1
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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2
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Niu X, Xu Z, Zhang Y, Zuo X, Chen C, Fang X. Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch. Nat Commun 2023; 14:7394. [PMID: 37968328 PMCID: PMC10651847 DOI: 10.1038/s41467-023-43232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg2+-induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg2+, the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.
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Affiliation(s)
- Xiaolin Niu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhonghe Xu
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yufan Zhang
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Chunlai Chen
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
| | - Xianyang Fang
- Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Key Laboratory of RNA Science and Engineering, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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3
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Fernandes GFS, Scarim CB, Kim SH, Wu J, Castagnolo D. Oxazolidinones as versatile scaffolds in medicinal chemistry. RSC Med Chem 2023; 14:823-847. [PMID: 37252095 PMCID: PMC10211318 DOI: 10.1039/d2md00415a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/06/2023] [Indexed: 11/19/2023] Open
Abstract
Oxazolidinone is a five-member heterocyclic ring with several biological applications in medicinal chemistry. Among the three possible isomers, 2-oxazolidinone is the most investigated in drug discovery. Linezolid was pioneered as the first approved drug containing an oxazolidinone ring as the pharmacophore group. Numerous analogues have been developed since its arrival on the market in 2000. Some have succeeded in reaching the advanced stages of clinical studies. However, most oxazolidinone derivatives reported in recent decades have not reached the initial stages of drug development, despite their promising pharmacological applications in a variety of therapeutic areas, including antibacterial, antituberculosis, anticancer, anti-inflammatory, neurologic, and metabolic diseases, among other areas. Therefore, this review article aims to compile the efforts of medicinal chemists who have explored this scaffold over the past decades and highlight the potential of the class for medicinal chemistry.
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Affiliation(s)
| | - Cauê Benito Scarim
- Department of Drugs and Medicines, School of Pharmaceutical Sciences, São Paulo State University Araraquara 14800903 Brazil
| | - Seong-Heun Kim
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
- School of Cancer and Pharmaceutical Sciences, King's College London 150 Stamford Street SE1 9NH London UK
| | - Jingyue Wu
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
| | - Daniele Castagnolo
- Department of Chemistry, University College London 20 Gordon Street WC1H 0AJ London UK
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4
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Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents. Antibiotics (Basel) 2023; 12:antibiotics12030463. [PMID: 36978331 PMCID: PMC10044086 DOI: 10.3390/antibiotics12030463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular docking. It would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. We examined the performance of five molecular docking programs (AutoDock 4, AutoDock Vina, DOCK 6, rDock, and RLDock) for their ability to model ribosomal–ligand interactions with oxazolidinones. Eleven ribosomal crystal structures with oxazolidinones as the ligands were docked. The accuracy was evaluated by calculating the docked complexes’ root-mean-square deviation (RMSD) and the program’s internal scoring function. The rankings for each program based on the median RMSD between the native and predicted were DOCK 6 > AD4 > Vina > RDOCK >> RLDOCK. Results demonstrate that the top-performing program, DOCK 6, could accurately replicate the ligand binding in only four of the eleven ribosomes due to the poor electron density of said ribosomal structures. In this study, we have further benchmarked the performance of the DOCK 6 docking algorithm and scoring in improving virtual screening (VS) enrichment using the dataset of 285 oxazolidinone derivatives against oxazolidinone binding sites in the S. aureus ribosome. However, there was no clear trend between the structure and activity of the oxazolidinones in VS. Overall, the docking performance indicates that the RNA pocket’s high flexibility does not allow for accurate docking prediction, highlighting the need to validate VS. protocols for ligand-RNA before future use. Later, we developed a re-scoring method incorporating absolute docking scores and molecular descriptors, and the results indicate that the descriptors greatly improve the correlation of docking scores and pMIC values. Morgan fingerprint analysis was also used, suggesting that DOCK 6 underpredicted molecules with tail modifications with acetamide, n-methylacetamide, or n-ethylacetamide and over-predicted molecule derivatives with methylamino bits. Alternatively, a ligand-based approach similar to a field template was taken, indicating that each derivative’s tail groups have strong positive and negative electrostatic potential contributing to microbial activity. These results indicate that one should perform VS. campaigns of ribosomal antibiotics with care and that more comprehensive strategies, including molecular dynamics simulations and relative free energy calculations, might be necessary in conjunction with VS. and docking.
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5
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Hossain MI, Myers M, Herath D, Aldhumani AH, Boesger H, Hines JV. 4-Aminoquinolines modulate RNA structure and function: Pharmacophore implications of a conformationally restricted polyamine. Biochem Biophys Res Commun 2023; 644:55-61. [PMID: 36630735 PMCID: PMC10473465 DOI: 10.1016/j.bbrc.2022.12.080] [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: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
RNA structure plays an important role in regulating cellular function and there is a significant emerging interest in targeting RNA for drug discovery. Here we report the identification of 4-aminoquinolines as modulators of RNA structure and function. Aminoquinolines have a broad range of pharmacological activities, but their specific mechanism of action is often not fully understood. Using electrophoretic mobility shift assays and enzymatic probing we identified 4-aminoquinolines that bind the stem-loop II motif (s2m) of SARS-CoV-2 RNA site-specifically and induce dimerization. Using fluorescence-based RNA binding and T-box riboswitch functional assays we identified that hydroxychloroquine binds the T-box riboswitch antiterminator RNA element and inhibits riboswitch function. Based on its structure and riboswitch dose-response activity we identified that the antagonist activity of hydroxychloroquine is consistent with it being a conformationally restricted analog of the polyamine spermidine. Given the known role that polyamines play in RNA function, the identification of an RNA binding ligand with the pharmacophore of a conformationally restricted polyamine has significant implications for further elucidation of RNA structure-function relationships and RNA-targeted drug discovery.
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Affiliation(s)
- Md Ismail Hossain
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Mason Myers
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Honors Tutorial College, Ohio University, Athens, OH, 45701, USA
| | - Danushika Herath
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Ali H Aldhumani
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Hannah Boesger
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, USA; Honors Tutorial College, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
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6
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Huguenot F, Vidal M. Phenyloxycarbonyl (Phoc) Carbamate: Chemioselective Reactivity and Tetra- n-butylammonium Fluoride Deprotection Study. ACS OMEGA 2022; 7:44861-44868. [PMID: 36530256 PMCID: PMC9753175 DOI: 10.1021/acsomega.2c04979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/12/2022] [Indexed: 06/17/2023]
Abstract
We present the results of the chemoselective reactivity of phenylcarbamates. Phenylcarbamates of primary amines are reactive to form urea, and phenylcarbamates of secondary amines can be used as tags due to the existence of rotamers. Moreover, deprotection attempts to to recover the primary amines in use of a catalytic amount of TBAF show the possibility of obtaining the symmetrical urea from the corresponding phenylcarbamate. We have begun the study of the transformation of Phoc carbamates into the corresponding free amines by TBAF. We present here our most significant results concerning the sensitivity of this reaction in terms of the solvent and substrate.
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Affiliation(s)
- Florent Huguenot
- CNRS
UMR 8038 CiTCoM, Université de Paris, Faculté de Pharmacie
de Paris, 4 Avenue de
l’observatoire, Paris 75006, France
- INSERM
U 1268 Medicinal Chemistry and Translational Research, Paris 75006, France
| | - Michel Vidal
- CNRS
UMR 8038 CiTCoM, Université de Paris, Faculté de Pharmacie
de Paris, 4 Avenue de
l’observatoire, Paris 75006, France
- INSERM
U 1268 Medicinal Chemistry and Translational Research, Paris 75006, France
- UF
Biologie du médicament—Toxicologie, Hôpital Cochin, AP-HP, 27 Rue du Faubourg Saint
Jacques, Paris 75014, France
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7
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Giarimoglou N, Kouvela A, Maniatis A, Papakyriakou A, Zhang J, Stamatopoulou V, Stathopoulos C. A Riboswitch-Driven Era of New Antibacterials. Antibiotics (Basel) 2022; 11:antibiotics11091243. [PMID: 36140022 PMCID: PMC9495366 DOI: 10.3390/antibiotics11091243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Riboswitches are structured non-coding RNAs found in the 5′ UTR of important genes for bacterial metabolism, virulence and survival. Upon the binding of specific ligands that can vary from simple ions to complex molecules such as nucleotides and tRNAs, riboswitches change their local and global mRNA conformations to affect downstream transcription or translation. Due to their dynamic nature and central regulatory role in bacterial metabolism, riboswitches have been exploited as novel RNA-based targets for the development of new generation antibacterials that can overcome drug-resistance problems. During recent years, several important riboswitch structures from many bacterial representatives, including several prominent human pathogens, have shown that riboswitches are ideal RNA targets for new compounds that can interfere with their structure and function, exhibiting much reduced resistance over time. Most interestingly, mainstream antibiotics that target the ribosome have been shown to effectively modulate the regulatory behavior and capacity of several riboswitches, both in vivo and in vitro, emphasizing the need for more in-depth studies and biological evaluation of new antibiotics. Herein, we summarize the currently known compounds that target several main riboswitches and discuss the role of mainstream antibiotics as modulators of T-box riboswitches, in the dawn of an era of novel inhibitors that target important bacterial regulatory RNAs.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Ag. Paraskevi, 15341 Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-997932
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8
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Giarimoglou N, Kouvela A, Patsi I, Zhang J, Stamatopoulou V, Stathopoulos C. Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action. Nucleic Acids Res 2022; 50:5834-5849. [PMID: 35580054 PMCID: PMC9177973 DOI: 10.1093/nar/gkac359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 01/27/2023] Open
Abstract
T-box riboswitches (T-boxes) are essential RNA regulatory elements with a remarkable structural diversity, especially among bacterial pathogens. In staphylococci, all glyS T-boxes synchronize glycine supply during synthesis of nascent polypeptides and cell wall formation and are characterized by a conserved and unique insertion in their antiterminator/terminator domain, termed stem Sa. Interestingly, in Staphylococcus aureus the stem Sa can accommodate binding of specific antibiotics, which in turn induce robust and diverse effects on T-box-mediated transcription. In the present study, domain swap mutagenesis and probing analysis were performed to decipher the role of stem Sa. Deletion of stem Sa significantly reduces both the S. aureus glyS T-box-mediated transcription readthrough levels and the ability to discriminate among tRNAGly isoacceptors, both in vitro and in vivo. Moreover, the deletion inverted the previously reported stimulatory effects of specific antibiotics. Interestingly, stem Sa insertion in the terminator/antiterminator domain of Geobacillus kaustophilus glyS T-box, which lacks this domain, resulted in elevated transcription in the presence of tigecycline and facilitated discrimination among proteinogenic and nonproteinogenic tRNAGly isoacceptors. Overall, stem Sa represents a lineage-specific structural feature required for efficient staphylococcal glyS T-box-mediated transcription and it could serve as a species-selective druggable target through its ability to modulate antibiotic binding.
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Affiliation(s)
- Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Adamantia Kouvela
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ioanna Patsi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
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9
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Wencker FDR, Marincola G, Schoenfelder SMK, Maaß S, Becher D, Ziebuhr W. Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay. Nucleic Acids Res 2021; 49:2192-2212. [PMID: 33450025 PMCID: PMC7913692 DOI: 10.1093/nar/gkaa1277] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/18/2020] [Accepted: 01/08/2021] [Indexed: 11/12/2022] Open
Abstract
In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5′ untranslated region (met leader RNA) of the S. aureus metICFE-mdh operon controls downstream gene transcription upon interaction with uncharged methionyl-tRNA. met leader and metICFE-mdh (m)RNAs undergo RNase-mediated degradation in a process whose molecular details are poorly understood. Here we determined the secondary structure of the met leader RNA and found the element to harbor, beyond other conserved T-box riboswitch structural features, a terminator helix which is target for RNase III endoribonucleolytic cleavage. As the terminator is a thermodynamically highly stable structure, it also forms posttranscriptionally in met leader/ metICFE-mdh read-through transcripts. Cleavage by RNase III releases the met leader from metICFE-mdh mRNA and initiates RNase J-mediated degradation of the mRNA from the 5′-end. Of note, metICFE-mdh mRNA stability varies over the length of the transcript with a longer lifespan towards the 3′-end. The obtained data suggest that coordinated RNA decay represents another checkpoint in a complex regulatory network that adjusts costly methionine biosynthesis to current metabolic requirements.
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Affiliation(s)
- Freya D R Wencker
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg 97080, Germany
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg 97080, Germany
| | - Sonja M K Schoenfelder
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg 97080, Germany
| | - Sandra Maaß
- Institute of Microbiology, University of Greifswald, Greifswald 17489, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald 17489, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg 97080, Germany
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10
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Aldhumani AH, Hossain MI, Fairchild EA, Boesger H, Marino EC, Myers M, Hines JV. RNA sequence and ligand binding alter conformational profile of SARS-CoV-2 stem loop II motif. Biochem Biophys Res Commun 2021; 545:75-80. [PMID: 33545635 PMCID: PMC7834705 DOI: 10.1016/j.bbrc.2021.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
Abstract
Antiviral drug discovery continues to be an essential complement to vaccine development for overcoming the global pandemic caused by SARS-CoV-2. The genomic RNA of SARS-CoV-2 contains structural elements important for viral replication and/or pathogenesis making them potential therapeutic targets. Here we report on the stem-loop II motif, a highly conserved noncoding RNA element. Based on our homology model we determined that the G to U transversion in the SARS-CoV-2 stem-loop II motif (S2MG35U) forms a C–U base-pair isosteric to the C-G base-pair in the early 2000’s SARS-CoV (S2M). In addition, chemo-enzymatic probing and molecular dynamics simulations indicate the S2MG35U conformational profile is altered compared to S2M in the apical loop region. We explored S2MG35U as a potential drug target by docking a library of FDA approved drugs. Enzymatic probing of the best docking ligands (aminoglycosides and polymyxins) indicated that polymyxin binding alters the conformational profile and/or secondary structure of the RNA. The SARS-CoV-2 stem-loop II motif conformational differences due to nucleotide transversion and ligand binding are highly significant and provide insight for future drug discovery efforts since the conformation of noncoding RNA elements affects their function.
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Affiliation(s)
- Ali H Aldhumani
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Md Ismail Hossain
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Emily A Fairchild
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States
| | - Hannah Boesger
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Emily C Marino
- Department of Biological Sciences, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Mason Myers
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States; Honors Tutorial College, Ohio University, Athens, OH, 45701, United States
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Ohio University, Athens, OH, 45701, United States.
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11
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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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12
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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: 0.5] [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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13
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Demir E, Sari O, Çetinkaya Y, Atmaca U, Sağ Erdem S, Çelik M. One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway. Beilstein J Org Chem 2020; 16:1805-1819. [PMID: 32765796 PMCID: PMC7385335 DOI: 10.3762/bjoc.16.148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/02/2020] [Indexed: 11/23/2022] Open
Abstract
The one-pot reaction of chlorosulfonyl isocyanate (CSI) with epoxides having phenyl, benzyl and fused cyclic alkyl groups in different solvents under mild reaction conditions without additives and catalysts was studied. Oxazolidinones and five-membered cyclic carbonates were obtained in ratios close to 1:1 in the cyclization reactions. The best yields of these compounds were obtained in dichloromethane (DCM). Together with 16 known compounds, two novel oxazolidinone derivatives and two novel cyclic carbonates were synthesized with an efficient and straightforward method. Compared to the existing methods, the synthetic approach presented here provides the following distinct advantageous: being a one-pot reaction with metal-free reagent, having shorter reaction times, good yields and a very simple purification method. Moreover, using the density functional theory (DFT) method at the M06-2X/6-31+G(d,p) level of theory the mechanism of the cycloaddition reactions has been elucidated. The further investigation of the potential energy surfaces associated with two possible channels leading to oxazolidinones and five-membered cyclic carbonates disclosed that the cycloaddition reaction proceeds via an asynchronous concerted mechanism in gas phase and in DCM.
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Affiliation(s)
- Esra Demir
- Department of Chemistry, Faculty of Science, Atatürk University, 25240 Erzurum, Turkey
| | - Ozlem Sari
- Department of Chemistry, Faculty of Arts and Sciences, Kırşehir Ahi Evran University, 40100 Kırşehir, Turkey
| | - Yasin Çetinkaya
- Department of Food Technology, Oltu Vocational School, Atatürk University, 25400 Oltu, Erzurum, Turkey
| | - Ufuk Atmaca
- Department of Chemistry, Faculty of Science, Atatürk University, 25240 Erzurum, Turkey.,Department of Food Technology, Oltu Vocational School, Atatürk University, 25400 Oltu, Erzurum, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Goztepe Campus, 34722 Istanbul, Turkey
| | - Murat Çelik
- Department of Chemistry, Faculty of Science, Atatürk University, 25240 Erzurum, Turkey
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14
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Synthesis of Chiral 5‐Aryl‐2‐oxazolidinones via Halohydrin Dehalogenase‐Catalyzed Enantio‐ and Regioselective Ring‐Opening of Styrene Oxides. Adv Synth Catal 2020. [DOI: 10.1002/adsc.201901412] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Suddala KC, Zhang J. An evolving tale of two interacting RNAs-themes and variations of the T-box riboswitch mechanism. IUBMB Life 2019; 71:1167-1180. [PMID: 31206978 DOI: 10.1002/iub.2098] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/10/2019] [Indexed: 01/10/2023]
Abstract
T-box riboswitches are a widespread class of structured noncoding RNAs in Gram-positive bacteria that regulate the expression of amino acid-related genes. They form negative feedback loops to maintain steady supplies of aminoacyl-transfer RNAs (tRNAs) to the translating ribosomes. T-box riboswitches are located in the 5' leader regions of mRNAs that they regulate and directly bind to their cognate tRNA ligands. T-boxes further sense the aminoacylation state of the bound tRNAs and, based on this readout, regulate gene expression at the level of transcription or translation. T-box riboswitches consist of two conserved domains-a 5' Stem I domain that is involved in specific tRNA recognition and a 3' antiterminator/antisequestrator (or discriminator) domain that senses the amino acid on the 3' end of the bound tRNA. Interaction of the 3' end of an uncharged but not charged tRNA with a thermodynamically weak discriminator domain stabilizes it to promote transcription readthrough or translation initiation. Recent biochemical, biophysical, and structural studies have provided high-resolution insights into the mechanism of tRNA recognition by Stem I, several structural models of full-length T-box-tRNA complexes, mechanism of amino acid sensing by the antiterminator domain, as well as kinetic details of tRNA binding to the T-box riboswitches. In addition, translation-regulating T-box riboswitches have been recently characterized, which presented key differences from the canonical transcriptional T-boxes. Here, we review the recent developments in understanding the T-box riboswitch mechanism that have employed various complementary approaches. Further, the regulation of multiple essential genes by T-boxes makes them very attractive drug targets to combat drug resistance. The recent progress in understanding the biochemical, structural, and dynamic aspects of the T-box riboswitch mechanism will enable more precise and effective targeting with small molecules. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1167-1180, 2019.
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Affiliation(s)
- Krishna C Suddala
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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16
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Frohlich KM, Weintraub SF, Bell JT, Todd GC, Väre VYP, Schneider R, Kloos ZA, Tabe ES, Cantara WA, Stark CJ, Onwuanaibe UJ, Duffy BC, Basanta-Sanchez M, Kitchen DB, McDonough KA, Agris PF. Discovery of Small-Molecule Antibiotics against a Unique tRNA-Mediated Regulation of Transcription in Gram-Positive Bacteria. ChemMedChem 2019; 14:758-769. [PMID: 30707489 DOI: 10.1002/cmdc.201800744] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/24/2019] [Indexed: 01/24/2023]
Abstract
The emergence of multidrug-resistant bacteria necessitates the identification of unique targets of intervention and compounds that inhibit their function. Gram-positive bacteria use a well-conserved tRNA-responsive transcriptional regulatory element in mRNAs, known as the T-box, to regulate the transcription of multiple operons that control amino acid metabolism. T-box regulatory elements are found only in the 5'-untranslated region (UTR) of mRNAs of Gram-positive bacteria, not Gram-negative bacteria or the human host. Using the structure of the 5'UTR sequence of the Bacillus subtilis tyrosyl-tRNA synthetase mRNA T-box as a model, in silico docking of 305 000 small compounds initially yielded 700 as potential binders that could inhibit the binding of the tRNA ligand. A single family of compounds inhibited the growth of Gram-positive bacteria, but not Gram-negative bacteria, including drug-resistant clinical isolates at minimum inhibitory concentrations (MIC 16-64 μg mL-1 ). Resistance developed at an extremely low mutational frequency (1.21×10-10 ). At 4 μg mL-1 , the parent compound PKZ18 significantly inhibited in vivo transcription of glycyl-tRNA synthetase mRNA. PKZ18 also inhibited in vivo translation of the S. aureus threonyl-tRNA synthetase protein. PKZ18 bound to the Specifier Loop in vitro (Kd ≈24 μm). Its core chemistry necessary for antibacterial activity has been identified. These findings support the T-box regulatory mechanism as a new target for antibiotic discovery that may impede the emergence of resistance.
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Affiliation(s)
- Kyla M Frohlich
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: Regeneron Inc., Rensselaer, NY, USA
| | - Spencer F Weintraub
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: New York Medical College, Valhalla, NY, USA
| | - Janeen T Bell
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: Albany Medical College, Center for Physician Assistant Studies, Albany, NY, USA
| | - Gabrielle C Todd
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ville Y P Väre
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ryan Schneider
- Department of Biomedical Sciences, School of Public Health, University at Albany - State University of New York, P.O. Box 22002, Albany, NY, 12201, USA
| | - Zachary A Kloos
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, P.O. Box 22002, Albany, NY, 12201-2002, USA.,Current address: Molecular, Cellular and Developmental Biology, Yale University, West Haven, CT, USA
| | - Ebot S Tabe
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, P.O. Box 22002, Albany, NY, 12201-2002, USA.,Current address: Albany College of Pharmacy and Health Sciences, Albany, NY, USA
| | - William A Cantara
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Caren J Stark
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Urenna J Onwuanaibe
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Bryan C Duffy
- Albany Molecular Research Incorporated, 26 Corporate Circle, Albany, NY, 12203, USA.,Current address: New York State Department of Health, Albany, NY, USA
| | - Maria Basanta-Sanchez
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: Waters Corporation, Pleasanton, CA, USA
| | - Douglas B Kitchen
- Albany Molecular Research Incorporated, 26 Corporate Circle, Albany, NY, 12203, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany - State University of New York, P.O. Box 22002, Albany, NY, 12201, USA.,Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, P.O. Box 22002, Albany, NY, 12201-2002, USA
| | - Paul F Agris
- The RNA Institute and the Department of Biological Sciences, University at Albany - State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA.,Current address: Duke University, Medical School, Durham, NC, USA
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17
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Abstract
The T-box riboswitch is a unique, RNA-based regulatory mechanism that modulates expression of a wide variety of amino acid-related genes, predominantly in Firmicutes. RNAs of this class selectively bind a specific cognate tRNA, utilizing recognition of the tRNA anticodon and other tRNA features. The riboswitch monitors the aminoacylation status of the tRNA to induce expression of the regulated downstream gene(s) at the level of transcription antitermination or derepression of translation initiation in response to reduced tRNA charging via stabilization of an antiterminator or antisequestrator. Recent biochemical and structural studies have revealed new features of tRNA recognition that extend beyond the initially identified Watson-Crick base-pairing of a codon-like sequence in the riboswitch with the tRNA anticodon, and residues in the antiterminator or antisequestrator with the tRNA acceptor end. These studies have revealed new tRNA contacts and new modes of riboswitch function and ligand recognition that expand our understanding of RNA-RNA recognition and the biological roles of tRNA.
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18
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Stamatopoulou V, Apostolidi M, Li S, Lamprinou K, Papakyriakou A, Zhang J, Stathopoulos C. Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors. Nucleic Acids Res 2017; 45:10242-10258. [PMID: 28973457 PMCID: PMC5622331 DOI: 10.1093/nar/gkx663] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/18/2017] [Indexed: 11/14/2022] Open
Abstract
Recently, it was discovered that exposure to mainstream antibiotics activate numerous bacterial riboregulators that control antibiotic resistance genes including metabolite-binding riboswitches and other transcription attenuators. However, the effects of commonly used antibiotics, many of which exhibit RNA-binding properties, on the widespread T-box riboswitches, remain unknown. In Staphylococcus aureus, a species-specific glyS T-box controls the supply of glycine for both ribosomal translation and cell wall synthesis, making it a promising target for next-generation antimicrobials. Here, we report that specific protein synthesis inhibitors could either significantly increase T-box-mediated transcription antitermination, while other compounds could suppress it, both in vitro and in vivo. In-line probing of the full-length T-box combined with molecular modelling and docking analyses suggest that the antibiotics that promote transcription antitermination stabilize the T-box:tRNA complex through binding specific positions on stem I and the Staphylococcal-specific stem Sa. By contrast, the antibiotics that attenuate T-box transcription bind to other positions on stem I and do not interact with stem Sa. Taken together, our results reveal that the transcription of essential genes controlled by T-box riboswitches can be directly modulated by commonly used protein synthesis inhibitors. These findings accentuate the regulatory complexities of bacterial response to antimicrobials that involve multiple riboregulators.
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Affiliation(s)
| | - Maria Apostolidi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
| | - Katerina Lamprinou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, 50 South Drive, Bethesda, MD 20892, USA
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19
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RNA as a small molecule druggable target. Bioorg Med Chem Lett 2017; 27:5083-5088. [PMID: 29097169 DOI: 10.1016/j.bmcl.2017.10.052] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/11/2017] [Accepted: 10/22/2017] [Indexed: 12/20/2022]
Abstract
Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents.
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20
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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: 56] [Impact Index Per Article: 8.0] [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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21
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Qian B, Xiong H, Zhu N, Ye C, Jian W, Bao H. Copper-catalyzed diesterification of 1,3-diene for the synthesis of allylic diester compounds. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.06.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Cheng BB, Yu B, Hu CW. Indirect conversion of ambient pressure CO 2 into oxazolidin-2-ones by a copper-based magnetic nanocatalyst. RSC Adv 2016; 6:87179-87187. [DOI: 10.1039/c6ra15857a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
A magnetically recyclable Cu-based catalytic system was developed for the indirect conversion of ambient pressure of CO2 into oxazolidin-2-ones.
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Affiliation(s)
- Bin-Bin Cheng
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- P. R. China
| | - Bing Yu
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- P. R. China
| | - Chang-Wen Hu
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- P. R. China
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23
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C. Bergmeier S, Fang F, Maciagiewicz I. A Synthesis of Hexahydro-H-oxazolo[3,4-a]pyrazin-3-ones from Fused Aziridines. HETEROCYCLES 2016. [DOI: 10.3987/com-15-s(t)24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Liu J, Zeng C, Hogan V, Zhou S, Monwar MM, Hines JV. Identification of Spermidine Binding Site in T-box Riboswitch Antiterminator RNA. Chem Biol Drug Des 2015; 87:182-9. [PMID: 26348362 DOI: 10.1111/cbdd.12660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/24/2015] [Accepted: 08/14/2015] [Indexed: 01/08/2023]
Abstract
The T-box transcription antitermination riboswitch controls bacterial gene expression by structurally responding to uncharged, cognate tRNA. Previous studies indicated that cofactors, such as the polyamine spermidine, might serve a specific functional role in enhancing riboswitch efficacy. As riboswitch function depends on key RNA structural changes involving the antiterminator element, the interaction of spermidine with the T-box riboswitch antiterminator element was investigated. Spermidine binds antiterminator model RNA with high affinity (micromolar Kd ) based on isothermal titration calorimetry and fluorescence-monitored binding assays. NMR titration studies, molecular modeling, and inline and enzymatic probing studies indicate that spermidine binds at the 3' portion of the highly conserved seven-nucleotide bulge in the antiterminator. Together, these results support the conclusion that spermidine binds the T-box antiterminator RNA preferentially in a location important for antiterminator function. The implications of these findings are significant both for better understanding of the T-box riboswitch mechanism and for antiterminator-targeted drug discovery efforts.
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Affiliation(s)
- Jia Liu
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Chunxi Zeng
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Vivian Hogan
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Md Masud Monwar
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V Hines
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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25
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Abstract
The T box riboswitch is an intriguing potential target for antibacterial drug discovery. Found primarily in Gram-positive bacteria, the riboswitch regulates gene expression by selectively responding to uncharged tRNA to control transcription readthrough. Polyamines and molecular crowding are known to specifically affect RNA function, but their effect on T box riboswitch efficacy and tRNA affinity have not been fully characterized. A fluorescence-monitored in vitro transcription assay was developed to readily quantify these molecular interactions and to provide a moderate-throughput functional assay for a comprehensive drug discovery screening cascade. The polyamine spermidine specifically enhanced T box riboswitch readthrough efficacy with an EC50 = 0.58 mM independent of tRNA binding. Molecular crowding, simulated by the addition of polyethylene glycol, had no effect on tRNA affinity for the riboswitch, but did reduce the efficacy of tRNA-induced readthrough. These results indicate that the T box riboswitch tRNA affinity and readthrough efficacy are intricately modulated by environmental factors.
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26
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T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions. Proc Natl Acad Sci U S A 2015; 112:1113-8. [PMID: 25583497 DOI: 10.1073/pnas.1424175112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The T box riboswitch regulates many amino acid-related genes in Gram-positive bacteria. T box riboswitch-mediated gene regulation was shown previously to occur at the level of transcription attenuation via structural rearrangements in the 5' untranslated (leader) region of the mRNA in response to binding of a specific uncharged tRNA. In this study, a novel group of isoleucyl-tRNA synthetase gene (ileS) T box leader sequences found in organisms of the phylum Actinobacteria was investigated. The Stem I domains of these RNAs lack several highly conserved elements that are essential for interaction with the tRNA ligand in other T box RNAs. Many of these RNAs were predicted to regulate gene expression at the level of translation initiation through tRNA-dependent stabilization of a helix that sequesters a sequence complementary to the Shine-Dalgarno (SD) sequence, thus freeing the SD sequence for ribosome binding and translation initiation. We demonstrated specific binding to the cognate tRNA(Ile) and tRNA(Ile)-dependent structural rearrangements consistent with regulation at the level of translation initiation, providing the first biochemical demonstration, to our knowledge, of translational regulation in a T box riboswitch.
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27
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Fluorescence assays for monitoring RNA-ligand interactions and riboswitch-targeted drug discovery screening. Methods Enzymol 2014; 550:363-83. [PMID: 25605395 DOI: 10.1016/bs.mie.2014.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches and other noncoding regulatory RNA are intriguing targets for the development of therapeutic agents. A significant challenge in the drug discovery process, however, is the identification of potent compounds that bind the target RNA specifically and disrupt its function. Essential to this process is an effectively designed cascade of screening assays. A screening cascade for identifying compounds that target the T box riboswitch antiterminator element is described. In the primary assays, moderate to higher throughput screening of compound libraries is achieved by combining the sensitivity of fluorescence techniques with functionally relevant assays. Active compounds are then validated and the binding to target RNA further characterized in secondary assays. The cascade of assays monitor ligand-induced changes in the steady-state fluorescence of an attached dye or internally incorporated 2-aminopurine; the fluorescence anisotropy of an RNA complex; and, the thermal denaturation fluorescence profile of a fluorophore-quencher labeled RNA. While the assays described have been developed for T box riboswitch-targeted drug discovery, the fluorescence methods and screening cascade design principles can be applied to drug discovery efforts targeted toward other medicinally relevant noncoding RNA.
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28
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Substrate scope and stereocontrol in the Rh(II)-catalysed oxyamination of allylic carbamates. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Slama S, Besbes R. Stereoselective synthesis of erythro-β-chloroamines and their conversion into functionalized trans-oxazolidin-2-ones. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Henkin TM. The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:959-963. [PMID: 24816551 DOI: 10.1016/j.bbagrm.2014.04.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 12/23/2022]
Abstract
The T box riboswitch is a cis-acting regulatory RNA that controls expression of amino acid-related genes in response to the aminoacylation state of a specific tRNA. Multiple genes in the same organism can utilize this mechanism, with each gene responding independently to its cognate tRNA. The uncharged tRNA interacts directly with the regulatory RNA element, and this interaction promotes readthrough of an intrinsic transcriptional termination site upstream of the regulated coding sequence. A second class of T box elements uses a similar tRNA-dependent response to regulate translation initiation. This review will describe the current state of our knowledge about this regulatory system. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Tina M Henkin
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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31
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Paddock RL, Adhikari D, Lord RL, Baik MH, Nguyen ST. [(Salcen)CrIII + Lewis base]-catalyzed synthesis of N-aryl-substituted oxazolidinones from epoxides and aryl isocyanates. Chem Commun (Camb) 2014; 50:15187-90. [DOI: 10.1039/c4cc07421a] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
[(Salcen)CrIII + Lewis base] was found to be a highly active and selective catalyst system in the [2+3] cycloaddition reaction between epoxides and isocyanates to form 5-oxazolidinones.
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Affiliation(s)
- Robert L. Paddock
- Department of Chemistry and the Institute of Catalysis for Energy Processes
- Northwestern University
- Evanston, USA
| | - Debashis Adhikari
- Department of Chemistry and the Institute of Catalysis for Energy Processes
- Northwestern University
- Evanston, USA
- Department of Chemistry
- Indiana University
| | - Richard L. Lord
- Department of Chemistry and the Institute of Catalysis for Energy Processes
- Northwestern University
- Evanston, USA
| | - Mu-Hyun Baik
- Department of Chemistry
- Indiana University
- Bloomington, USA
| | - SonBinh T. Nguyen
- Department of Chemistry and the Institute of Catalysis for Energy Processes
- Northwestern University
- Evanston, USA
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Murakami T. Synthesis of all four stereoisomers of 5-formyl-4-hydroxymethyl-1,3-oxazolidin-2-ones from d-glucosamine. Carbohydr Res 2013; 375:47-54. [DOI: 10.1016/j.carres.2013.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/16/2013] [Accepted: 04/17/2013] [Indexed: 12/01/2022]
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Studies on the ring opening reactions of 3-oxa-1-azabicyclo[3.1.0]hexan-2-ones. Synthesis of aminomethyl oxazolidinones and aziridinyl ureas. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Jentzsch F, Hines JV. Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery. BMC Bioinformatics 2012; 13 Suppl 2:S5. [PMID: 22536868 PMCID: PMC3375634 DOI: 10.1186/1471-2105-13-s2-s5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background The T box riboswitch controls bacterial transcription by structurally responding to tRNA aminoacylation charging ratios. Knowledge of the thermodynamic stability difference between two competing structural elements within the riboswitch, the terminator and the antiterminator, is critical for effective T box-targeted drug discovery. Methods The ΔG of aminoacyl tRNA synthetase (aaRS) T box riboswitch terminators and antiterminators was predicted using DINAMelt and the resulting ΔΔG (ΔGTerminator - ΔGAntiterminator) values were compared. Results Average ΔΔG values did not differ significantly between the bacterial species analyzed, but there were significant differences based on the type of aaRS. Conclusions The data indicate that, of the bacteria studied, there is little potential for drug targeting based on overall bacteria-specific thermodynamic differences of the T box antiterminator vs. terminator stability, but that aaRS-specific thermodynamic differences could possibly be exploited for designing drug specificity.
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Abstract
RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void.
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Affiliation(s)
- Lirui Guan
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
| | - Matthew D. Disney
- Department of Chemistry, The Kellogg School of Science
and Technology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458,
United States
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Fang F, Vogel M, Hines JV, Bergmeier SC. Fused ring aziridines as a facile entry into triazole fused tricyclic and bicyclic heterocycles. Org Biomol Chem 2012; 10:3080-91. [DOI: 10.1039/c2ob07042a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhou S, Acquaah-Harrison G, Jack KD, Bergmeier SC, Hines JV. Ligand-induced changes in T box antiterminator RNA stability. Chem Biol Drug Des 2011; 79:202-8. [PMID: 22117759 DOI: 10.1111/j.1747-0285.2011.01274.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
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Affiliation(s)
- Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Zhou S, Means JA, Acquaah-Harrison G, Bergmeier SC, Hines JV. Characterization of a 1,4-disubstituted 1,2,3-triazole binding to T box antiterminator RNA. Bioorg Med Chem 2011; 20:1298-302. [PMID: 22230198 DOI: 10.1016/j.bmc.2011.12.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/05/2011] [Accepted: 12/10/2011] [Indexed: 10/14/2022]
Abstract
The T box riboswitch regulates the transcription of many bacterial genes by structurally responding to cognate non-aminoacylated (uncharged) tRNA. The riboswitch contains multiple conserved RNA elements including a key structural element, the antiterminator, which binds the tRNA acceptor end nucleotides. Previous studies identified a lead 1,4-disubstituted 1,2,3-triazole, GHB-7, that disrupted formation of a tRNA-antiterminator RNA model complex. The affinity and molecular interactions of GHB-7 binding to antiterminator model RNA were characterized as part of a comprehensive T box antiterminator RNA-targeted drug discovery project. In-line probing, UV-monitored thermal denaturation and docking studies all consistently indicated that GHB-7 likely binds to the bulge region of the antiterminator, reduces the flexibility of the bulge nucleotides and, overall, stabilizes the RNA secondary structure. These results begin to elucidate possible mechanisms for ligand-induced inhibition of tRNA binding to T box antiterminator RNA and contribute to the knowledge of how small molecules bind relatively simple RNA structural elements such as bulges.
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Affiliation(s)
- S Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Zhou S, Acquaah-Harrison G, Bergmeier SC, Hines JV. Anisotropy studies of tRNA-T box antiterminator RNA complex in the presence of 1,4-disubstituted 1,2,3-triazoles. Bioorg Med Chem Lett 2011; 21:7059-63. [PMID: 22001091 DOI: 10.1016/j.bmcl.2011.09.095] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 09/21/2011] [Accepted: 09/22/2011] [Indexed: 10/17/2022]
Abstract
The binding of tRNA to the T box antiterminator RNA element is a critical component of the T box riboswitch mechanism that regulates essential genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened for disruption of the tRNA-T box antiterminator RNA interaction using a fluorescence anisotropy-based assay. Several compounds reduced the anisotropy greater than 50% likely indicating significant competition for binding antiterminator RNA. General structure-activity trends indicated that the substituents at both N-1 and C-4 likely are involved in ligand binding. In addition, the anisotropy of the complex was significantly decreased not only by ligands with the possibility for electrostatic interactions with the RNA, but also by ligands with the potential for π-π stacking or other hydrophobic interactions indicating that these non-electrostatic interactions could possibly be utilized in the future development of compounds that target and disrupt the function of this medicinally important riboswitch.
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Affiliation(s)
- S Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio 45701, USA
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