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Ghosh P, Phadte A, Bhojappa B, Palani S, Srivatsan S. Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase. Nucleic Acids Res 2025; 53:gkaf108. [PMID: 40173016 PMCID: PMC11963764 DOI: 10.1093/nar/gkaf108] [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: 09/23/2024] [Revised: 01/10/2025] [Accepted: 02/12/2025] [Indexed: 04/04/2025] Open
Abstract
Given the emerging use of terminal deoxynucleotidyl transferase (TdT) in biotechnology and its clinical potential as a cancer marker and target, the development of a versatile probe system to study its processivity, substrate properties, and inhibition is highly desired. Here, we demonstrate a multilayered application of a series of environment-sensitive fluorescent 2'-deoxynucleotide probes that harness the activity of TdT in accessing site-specifically functionalized DNA oligonucleotides and devising a real-time fluorescence platform to monitor the enzyme activity and identify potential inhibitors. The nucleotides constructed by coupling heterocycles of progressively increasing chemical modifications (selenophene, benzothiophene, benzofuran, and fluorobenzofuran) at the C5 position of 2'-deoxyuridine serve as suitable substrates for TdT, albeit differences in incorporation efficiency. A battery of experiments provided valuable insights into the scope of this functionalization method. It revealed how a fine balance between steric hindrance and stacking interaction between the heterocycle moiety and primer 3'-end nucleobase in the active site modulates the recognition and processing of nucleotides based on their size. Remarkably, the excellent responsiveness of benzofuran-modified dUTP enabled the design of fluorescence assays to estimate TdT activity, and detect nucleotide and non-nucleotide inhibitors. The findings obtained using our probes should significantly advance TdT-based functionalization, diagnostic, and therapeutic strategies.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Apeksha A Phadte
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Bindu Bhojappa
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, C.V. Raman Road, Bengaluru 560012, India
| | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, C.V. Raman Road, Bengaluru 560012, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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2
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Ghosh P, Betz K, Gutfreund C, Pal A, Marx A, Srivatsan SG. Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes. Angew Chem Int Ed Engl 2025; 64:e202414319. [PMID: 39428682 DOI: 10.1002/anie.202414319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 10/22/2024]
Abstract
Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes. These nucleotides include SedUTP, BFdUTP and FBFdUTP, which bear selenophene, benzofuran and fluorobenzofuran, respectively, at the C5 position of uracil, and exhibit high conformational sensitivity. SedUTP and FBFdUTP serve as dual-app probes, combining a fluorophore with X-ray anomalous scattering Se or 19F NMR labels. Our study reveals that the size of the heterocycle influences how DNA polymerase families A and B incorporate these modified nucleotides during single nucleotide incorporation and primer extension reactions. Remarkably, the responsiveness of FBFdUTP enabled real-time monitoring of the binary complex formation and polymerase activity through fluorescence and 19F NMR spectroscopy. Comparative analysis of incorporation profiles, fluorescence, 19F NMR data, and crystal structures of ternary complexes highlights the plasticity of the enzyme. Key insight is provided into the role of gatekeeper amino acids (Arg660 and Arg587) in accommodating and processing these modified substrates, offering a structural basis for next-generation nucleotide probe development.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Cédric Gutfreund
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Arindam Pal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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3
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Tomita S, Nagai-Okatani C. Expanding the recognition of monosaccharides and glycans: A comprehensive analytical approach using chemical-nose/tongue technology and a comparison to lectin microarrays. BBA ADVANCES 2024; 7:100129. [PMID: 39790466 PMCID: PMC11714387 DOI: 10.1016/j.bbadva.2024.100129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Accepted: 12/07/2024] [Indexed: 01/12/2025] Open
Abstract
Chemical-nose/tongue technologies are emerging as promising analytical tools for glycan analysis. After briefly introducing the importance of glycans and their analytical methods, including the lectin microarray (LMA) as one of the gold standards, the fundamental principles underlying chemical noses/tongues are explained and various applications for monosaccharides and glycans are introduced. Then, the similarities and differences of these two approaches are discussed. While both technologies aim to comprehensively profile biospecimens based on 'interaction patterns' between multiple recognition probes and analytes, each has its own strengths. LMAs excel at specific, targeted analysis based on defined lectin-glycan interactions, whereas chemical nose/tongue offers greater flexibility and expandability in terms of system design, making it well-suited for discovering unknown glycan profiles and detecting broader differences in glycan mixtures. In the future, chemical-nose/tongue technologies may be applied to niche areas in glycan analysis and become powerful tools that complement LMA techniques.
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Affiliation(s)
- Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Chiaki Nagai-Okatani
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
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4
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Hegde S, Akhter S, Tang Z, Qi C, Yu C, Lewicka A, Liu Y, Koirala K, Reibarkh M, Battaile KP, Cooper A, Lovell S, Holmstrom ED, Wang X, Piccirilli JA, Gao Q, Miao Y, Wang J. Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618236. [PMID: 39464119 PMCID: PMC11507752 DOI: 10.1101/2024.10.14.618236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated Molecular Dynamics (GaMD) simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity-relationship (SAR) studies and transverse relaxation measurements by NMR spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Strikingly, small structure perturbations on these key contributors, such as the addition of a methyl group that disrupts the planarity of the ligand resulted in > 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders.
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Affiliation(s)
- Shalakha Hegde
- Section of Genetic Medicine, Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, IL, USA
- These authors contributed equally
| | - Sana Akhter
- Pharmacology and Computational Medicine Program, University of North Carolina, Chapel Hill, NC, USA
- These authors contributed equally
| | - Zhichao Tang
- Section of Genetic Medicine, Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, IL, USA
- These authors contributed equally
| | - Chang Qi
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Chenguang Yu
- Calibr-Skaggs Institute for Innovative Medicines, The Scripps Research Institute, La Jolla, CA, USA
| | - Anna Lewicka
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Yu Liu
- Department of Chemistry, Rockhurst University, Kansas City, MO, USA
| | - Kushal Koirala
- Pharmacology and Computational Medicine Program, University of North Carolina, Chapel Hill, NC, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ, USA
| | | | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, USA
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, USA
| | - Erik D. Holmstrom
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Xiao Wang
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
- Department of Chemistry, Physical Sciences Division, University of Chicago, Chicago, IL, USA
| | - Qi Gao
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ, USA
| | - Yinglong Miao
- Pharmacology and Computational Medicine Program, University of North Carolina, Chapel Hill, NC, USA
| | - Jingxin Wang
- Section of Genetic Medicine, Department of Medicine, Biological Sciences Division, University of Chicago, Chicago, IL, USA
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5
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Dutta S, Srivatsan SG. Enzymatic Functionalization of RNA Oligonucleotides by Terminal Uridylyl Transferase Using Fluorescent and Clickable Nucleotide Analogs. Chem Asian J 2024; 19:e202400475. [PMID: 38949615 DOI: 10.1002/asia.202400475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
We report a systematic study on controlling the enzyme activity of a terminal uridylyl transferase (TUTase) called SpCID1, which provides methods to effect site-specific incorporation of a single modified nucleotide analog at the 3'-end of an RNA oligonucleotide (ON). Responsive heterocycle-modified fluorescent UTP probes that are useful in analyzing non-canonical nucleic acid structures and azide- and alkyne-modified UTP analogs that are compatible for chemoenzymatic functionalization were used as study systems. In the first strategy, we balanced the concentration of essential metal ion cofactors (Mg2+ and Mn2+ ions) to restrict the processivity of the enzyme, which gave a very good control on the incorporation of clickable nucleotide analogs. In the second approach, borate that complexes with 2' and 3' oxygen atoms of a ribose sugar was used as a reversibly binding chelator to block repeated addition of nucleotide analogs. Notably, in the presence of heterocycle-modified fluorescent UTPs, we obtained single-nucleotide incorporated RNA products in reasonable yields, while with clickable nucleotides yields were very good. Further, 3'-end azide- and alkyne-labeled RNA ONs were post-enzymatically functionalized by CuAAC and SPAAC reactions with fluorescent probes. These strategies broaden the scope of TUTase in site-specifically installing modifications of different types onto RNA for various applications.
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Affiliation(s)
- Swagata Dutta
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune, 411008, India
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6
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Xie DD, Song R, Cheng X, Zhang H, Wei YF, Gao F. From Intercalation to External Binding: Ru(II) Complexes with a Spiro Ligand for TAR RNA Selective Binding and HIV-1 Reverse Transcriptase Inhibition. Inorg Chem 2024; 63:12342-12349. [PMID: 38904258 DOI: 10.1021/acs.inorgchem.4c01815] [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: 06/22/2024]
Abstract
As a typical RNA virus, the genetic information on HIV-1 is entirely stored in RNA. The reverse transcription activity of HIV-1 reverse transcriptase (RT) plays a crucial role in the replication and transmission of the virus. Non-nucleoside RT inhibitors (NNRTIs) block the function of RT by binding to the RNA binding site on RT, with very few targeting viral RNA. In this study, by transforming planar conjugated ligands into a spiro structure, we convert classical Ru(II) DNA intercalators into a nonintercalator. This enables selective binding to HIV-1 transactivation response (TAR) RNA on the outer side of nucleic acids through dual interactions involving hydrogen bonds and electrostatic attraction, effectively inhibiting HIV-1 RT and serving as a selective fluorescence probe for TAR RNA.
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Affiliation(s)
- Dan-Dan Xie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Ran Song
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Xiaohong Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
| | - Yuan-Fang Wei
- Guangzhou Quality Supervision and Testing Institute, Guangzhou 511400, P. R. China
| | - Feng Gao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education; School of Pharmacy, Yunnan University, Kunming 650500, P. R. China
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7
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Ito Y, Tanaka H, Murakami A, Fuchi Y, Hari Y. Synthesis of fluorescent 5-heteroarylpyrimidine-containing oligonucleotides via post-synthetic trifluoromethyl conversion. Org Biomol Chem 2024; 22:3510-3517. [PMID: 38619422 DOI: 10.1039/d4ob00402g] [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: 04/16/2024]
Abstract
Post-synthetic conversion of the trifluoromethyl group to a heteroaryl group at the C5 position of the pyrimidine base in DNA oligonucleotides was achieved. Specifically, the oligonucleotides containing 5-trifluoromethylpyrimidine bases were treated with o-phenylenediamines and o-aminothiophenols as nucleophiles to afford the corresponding 5-(benzimidazol-2-yl)- and 5-(benzothiazol-2-yl)-pyrimidine-modified bases. Furthermore, evaluation of the fluorescence properties of the obtained oligonucleotides revealed that among them the oligonucleotide containing 5-(5-methylbenzimidazol-2-yl)cytosine exhibited the highest fluorescence intensity. These results indicated that post-synthetic trifluoromethyl conversion, which is practical and operationally simple, is a powerful tool for exploring functional oligonucleotides.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Hisato Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Ayana Murakami
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yasufumi Fuchi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
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8
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Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
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9
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Neitz H, Höbartner C. A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker. Chem Commun (Camb) 2023; 59:12003-12006. [PMID: 37727895 DOI: 10.1039/d3cc03796g] [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: 09/21/2023]
Abstract
We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detection of a specific DNA sequence.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
- Center for Nanosystems Chemistry (CNC), University of Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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10
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Heel S, Bartosik K, Juen F, Kreutz C, Micura R, Breuker K. Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer. J Am Chem Soc 2023; 145:15284-15294. [PMID: 37420313 PMCID: PMC10360057 DOI: 10.1021/jacs.3c02774] [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: 03/16/2023] [Indexed: 07/09/2023]
Abstract
Understanding how ligands bind to ribonucleic acids (RNA) is important for understanding RNA recognition in biological processes and drug development. Here, we have studied neomycin B binding to neomycin-sensing riboswitch aptamer constructs by native top-down mass spectrometry (MS) using electrospray ionization (ESI) and collisionally activated dissociation (CAD). Our MS data for a 27 nt aptamer construct reveal the binding site and ligand interactions, in excellent agreement with the structure derived from nuclear magnetic resonance (NMR) studies. Strikingly, for an extended 40 nt aptamer construct, which represents the sequence with the highest regulatory factor for riboswitch function, we identified two binding motifs for neomycin B binding, one corresponding to the bulge-loop motif of the 27 nt construct and the other one in the minor groove of the lower stem, which according to the MS data are equally populated. By replacing a noncanonical with a canonical base pair in the lower stem of the 40 nt aptamer, we can reduce binding to the minor groove motif from ∼50 to ∼30%. Conversely, the introduction of a CUG/CUG motif in the lower stem shifts the binding equilibrium in favor of minor groove binding. The MS data reveal site-specific and stoichiometry-resolved information on aminoglycoside binding to RNA that is not directly accessible by other methods and underscore the role of noncanonical base pairs in RNA recognition by aminoglycosides.
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Affiliation(s)
- Sarah
Viola Heel
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Karolina Bartosik
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Fabian Juen
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry
and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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11
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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: 6] [Impact Index Per Article: 3.0] [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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12
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Chen J, Hickey BL, Gao Z, Raz AAP, Hooley RJ, Zhong W. Sensing Base Modifications in Non-Canonically Folded DNA with an Optimized Host:Guest Sensing Array. ACS Sens 2022; 7:2164-2169. [PMID: 35917160 DOI: 10.1021/acssensors.2c00839] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An arrayed host:guest fluorescence sensor system can discriminate DNA G-quadruplex structures that differ only in the presence of single oxidation or methylation modification in the guanine base. These small modifications make subtle changes to G4 folding that are often not detectable by CD but induce differential fluorescence responses in the array. The sensing is functional in diluted serum and is capable of distinguishing individual modifications in DNA mixtures, providing a powerful method of detecting folding changes caused by DNA damage.
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13
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Falco N, Garfio CM, Spitalny L, Spitale RC. A Fluorescent Reverse-Transcription Assay to Detect Chemical Adducts on RNA. Biochemistry 2022; 61:1665-1668. [PMID: 35876726 PMCID: PMC10010264 DOI: 10.1021/acs.biochem.2c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we detail a novel reverse-transcription (RT) assay to directly detect chemical adducts on RNA. We optimize a fluorescence quenching assay to detect RT polymerization and employ our approach to detect N1-alkylation of inosine, an important post-transcriptional modification, using a phenylacrylamide as a model compound. We anticipate our approach can be expanded to identify novel reagents that form adducts with RNA and further explored to understand the relationship between RT processivity and natural post-transcriptional modifications in RNA.
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14
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Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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15
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Zhong W, Hooley RJ. Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts. Acc Chem Res 2022; 55:1035-1046. [PMID: 35302733 DOI: 10.1021/acs.accounts.2c00026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe3+ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe3+ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.
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16
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Pu F, Ren J, Qu X. Recent progress in sensor arrays using nucleic acid as sensing elements. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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17
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18
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DNA-encoded library versus RNA-encoded library selection enables design of an oncogenic noncoding RNA inhibitor. Proc Natl Acad Sci U S A 2022; 119:2114971119. [PMID: 35110406 PMCID: PMC8833215 DOI: 10.1073/pnas.2114971119] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/31/2022] Open
Abstract
Drug discovery generally investigates one target at a time, in sharp contrast to living organisms, which mold ligands and targets by evolution of highly complex molecular interaction networks. We recapitulate this modality of discovery by encoding drug structures in DNA, allowing the entire DNA-encoded library to interact with thousands of RNA fold targets, and then decoding both drug and target by sequencing. This information serves as a filter to identify human RNAs aberrantly produced in cancer that are also binding partners of the discovered ligand, leading to a precision medicine candidate that selectively ablates an oncogenic noncoding RNA, reversing a disease-associated phenotype in cells. Nature evolves molecular interaction networks through persistent perturbation and selection, in stark contrast to drug discovery, which evaluates candidates one at a time by screening. Here, nature’s highly parallel ligand-target search paradigm is recapitulated in a screen of a DNA-encoded library (DEL; 73,728 ligands) against a library of RNA structures (4,096 targets). In total, the screen evaluated ∼300 million interactions and identified numerous bona fide ligand–RNA three-dimensional fold target pairs. One of the discovered ligands bound a 5′GAG/3′CCC internal loop that is present in primary microRNA-27a (pri-miR-27a), the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand was cell active, potently and selectively inhibiting pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells. By exploiting evolutionary principles at the earliest stages of drug discovery, it is possible to identify high-affinity and selective target–ligand interactions and predict engagements in cells that short circuit disease pathways in preclinical disease models.
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19
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Zhang X, Feng X, Zhou LL, Liu B, Chen Z, Zuo X. A colorimetric sensor array for rapid discrimination of edible oil species based on a halogen ion exchange reaction between CsPbBr 3 and iodide. Analyst 2022; 147:404-409. [DOI: 10.1039/d1an02109e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halogen exchange of iodides with CsPbBr3 NCs generates CsPbI3, which differs in its content and directly causes different photoluminescence responses.
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Affiliation(s)
- Xin Zhang
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Xiaowei Feng
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Leon Lee Zhou
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Bin Liu
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Zhengbo Chen
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Xia Zuo
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
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20
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Tang Z, Akhter S, Ramprasad A, Wang X, Reibarkh M, Wang J, Aryal S, Thota SS, Zhao J, Douglas JT, Gao P, Holmstrom ED, Miao Y, Wang J. Recognition of single-stranded nucleic acids by small-molecule splicing modulators. Nucleic Acids Res 2021; 49:7870-7883. [PMID: 34283224 PMCID: PMC8373063 DOI: 10.1093/nar/gkab602] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Risdiplam is the first approved small-molecule splicing modulator for the treatment of spinal muscular atrophy (SMA). Previous studies demonstrated that risdiplam analogues have two separate binding sites in exon 7 of the SMN2 pre-mRNA: (i) the 5'-splice site and (ii) an upstream purine (GA)-rich binding site. Importantly, the sequence of this GA-rich binding site significantly enhanced the potency of risdiplam analogues. In this report, we unambiguously determined that a known risdiplam analogue, SMN-C2, binds to single-stranded GA-rich RNA in a sequence-specific manner. The minimum required binding sequence for SMN-C2 was identified as GAAGGAAGG. We performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which captured spontaneous binding of a risdiplam analogue to the target nucleic acids. We uncovered, for the first time, a ligand-binding pocket formed by two sequential GAAG loop-like structures. The simulation findings were highly consistent with experimental data obtained from saturation transfer difference (STD) NMR and structure-affinity-relationship studies of the risdiplam analogues. Together, these studies illuminate us to understand the molecular basis of single-stranded purine-rich RNA recognition by small-molecule splicing modulators with an unprecedented binding mode.
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Affiliation(s)
- Zhichao Tang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Ankita Ramprasad
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Xiao Wang
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Mikhail Reibarkh
- Analytical Research & Development, Merck and Co., Inc., Kenilworth, NJ 07033, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Sadikshya Aryal
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Srinivas S Thota
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Justin T Douglas
- Nuclear Magnetic Resonance Lab, University of Kansas, Lawrence, KS 66045, USA
| | - Philip Gao
- Protein Production Group, University of Kansas, Lawrence, KS 66047, USA
| | - Erik D Holmstrom
- Department of Molecular Biosciences and Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
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21
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Chen J, Gill AD, Hickey BL, Gao Z, Cui X, Hooley RJ, Zhong W. Machine Learning Aids Classification and Discrimination of Noncanonical DNA Folding Motifs by an Arrayed Host:Guest Sensing System. J Am Chem Soc 2021; 143:12791-12799. [PMID: 34346209 DOI: 10.1021/jacs.1c06031] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An arrayed host:guest fluorescence sensor system can discriminate among and classify multiple different noncanonical DNA structures by exploiting selective molecular recognition. The sensor is highly selective and can discriminate between folds as similar as native G-quadruplexes and those with bulges or vacancies. The host and guest can form heteroternary complexes with DNA strands, with the host acting as mediator between the DNA and dye, modulating the emission. By applying machine learning algorithms to the sensing data, prediction of the folding state of unknown DNA strands is possible with high fidelity.
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22
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Selective discrimination and classification of G-quadruplex structures with a host-guest sensing array. Nat Chem 2021; 13:488-495. [PMID: 33795843 DOI: 10.1038/s41557-021-00647-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/27/2021] [Indexed: 02/01/2023]
Abstract
The secondary structures of nucleic acids have an important influence on their cellular functions but can be difficult to identify and classify quickly. Here, we show that an arrayed suite of synthetic hosts and dyes is capable of fluorescence detection of oligonucleotide secondary structures. Multivariate analysis of different fluorescence enhancements-generated using cationic dyes that show affinity for both DNA G-quadruplexes and the synthetic hosts-enables discrimination between G-quadruplex structures of identical length and highly similar topological types. Different G-quadruplexes that display the same folding topology can also be easily differentiated by the number of G-quartets and sequence differences at the 3' or 5' ends. The array is capable of both differentiation and classification of the G-quadruplex structures at the same time. This simple non-invasive sensing method does not require the discovery and synthesis of specific G-quadruplex binding ligands, but employs a simple multicomponent approach to ensure wide applicability.
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23
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Liu H, Rauch S, Dickinson BC. Programmable technologies to manipulate gene expression at the RNA level. Curr Opin Chem Biol 2021; 64:27-37. [PMID: 33930627 DOI: 10.1016/j.cbpa.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
RNA has long been an enticing therapeutic target, but is now garnering increased attention, largely driven by clinical successes of RNA interference-based drugs. While gene knockdown by well-established RNA interference- and other oligonucleotide-based strategies continues to advance in the clinic, the repertoire of targetable effectors capable of altering gene expression at the RNA level is also rapidly expanding. In this review, we focus on several recently developed bifunctional molecular technologies that both interact with and act upon a target RNA. These new approaches for programmable RNA knockdown, editing, splicing, translation, and chemical modifications stand to provide impactful new modalities for therapeutic development in the coming decades.
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Affiliation(s)
- Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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24
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Falese JP, Donlic A, Hargrove AE. Targeting RNA with small molecules: from fundamental principles towards the clinic. Chem Soc Rev 2021; 50:2224-2243. [PMID: 33458725 PMCID: PMC8018613 DOI: 10.1039/d0cs01261k] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent advances in our understanding of RNA biology have uncovered crucial roles for RNA in multiple disease states, ranging from viral and bacterial infections to cancer and neurological disorders. As a result, multiple laboratories have become interested in developing drug-like small molecules to target RNA. However, this development comes with multiple unique challenges. For example, RNA is inherently dynamic and has limited chemical diversity. In addition, promiscuous RNA-binding ligands are often identified during screening campaigns. This Tutorial Review overviews important considerations and advancements for generating RNA-targeted small molecules, ranging from fundamental chemistry to promising small molecule examples with demonstrated clinical efficacy. Specifically, we begin by exploring RNA functional classes, structural hierarchy, and dynamics. We then discuss fundamental RNA recognition principles along with methods for small molecule screening and RNA structure determination. Finally, we review unique challenges and emerging solutions from both the RNA and small molecule perspectives for generating RNA-targeted ligands before highlighting a selection of the "Greatest Hits" to date. These molecules target RNA in a variety of diseases, including cancer, neurodegeneration, and viral infection, in cellular and animal model systems. Additionally, we explore the recently FDA-approved small molecule regulator of RNA splicing, risdiplam, for treatment of spinal muscular atrophy. Together, this Tutorial Review showcases the fundamental role of chemical and molecular recognition principles in enhancing our understanding of RNA biology and contributing to the rapidly growing number of RNA-targeted probes and therapeutics. In particular, we hope this widely accessible review will serve as inspiration for aspiring small molecule and/or RNA researchers.
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Affiliation(s)
- James P Falese
- Duke University School of Medicine, Department of Biochemistry, Durham, North Carolina, USA.
| | - Anita Donlic
- Princeton University, Department of Chemical and Biological Engineering, Princeton, New Jersey, USA
| | - Amanda E Hargrove
- Duke University School of Medicine, Department of Biochemistry, Durham, North Carolina, USA. and Duke University, Department of Chemistry, Durham, North Carolina, USA
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25
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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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26
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Ursu A, Childs-Disney JL, Andrews RJ, O'Leary CA, Meyer SM, Angelbello AJ, Moss WN, Disney MD. Design of small molecules targeting RNA structure from sequence. Chem Soc Rev 2020; 49:7252-7270. [PMID: 32935689 PMCID: PMC7707016 DOI: 10.1039/d0cs00455c] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and discovery of small molecule medicines has largely been focused on a small number of druggable protein families. A new paradigm is emerging, however, in which small molecules exert a biological effect by interacting with RNA, both to study human disease biology and provide lead therapeutic modalities. Due to this potential for expanding target pipelines and treating a larger number of human diseases, robust platforms for the rational design and optimization of small molecules interacting with RNAs (SMIRNAs) are in high demand. This review highlights three major pillars in this area. First, the transcriptome-wide identification and validation of structured RNA elements, or motifs, within disease-causing RNAs directly from sequence is presented. Second, we provide an overview of high-throughput screening approaches to identify SMIRNAs as well as discuss the lead identification strategy, Inforna, which decodes the three-dimensional (3D) conformation of RNA motifs with small molecule binding partners, directly from sequence. An emphasis is placed on target validation methods to study the causality between modulating the RNA motif in vitro and the phenotypic outcome in cells. Third, emergent modalities that convert occupancy-driven mode of action SMIRNAs into event-driven small molecule chemical probes, such as RNA cleavers and degraders, are presented. Finally, the future of the small molecule RNA therapeutics field is discussed, as well as hurdles to overcome to develop potent and selective RNA-centric chemical probes.
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Affiliation(s)
- Andrei Ursu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Collin A O'Leary
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Samantha M Meyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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27
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Armstrong I, Aldhumani AH, Schopis JL, Fang F, Parsons E, Zeng C, Hossain MI, Bergmeier SC, Hines JV. RNA drug discovery: Conformational restriction enhances specific modulation of the T-box riboswitch function. Bioorg Med Chem 2020; 28:115696. [PMID: 33069065 DOI: 10.1016/j.bmc.2020.115696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
Antibacterial drug resistance is a global health concern that requires multiple solution approaches including development of new antibacterial compounds acting at novel targets. Targeting regulatory RNA is an emerging area of drug discovery. The T-box riboswitch is a regulatory RNA mechanism that controls gene expression in Gram-positive bacteria and is an exceptional, novel target for antibacterial drug design. We report the design, synthesis and activity of a series of conformationally restricted oxazolidinone-triazole compounds targeting the highly conserved antiterminator RNA element of the T-box riboswitch. Computational binding energies correlated with experimentally-derived Kd values indicating the predictive capabilities for docking studies within this series of compounds. The conformationally restricted compounds specifically inhibited T-box riboswitch function and not overall transcription. Complex disruption, computational docking and RNA binding specificity data indicate that inhibition may result from ligand binding to an allosteric site. These results highlight the importance of both ligand affinity and RNA conformational outcome for targeted RNA drug design.
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Affiliation(s)
- Ian Armstrong
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Ali H Aldhumani
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Jia L Schopis
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Fang Fang
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Eric Parsons
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Chunxi Zeng
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH 45701, USA
| | - Md Ismail Hossain
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Stephen C Bergmeier
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Edison Biotechnology Institute, Konneker Laboratories, Ohio University, Athens, OH 45701, USA
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH 45701, USA.
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28
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Chillón I, Marcia M. The molecular structure of long non-coding RNAs: emerging patterns and functional implications. Crit Rev Biochem Mol Biol 2020; 55:662-690. [PMID: 33043695 DOI: 10.1080/10409238.2020.1828259] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts that regulate vital cellular processes and are crucially connected to diseases. Despite their unprecedented molecular complexity, it is emerging that lncRNAs possess distinct structural motifs. Remarkably, the 3D shape and topology of full-length, native lncRNAs have been visualized for the first time in the last year. These studies reveal that lncRNA structures dictate lncRNA functions. Here, we review experimentally determined lncRNA structures and emphasize that lncRNA structural characterization requires synergistic integration of computational, biochemical and biophysical approaches. Based on these emerging paradigms, we discuss how to overcome the challenges posed by the complex molecular architecture of lncRNAs, with the goal of obtaining a detailed understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Isabel Chillón
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, Grenoble, France
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29
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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: 29] [Impact Index Per Article: 5.8] [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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30
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Yang Z, Fan L, Fan X, Hou M, Cao Z, Ding Y, Zhang W. Porphyrin-GO Nanocomposites Based NIR Fluorescent Sensor Array for Heparin Sensing and Quality Control. Anal Chem 2020; 92:6727-6733. [DOI: 10.1021/acs.analchem.0c00808] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhiyu Yang
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Liangfei Fan
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Xia Fan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Meiting Hou
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Zhiyuan Cao
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
| | - Yubin Ding
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, People’s Republic of China
| | - Weihua Zhang
- Jiangsu Key Laboratory of Pesticide Science, Department of Chemistry, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People’s Republic of China
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31
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Van Meter EN, Onyango JA, Teske KA. A review of currently identified small molecule modulators of microRNA function. Eur J Med Chem 2020; 188:112008. [DOI: 10.1016/j.ejmech.2019.112008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]
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32
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Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019; 167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022] Open
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33
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Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res 2019; 47:1523-1531. [PMID: 30481318 PMCID: PMC6379670 DOI: 10.1093/nar/gky1197] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Paul T Wille
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Alisha N Jones
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Jasmina Bogdanovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Eric Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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34
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Padroni G, Eubanks CS, Hargrove AE. Differentiation and classification of RNA motifs using small molecule-based pattern recognition. Methods Enzymol 2019; 623:101-130. [PMID: 31239043 PMCID: PMC6891821 DOI: 10.1016/bs.mie.2019.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Understanding how to design small molecules that target coding and non-coding RNA has the potential to exponentially increase the number of therapeutically-relevant druggable targets, which are currently mostly proteins. However, there is limited information on the principles at the basis of RNA recognition. In this chapter, we describe a pattern-based technique that can be used for the simultaneous elucidation of RNA motifs and small molecule features for RNA selective recognition, termed Pattern Recognition of RNA by Small Molecules (PRRSM). We provide protocols for the computational design and synthetic preparation of an RNA training set as well as how to perform the assay in plate reader format. Furthermore, we provide details on how to perform and interpret the statistical analysis and indicate possible future extensions of the technique. By combining insights into characteristics of the small molecules and of the RNA that leads to differentiation, PRRSM promises to accelerate the elucidation of the determinants at the basis of RNA recognition.
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Affiliation(s)
- Giacomo Padroni
- Department of Chemistry, Duke University, Durham, NC, United States
| | | | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, NC, United States.
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35
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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: 0.7] [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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36
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Thompson RD, Baisden JT, Zhang Q. NMR characterization of RNA small molecule interactions. Methods 2019; 167:66-77. [PMID: 31128236 DOI: 10.1016/j.ymeth.2019.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/25/2023] Open
Abstract
Exciting discoveries of naturally occurring ligand-sensing and disease-linked noncoding RNAs have promoted significant interests in understanding RNA-small molecule interactions. NMR spectroscopy is a powerful tool for characterizing intermolecular interactions. In this review, we describe protocols and approaches for applying NMR spectroscopy to investigate interactions between RNA and small molecules. We review protocols for RNA sample preparation, methods for identifying RNA-binding small molecules, approaches for mapping RNA-small molecule interactions, determining complex structures, and characterizing binding kinetics. We hope this review will provide a guideline to streamline NMR applications in studying RNA-small molecule interactions, facilitating both basic mechanistic understandings of RNA functions and translational efforts in developing RNA-targeted therapeutics.
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Affiliation(s)
- Rhese D Thompson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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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: 34] [Impact Index Per Article: 5.7] [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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Eubanks CS, Zhao B, Patwardhan NN, Thompson RD, Zhang Q, Hargrove AE. Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules. J Am Chem Soc 2019; 141:5692-5698. [DOI: 10.1021/jacs.8b09665] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Sabale PM, Tanpure AA, Srivatsan SG. Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe. Org Biomol Chem 2019; 16:4141-4150. [PMID: 29781489 PMCID: PMC6086326 DOI: 10.1039/c8ob00646f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Double-stranded segments of a genome that can potentially form G-quadruplex (GQ) and/or i-motif (iM) structures are considered to be important regulatory elements. Hence, the development of a common probe that can detect GQ and iM structures and also distinguish them from a duplex structure will be highly useful in understanding the propensity of such segments to adopt duplex or non-canonical four-stranded structures. Here, we describe the utility of a conformation-sensitive fluorescent nucleoside analog, which was originally developed as a GQ sensor, in detecting the iM structures of C-rich DNA oligonucleotides (ONs). The analog is based on a 5-(benzofuran-2-yl)uracil scaffold, which when incorporated into C-rich ONs (e.g., telomeric repeats) fluorescently distinguishes an iM from random coil and duplex structures. Steady-state and time-resolved fluorescence techniques enabled the determination of transition pH for the transformation of a random coil to an iM structure. Furthermore, a qualitative understanding on the relative population of duplex and GQ/iM forms under physiological conditions could be gained by correlating the fluorescence, CD and thermal melting data. Taken together, this sensor could provide a general platform to profile double-stranded promoter regions in terms of their ability to adopt four-stranded structures, and also could support approaches to discover functional GQ and iM binders.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India.
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40
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Yan H, Zhou M, Bhattarai U, Song Y, Zheng M, Cai J, Liang FS. Cyclic Peptidomimetics as Inhibitor for miR-155 Biogenesis. Mol Pharm 2019; 16:914-920. [PMID: 30601666 PMCID: PMC8513084 DOI: 10.1021/acs.molpharmaceut.8b01247] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
miR-155 plays key promoting roles in several cancers and emerges as an important anticancer therapeutic target. However, the discovery of small molecules that target RNAs is challenging. Peptidomimetics have been shown to be a rich source for discovering novel ligands to regulate cellular proteins. However, the potential of using peptidomimetics for RNA targeting is relatively unexplored. To this end, we designed and synthesized members of a novel 320 000 compound macrocyclic peptidomimetic library. An affinity-based screening protocol led to the identification of a pre-miR-155 binder that inhibits oncogenic miR-155 maturation in vitro and in cell and induces cancer cell apoptosis. The results of this investigation demonstrate that macrocyclic peptidomimetics could serve as a new scaffold for RNA targeting.
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Affiliation(s)
- Hao Yan
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Mi Zhou
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Umesh Bhattarai
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Yabin Song
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
| | - Mengmeng Zheng
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology, University of New Mexico, 300 Terrace Street NE, Albuquerque, New Mexico 87131, United States
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41
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Zuffo M, Xie X, Granzhan A. Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA. Chemistry 2019; 25:1812-1818. [DOI: 10.1002/chem.201805422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Michela Zuffo
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Xiao Xie
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
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42
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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: 2.3] [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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43
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Fedorova O, Jagdmann GE, Adams RL, Yuan L, Van Zandt MC, Pyle AM. Small molecules that target group II introns are potent antifungal agents. Nat Chem Biol 2018; 14:1073-1078. [PMID: 30323219 PMCID: PMC6239893 DOI: 10.1038/s41589-018-0142-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 08/29/2018] [Indexed: 11/09/2022]
Abstract
Specific RNA structures control numerous metabolic processes that impact human health, and yet efforts to target RNA structures de novo have been limited. In eukaryotes, the self-splicing group II intron is a mitochondrial RNA tertiary structure that is absent in vertebrates but essential for respiration in plants, fungi and yeast. Here we show that this RNA can be targeted through a process of high-throughput in vitro screening, SAR and lead optimization, resulting in high-affinity compounds that specifically inhibit group IIB intron splicing in vitro and in vivo and lack toxicity in human cells. The compounds are potent growth inhibitors of the pathogen Candida parapsilosis, displaying antifungal activity comparable to that of amphotericin B. These studies demonstrate that RNA tertiary structures can be successfully targeted de novo, resulting in pharmacologically valuable compounds.
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Affiliation(s)
- Olga Fedorova
- Howard Hughes Medical Institute, New Haven, CT, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Rebecca L Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Lin Yuan
- New England Discovery Partners, Branford, CT, USA
| | | | - Anna Marie Pyle
- Howard Hughes Medical Institute, New Haven, CT, USA. .,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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44
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Donlic A, Hargrove AE. Targeting RNA in mammalian systems with small molecules. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1477. [PMID: 29726113 PMCID: PMC6002909 DOI: 10.1002/wrna.1477] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]
Abstract
The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, Durham, North Carolina
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina
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45
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Eubanks CS, Hargrove AE. Sensing the impact of environment on small molecule differentiation of RNA sequences. Chem Commun (Camb) 2018; 53:13363-13366. [PMID: 29199743 DOI: 10.1039/c7cc07157d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Using pattern recognition of RNA with small molecules (PRRSM) with fluorescent RNA chemosensors and aminoglycosides, we reveal the impact of changing environmental conditions on the differentiation of a range of RNA structures as well as the ability to predict different sequence/size compositions of five canonical RNA motifs.
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46
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Zhang W, Gao N, Cui J, Wang C, Wang S, Zhang G, Dong X, Zhang D, Li G. AIE-doped poly(ionic liquid) photonic spheres: a single sphere-based customizable sensing platform for the discrimination of multi-analytes. Chem Sci 2017; 8:6281-6289. [PMID: 28989662 PMCID: PMC5628402 DOI: 10.1039/c7sc02409f] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
By simultaneously exploiting the unique properties of ionic liquids and aggregation-induced emission (AIE) luminogens, as well as photonic structures, a novel customizable sensing system for multi-analytes was developed based on a single AIE-doped poly(ionic liquid) photonic sphere. It was found that due to the extraordinary multiple intermolecular interactions involved in the ionic liquid units, one single sphere could differentially interact with broader classes of analytes, thus generating response patterns with remarkable diversity. Moreover, the optical properties of both the AIE luminogen and photonic structure integrated in the poly(ionic liquid) sphere provide multidimensional signal channels for transducing the involved recognition process in a complementary manner and the acquisition of abundant and sufficient sensing information could be easily achieved on only one sphere sensor element. More importantly, the sensing performance of our poly(ionic liquid) photonic sphere is designable and customizable through a simple ion-exchange reaction and target-oriented multi-analyte sensing can be conveniently realized using a selective receptor species, such as counterions, showing great flexibility and extendibility. The power of our single sphere-based customizable sensing system was exemplified by the successful on-demand detection and discrimination of four multi-analyte challenge systems: all 20 natural amino acids, nine important phosphate derivatives, ten metal ions and three pairs of enantiomers. To further demonstrate the potential of our spheres for real-life application, 20 amino acids in human urine and their 26 unprecedented complex mixtures were also discriminated between by the single sphere-based array.
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Affiliation(s)
- Wanlin Zhang
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
| | - Ning Gao
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
| | - Jiecheng Cui
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
| | - Chen Wang
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
| | - Shiqiang Wang
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
| | - Guanxin Zhang
- Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China .
| | - Xiaobiao Dong
- Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China .
| | - Deqing Zhang
- Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 , P. R. China .
| | - Guangtao Li
- Department of Chemistry , Key Lab of Organic Optoelectronics and Molecular Engineering , Tsinghua University , Beijing 100084 , P. R. China .
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47
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Sun S, Jiang K, Qian S, Wang Y, Lin H. Applying Carbon Dots-Metal Ions Ensembles as a Multichannel Fluorescent Sensor Array: Detection and Discrimination of Phosphate Anions. Anal Chem 2017; 89:5542-5548. [DOI: 10.1021/acs.analchem.7b00602] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shan Sun
- Key Laboratory of Graphene Technologies and Applications of Zhejiang Province, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences (CAS), Ningbo 315201, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Kai Jiang
- Key Laboratory of Graphene Technologies and Applications of Zhejiang Province, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences (CAS), Ningbo 315201, P. R. China
| | - Sihua Qian
- Key Laboratory of Graphene Technologies and Applications of Zhejiang Province, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences (CAS), Ningbo 315201, P. R. China
| | - Yuhui Wang
- Key Laboratory of Graphene Technologies and Applications of Zhejiang Province, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences (CAS), Ningbo 315201, P. R. China
| | - Hengwei Lin
- Key Laboratory of Graphene Technologies and Applications of Zhejiang Province, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences (CAS), Ningbo 315201, P. R. China
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48
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Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. MEDCHEMCOMM 2017; 8:1022-1036. [PMID: 28798862 PMCID: PMC5546750 DOI: 10.1039/c6md00729e] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/14/2017] [Indexed: 12/23/2022]
Abstract
Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic routes for combinatorial C(5)- and C(6)-diversification. Iterative modifications at the C(5)- and C(6)- positions yielded derivative 24, which demonstrated a 100-fold increase in activity over the parent dimethylamiloride in peptide displacement assays. NMR chemical shift mapping was performed using the 2D SOFAST- [1H-13C] HMQC NMR method, which allowed for facile and rapid evaluation of binding modes for all library members. Cheminformatic analysis revealed distinct differences between selective and non-selective ligands. In this study, we evolved dimethylamiloride from a weak TAR ligand to one of the tightest binding selective TAR ligands reported to date through a novel combination of synthetic methods and analytical techniques. We expect these methods to allow for rapid library expansion and tuning of the amiloride scaffold for a range of RNA targets and for SOFAST NMR to allow unprecedented evaluation of small molecule:RNA interactions.
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Affiliation(s)
- Neeraj N. Patwardhan
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Laura R. Ganser
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Gary J. Kapral
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Christopher S. Eubanks
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Janghyun Lee
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Bharathwaj Sathyamoorthy
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Amanda E. Hargrove
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| |
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