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Nagasawa R, Onizuka K, Komatsu KR, Miyashita E, Murase H, Ojima K, Ishikawa S, Ozawa M, Saito H, Nagatsugi F. Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries. Commun Chem 2024; 7:98. [PMID: 38693284 DOI: 10.1038/s42004-024-01181-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
The large-scale analysis of small-molecule binding to diverse RNA structures is key to understanding the required interaction properties and selectivity for developing RNA-binding molecules toward RNA-targeted therapies. Here, we report a new system for performing the large-scale analysis of small molecule-RNA interactions using a multiplexed pull-down assay with RNA structure libraries. The system profiled the RNA-binding landscapes of G-clamp and thiazole orange derivatives, which recognizes an unpaired guanine base and are good probes for fluorescent indicator displacement (FID) assays, respectively. We discuss the binding preferences of these molecules based on their large-scale affinity profiles. In addition, we selected combinations of fluorescent indicators and different ranks of RNA based on the information and screened for RNA-binding molecules using FID. RNAs with high- and intermediate-rank RNA provided reliable results. Our system provides fundamental information about small molecule-RNA interactions and facilitates the discovery of novel RNA-binding molecules.
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Affiliation(s)
- Ryosuke Nagasawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan.
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Miyagi, 980-8577, Japan.
| | - Kaoru R Komatsu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Emi Miyashita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Hirotaka Murase
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | - Kanna Ojima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Shunya Ishikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan.
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Miyagi, 980-8578, Japan.
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2
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Takashima Y, Murata A, Iida K, Sugai A, Hagiwara M, Nakatani K. Method for Identifying Sequence Motifs in Pre-miRNAs for Small-Molecule Binding. ACS Chem Biol 2022; 17:2817-2827. [PMID: 36150699 PMCID: PMC9594041 DOI: 10.1021/acschembio.2c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Non-coding RNAs are emerging targets for drug development because they are involved in various cellular processes. However, there are a few reliable design strategies for small molecules that can target RNAs. This paper reports a simple and efficient method to comprehensively analyze RNA motifs that can be bound by a specific small molecule. The method involves Dicer-mediated pre-miRNA cleavage and subsequent analysis of the reaction products by high-throughput sequencing. A pre-miRNA mutant library containing a randomized region at the Dicer cleavage site was used as the substrate for the reaction. Sequencing analysis of the products of the reaction carried out in the presence or absence of a synthetic small molecule identified the pre-miRNA mutants whose Dicer-mediated cleavage was significantly altered by the addition of the small molecule. The binding of the small molecule to the identified pre-miRNA mutants was confirmed by surface plasmon resonance, demonstrating the feasibility of our method.
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Affiliation(s)
- Yusuke Takashima
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan,
| | - Kei Iida
- Medical
Research Support Center, Kyoto University
Graduate School of Medicine, Konoecho Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ayako Sugai
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Masatoshi Hagiwara
- Department
of Anatomy and Developmental Biology, Kyoto
University Graduate School of Medicine, Konoecho Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific
and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan,
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3
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Sato Y, Miura H, Tanabe T, Okeke CU, Kikuchi A, Nishizawa S. Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule. Anal Chem 2022; 94:7814-7822. [PMID: 35604144 DOI: 10.1021/acs.analchem.1c05488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new class of triplex-forming peptide nucleic acid (PNA)-based fluorogenic probes for sensing of the panhandle structure of the influenza A virus (IAV) RNA promoter region. Here, a small molecule (DPQ) capable of selectively binding to the internal loop structure was conjugated with triplex-forming forced intercalation of the thiazole orange (tFIT) probe with natural PNA nucleobases. The resulting conjugate, tFIT-DPQ, showed a significant light-up response (83-fold) upon strong (Kd = 107 nM) and structure-selective binding to the IAV RNA promoter region under physiological conditions (pH 7.0, 100 mM NaCl). We demonstrated the conjugation of these two units through the suitable spacer was key to show useful binding and fluorogenic signaling functions. tFIT-DPQ facilitated the sensitive and selective detection of IAV RNA based on its binding to the promoter region. Furthermore, we found that tFIT-DPQ could work as a sensitive indicator for screening of test compounds targeting the IAV RNA promoter region in the fluorescence indicator displacement assay.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiromasa Miura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Chioma Uche Okeke
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Akiko Kikuchi
- Department of Kampo and Integrative Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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4
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Mukherjee S, Murata A, Ishida R, Sugai A, Dohno C, Hamada M, Krishna S, Nakatani K. HT-SELEX-based identification of binding pre-miRNA hairpin-motif for small molecules. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:165-174. [PMID: 34976435 PMCID: PMC8685993 DOI: 10.1016/j.omtn.2021.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022]
Abstract
Selective targeting of biologically relevant RNAs with small molecules is a long-standing challenge due to the lack of clear understanding of the binding RNA motifs for small molecules. The standard SELEX procedure allows the identification of specific RNA binders (aptamers) for the target of interest. However, more effort is needed to identify and characterize the sequence-structure motifs in the aptamers important for binding to the target. Herein, we described a strategy integrating high-throughput (HT) sequencing with conventional SELEX followed by bioinformatic analysis to identify aptamers with high binding affinity and target specificity to unravel the sequence-structure motifs of pre-miRNA, which is essential for binding to the recently developed new water-soluble small-molecule CMBL3aL. To confirm the fidelity of this approach, we investigated the binding of CMBL3aL to the identified motifs by surface plasmon resonance (SPR) spectroscopy and its potential regulatory activity on dicer-mediated cleavage of the obtained aptamers and endogenous pre-miRNAs comprising the identified motif in its hairpin loop. This new approach would significantly accelerate the identification process of binding sequence-structure motifs of pre-miRNA for the compound of interest and would contribute to increase the spectrum of biomedical application.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bellary Road, Bangalore 560065, India
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Ryoga Ishida
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ayako Sugai
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Sudhir Krishna
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bellary Road, Bangalore 560065, India
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (SANKEN), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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5
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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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6
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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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7
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Winkle M, El-Daly SM, Fabbri M, Calin GA. Noncoding RNA therapeutics - challenges and potential solutions. Nat Rev Drug Discov 2021; 20:629-651. [PMID: 34145432 PMCID: PMC8212082 DOI: 10.1038/s41573-021-00219-z] [Citation(s) in RCA: 786] [Impact Index Per Article: 262.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Therapeutic targeting of noncoding RNAs (ncRNAs), such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), represents an attractive approach for the treatment of cancers, as well as many other diseases. Over the past decade, substantial effort has been made towards the clinical application of RNA-based therapeutics, employing mostly antisense oligonucleotides and small interfering RNAs, with several gaining FDA approval. However, trial results have so far been ambivalent, with some studies reporting potent effects whereas others demonstrated limited efficacy or toxicity. Alternative entities such as antimiRNAs are undergoing clinical testing, and lncRNA-based therapeutics are gaining interest. In this Perspective, we discuss key challenges facing ncRNA therapeutics - including issues associated with specificity, delivery and tolerability - and focus on promising emerging approaches that aim to boost their success.
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Affiliation(s)
- Melanie Winkle
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA
| | - Sherien M El-Daly
- Medical Biochemistry Department, Medical Research Division - Cancer Biology and Genetics Laboratory, Centre of Excellence for Advanced Sciences - National Research Centre, Cairo, Egypt
| | - Muller Fabbri
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - George A Calin
- Translational Molecular Pathology, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
- The RNA Interference and Non-codingRNA Center, MD Anderson Cancer Center, Texas State University, Houston, TX, USA.
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8
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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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9
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Shibata T, Nagano K, Ueyama M, Ninomiya K, Hirose T, Nagai Y, Ishikawa K, Kawai G, Nakatani K. Small molecule targeting r(UGGAA) n disrupts RNA foci and alleviates disease phenotype in Drosophila model. Nat Commun 2021; 12:236. [PMID: 33431896 PMCID: PMC7801683 DOI: 10.1038/s41467-020-20487-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here we report our discovery that naphthyridine carbamate dimer (NCD) targets disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31 (SCA31). Structural analysis of the NCD-UGGAA/UGGAA complex by nuclear magnetic resonance (NMR) spectroscopy clarifies the mode of binding that recognizes four guanines in the UGGAA/UGGAA pentad by hydrogen bonding with four naphthyridine moieties of two NCD molecules. Biological studies show that NCD disrupts naturally occurring RNA foci built on r(UGGAA)n repeat RNA known as nuclear stress bodies (nSBs) by interfering with RNA–protein interactions resulting in the suppression of nSB-mediated splicing events. Feeding NCD to larvae of the Drosophila model of SCA31 alleviates the disease phenotype induced by toxic r(UGGAA)n repeat RNA. These studies demonstrate that small molecules targeting toxic repeat RNAs are a promising chemical tool for studies on repeat expansion diseases. Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here the authors show the mechanism by which a small molecule targets the disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31.
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Affiliation(s)
- Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan
| | - Konami Nagano
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Morio Ueyama
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kinya Ishikawa
- Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Tokyo, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Ibaraki, Japan.
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A review: Biologically active 3,4-heterocycle-fused coumarins. Eur J Med Chem 2020; 212:113034. [PMID: 33276991 DOI: 10.1016/j.ejmech.2020.113034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/15/2020] [Accepted: 11/15/2020] [Indexed: 12/17/2022]
Abstract
The combination of heterocycles offers a new opportunity to create novel multicyclic compounds having improved biological activity. Coumarins are ubiquitous natural heterocycle widely adopted in the design of various biologically active compounds. Fusing different heterocycles with coumarin ring is one of the interesting approaches to generating novel hybrid molecules having highlighted biological activities. In the efforts to develop heterocyclic-fused coumarins, a wide range of 3,4-heterocycle-fused coumarins have been introduced bearing outstanding biological activity. The effect of heterocycles annulation at 3,4-positions of coumarin ring on the biological activity of the target structures were discussed. This review focuses on the important progress of 3,4-heterocycle-fused coumarins providing better insight for medicinal chemists on the design and preparation of biologically active heterocycle-fused coumarins with a significant therapeutic effect in the future.
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11
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Lee ETT, Sato Y, Nishizawa S. Small molecule-PNA oligomer conjugates for rRNA A-site at neutral pH for FID assays. Chem Commun (Camb) 2020; 56:14976-14979. [PMID: 33174546 DOI: 10.1039/d0cc06084d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A triplex-forming PNA oligomer conjugated with a naphthyridine derivative (ATMND-C2-NH2) showed high selectivity and strong binding for the bacterial rRNA A-site at pH 7.0 (Kd = 190 ± 72 nM), which was accompanied by fluorogenic signaling that allowed the potential use of this conjugate probe in fluorescent indicator displacement assays.
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Affiliation(s)
- En Ting Tabitha Lee
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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12
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Brzuzan P, Mazur-Marzec H, Florczyk M, Stefaniak F, Fidor A, Konkel R, Woźny M. Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea. Toxicol In Vitro 2020; 68:104951. [PMID: 32721573 DOI: 10.1016/j.tiv.2020.104951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022]
Abstract
We developed a cell sensor that detects the liver cancer-specific microRNA MIR92b-3p, involved in hepatocellular carcinoma development and hepatitis C virus infection. To validate our small-molecule screen that employs a Huh7 human hepatoma cell line stably transfected with a pmirGLO vector containing dual luciferase reporters, we used i) a MIR92b-3p antisense or a MIR92b-3p mimicking agent (concentrations from 0.1 pM to 100 nM), ii) expression of XIST, a long non-coding RNA that is a cellular target of MIR92b, and iii) ectopic expression of Luc2 luciferase. This reporter system was used to test four cyanopeptolins from a de novo library of peptides that were isolated from the Baltic Sea cyanobacteria Nostoc edaphicum strain CCNP1411. Exposure of the Huh7-pmirGLO-MIR92b-3p cells to increasing concentrations (from 10 nM to 100 μM) of the cyanopeptolins and microcystin-LR (MC-LR; a treatment control) did not lead to a dose-dependent restoration of the luciferase signal. Instead, when the reporter cells were treated with MC-LR, the luciferase signal decreased markedly, most likely due to non-target, toxic effects of MC-LR on the cells. Although the first use of this reporter system to screen selected Nostoc peptides did not identify inhibitors of MIR92b, this method provides a means to identify functional miRNA regulators and could be readily extended to other compounds.
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Affiliation(s)
- Paweł Brzuzan
- Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland.
| | | | - Maciej Florczyk
- Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Anna Fidor
- Division of Marine Biotechnology, University of Gdańsk, Gdańsk, Poland
| | - Robert Konkel
- Division of Marine Biotechnology, University of Gdańsk, Gdańsk, Poland
| | - Maciej Woźny
- Department of Environmental Biotechnology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland
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13
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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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14
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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15
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Umuhire Juru A, Patwardhan NN, Hargrove AE. Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions. ACS Chem Biol 2019; 14:824-838. [PMID: 31042354 DOI: 10.1021/acschembio.8b00945] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities ( Ka or Kd) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.
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Affiliation(s)
- Aline Umuhire Juru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Neeraj N. Patwardhan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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16
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Yan H, Liang FS. miRNA inhibition by proximity-enabled Dicer inactivation. Methods 2019; 167:117-123. [PMID: 31077820 DOI: 10.1016/j.ymeth.2019.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/22/2019] [Accepted: 05/05/2019] [Indexed: 11/17/2022] Open
Abstract
microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by the key biological roles and the therapeutic potential, developing methods for miRNA regulation has become an intense research area. Due to favorable pharmacological properties, small molecule-based miRNA inhibition emerges as a promising strategy and significant progresses have been made. However, it remains challenging to regulate miRNA using small molecules because of the inherent difficulty in RNA targeting and inhibition. Herein we outline the workflow of generating bifunctional small molecule inhibitors blocking miRNA biogenesis through proximity-enabled inactivation of Dicer, an enzyme required for the processing of precursor miRNA (pre-miRNA) into mature miRNA. By conjugating a weak Dicer inhibitor with a pre-miRNA binder, the inhibitor can be delivered to the Dicer processing site associated with the targeted pre-miRNA, and as a result inhibiting Dicer-mediated pre-miRNA processing. This protocol can be applicable in producing bifunctional inhibitors for different miRNAs.
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Affiliation(s)
- Hao Yan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
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17
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Vo T, Paul A, Kumar A, Boykin DW, Wilson WD. Biosensor-surface plasmon resonance: A strategy to help establish a new generation RNA-specific small molecules. Methods 2019; 167:15-27. [PMID: 31077819 DOI: 10.1016/j.ymeth.2019.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/15/2019] [Accepted: 05/04/2019] [Indexed: 12/13/2022] Open
Abstract
Biosensor surface plasmon resonance (SPR) is a highly sensitive technique and is most commonly used to decipher the interactions of biological systems including proteins and nucleic acids. Throughout the years, there have been significant efforts to develop SPR assays for studying protein-protein interactions, protein-DNA interactions, as well as small molecules to target DNAs that are of therapeutic interest. With the explosion of discovery of new RNA structures and functions, it is time to review the applications of SPR to RNA interaction studies, which have actually extended over a long time period. The primary advantage of SPR is its ability to measure affinities and kinetics in real time, along with being a label-free technique and utilizing relatively small quantities of materials. Recently, developments that use SPR to analyze the interactions of different RNA sequences with proteins and small molecules demonstrate the versatility of SPR as a powerful method in the analysis of the structure-function relationships, not only for biological macromolecules but also for potential drug candidates. This chapter will guide the reader through some background material followed by an extensive assay development to dissect the interactions of small molecules and RNA sequences using SPR as the critical method. The protocol includes (i) fundamental concepts of SPR, (ii) experimental design and execution, (iii) the immobilization of RNA using the streptavidin-biotin capturing method, and (iv) affinities and kinetics analyses of the interactions using specific example samples. The chapter also contains useful notes to address situations that might arise during the process. This assay demonstrates SPR as a valuable quantitative method used in the search for potential therapeutic agents that selectively target RNA.
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Affiliation(s)
- Tam Vo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA.
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18
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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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19
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Eubanks CS, Hargrove AE. RNA Structural Differentiation: Opportunities with Pattern Recognition. Biochemistry 2018; 58:199-213. [PMID: 30513196 DOI: 10.1021/acs.biochem.8b01090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Our awareness and appreciation of the many regulatory roles of RNA have dramatically increased in the past decade. This understanding, in addition to the impact of RNA in many disease states, has renewed interest in developing selective RNA-targeted small molecule probes. However, the fundamental guiding principles in RNA molecular recognition that could accelerate these efforts remain elusive. While high-resolution structural characterization can provide invaluable insight, examples of well-characterized RNA structures, not to mention small molecule:RNA complexes, remain limited. This Perspective provides an overview of the current techniques used to understand RNA molecular recognition when high-resolution structural information is unavailable. We will place particular emphasis on a new method, pattern recognition of RNA with small molecules (PRRSM), that provides rapid insight into critical components of RNA recognition and differentiation by small molecules as well as into RNA structural features.
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Affiliation(s)
- Christopher S Eubanks
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0354 , United States
| | - Amanda E Hargrove
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0354 , United States
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20
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Yagi Y, Aikawa H, Yamada T, Nakatani K. Expanding chemical space of DNA-binding molecules with three base-binding units. Bioorg Med Chem Lett 2018; 28:2894-2898. [PMID: 30025901 DOI: 10.1016/j.bmcl.2018.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
A new molecule NC3-3 designed to expand chemical space of parent molecule NCD by adding the third base-binding unit was reported. NC3-3 bound to the G-G mismatch in the 5'-CGG-3'/5'-CGG-3' motif but not to that in 5'-GGC-3'/5'-GGC-3'. This binding selectivity is similar to that reported for NCD. Fluorimetric screening of NCD and NC3-3 to dsDNA library containing yGw/xGz motifs showed that NC3-3 still kept the sequence selectivity as we observed for NCD-binding. The third naphthyridine heterocycle in NC3-3 affected the mode of the binding, but a little effect on the sequence selectivity.
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Affiliation(s)
- Yuki Yagi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Haruo Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, 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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21
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Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Small-molecule approaches toward the targeting of oncogenic miRNAs: roadmap for the discovery of RNA modulators. Future Med Chem 2016; 8:803-16. [DOI: 10.4155/fmc-2016-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
miRNAs are a recently discovered class of small noncoding RNAs implicated in the regulation of gene expression. The deregulation of miRNAs levels has been linked to the development of various cancers where oncogenic miRNAs are overexpressed and tumor suppressor miRNAs are underexpressed. Here we report the three main strategies developed in order to discover small-molecule drugs able to selectively interfere with oncogenic miRNAs: the high throughput screening of large libraries of compounds, the focused screening of small libraries of molecules that are known to be able to interact with RNA thus being supposed modulators of miRNAs pathway and the design of small molecules based on the secondary structure of targeted RNA and/or three-dimensional structure of enzymes involved in miRNAs pathway.
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23
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Yang Y, Qi X, Liu R, He Q, Yang C. One-pot transition-metal-free cascade synthesis of thieno[2,3-c]coumarins from chromones. RSC Adv 2016. [DOI: 10.1039/c6ra21776a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A one-pot transition-metal-free, base-mediated synthesis of a novel series of functionalized thieno[2,3-c]coumarins has been developed through a cascade reaction from chromones.
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Affiliation(s)
- Yuhong Yang
- State Key Laboratory of Drug Research
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Xueyu Qi
- State Key Laboratory of Drug Research
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Ruiling Liu
- State Key Laboratory of Drug Research
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Qian He
- State Key Laboratory of Drug Research
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Chunhao Yang
- State Key Laboratory of Drug Research
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
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