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Liu M, Xie DD, Guo YX, Zhao RY, Liu FD, Zhang H, Gao F. TAR RNA selective targeting ruthenium(II) complexes as HIV-1 reverse transcriptase inhibitors: On exploring structure-activity relationships of multiple positions. J Inorg Biochem 2024; 259:112664. [PMID: 39018747 DOI: 10.1016/j.jinorgbio.2024.112664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
HIV-1 reverse transcriptase (RT) inhibitors play a crucial role in the treatment of HIV by preventing the activity of the enzyme responsible for the replication of the virus. The HIV-1 Tat protein binds to transactivation response (TAR) RNA and recruits host factors to stimulate HIV-1 transcription. We have created a small library consisting of 4 × 6 polypyridyl Ru(II) complexes that selectively bind to TAR RNA, with targeting groups specific to HIV-1 TAR RNA. The molecule design was conducted by introducing hydroxyl or methoxy groups into an established potent TAR binder. The potential TAR binding ability was analysis from nature charge population and electrostatic potential by quantum chemistry calculations. Key modifications were found to be R1 and R3 groups. The most potent and selective TAR RNA binder was a3 with R1 = OH, R2 = H and R3 = Me. Through molecular recognition of hydrogen bonds and electrostatic attraction, they were able to firmly and selectively bind HIV-1 TAR RNA. Furthermore, they efficiently obstructed the contact between TAR RNA and Tat protein, and inhibited the reverse transcription activity of HIV-1 RT. The polypyridyl Ru(II) complexes were chemical and photo-stable, and sensitive and selective spectroscopic responses to TAR RNA. They exhibited little toxicity towards normal cells. Hence, this study might offer significant drug design approaches for researching AIDS and other illnesses associated with RT, including HCV, EBOV, and SARS-CoV-2. Moreover, it could contribute to fundamental research on the interactions of inorganic transition metal complexes with biomolecules.
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Affiliation(s)
- Meng Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Dan-Dan Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Yuan-Xiao Guo
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Run-Yu Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Fu-Dan Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Pharmacy, Yunnan University, Kunming 650050, PR China.
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2
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Lee ETT, Sato Y, Ujuagu AF, Nishizawa S. Forced intercalation-induced light-up peptides as fluorogenic indicators for the HIV-1 TAR RNA-ligand assay. Analyst 2024. [PMID: 38860915 DOI: 10.1039/d4an00530a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Fluorescence indicators capable of binding to human immunodeficiency virus-1 (HIV-1) trans-activation responsive (TAR) RNA are powerful tools for the exploratory studies of the identification of anti-HIV drug candidates. This work presents a new design strategy for fluorogenic indicators with a transactivator of transcription (Tat)-derived peptide based on the forced intercalation of thiazole orange (TO) dyes (FIT). The developed 9-mer FIT peptide (RKKRR-TO-RRR: named FiLuP) features the TO unit integrated onto a Dap (2,3-diaminopropionic acid) residue in the middle of the Tat peptide sequence; the Q (glutamic acid) residue in the Tat peptide (RKKRR-Q-RRR) is replaced with TO as if it were an amino acid surrogate. This facilitates a significant light-up response (450-fold at λem = 541 nm, Φfree = 0.0057, and Φbound = 0.61) upon binding to TAR RNA. The response of FiLuP is highly selective to TAR RNA over other non-cognate RNAs, and FiLuP maintains strong binding affinity (Kd = 1.0 ± 0.6 nM). Significantly, in contrast to previously developed Tat peptide-based FRET probes, FiLuP is able to discriminate between "competitive" and "noncompetitive" inhibitors when used in the fluorescence indicator displacement (FID) assay. The FID assay under stringent screening conditions is also possible, enabling super-strong competitive binders toward TAR RNA to be sieved out.
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Affiliation(s)
- En Ting Tabitha Lee
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Akunna F Ujuagu
- 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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3
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Gribling-Burrer AS, Bohn P, Smyth RP. Isoform-specific RNA structure determination using Nano-DMS-MaP. Nat Protoc 2024; 19:1835-1865. [PMID: 38347203 DOI: 10.1038/s41596-024-00959-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/12/2023] [Indexed: 06/12/2024]
Abstract
RNA structure determination is essential to understand how RNA carries out its diverse biological functions. In cells, RNA isoforms are readily expressed with partial variations within their sequences due, for example, to alternative splicing, heterogeneity in the transcription start site, RNA processing or differential termination/polyadenylation. Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) is a method for in situ isoform-specific RNA structure determination. Unlike similar methods that rely on short sequencing reads, Nano-DMS-MaP employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules to reveal their previously hidden structural differences. This Protocol describes the development and applications of Nano-DMS-MaP and outlines the main considerations for designing and implementing a successful experiment: from bench to data analysis. In cell probing experiments can be carried out by an experienced molecular biologist in 3-4 d. Data analysis requires good knowledge of command line tools and Python scripts and requires a further 3-5 d.
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Affiliation(s)
- Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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4
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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5
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Agarwal R, T RR, Smith JC. Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J Chem Inf Model 2023; 63:7444-7452. [PMID: 37972310 DOI: 10.1021/acs.jcim.3c01533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve the accuracy in the computation of binding strengths and poses. In the past decade, RNA has also emerged as a target class for new small-molecule drugs. However, most ligand docking programs have been validated and tested for proteins and not RNA. Here, we test the docking power (pose prediction accuracy) of three state-of-the-art docking protocols on 173 RNA-small molecule crystal structures. The programs are AutoDock4 (AD4) and AutoDock Vina (Vina), which were designed for protein targets, and rDock, which was designed for both protein and nucleic acid targets. AD4 performed relatively poorly. For RNA targets for which a crystal structure of a bound ligand used to limit the docking search space is available and for which the goal is to identify new molecules for the same pocket, rDock performs slightly better than Vina, with success rates of 48% and 63%, respectively. However, in the more common type of early-stage drug discovery setting, in which no structure of a ligand-target complex is known and for which a larger search space is defined, rDock performed similarly to Vina, with a low success rate of ∼27%. Vina was found to have bias for ligands with certain physicochemical properties, whereas rDock performs similarly for all ligand properties. Thus, for projects where no ligand-protein structure already exists, Vina and rDock are both applicable. However, the relatively poor performance of all methods relative to protein-target docking illustrates a need for further methods refinement.
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Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Rajitha Rajeshwar T
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
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6
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Wicks SL, Morgan BS, Wilson AW, Hargrove AE. Probing Bioactive Chemical Space to Discover RNA-Targeted Small Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551350. [PMID: 37577658 PMCID: PMC10418101 DOI: 10.1101/2023.07.31.551350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Small molecules have become increasingly recognized as invaluable tools to study RNA structure and function and to develop RNA-targeted therapeutics. To rationally design RNA-targeting ligands, a comprehensive understanding and explicit testing of small molecule properties that govern molecular recognition is crucial. To date, most studies have primarily evaluated properties of small molecules that bind RNA in vitro, with little to no assessment of properties that are distinct to selective and bioactive RNA-targeted ligands. Therefore, we curated an RNA-focused library, termed the Duke RNA-Targeted Library (DRTL), that was biased towards the physicochemical and structural properties of biologically active and non-ribosomal RNA-targeted small molecules. The DRTL represents one of the largest academic RNA-focused small molecule libraries curated to date with more than 800 small molecules. These ligands were selected using computational approaches that measure similarity to known bioactive RNA ligands and that diversify the molecules within this space. We evaluated DRTL binding in vitro to a panel of four RNAs using two optimized fluorescent indicator displacement assays, and we successfully identified multiple small molecule hits, including several novel scaffolds for RNA. The DRTL has and will continue to provide insights into biologically relevant RNA chemical space, such as the identification of additional RNA-privileged scaffolds and validation of RNA-privileged molecular features. Future DRTL screening will focus on expanding both the targets and assays used, and we welcome collaboration from the scientific community. We envision that the DRTL will be a valuable resource for the discovery of RNA-targeted chemical probes and therapeutic leads.
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Affiliation(s)
- Sarah L. Wicks
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Brittany S. Morgan
- Department of Chemistry & Biochemistry; University of Notre Dame; 123 McCourtney Hall Notre Dame, IN 46556
| | - Alexander W. Wilson
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Amanda E. Hargrove
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
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7
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Bagnolini G, Luu TB, Hargrove AE. Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA. RNA (NEW YORK, N.Y.) 2023; 29:473-488. [PMID: 36693763 PMCID: PMC10019373 DOI: 10.1261/rna.079497.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA structures regulate a wide range of processes in biology and disease, yet small molecule chemical probes or drugs that can modulate these functions are rare. Machine learning and other computational methods are well poised to fill gaps in knowledge and overcome the inherent challenges in RNA targeting, such as the dynamic nature of RNA and the difficulty of obtaining RNA high-resolution structures. Successful tools to date include principal component analysis, linear discriminate analysis, k-nearest neighbor, artificial neural networks, multiple linear regression, and many others. Employment of these tools has revealed critical factors for selective recognition in RNA:small molecule complexes, predictable differences in RNA- and protein-binding ligands, and quantitative structure activity relationships that allow the rational design of small molecules for a given RNA target. Herein we present our perspective on the value of using machine learning and other computation methods to advance RNA:small molecule targeting, including select examples and their validation as well as necessary and promising future directions that will be key to accelerate discoveries in this important field.
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Affiliation(s)
- Greta Bagnolini
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - TinTin B Luu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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8
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Feng Z, Zhang D, Guo H, Su W, Tian Y, Tian X. Lighting up RNA-specific multi-photon and super-resolution imaging using a novel zinc complex. NANOSCALE 2023; 15:5486-5493. [PMID: 36852659 DOI: 10.1039/d2nr05392f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Ribonucleic acid (RNA) probes are critical for understanding the role of RNA dynamics in cellular function but are in short supply due to the lack of optimized imaging systems and excellent fluorescence emission performance. Here, the terpyridine Zn(II) complex (Zn-T) with D-π-A configuration and bright aggregation-induced fluorescence emission (AIE) has been fabricated for the selective detection and real-time monitoring of RNA. Impressively, Zn-T exhibits a large Stokes shift and three-photon absorption (3PA) activity and responds specifically through hydrophobic interactions with an RNA pocket. The combination of AIE-assisted two-photon fluorescence and stimulated emission depletion (STED) microscopy of Zn-T for imaging nuclear RNA has higher spatial resolution and brightness, thus providing an imaging platform for studying RNA-related physiological or pathological processes.
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Affiliation(s)
- Zhihui Feng
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
| | - Dongxue Zhang
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
- Equipment and Material Department, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Guo
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Wenqing Su
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Yupeng Tian
- College of Chemistry and Chemical Engineering, Key Laboratory of Functional Inorganic Materials Chemistry of Anhui Province, Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized Materials, Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University) Ministry of Education, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Xiaohe Tian
- Huaxi MR Research Centre (HMRRC), Functional and Molecular Imaging Key Laboratory of Sichuan Province, Department of Radiology and National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610000, Sichuan Province, China.
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9
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An H, Elvers KT, Gillespie JA, Jones K, Atack JR, Grubisha O, Shelkovnikova TA. A toolkit for the identification of NEAT1_2/paraspeckle modulators. Nucleic Acids Res 2022; 50:e119. [PMID: 36099417 PMCID: PMC9723620 DOI: 10.1093/nar/gkac771] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
Paraspeckles are ribonucleoprotein granules assembled by NEAT1_2 lncRNA, an isoform of Nuclear Paraspeckle Assembly Transcript 1 (NEAT1). Dysregulation of NEAT1_2/paraspeckles has been linked to multiple human diseases making them an attractive drug target. However currently NEAT1_2/paraspeckle-focused translational research and drug discovery are hindered by a limited toolkit. To fill this gap, we developed and validated a set of tools for the identification of NEAT1_2 binders and modulators comprised of biochemical and cell-based assays. The NEAT1_2 triple helix stability element was utilized as the target in the biochemical assays, and the cellular assay ('ParaQuant') was based on high-content imaging of NEAT1_2 in fixed cells. As a proof of principle, these assays were used to screen a 1,200-compound FDA-approved drug library and a 170-compound kinase inhibitor library and to confirm the screening hits. The assays are simple to establish, use only commercially-available reagents and are scalable for higher throughput. In particular, ParaQuant is a cost-efficient assay suitable for any cells growing in adherent culture and amenable to multiplexing. Using ParaQuant, we identified dual PI3K/mTOR inhibitors as potent negative modulators of paraspeckles. The tools we describe herein should boost paraspeckle studies and help guide the search, validation and optimization of NEAT1_2/paraspeckle-targeted small molecules.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Karen T Elvers
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Jason A Gillespie
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Kimberley Jones
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - John R Atack
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Olivera Grubisha
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Cardiff CF10 3AT, UK.,Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
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10
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Guo YX, Liu M, Zhou YQ, Bi XD, Gao F. Terpyridyl ruthenium complexes as visible spectral probe for poly(A) RNA and bifunctional TAR RNA binders and HIV-1 reverse transcriptase inhibitors. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Wang MF, Li Y, Bi XD, Guo YX, Liu M, Zhang H, Gao F. Polypyridyl ruthenium complexes as bifunctional TAR RNA binders and HIV-1 reverse transcriptase inhibitors. J Inorg Biochem 2022; 234:111880. [DOI: 10.1016/j.jinorgbio.2022.111880] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/18/2022]
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12
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Yang R, Bi XD, Li Y, Liu M, Hu MQ, Zhao LM, Zhang H, Gao F. Scorpion-Shaped Zinc Porphyrins as Tetrafunctional TAR RNA Predators and HIV-1 Reverse Transcriptase Inhibitors. Inorg Chem 2022; 61:10774-10780. [PMID: 35796528 DOI: 10.1021/acs.inorgchem.2c00975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 reverse transcriptase (RT) inhibitors are fundamental to the discovery and development of anti-HIV drugs. Their main target is RT, and only a tiny number of them can bind to viral RNA. In this paper, five new Zn(II) porphyrin compounds were developed with different characters. ZnTPP4 has both the appearance and the functions of a scorpion with a rigid tail and stinger to selectively hunt HIV-1 TAR RNA based on the molecular recognition of hydrogen bonds, a fierce chelicera to bite RNA by metal coordination, mighty pedipalps to grasp the bound RNA by supramolecular inclusion, and a broad body maintaining the configuration of each functional area so that they can cooperate with each other and providing accommodation space for the bound RNA. This tetrafunctional Zn(II) porphyrin is relatively nontoxic to normal cells and can produce sensitive responses for RNA. Moreover, this work offers practical construction methodologies for medication of AIDS and other diseases closely related to RT like EBOV and SARS-CoV-2.
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Affiliation(s)
- Rong Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Xu-Dan Bi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Meng Liu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Man-Qi Hu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Li-Min Zhao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, P. R. China
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13
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Donlic A, Swanson EG, Chiu LY, Wicks SL, Umuhire Juru A, Cai Z, Kassam K, Laudeman C, Sanaba BG, Sugarman A, Han E, Tolbert BS, Hargrove AE. R-BIND 2.0: An Updated Database of Bioactive RNA-Targeting Small Molecules and Associated RNA Secondary Structures. ACS Chem Biol 2022; 17:1556-1566. [PMID: 35594415 PMCID: PMC9343015 DOI: 10.1021/acschembio.2c00224] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Discoveries of RNA roles in cellular physiology and pathology are increasing the need for new tools that modulate the structure and function of these biomolecules, and small molecules are proving useful. In 2017, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND) and discovered distinguishing physicochemical properties of RNA-targeting ligands, leading us to propose the existence of an "RNA-privileged" chemical space. Biennial updates of the database and the establishment of a website platform (rbind.chem.duke.edu) have provided new insights and tools to design small molecules based on the analyzed physicochemical and spatial properties. In this report and R-BIND 2.0 update, we refined the curation approach and ligand classification system as well as conducted analyses of RNA structure elements for the first time to identify new targeting strategies. Specifically, we curated and analyzed RNA target structural motifs to determine the properties of small molecules that may confer selectivity for distinct RNA secondary and tertiary structures. Additionally, we collected sequences of target structures and incorporated an RNA structure search algorithm into the website that outputs small molecules targeting similar motifs without a priori secondary structure knowledge. Cheminformatic analyses revealed that, despite the 50% increase in small molecule library size, the distinguishing properties of R-BIND ligands remained significantly different from that of proteins and are therefore still relevant to RNA-targeted probe discovery. Combined, we expect these novel insights and website features to enable the rational design of RNA-targeted ligands and to serve as a resource and inspiration for a variety of scientists interested in RNA targeting.
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Affiliation(s)
| | | | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Sarah L. Wicks
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Aline Umuhire Juru
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Zhengguo Cai
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Kamillah Kassam
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Chris Laudeman
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Bilva G. Sanaba
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Eunseong Han
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 441106, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27705, United States
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14
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Cai Z, Zafferani M, Akande OM, Hargrove AE. Quantitative Structure-Activity Relationship (QSAR) Study Predicts Small-Molecule Binding to RNA Structure. J Med Chem 2022; 65:7262-7277. [PMID: 35522972 PMCID: PMC9150105 DOI: 10.1021/acs.jmedchem.2c00254] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The diversity of RNA structural elements and their documented role in human diseases make RNA an attractive therapeutic target. However, progress in drug discovery and development has been hindered by challenges in the determination of high-resolution RNA structures and a limited understanding of the parameters that drive RNA recognition by small molecules, including a lack of validated quantitative structure-activity relationships (QSARs). Herein, we develop QSAR models that quantitatively predict both thermodynamic- and kinetic-based binding parameters of small molecules and the HIV-1 transactivation response (TAR) RNA model system. Small molecules bearing diverse scaffolds were screened against TAR using surface plasmon resonance. Multiple linear regression (MLR) combined with feature selection afforded robust models that allowed direct interpretation of the properties critical for both binding strength and kinetic rate constants. These models were validated with new molecules, and their accurate performance was confirmed via comparison to ensemble tree methods, supporting the general applicability of this platform.
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Affiliation(s)
- Zhengguo Cai
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Martina Zafferani
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Olanrewaju M. Akande
- Social
Science Research Institute, 140 Science Drive, Durham, North Carolina 27708, United States
| | - Amanda E. Hargrove
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States,. Phone: 919-660-1521. Fax: 919-660-1605
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15
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Arévalo DM, Anokhina VS, Swart OLR, Miller BL. Expanding the known structure space for RNA binding: a test of 2,5-diketopiperazine. Org Biomol Chem 2022; 20:606-612. [PMID: 34927652 PMCID: PMC8900054 DOI: 10.1039/d1ob01976g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
As the importance of RNA as a therapeutic target has become increasingly recognized, the need for new chemotypes able to bind RNA has grown in significance. We hypothesized that diketopiperazines (DKPs), common substructures in natural products and protein-targeting therapeutic agents, could serve as effective scaffolds for targeting RNA. To confirm this hypothesis, we designed and synthesized two analogs, one incorporating a DKP and one not, of compounds previously demonstrated to bind an RNA critical to the life cycle of HIV-1 with high affinity and specificity. Prior to compound synthesis, calculations employing density functional methods and molecular mechanics conformational searches were used to confirm that the DKP could present functionality in a similar (albeit not identical) orientation to the non DKP-containing compound. We found that both the DKP-containing and parent compound had similar affinities to the target RNA as measured by surface plasmon resonance (SPR). Both compounds were found to have modest but equal anti-HIV activity. These results establish the feasibility of using DKPs to target RNA.
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Affiliation(s)
- Diego M. Arévalo
- Department of Chemistry, University of Rochester, Rochester, NY 14642, USA
| | - Viktoriya S. Anokhina
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA
| | - Oliver L. R. Swart
- Department of Chemistry, University of Rochester, Rochester, NY 14642, USA
| | - Benjamin L. Miller
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, USA,Department of Dermatology, University of Rochester, Rochester, NY 14642, USA
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16
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Zafferani M, Haddad C, Luo L, Davila-Calderon J, Chiu LY, Mugisha CS, Monaghan AG, Kennedy AA, Yesselman JD, Gifford RJ, Tai AW, Kutluay SB, Li ML, Brewer G, Tolbert BS, Hargrove AE. Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures. SCIENCE ADVANCES 2021; 7:eabl6096. [PMID: 34826236 PMCID: PMC8626076 DOI: 10.1126/sciadv.abl6096] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/06/2021] [Indexed: 05/15/2023]
Abstract
The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, emphasized the urgent need for development of novel antivirals. Small-molecule chemical probes offer both to reveal aspects of virus replication and to serve as leads for antiviral therapeutic development. Here, we report on the identification of amiloride-based small molecules that potently inhibit OC43 and SARS-CoV-2 replication through targeting of conserved structured elements within the viral 5′-end. Nuclear magnetic resonance–based structural studies revealed specific amiloride interactions with stem loops containing bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Amilorides represent the first antiviral small molecules that target RNA structures within the 5′ untranslated regions and proximal region of the CoV genomes. These molecules will serve as chemical probes to further understand CoV RNA biology and can pave the way for the development of specific CoV RNA–targeted antivirals.
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Affiliation(s)
- Martina Zafferani
- Chemistry Department, Duke University, 124 Science Drive, Durham, NC 27705, USA
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 441106, USA
| | - Le Luo
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 441106, USA
| | | | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 441106, USA
| | - Christian Shema Mugisha
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Adeline G. Monaghan
- Chemistry Department, Duke University, 124 Science Drive, Durham, NC 27705, USA
| | - Andrew A. Kennedy
- Department of Internal Medicine and Department of Microbiology and Immunology, University of Michigan, 1150 W Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Joseph D. Yesselman
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd., Bearsden, Glasgow G61 1QH, UK
| | - Andrew W. Tai
- Department of Internal Medicine and Department of Microbiology and Immunology, University of Michigan, 1150 W Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 441106, USA
| | - Amanda E. Hargrove
- Chemistry Department, Duke University, 124 Science Drive, Durham, NC 27705, USA
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17
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Sosic A, Göttlich R, Fabris D, Gatto B. B-CePs as cross-linking probes for the investigation of RNA higher-order structure. Nucleic Acids Res 2021; 49:6660-6672. [PMID: 34125908 PMCID: PMC8266612 DOI: 10.1093/nar/gkab468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 11/12/2022] Open
Abstract
Elucidating the structure of RNA and RNA ensembles is essential to understand biological functions. In this work, we explored the previously uncharted reactivity of bis-chloropiperidines (B-CePs) towards RNA. We characterized at the molecular level the different adducts induced by the fast reacting compound B-CeP 1 with RNA. Following an approach based on solution thermal melting coupled with ESI mass spectrometry (STHEM-ESI), we proved the ability of B-CePs to induce inter-molecular cross-links between guanines in double stranded RNA. These results open the possibility of using B-CePs as structural probes for investigating higher-order structures, such as the kissing loop complex established by the dimerization initiation site (DIS) of the HIV-1 genome. We confirmed the potential of B-CePs to reveal the identity of RNA structures involved in long-range interactions, expecting to benefit the characterization of samples that are not readily amenable to traditional high-resolution techniques, and thus promoting the elucidation of pertinent RNA systems associated with old and new diseases.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Dan Fabris
- Departments of Chemistry and Biological Sciences, University at Albany-SUNY, Albany, NY, 12222, USA
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
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18
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Bush JA, Williams CC, Meyer SM, Tong Y, Haniff HS, Childs-Disney JL, Disney MD. Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models. ACS Chem Biol 2021; 16:1111-1127. [PMID: 34166593 PMCID: PMC8867596 DOI: 10.1021/acschembio.1c00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interrogation and manipulation of biological systems by small molecules is a powerful approach in chemical biology. Ideal compounds selectively engage a target and mediate a downstream phenotypic response. Although historically small molecule drug discovery has focused on proteins and enzymes, targeting RNA is an attractive therapeutic alternative, as many disease-causing or -associated RNAs have been identified through genome-wide association studies. As the field of RNA chemical biology emerges, the systematic evaluation of target validation and modulation of target-associated pathways is of paramount importance. In this Review, through an examination of case studies, we outline the experimental characterization, including methods and tools, to evaluate comprehensively the impact of small molecules that target RNA on cellular phenotype.
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Affiliation(s)
- Jessica A Bush
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Christopher C Williams
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Yuquan Tong
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- The Scripps Research Institute, Department of Chemistry, 130 Scripps Way, Jupiter, Florida 33458, United States
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19
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Cardenas G, Menger MFSJ, Ramos-Berdullas N, Sánchez-Murcia PA. Deciphering the Chemical Basis of Fluorescence of a Selenium-Labeled Uracil Probe when Bound at the Bacterial Ribosomal A-Site. Chemistry 2021; 27:4927-4931. [PMID: 33368691 DOI: 10.1002/chem.202004818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Indexed: 12/23/2022]
Abstract
We unveil in this work the main factors that govern the turn-on/off fluorescence of a Se-modified uracil probe at the ribosomal RNA A-site. Whereas the constraint into an "in-plane" conformation of the two rings of the fluorophore is the main driver for the observed turn-on fluorescence emission in the presence of the antibiotic paromomycin, the electrostatics of the environment plays a minor role during the emission process. Our computational strategy clearly indicates that, in the absence of paromomycin, the probe prefers conformations that show a dark S1 electronic state with participation of nπ* electronic transition contributions between the selenium atom and the π-system of the uracil moiety.
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Affiliation(s)
- Gustavo Cardenas
- Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - Maximilian F S J Menger
- Zernike Institute for Advanced Materials, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nicolás Ramos-Berdullas
- Department of Physical Chemistry, University of Vigo, Lagoas Marcosende s/n, 36310, Vigo, Spain
| | - Pedro A Sánchez-Murcia
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090, Vienna, Austria.,Present address: Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingstalstraße 6/III, 8010, Graz, Austria
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20
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Martina Z, Christina H, Le L, Jesse DC, Liang YC, Christian SM, Monaghan AG, Kennedy AA, Yesselman JD, Gifford RR, Tai AW, Kutluay SB, Li ML, Brewer G, Tolbert BS, Hargrove AE. Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.05.409821. [PMID: 33299997 PMCID: PMC7724665 DOI: 10.1101/2020.12.05.409821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, has rendered our understanding of coronavirus biology more essential than ever. Small molecule chemical probes offer to both reveal novel aspects of virus replication and to serve as leads for antiviral therapeutic development. The RNA-biased amiloride scaffold was recently tuned to target a viral RNA structure critical for translation in enterovirus 71, ultimately uncovering a novel mechanism to modulate positive-sense RNA viral translation and replication. Analysis of CoV RNA genomes reveal many conserved RNA structures in the 5'-UTR and proximal region critical for viral translation and replication, including several containing bulge-like secondary structures suitable for small molecule targeting. Following phylogenetic conservation analysis of this region, we screened an amiloride-based small molecule library against a less virulent human coronavirus, OC43, to identify lead ligands. Amilorides inhibited OC43 replication as seen in viral plaque assays. Select amilorides also potently inhibited replication competent SARS-CoV-2 as evident in the decreased levels of cell free virions in cell culture supernatants of treated cells. Reporter screens confirmed the importance of RNA structures in the 5'-end of the viral genome for small molecule activity. Finally, NMR chemical shift perturbation studies of the first six stem loops of the 5'-end revealed specific amiloride interactions with stem loops 4, 5a, and 6, all of which contain bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Taken together, the use of multiple orthogonal approaches allowed us to identify the first small molecules aimed at targeting RNA structures within the 5'-UTR and proximal region of the CoV genome. These molecules will serve as chemical probes to further understand CoV RNA biology and can pave the way for the development of specific CoV RNA-targeted antivirals.
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Affiliation(s)
- Zafferani Martina
- Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705
| | - Haddad Christina
- Department of Chemistry, Case Western Reserve University, Cleveland OH 441106
| | - Luo Le
- Department of Chemistry, Case Western Reserve University, Cleveland OH 441106
| | | | - Yuan-Chiu Liang
- Department of Chemistry, Case Western Reserve University, Cleveland OH 441106
| | - Shema Mugisha Christian
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Adeline G. Monaghan
- Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705
| | - Andrew A. Kennedy
- Department of Internal Medicine and Department of Microbiology & Immunology, University of Michigan, 1150 W Medical Center Dr, Ann Arbor MI 48109
| | - Joseph D. Yesselman
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Robert R. Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, UK, G61 1QH
| | - Andrew W. Tai
- Department of Internal Medicine and Department of Microbiology & Immunology, University of Michigan, 1150 W Medical Center Dr, Ann Arbor MI 48109
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ USA 08854
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane West, Piscataway, NJ USA 08854
| | - Blanton S. Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland OH 441106
| | - Amanda E. Hargrove
- Chemistry Department, Duke University, 124 Science Drive; Durham, NC USA 27705
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21
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Abstract
The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In particular, RNAs tend to be more dynamic and offer less chemical functionality than proteins, and biologically active ligands must compete with the highly abundant and highly structured RNA of the ribosome. Indeed, the only small molecule drug targeting RNA other than the ribosome was just approved in August 2020, and our recent survey of the literature revealed fewer than 150 reported chemical probes that target non-ribosomal RNA in biological systems. This Feature outlines our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition by analyzing patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. First, we synthesized libraries based on RNA binding scaffolds that allowed us to reveal general principles in small molecule:recognition and to ask precise chemical questions about drivers of affinity and selectivity. Elaboration of these scaffolds has led to recognition of medicinally relevant RNA targets, including viral and long noncoding RNA structures. More globally, we identified physicochemical, structural, and spatial properties of biologically active RNA ligands that are distinct from those of protein-targeted ligands, and we have provided the dataset and associated analytical tools as part of a publicly available online platform to facilitate RNA ligand discovery. At the same time, we used pattern recognition protocols to identify RNA topologies that can be differentially recognized by small molecules and have elaborated this technique to visualize conformational changes in RNA secondary structure. These fundamental insights into the drivers of RNA recognition in vitro have led to functional targeting of RNA structures in biological systems. We hope that these initial guiding principles, as well as the approaches and assays developed in their pursuit, will enable rapid progress toward the development of RNA-targeted chemical probes and ultimately new therapeutic approaches to a wide range of deadly human diseases.
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Affiliation(s)
- Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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22
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Umuhire Juru A, Cai Z, Jan A, Hargrove AE. Template-guided selection of RNA ligands using imine-based dynamic combinatorial chemistry. Chem Commun (Camb) 2020; 56:3555-3558. [PMID: 32104839 DOI: 10.1039/d0cc00266f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This study establishes the applicability of imine-based dynamic combinatorial chemistry to discover non-covalent ligands for RNA targets. We elucidate properties underlying the reactivity of arylamines and demonstrate target-guided amplification of tight binders in an amiloride-based dynamic library.
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Affiliation(s)
- Aline Umuhire Juru
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Zhengguo Cai
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Adina Jan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
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23
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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24
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Costales MG, Childs-Disney JL, Haniff HS, Disney MD. How We Think about Targeting RNA with Small Molecules. J Med Chem 2020; 63:8880-8900. [PMID: 32212706 PMCID: PMC7486258 DOI: 10.1021/acs.jmedchem.9b01927] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA offers nearly unlimited potential as a target for small molecule chemical probes and lead medicines. Many RNAs fold into structures that can be selectively targeted with small molecules. This Perspective discusses molecular recognition of RNA by small molecules and highlights key enabling technologies and properties of bioactive interactions. Sequence-based design of ligands targeting RNA has established rules for affecting RNA targets and provided a potentially general platform for the discovery of bioactive small molecules. The RNA targets that contain preferred small molecule binding sites can be identified from sequence, allowing identification of off-targets and prediction of bioactive interactions by nature of ligand recognition of functional sites. Small molecule targeted degradation of RNA targets (ribonuclease-targeted chimeras, RIBOTACs) and direct cleavage by small molecules have also been developed. These growing technologies suggest that the time is right to provide small molecule chemical probes to target functionally relevant RNAs throughout the human transcriptome.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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25
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Ursu A, Childs-Disney JL, Angelbello AJ, Costales MG, Meyer SM, Disney MD. Gini Coefficients as a Single Value Metric to Define Chemical Probe Selectivity. ACS Chem Biol 2020; 15:2031-2040. [PMID: 32568503 PMCID: PMC7442733 DOI: 10.1021/acschembio.0c00486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Selectivity is a key requirement of high-quality chemical probes and lead medicines; however, methods to quantify and compare the selectivity of small molecules have not been standardized across the field. Herein, we discuss the origins and use of a comprehensive, single value term to quantify selectivity, the Gini coefficient. Case studies presented include compounds that target protein kinases, small molecules that bind RNA structures, and small molecule chimeras that bind to and degrade the target RNA. With an increasing number of transcriptome- and proteome-wide studies, we submit that reporting Gini coefficients as a quantitative descriptor of selectivity should be used broadly.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | | | | | | | - Samantha M. Meyer
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458
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26
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Padroni G, Patwardhan NN, Schapira M, Hargrove AE. Systematic analysis of the interactions driving small molecule-RNA recognition. RSC Med Chem 2020; 11:802-813. [PMID: 33479676 DOI: 10.1039/d0md00167h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are becoming an important target class in drug discovery. However, the principles for designing RNA-binding small molecules are yet to be fully uncovered. In this study, we examined the Protein Data Bank (PDB) to highlight privileged interactions underlying small molecule-RNA recognition. By comparing this analysis with previously determined small molecule-protein interactions, we find that RNA recognition is driven mostly by stacking and hydrogen bonding interactions, while protein recognition is instead driven by hydrophobic effects. Furthermore, we analyze patterns of interactions to highlight potential strategies to tune RNA recognition, such as stacking and cation-π interactions that favor purine and guanine recognition, and note an unexpected paucity of backbone interactions, even for cationic ligands. Collectively, this work provides further understanding of RNA-small molecule interactions that may inform the design of small molecules targeting RNA.
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Affiliation(s)
- G Padroni
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - N N Patwardhan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - M Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - A E Hargrove
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
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27
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Sato Y. Design of Fluorescent Peptide Nucleic Acid Probes Carrying Cyanine Dyes for Targeting Double-Stranded RNAs for Analytical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
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28
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Human cytomegalovirus-encoded MicroRNAs: A master regulator of latent infection. INFECTION GENETICS AND EVOLUTION 2020; 78:104119. [DOI: 10.1016/j.meegid.2019.104119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 11/06/2019] [Accepted: 11/14/2019] [Indexed: 01/08/2023]
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29
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Benhamou RI, Angelbello AJ, Andrews RJ, Wang ET, Moss WN, Disney MD. Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide. ACS Chem Biol 2020; 15:485-493. [PMID: 31927948 PMCID: PMC7081929 DOI: 10.1021/acschembio.9b00958] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Myotonic dystrophy type 2 (DM2) is a genetically defined muscular dystrophy that is caused by an expanded repeat of r(CCUG) [r(CCUG)exp] in intron 1 of a CHC-type zinc finger nucleic acid binding protein (CNBP) pre-mRNA. Various mechanisms contribute to DM2 pathology including pre-mRNA splicing defects caused by sequestration of the RNA splicing regulator muscleblind-like-1 (MBNL1) by r(CCUG)exp. Herein, we study the biological impacts of the molecular recognition of r(CCUG)exp's structure by a designer dimeric small molecule that directly cleaves the RNA in patient-derived cells. The compound is comprised of two RNA-binding modules conjugated to a derivative of the natural product bleomycin. Careful design of the chimera affords RNA-specific cleavage, as attachment of the bleomycin cleaving module was done in a manner that disables DNA cleavage. The chimeric cleaver is more potent than the parent binding compound for alleviating DM2-associated defects. Importantly, oligonucleotides targeting the r(CCUG)exp sequence for cleavage exacerbate DM2 defects due to recognition of a short r(CCUG) sequence that is embedded in CNBP, argonaute-1 (AGO1), and MBNL1, reducing their levels. The latter event causes a greater depletion of functional MBNL1 than the amount already sequestered by r(CCUG)exp. Thus, compounds targeting RNA structures can have functional advantages over oligonucleotides that target the sequence in some disease settings, particularly in DM2.
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Affiliation(s)
- Raphael I Benhamou
- Department of Chemistry , The Scripps Research Institute , 110 Scripps Way , Jupiter , Florida 33458 , United States
| | - Alicia J Angelbello
- Department of Chemistry , The Scripps Research Institute , 110 Scripps Way , Jupiter , Florida 33458 , United States
| | - Ryan J Andrews
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology , Iowa State University , Ames , Iowa 50011 , United States
| | - Eric T Wang
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, UF Genetics Institute , University of Florida , 2033 Mowry Road , Gainesville , Florida 32610 , United States
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry, and Molecular Biology , Iowa State University , Ames , Iowa 50011 , United States
| | - Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , 110 Scripps Way , Jupiter , Florida 33458 , United States
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30
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Martin C, De Piccoli S, Gaysinski M, Becquart C, Azoulay S, Di Giorgio A, Duca M. Unveiling RNA‐Binding Properties of Verapamil and Preparation of New Derivatives as Inhibitors of HIV‐1 Tat‐TAR Interaction. Chempluschem 2020. [DOI: 10.1002/cplu.201900650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Céline Martin
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Serena De Piccoli
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Marc Gaysinski
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Cécile Becquart
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Stéphane Azoulay
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Audrey Di Giorgio
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
| | - Maria Duca
- Université Côte d'Azur Institute of Chemistry of Nice (ICN) 28 avenue Valrose 06100 Nice France
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31
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Morgan BS, Sanaba BG, Donlic A, Karloff DB, Forte JE, Zhang Y, Hargrove AE. R-BIND: An Interactive Database for Exploring and Developing RNA-Targeted Chemical Probes. ACS Chem Biol 2019; 14:2691-2700. [PMID: 31589399 DOI: 10.1021/acschembio.9b00631] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many researchers from entering the field. To facilitate the discovery of RNA-targeted chemical probes and their subsequent applications, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND). This collection contains an array of information on reported chemical probes that target non-rRNA and have biological activity, and analysis has led to the discovery of RNA-privileged properties. Herein, we developed an online platform to make this information freely available to the community, offering search options, a suite of tools for probe development, and an updated R-BIND data set with detailed experimental information for each probe. We repeated the previous cheminformatics analysis on the updated R-BIND list and found that the distinguishing physicochemical, structural, and spatial properties remained unchanged, despite an almost 50% increase in the database size. Further, we developed several user-friendly tools, including queries based on cheminformatic parameters, experimental details, functional groups, and substructures. In addition, a nearest neighbor algorithm can assess the similarity of user-uploaded molecules to R-BIND ligands. These tools and resources can be used to design small molecule libraries, optimize lead ligands, or select targets, probes, assays, and control experiments. Chemical probes are critical to the study and discovery of novel functions for RNA, and we expect this resource to greatly assist researchers in exploring and developing successful RNA-targeted probes.
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Affiliation(s)
- Brittany S. Morgan
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - Bilva G. Sanaba
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Anita Donlic
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
| | - Diane B. Karloff
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jordan E. Forte
- Wake Forest School of Medicine, 475 Vine Street, Winston Salem, North Carolina 27101, United States
| | - Yuqi Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Amanda E. Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27705, United States
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32
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Patwardhan NN, Cai Z, Umuhire Juru A, Hargrove AE. Driving factors in amiloride recognition of HIV RNA targets. Org Biomol Chem 2019; 17:9313-9320. [PMID: 31612165 PMCID: PMC6909927 DOI: 10.1039/c9ob01702j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Noncoding RNAs are increasingly promising drug targets yet ligand design is hindered by a paucity of methods that reveal driving factors in selective small molecule : RNA interactions, particularly given the difficulties of high-resolution structural characterization. HIV RNAs are excellent model systems for method development given their targeting history, known structure-function relationships, and the unmet need for more effective treatments. Herein we report a strategy combining synthetic diversification, profiling against multiple RNA targets, and predictive cheminformatic analysis to identify driving factors for selectivity and affinity of small molecules for distinct HIV RNA targets. Using this strategy, we discovered improved ligands for multiple targets and the first ligands for ESSV, an exonic splicing silencer critical to replication. Computational analysis revealed guiding principles for future designs and a predictive cheminformatics model of small molecule : RNA binding. These methods are expected to facilitate progress toward selective targeting of disease-causing RNAs.
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Affiliation(s)
- Neeraj N Patwardhan
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27705, USA.
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33
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Cheng MSQ, Su MXX, Wang MXN, Sun MZY, Ou TM. Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions. Methods 2019; 167:124-133. [PMID: 31185274 DOI: 10.1016/j.ymeth.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.
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Affiliation(s)
- Miss Sui-Qi Cheng
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Xiao-Xuan Su
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China.
| | - Miss Xiao-Na Wang
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Zhi-Yin Sun
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Tian-Miao Ou
- Sun Yat-Sen University, School of Pharmaceutical Sciences, 132 Waihuan East Road, Guangzhou University City, Guangzhou, Guangdong, China.
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34
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Calabrese DR, Connelly CM, Schneekloth JS. Ligand-observed NMR techniques to probe RNA-small molecule interactions. Methods Enzymol 2019; 623:131-149. [PMID: 31239044 DOI: 10.1016/bs.mie.2019.05.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A growing understanding of the structure and function of RNA has revealed it as a key regulator of gene expression and disease. A multitude of noncoding functions apart from the central roles of RNA in coding for and facilitating protein biogenesis has stimulated research into RNA as a pharmacological target. Despite many exciting advances, RNA remains an understudied target for small molecules, and techniques to investigate RNA-binding molecules are still emerging. A key stumbling block in this area has been validation of RNA-small molecule interactions. Our laboratory has recently used multiple ligand-observed NMR techniques in this regard, including CPMG and WaterLOGSY. This work describes methods to use these techniques in the context of studying RNA-ligand interactions.
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Colleen M Connelly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, United States.
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35
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Hewitt WM, Calabrese DR, Schneekloth JS. Evidence for ligandable sites in structured RNA throughout the Protein Data Bank. Bioorg Med Chem 2019; 27:2253-2260. [PMID: 30982658 PMCID: PMC8283815 DOI: 10.1016/j.bmc.2019.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
Abstract
RNA has attracted considerable attention as a target for small molecules. However, methods to identify, study, and characterize suitable RNA targets have lagged behind strategies for protein targets. One approach that has received considerable attention for protein targets has been to utilize computational analysis to investigate ligandable "pockets" on proteins that are amenable to small molecule binding. These studies have shown that selected physical properties of pockets are important parameters that govern the ability of a structure to bind to small molecules. This work describes a similar analysis to study pockets on all RNAs in the Protein Data Bank (PDB). Using parameters such as buriedness, hydrophobicity, volume, and other properties, the set of all RNAs is analyzed and compared to all proteins. Considerable overlap is observed between the properties of pockets on RNAs and proteins. Thus, many RNAs are capable of populating conformations with pockets that are likely suitable for small molecule binding. Further, principal moment of inertia (PMI) calculations reveal that liganded RNAs exist in diverse structural space, much of which overlaps with protein structural space. Taken together, these results suggest that complex folded RNAs adopt unique structures with pockets that may represent viable opportunities for small molecule targeting.
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Affiliation(s)
- William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, United States.
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36
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Dynamic combinatorial chemistry as a rapid method for discovering sequence-selective RNA-binding compounds. Methods Enzymol 2019; 623:67-84. [PMID: 31239058 DOI: 10.1016/bs.mie.2019.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ever-growing number of RNA species that are recognized as having a role in human disease is driving a demand for novel molecular probes and therapeutics. Producing sequence-selective RNA-binding molecules remains a substantial challenge, however. One approach that has been successful in producing molecules with high affinity and specificity for disease-relevant RNAs is the use of dynamic combinatorial chemistry, a fragment-based method in which fragments combine reversibly in the presence of the target. We describe methods for the design, synthesis, and screening of dynamic combinatorial libraries targeting RNA.
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37
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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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38
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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39
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Anokhina VS, McAnany JD, Ciesla JH, Hilimire TA, Santoso N, Miao H, Miller BL. Enhancing the ligand efficiency of anti-HIV compounds targeting frameshift-stimulating RNA. Bioorg Med Chem 2019; 27:2972-2977. [PMID: 31101492 DOI: 10.1016/j.bmc.2019.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/22/2019] [Accepted: 05/07/2019] [Indexed: 11/29/2022]
Abstract
Ribosomal frameshifting, a process whereby a translating ribosome is diverted from one reading frame to another on a contiguous mRNA, is an important regulatory mechanism in biology and an opportunity for therapeutic intervention in several human diseases. In HIV, ribosomal frameshifting controls the ratio of Gag and Gag-Pol, two polyproteins critical to the HIV life cycle. We have previously reported compounds able to selectively bind an RNA stemloop within the Gag-Pol mRNA; these compounds alter the production of Gag-Pol in a manner consistent with increased frameshifting. Importantly, they also display antiretroviral activity in human T-cells. Here, we describe new compounds with significantly reduced molecular weight, but with substantially maintained affinity and anti-HIV activity. These results suggest that development of more "ligand efficient" enhancers of ribosomal frameshifting is an achievable goal.
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Affiliation(s)
- Viktoriya S Anokhina
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, United States
| | - John D McAnany
- Department of Chemistry, University of Rochester, Rochester, NY 14642, United States
| | - Jessica H Ciesla
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, United States
| | - Thomas A Hilimire
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, United States
| | - Netty Santoso
- Department of Biostatistics, University of Rochester, Rochester, NY 14642, United States
| | - Hongyu Miao
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, United States
| | - Benjamin L Miller
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642, United States; Department of Dermatology, University of Rochester, Rochester, NY 14642, United States.
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40
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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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41
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Patwardhan NN, Cai Z, Newson CN, Hargrove AE. Fluorescent peptide displacement as a general assay for screening small molecule libraries against RNA. Org Biomol Chem 2019; 17:1778-1786. [PMID: 30468226 DOI: 10.1039/c8ob02467g] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A prominent hurdle in developing small molecule probes against RNA is the relative scarcity of general screening methods. In this study, we demonstrate the application of a fluorescent peptide displacement assay to screen small molecule probes against four different RNA targets. The designed experimental protocol combined with statistical analysis provides a fast and convenient method to simultaneously evaluate small molecule libraries against different RNA targets and classify them based on affinity and selectivity patterns.
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Affiliation(s)
- Neeraj N Patwardhan
- Department of Chemistry, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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42
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Costales MG, Hoch DG, Abegg D, Childs-Disney JL, Velagapudi SP, Adibekian A, Disney MD. A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin. J Am Chem Soc 2019; 141:2960-2974. [PMID: 30726072 DOI: 10.1021/jacs.8b10558] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A small molecule (1) with overlapping affinity for two microRNA (miRNA) precursors was used to inform design of a dimeric compound (2) selective for one of the miRNAs. In particular, 2 selectively targets the microRNA(miR)-515 hairpin precursor to inhibit production of miR-515 that represses sphingosine kinase 1 (SK1), a key enzyme in the biosynthesis of sphingosine 1-phosphate (S1P). Application of 2 to breast cancer cells enhanced SK1 and S1P levels, triggering a migratory phenotype. Knockout of SK1, forced overexpression of miR-515, and application of a small molecule SK1 inhibitor all ablated 2's effect on phenotype, consistent with its designed mode of action. Target profiling studies via Chem-CLIP showed that 2 bound selectively to the miR-515 hairpin precursor in cells. Global neoprotein synthesis upon addition of 2 to MCF-7 breast cancer cells demonstrated 2's selectivity and upregulation of cancer-associated proteins regulated by S1P. The most upregulated protein was human epidermal growth factor receptor 2 (ERBB2/HER2), which is regulated by the SK1/S1P pathway and is normally not expressed in MCF-7 cells. Like triple negative breast cancer (TNBC) cells, the lack of HER2 renders them insusceptible to Herceptin and its antibody-drug conjugate Kadcyla. In addition to proteomics, an RNA-seq study supports that 2 has limited off target effects and other studies support that 2 is more selective than an oligonucleotide. We therefore hypothesized that 2 could sensitize MCF-7 cells to anti-HER2 therapies. Indeed, application of 2 sensitized cells to Herceptin. These results were confirmed in two other cell lines that express miR-515 and are HER2-, the hepatocellular carcinoma cell line HepG2 and the TNBC line MDA-MB-231. Importantly, normal breast epithelial cells (MCF-10A) that do not express miR-515 are not affected by 2. These observations suggest a precision medicine approach to sensitize HER2- cancers to approved anticancer medicines. This study has implications for broadening the therapeutic utility of known targeted cancer therapeutics by using a secondary targeted approach to render otherwise insensitive cells, sensitive to a targeted therapeutic.
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Affiliation(s)
- Matthew G Costales
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Dominic G Hoch
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Daniel Abegg
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Jessica L Childs-Disney
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Sai Pradeep Velagapudi
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Alexander Adibekian
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
| | - Matthew D Disney
- Department of Chemistry , The Scripps Research Institute , 130 Scripps Way , Jupiter , Florida 33458 , United States
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43
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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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44
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Abstract
While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.
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45
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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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