1
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Heel SV, Breuker K. Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry. Chempluschem 2024; 89:e202400178. [PMID: 38758051 DOI: 10.1002/cplu.202400178] [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: 03/06/2024] [Revised: 04/13/2024] [Indexed: 05/18/2024]
Abstract
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
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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
| | - 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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2
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Matzel T, Martin MW, Herr A, Wacker A, Richter C, Sreeramulu S, Schwalbe H. NMR characterization and ligand binding site of the stem-loop 2 motif from the Delta variant of SARS-CoV-2. RNA (NEW YORK, N.Y.) 2024; 30:779-794. [PMID: 38565242 PMCID: PMC11182009 DOI: 10.1261/rna.079902.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
The stem-loop 2 motif (s2m) in SARS-CoV-2 (SCoV-2) is located in the 3'-UTR. Although s2m has been reported to display characteristics of a mobile genomic element that might lead to an evolutionary advantage, its function has remained unknown. The secondary structure of the original SCoV-2 RNA sequence (Wuhan-Hu-1) was determined by NMR in late 2020, delineating the base-pairing pattern and revealing substantial differences in secondary structure compared to SARS-CoV-1 (SCoV-1). The existence of a single G29742-A29756 mismatch in the upper stem of s2m leads to its destabilization and impedes a complete NMR analysis. With Delta, a variant of concern has evolved with one mutation compared to the original sequence that replaces G29742 by U29742. We show here that this mutation results in a more defined structure at ambient temperature accompanied by a rise in melting temperature. Consequently, we were able to identify >90% of the relevant NMR resonances using a combination of selective RNA labeling and filtered 2D NOESY as well as 4D NMR experiments. We present a comprehensive NMR analysis of the secondary structure, (sub)nanosecond dynamics, and ribose conformation of s2m Delta based on heteronuclear 13C NOE and T 1 measurements and ribose carbon chemical shift-derived canonical coordinates. We further show that the G29742U mutation in Delta has no influence on the druggability of s2m compared to the Wuhan-Hu-1 sequence. With the assignment at hand, we identify the flexible regions of s2m as the primary site for small molecule binding.
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Affiliation(s)
- Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Maria Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Alexander Herr
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
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3
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Hymon D, Martins J, Richter C, Sreeramulu S, Wacker A, Ferner J, Patwardhan NN, Hargrove AE, Schwalbe H. NMR 1H, 19F-based screening of the four stem-looped structure 5_SL1-SL4 located in the 5'-untranslated region of SARS-CoV 2 RNA. RSC Med Chem 2024; 15:165-177. [PMID: 38283228 PMCID: PMC10809358 DOI: 10.1039/d3md00322a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/16/2023] [Indexed: 01/30/2024] Open
Abstract
Development of new antiviral medication against the beta-coronavirus SARS-CoV-2 (SCoV2) is actively being pursued. Both NMR spectroscopy and crystallography as structural screening technologies have been utilised to screen the viral proteome for binding to fragment libraries. Here, we report on NMR screening of elements of the viral RNA genome with two different ligand libraries using 1H-NMR-screening experiments and 1H and 19F NMR-screening experiments for fluorinated compounds. We screened against the 5'-terminal 119 nucleotides located in the 5'-untranslated region of the RNA genome of SCoV2 and further dissected the four stem-loops into its constituent RNA elements to test specificity of binding of ligands to shorter and longer viral RNA stretches. The first library (DRTL-F library) is enriched in ligands binding to RNA motifs, while the second library (DSI-poised library) represents a fragment library originally designed for protein screening. Conducting screens with two different libraries allows us to compare different NMR screening methodologies, describe NMR screening workflows, validate the two different fragment libraries, and derive initial leads for further downstream medicinal chemistry optimisation.
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Affiliation(s)
- Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Jason Martins
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
| | | | - Amanda E Hargrove
- Department of Chemistry, Duke University Durham North Carolina 27708 USA
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt/Main Germany
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4
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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] [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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5
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Geng A, Ganser L, Roy R, Shi H, Pratihar S, Case DA, Al-Hashimi HM. An RNA excited conformational state at atomic resolution. Nat Commun 2023; 14:8432. [PMID: 38114465 PMCID: PMC10730710 DOI: 10.1038/s41467-023-43673-6] [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: 05/25/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
Sparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational modeling, we determined the 3D structural ensemble formed by a short-lived (lifetime ~2.1 ms) lowly-populated (~0.4%) conformational state in HIV-1 TAR RNA. Through a strand register shift, the excited conformational state completely remodels the 3D structure of the ground state (RMSD from the ground state = 7.2 ± 0.9 Å), forming a surprisingly more ordered conformational ensemble rich in non-canonical mismatches. The structure impedes the formation of the motifs recognized by Tat and the super elongation complex, explaining why this alternative TAR conformation cannot activate HIV-1 transcription. The ability to determine the 3D structures of fleeting RNA states using the presented methodology holds great promise for our understanding of RNA biology, disease mechanisms, and the development of RNA-targeting therapeutics.
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Affiliation(s)
- Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Laura Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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6
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Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
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Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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7
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Wicks SL, Morgan BS, Wilson AW, Hargrove AE. Probing Bioactive Chemical Space to Discover RNA-Targeted Small Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551350. [PMID: 37577658 PMCID: PMC10418101 DOI: 10.1101/2023.07.31.551350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Small molecules have become increasingly recognized as invaluable tools to study RNA structure and function and to develop RNA-targeted therapeutics. To rationally design RNA-targeting ligands, a comprehensive understanding and explicit testing of small molecule properties that govern molecular recognition is crucial. To date, most studies have primarily evaluated properties of small molecules that bind RNA in vitro, with little to no assessment of properties that are distinct to selective and bioactive RNA-targeted ligands. Therefore, we curated an RNA-focused library, termed the Duke RNA-Targeted Library (DRTL), that was biased towards the physicochemical and structural properties of biologically active and non-ribosomal RNA-targeted small molecules. The DRTL represents one of the largest academic RNA-focused small molecule libraries curated to date with more than 800 small molecules. These ligands were selected using computational approaches that measure similarity to known bioactive RNA ligands and that diversify the molecules within this space. We evaluated DRTL binding in vitro to a panel of four RNAs using two optimized fluorescent indicator displacement assays, and we successfully identified multiple small molecule hits, including several novel scaffolds for RNA. The DRTL has and will continue to provide insights into biologically relevant RNA chemical space, such as the identification of additional RNA-privileged scaffolds and validation of RNA-privileged molecular features. Future DRTL screening will focus on expanding both the targets and assays used, and we welcome collaboration from the scientific community. We envision that the DRTL will be a valuable resource for the discovery of RNA-targeted chemical probes and therapeutic leads.
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Affiliation(s)
- Sarah L. Wicks
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Brittany S. Morgan
- Department of Chemistry & Biochemistry; University of Notre Dame; 123 McCourtney Hall Notre Dame, IN 46556
| | - Alexander W. Wilson
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
| | - Amanda E. Hargrove
- Department of Chemistry; Duke University; 124 Science Drive; Durham, NC 27708
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8
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Taghavi A, Baisden JT, Childs-Disney JL, Yildirim I, Disney M. Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies. Nucleic Acids Res 2023; 51:5325-5340. [PMID: 37216594 PMCID: PMC10287959 DOI: 10.1093/nar/gkad403] [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: 01/08/2023] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
G4C2 and G2C4 repeat expansions in chromosome 9 open reading frame 72 (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), or c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats [r(G4C2)exp] and G2C4 repeats [r(G2C4)exp]. The c9ALS/FTD repeat expansions are highly structured, and structural studies showed that r(G4C2)exp predominantly folds into a hairpin with a periodic array of 1 × 1 G/G internal loops and a G-quadruplex. A small molecule probe revealed that r(G4C2)exp also adopts a hairpin structure with 2 × 2 GG/GG internal loops. We studied the conformational dynamics adopted by 2 × 2 GG/GG loops using temperature replica exchange molecular dynamics (T-REMD) and further characterized the structure and underlying dynamics using traditional 2D NMR techniques. These studies showed that the loop's closing base pairs influence both structure and dynamics, particularly the configuration adopted around the glycosidic bond. Interestingly, r(G2C4) repeats, which fold into an array of 2 × 2 CC/CC internal loops, are not as dynamic. Collectively, these studies emphasize the unique sensitivity of r(G4C2)exp to small changes in stacking interactions, which is not observed in r(G2C4)exp, providing important considerations for further principles in structure-based drug design.
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Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jared T Baisden
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
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9
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Marušič M, Toplishek M, Plavec J. NMR of RNA - Structure and interactions. Curr Opin Struct Biol 2023; 79:102532. [PMID: 36746110 DOI: 10.1016/j.sbi.2023.102532] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/11/2022] [Accepted: 12/19/2022] [Indexed: 02/07/2023]
Abstract
RNA was shown to have a more substantial role in the regulation of diverse cellular processes than anticipated until recently. Answers to questions what is the structure of specific RNAs, how structure changes to accommodate different functional roles, and how RNA senses other biomolecules and changes its fold upon interaction create a complete representation of RNA involved in cellular processes. Nuclear magnetic resonance (NMR) spectroscopy encompasses a collection of methods and approaches that offer insight into several structural aspects of RNAs. We review the most recent advances in the field of viral, long non-coding, regulatory, and four-stranded RNAs, with an emphasis on the detection of dynamic sub-states and in view of chemical modifications that expand RNA's function.
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Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Maria Toplishek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia; University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia; EN-FIST Centre of Excellence, Cesta OF 13, Ljubljana, Slovenia.
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10
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Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
Abstract
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts have yielded a large collection of proteins that are capable of RNA binding in the absence of conventional RNA recognition domains. Many of the recently identified RNA interaction motifs fall into intrinsically disordered protein regions (IDRs). While the recognition mode and specificity of globular RNA binding elements have been thoroughly investigated and described, much less is known about the way IDRs can recognize their RNA partners. Our aim was to summarize the current state of structural knowledge on the RNA binding modes of disordered protein regions and to propose a classification system based on their sequential and structural properties. Through a detailed structural analysis of the complexes that contain disordered protein regions binding to RNA, we found two major binding modes that represent different recognition strategies and, most likely, functions. We compared these examples with DNA binding disordered proteins and found key differences stemming from the nucleic acids as well as similar binding strategies, implying a broader substrate acceptance by these proteins. Due to the very limited number of known structures, we integrated molecular dynamics simulations in our study, whose results support the proposed structural preferences of specific RNA‐binding IDRs. To broaden the scope of our review, we included a brief analysis of RNA‐binding small molecules and compared their structural characteristics and RNA recognition strategies to the RNA‐binding IDRs. This article is categorized under:RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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Affiliation(s)
- András Zeke
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Schád
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Horváth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rawan Abukhairan
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Beáta Szabó
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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11
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Kim HU, Jung HS. Cryo-EM as a powerful tool for drug discovery: recent structural based studies of SARS-CoV-2. Appl Microsc 2021; 51:13. [PMID: 34562174 PMCID: PMC8464538 DOI: 10.1186/s42649-021-00062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has arisen as a global pandemic affecting the respiratory system showing acute respiratory distress syndrome (ARDS). However, there is no targeted therapeutic agent yet and due to the growing cases of infections and the rising death tolls, discovery of the possible drug is the need of the hour. In general, the study for discovering therapeutic agent for SARS-CoV-2 is largely focused on large-scale screening with fragment-based drug discovery (FBDD). With the recent advancement in cryo-electron microscopy (Cryo-EM), it has become one of the widely used tools in structural biology. It is effective in investigating the structure of numerous proteins in high-resolution and also had an intense influence on drug discovery, determining the binding reaction and regulation of known drugs as well as leading the design and development of new drug candidates. Here, we review the application of cryo-EM in a structure-based drug design (SBDD) and in silico screening of the recently acquired FBDD in SARS-CoV-2. Such insights will help deliver better understanding in the procurement of the effective remedial solution for this pandemic.
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Affiliation(s)
- Han-Ul Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, 24341, Gangwon-do, Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1, Kangwondaehak-gil, Chuncheon-si, 24341, Gangwon-do, Korea.
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12
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Martin WJ, Grandi P, Marcia M. Screening strategies for identifying RNA- and ribonucleoprotein-targeted compounds. Trends Pharmacol Sci 2021; 42:758-771. [PMID: 34215444 DOI: 10.1016/j.tips.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022]
Abstract
The past few years have witnessed important breakthroughs in the identification of compounds that specifically bind and regulate RNAs and in optimizing them for therapeutic use. Here, we review successful and unsuccessful approaches in screening for RNA-targeted small molecules. We discuss advantages and disadvantages of the different screening techniques and variables that affect the outcome of RNA-screening projects. We also highlight key challenges that hamper the development of quality RNA ligands, especially the still-low availability of RNA-specific compound libraries and the poor understanding of RNA structural dynamics. We conclude that the development of new RNA-targeting drugs would greatly benefit from integration of the power of high-throughput screening technologies with improved biochemical, structural, and computational characterization of RNA targets.
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Affiliation(s)
- William J Martin
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, 69117 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Paola Grandi
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, 69117 Heidelberg, Germany
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble 38042, France.
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13
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Maucort C, Vo DD, Aouad S, Charrat C, Azoulay S, Di Giorgio A, Duca M. Design and Implementation of Synthetic RNA Binders for the Inhibition of miR-21 Biogenesis. ACS Med Chem Lett 2021; 12:899-906. [PMID: 34141067 DOI: 10.1021/acsmedchemlett.0c00682] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/03/2021] [Indexed: 12/17/2022] Open
Abstract
Targeting RNAs using small molecules is an emerging field of medicinal chemistry and holds promise for the discovery of efficient tools for chemical biology. MicroRNAs are particularly interesting targets since they are involved in a number of pathologies such as cancers. Indeed, overexpressed microRNAs in cancer are oncogenic and various series of inhibitors of microRNAs biogenesis have been developed in recent years. Here, we describe the structure-based design of new efficient inhibitors of microRNA-21. Starting from a previously identified hit, we performed biochemical studies and molecular docking to design a new series of optimized conjugates of neomycin aminoglycoside with artificial nucleobases and amino acids. Investigation about the mode of action and the site of the interaction of the newly synthesized compounds allowed for the description of structure-activity relationships and the identification of the most important parameters for miR-21 inhibition.
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Affiliation(s)
- Chloé Maucort
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Duc Duy Vo
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Samy Aouad
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Coralie Charrat
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Stéphane Azoulay
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Audrey Di Giorgio
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
| | - Maria Duca
- Université Côte d’Azur, CNRS, Institute of Chemistry of Nice (ICN), 28 avenue Valrose, 06100 Nice, France
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Umuhire Juru A, Hargrove AE. Frameworks for targeting RNA with small molecules. J Biol Chem 2021; 296:100191. [PMID: 33334887 PMCID: PMC7948454 DOI: 10.1074/jbc.rev120.015203] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/31/2022] Open
Abstract
Since the characterization of mRNA in 1961, our understanding of the roles of RNA molecules has significantly grown. Beyond serving as a link between DNA and proteins, RNA molecules play direct effector roles by binding to various ligands, including proteins, DNA, other RNAs, and metabolites. Through these interactions, RNAs mediate cellular processes such as the regulation of gene transcription and the enhancement or inhibition of protein activity. As a result, the misregulation of RNA molecules is often associated with disease phenotypes, and RNA molecules have been increasingly recognized as potential targets for drug development efforts, which in the past had focused primarily on proteins. Although both small molecule-based and oligonucleotide-based therapies have been pursued in efforts to target RNA, small-molecule modalities are often favored owing to several advantages including greater oral bioavailability. In this review, we discuss three general frameworks (sets of premises and hypotheses) that, in our view, have so far dominated the discovery of small-molecule ligands for RNA. We highlight the unique merits of each framework as well as the pitfalls associated with exclusive focus of ligand discovery efforts within only one framework. Finally, we propose that RNA ligand discovery can benefit from using progress made within these three frameworks to move toward a paradigm that formulates RNA-targeting questions at the level of RNA structural subclasses.
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Affiliation(s)
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina, USA.
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