightness, working over a wide pH range enabled by a "switchable reaction" of the heterocyclic backbone. The strength and nature of fluorescence were probed via spectroscopic methods and density functional theory calculations on the molecular level, respectively. Along with the potent anticancer activity, which was demonstrated using MTT and clonogenic assays with high fluorescent brightness in the cytoplasm, SLI 3fd could be established as a modeled self-monitoring drug in cancer therapy.
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Affiliation(s)
- Fu-Chao Yu
- Key
Laboratory of Medicinal Chemistry for Natural Resource (Ministry of
Education), Yunnan Provincial Engineering Research Center in University
for Crude Drugs and Pharmaceutical Intermediates, School of Chemical
Science and Technology, Yunnan University, Kunming 650091, P. R. China
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Xin-Rong Lin
- Department of Chemistry and Department of
Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Zhi-Cheng Liu
- Key
Laboratory of Medicinal Chemistry for Natural Resource (Ministry of
Education), Yunnan Provincial Engineering Research Center in University
for Crude Drugs and Pharmaceutical Intermediates, School of Chemical
Science and Technology, Yunnan University, Kunming 650091, P. R. China
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Ji-Hong Zhang
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Fei-Fei Liu
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Wei Wu
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Yu-Lu Ma
- Key
Laboratory of Medicinal Chemistry for Natural Resource (Ministry of
Education), Yunnan Provincial Engineering Research Center in University
for Crude Drugs and Pharmaceutical Intermediates, School of Chemical
Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Wen-Wen Qu
- Faculty of Life Science
and Technology and Faculty of Science, Kunming University
of Science and Technology, Kunming 650504, P. R. China
| | - Sheng-Jiao Yan
- Key
Laboratory of Medicinal Chemistry for Natural Resource (Ministry of
Education), Yunnan Provincial Engineering Research Center in University
for Crude Drugs and Pharmaceutical Intermediates, School of Chemical
Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Jun Lin
- Key
Laboratory of Medicinal Chemistry for Natural Resource (Ministry of
Education), Yunnan Provincial Engineering Research Center in University
for Crude Drugs and Pharmaceutical Intermediates, School of Chemical
Science and Technology, Yunnan University, Kunming 650091, P. R. China
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14
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Qi L, Zhang J, He T, Huo Y, Zhang ZQ. Probing interaction of a fluorescent ligand with HIV TAR RNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:93-98. [PMID: 27611591 DOI: 10.1016/j.saa.2016.08.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/15/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.
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MESH Headings
- Aminacrine/analogs & derivatives
- Aminacrine/chemistry
- Aminacrine/metabolism
- Aminacrine/pharmacology
- Binding, Competitive
- Circular Dichroism
- Drug Evaluation, Preclinical/methods
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Framycetin/chemistry
- Framycetin/metabolism
- HIV Long Terminal Repeat
- Models, Molecular
- Molecular Docking Simulation
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Tian He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China.
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15
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MnO2 nanosheet-assisted ligand-DNA interaction-based fluorescence polarization biosensor for the detection of Ag+ ions. Biosens Bioelectron 2017; 87:566-571. [DOI: 10.1016/j.bios.2016.08.093] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/17/2016] [Accepted: 08/26/2016] [Indexed: 11/30/2022]
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16
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A ratiometric fluorescence RRE RNA-targeted assay for a new fluorescence ligand. Biosens Bioelectron 2016; 86:287-292. [DOI: 10.1016/j.bios.2016.06.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/01/2016] [Accepted: 06/18/2016] [Indexed: 11/18/2022]
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17
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Qi L, Huo Y, Wang H, Zhang J, Dang FQ, Zhang ZQ. Fluorescent DNA-Protected Silver Nanoclusters for Ligand-HIV RNA Interaction Assay. Anal Chem 2015; 87:11078-83. [PMID: 26447651 DOI: 10.1021/acs.analchem.5b03166] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Studying ligand-biomacromolecule interactions provides opportunities for creating new compounds that can efficiently regulate specific biological processes. Ribonucleic acid (RNA) molecules have become attractive drug targets since the discovery of their roles in modulating gene expression, while only a limited number of studies have investigated interactions between ligands and functional RNA molecules, especially those based on nanotechnology. DNA-protected silver nanoclusters (AgNCs) were used to investigate ligand-RNA interactions for the first time in this study. The anthracycline anticancer drug mitoxantrone (MTX) was found to quench the fluorescence of AgNCs. After adding human immunodeficiency virus trans-activation responsive region (TAR) RNA or Rev-response element (RRE) RNA to AgNCs-MTX mixtures, the fluorescence of the AgNCs recovered due to interactions between MTX with RNAs. The binding constants and number of binding sites of MTX to TAR and RRE RNA were determined through theoretical calculations. MTX-RNA interactions were further confirmed in fluorescence polarization and mass spectrometry experiments. The mechanism of MTX-based fluorescence quenching of the AgNCs was also explored. This study provides a new strategy for ligand-RNA binding interaction assay.
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Huan Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Fu-Quan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
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18
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Fukuzumi T, Murata A, Aikawa H, Harada Y, Nakatani K. Exploratory Study on the RNA-Binding Structural Motifs by Library Screening Targeting pre-miRNA-29 a. Chemistry 2015; 21:16859-67. [DOI: 10.1002/chem.201502913] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 12/31/2022]
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19
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Chow CF, Ho PY, Wong WL, Gong CB. A Multifunctional Bimetallic Molecular Device for Ultrasensitive Detection, Naked-Eye Recognition, and Elimination of Cyanide Ions. Chemistry 2015. [PMID: 26198787 DOI: 10.1002/chem.201501448] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Cheuk-Fai Chow
- Department of Science and Environmental Studies, Centre for Education in Environmental Sustainability, The Hong Kong Institute of Education, 10 Lo Ping Road, Tai Po Hong Kong SAR (P.R. China).
| | - Pui-Yu Ho
- Department of Science and Environmental Studies, Centre for Education in Environmental Sustainability, The Hong Kong Institute of Education, 10 Lo Ping Road, Tai Po Hong Kong SAR (P.R. China)
| | - Wing-Leung Wong
- Department of Science and Environmental Studies, Centre for Education in Environmental Sustainability, The Hong Kong Institute of Education, 10 Lo Ping Road, Tai Po Hong Kong SAR (P.R. China)
| | - Cheng-Bin Gong
- College of Chemistry and Chemical Engineering, Southwest University, Chong Qing (P.R. China)
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20
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Joly JP, Mata G, Eldin P, Briant L, Fontaine-Vive F, Duca M, Benhida R. Artificial Nucleobase-Amino Acid Conjugates: A New Class of TAR RNA Binding Agents. Chemistry 2014; 20:2071-9. [DOI: 10.1002/chem.201303664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Indexed: 12/23/2022]
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21
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Murata A, Harada Y, Fukuzumi T, Nakatani K. Fluorescent indicator displacement assay of ligands targeting 10 microRNA precursors. Bioorg Med Chem 2013; 21:7101-6. [PMID: 24084297 DOI: 10.1016/j.bmc.2013.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/04/2013] [Accepted: 09/04/2013] [Indexed: 11/15/2022]
Abstract
Fluorescent indicator displacement (FID) assay is a rapid and convenient assay for identifying new ligands that bind to the target molecules. In our previous studies, we have shown that a series of 2,7-diaminoalkoxy xanthone and thioxanthone derivatives can be used as fluorescent indicators for detecting the interaction between RNA and a ligand. The xanthone and thioxanthone fluorochromes showed efficient fluorescence quenching upon binding to target RNA. Subsequent displacement of the bound-fluorochrome with a ligand that binds more strongly to the target RNA led to the recovery of the fluorescence by releasing the fluorochrome from RNA. Here we report a pilot screening of a chemical library that contains 9600 structurally diverse compounds for molecules that bind to a specific miRNA precursor using the FID assay.
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Affiliation(s)
- Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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22
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Murata A, Fukuzumi T, Umemoto S, Nakatani K. Xanthone derivatives as potential inhibitors of miRNA processing by human Dicer: targeting secondary structures of pre-miRNA by small molecules. Bioorg Med Chem Lett 2012; 23:252-5. [PMID: 23164709 DOI: 10.1016/j.bmcl.2012.10.108] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/25/2012] [Indexed: 10/27/2022]
Abstract
In recent years, various biological processes have been found to be regulated by miRNA-mediated gene silencing. A small molecule that modulate the miRNA pathway will provide the biological tool for elucidating mechanisms of miRNA-mediated gene regulation, and can be the drug lead for miRNA related diseases. In this study, we demonstrated that an aminoalkoxy-substituted thioxanthone derivative interferes Dicer-mediated processing of pre-miRNA. Information about the interaction between these xanthone derivatives and pre-miRNAs will enable us to design and develop new small molecule-based inhibitors for miRNA pathway.
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Affiliation(s)
- Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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