Generic placeholder image

Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 1573-4064
ISSN (Online): 1875-6638

Current Frontiers

New Approaches in Sensing and Targeting Bacterial rRNA A-site

Author(s): Preethi Parameswaran, Nihar Ranjan* and Swaran J.S. Flora*

Volume 17, Issue 4, 2021

Published on: 11 October, 2019

Page: [299 - 309] Pages: 11

DOI: 10.2174/1573406415666191011160035

Price: $65

Abstract

New chemical agents that could combat increasing antibiotic resistance are urgently needed. In this mini-review, an old but highly relevant RNA sequence which is crucial for the continuation of bacterial life-cycle is covered. Some of the most significant advances of the last decade in sensing and targeting the bacterial rRNA A-site: a well-validated binding site of proverbially known aminoglycoside antibiotics are described. Some of the major advances in direct sensing of the bacterial decoding side (A-site) are described and also new fluorescent molecules that are capable of detecting lead compounds through high-throughput assays by displacement of fluorescent probe molecules are highlighted. Lastly, some of the recently discovered non-aminoglycoside small molecule binders of bacterial rRNA A-site as a new class of molecules that could provide future scaffolds and molecules for developing new antibacterial agents have been discussed.

Keywords: A-site, rRNA, FRET, antimicrobial agents, drug discovery, antimicrobial agents, drug discovery, Mycobacterium tuberculosis.

Next »
Graphical Abstract
[1]
Orgel, L.E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol., 2004, 39(2), 99-123.
[http://dx.doi.org/10.1080/10409230490460765] [PMID: 15217990]
[2]
Ranjan, N.; Arya, D.P. Linker dependent intercalation of bisbenzimidazole-aminosugars in an RNA duplex; selectivity in RNA vs. DNA binding. Bioorg. Med. Chem. Lett., 2016, 26(24), 5989-5994.
[http://dx.doi.org/10.1016/j.bmcl.2016.10.076] [PMID: 27884695]
[3]
Fourmy, D.; Recht, M.I.; Puglisi, J.D. Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNA. J. Mol. Biol., 1998, 277(2), 347-362.
[http://dx.doi.org/10.1006/jmbi.1997.1552] [PMID: 9514735]
[4]
Kling, D.; Chow, C.S.; Mobashery, S. “Binding of Antibiotics to the Aminoacyl-tRNA Site of Bacterial Ribosomes” in Aminoglycoside Antibiotics: From Chemical Biology to Drug Discovery. John Wiley & Sons, Inc. (Ed. D. P. Arya); , 2007, pp. 225-233.
[http://dx.doi.org/10.1002/9780470149676.ch7]
[5]
Arya, D.P. Aminoglycoside antibiotics: from chemical biology to drug discovery, 2nd ed; John Wiley & Sons, 2007, pp. 181-207.
[http://dx.doi.org/10.1002/9780470149676]
[6]
Davies, J. In the beginning there was streptomycin. Aminoglycoside Antibiotics; John Wiley & Sons, Inc: New Jersey, 2007, pp. 1-13.
[7]
Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell, 2002, 108(4), 557-572.
[http://dx.doi.org/10.1016/S0092-8674(02)00619-0] [PMID: 11909526]
[8]
Zaman, G.J.; Michiels, P.J.; van Boeckel, C.A. Targeting RNA: new opportunities to address drugless targets. Drug Discov. Today, 2003, 8(7), 297-306.
[http://dx.doi.org/10.1016/S1359-6446(03)02624-2] [PMID: 12654542]
[9]
King, A.; Watkins, D.; Kumar, S.; Ranjan, N.; Gong, C.; Whitlock, J.; Arya, D.P. Characterization of ribosomal binding and antibacterial activities using two orthogonal high-throughput screens. Antimicrob. Agents Chemother., 2013, 57(10), 4717-4726.
[http://dx.doi.org/10.1128/AAC.00671-13] [PMID: 23856777]
[10]
Kukielski, C.; Maiti, K.; Bhaduri, S.; Story, S.; Arya, D.P. Rapid solid-phase syntheses of a peptidic-aminoglycoside library. Tetrahedron, 2018, 74, 4418-4428.
[http://dx.doi.org/10.1016/j.tet.2018.07.012]
[11]
Tor, Y. The ribosomal A-site as an inspiration for the design of RNA binders. Biochimie, 2006, 88(8), 1045-1051.
[http://dx.doi.org/10.1016/j.biochi.2006.03.005] [PMID: 16581175]
[12]
Barbieri, C.M.; Kaul, M.; Pilch, D.S. Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site. Tetrahedron, 2007, 63(17), 3567-6574.
[http://dx.doi.org/10.1016/j.tet.2006.08.107] [PMID: 18431442]
[13]
Sato, Y.; Rokugawa, M.; Ito, S.; Yajima, S.; Sugawara, H.; Teramae, N.; Nishizawa, S. Fluorescent trimethylated naphthyridine derivative with an aminoalkyl side chain as the tightest non‐aminoglycoside ligand for the bacterial A‐site RNA. Chemistry, 2018, 24(52), 13862-13870.
[http://dx.doi.org/10.1002/chem.201802320] [PMID: 29971862]
[14]
Srivatsan, S.G.; Tor, Y. Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation, and utilization. J. Am. Chem. Soc., 2007, 129(7), 2044-2053.
[http://dx.doi.org/10.1021/ja066455r] [PMID: 17256858]
[15]
Xie, Y.; Dix, A.V.; Tor, Y. FRET enabled real time detection of RNA-small molecule binding. J. Am. Chem. Soc., 2009, 131(48), 17605-17614.
[http://dx.doi.org/10.1021/ja905767g] [PMID: 19908830]
[16]
Michael, K.; Wang, H.; Tor, Y. Enhanced RNA binding of dimerized aminoglycosides. Bioorg. Med. Chem., 1999, 7(7), 1361-1371.
[http://dx.doi.org/10.1016/S0968-0896(99)00071-1] [PMID: 10465410]
[17]
Boer, J.; Blount, K.F.; Luedtke, N.W.; Elson‐Schwab, L.; Tor, Y. RNA‐selective modification by a platinum (II) complex conjugated to amino‐and guanidinoglycosides. Angew. Chem. Int. Ed., 2005, 44(6), 927-932.
[http://dx.doi.org/10.1002/anie.200461182] [PMID: 15630712]
[18]
Boger, D.L.; Fink, B.E.; Brunette, S.R.; Tse, W.C.; Hedrick, M.P.A. A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity. J. Am. Chem. Soc., 2001, 123(25), 5878-5891.
[http://dx.doi.org/10.1021/ja010041a] [PMID: 11414820]
[19]
Tse, W.C.; Boger, D.L. A fluorescent intercalator displacement assay for establishing DNA binding selectivity and affinity. Acc. Chem. Res., 2004, 37(1), 61-69.
[http://dx.doi.org/10.1021/ar030113y] [PMID: 14730995]
[20]
Xi, H.; Davis, E.; Ranjan, N.; Xue, L.; Hyde-Volpe, D.; Arya, D.P. Thermodynamics of nucleic acid “shape readout” by an aminosugar. Biochemistry, 2011, 50(42), 9088-9113.
[http://dx.doi.org/10.1021/bi201077h] [PMID: 21863895]
[21]
Watkins, D.; Norris, F.A.; Kumar, S.; Arya, D.P. A fluorescence-based screen for ribosome binding antibiotics. Anal. Biochem., 2013, 434(2), 300-307.
[http://dx.doi.org/10.1016/j.ab.2012.12.003] [PMID: 23262284]
[22]
Yu, L.; Oost, T.K.; Schkeryantz, J.M.; Yang, J.; Janowick, D.; Fesik, S.W. Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA. J. Am. Chem. Soc., 2003, 125(15), 4444-4450.
[http://dx.doi.org/10.1021/ja021354o] [PMID: 12683814]
[23]
Alvarez-Pez, J.M.; Ballesteros, L.; Talavera, E.; Yguerabide, J. Fluorescein excited-state proton exchange reactions: Nanosecond emission kinetics and correlation with steady-state fluorescence intensity. J. Phys. Chem. A, 2001, 105, 6320-6332.
[http://dx.doi.org/10.1021/jp010372+]
[24]
Alper, P.B.; Hendrix, M.; Sears, P.; Wong, C. Probing the specificity of aminoglycoside− ribosomal RNA interactions with designed synthetic analogs. J. Am. Chem. Soc., 1998, 120, 1965-1978.
[http://dx.doi.org/10.1021/ja972599h]
[25]
Sjöback, R.; Nygren, J.; Kubista, M. Characterization of fluorescein-oligonucleotide conjugates and measurement of local electrostatic potential. Biopolymers, 1998, 46(7), 445-453.
[http://dx.doi.org/10.1002/(SICI)1097-0282(199812)46:7<445:AID-BIP2>3.0.CO;2-5] [PMID: 9838871]
[26]
Watkins, D.; Gong, C.; Kellish, P.; Arya, D.P. Probing A-form DNA: A fluorescent aminosugar probe and dual recognition by anthraquinone-neomycin conjugates. Bioorg. Med. Chem., 2017, 25(4), 1309-1319.
[http://dx.doi.org/10.1016/j.bmc.2016.11.003] [PMID: 28129992]
[27]
Degtyareva, N.N.; Gong, C.; Story, S.; Levinson, N.S.; Oyelere, A.K.; Green, K.D.; Garneau-Tsodikova, S.; Arya, D.P. Antimicrobial activity, AME resistance, and A-Site binding studies of anthraquinone–neomycin conjugates. ACS Infect. Dis., 2017, 3(3), 206-215.
[http://dx.doi.org/10.1021/acsinfecdis.6b00176] [PMID: 28103015]
[28]
Jiang, L.; Watkins, D.; Jin, Y.; Gong, C.; King, A.; Washington, A.Z.; Green, K.D.; Garneau-Tsodikova, S.; Oyelere, A.K.; Arya, D.P. Rapid synthesis, RNA binding, and antibacterial screening of a peptidic-aminosugar (PA) library. ACS Chem. Biol., 2015, 10(5), 1278-1289.
[http://dx.doi.org/10.1021/cb5010367] [PMID: 25706406]
[29]
Ghosh, A.; Degyatoreva, N.; Kukielski, C.; Story, S.; Bhaduri, S.; Maiti, K.; Nahar, S.; Ray, A.; Arya, D.P.; Maiti, S. Targeting miRNA by tunable small molecule binders: peptidic aminosugar mediated interference in miR-21 biogenesis reverts epithelial to mesenchymal transition. MedChemComm, 2018, 9(7), 1147-1154.
[http://dx.doi.org/10.1039/C8MD00092A] [PMID: 30109002]
[30]
Jin, Y.; Watkins, D.; Degtyareva, N.N.; Green, K.D.; Spano, M.N.; Garneau-Tsodikova, S.; Arya, D.P. Arginine-linked neomycin B dimers: synthesis, rRNA binding, and resistance enzyme activity. MedChemComm, 2016, 7(1), 164-169.
[http://dx.doi.org/10.1039/C5MD00427F] [PMID: 26811742]
[31]
Sato, Y.; Yajima, S.; Taguchi, A.; Baba, K.; Nakagomi, M.; Aiba, Y.; Nishizawa, S. Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA. Chem. Commun. (Camb.), 2019, 55(22), 3183-3186.
[http://dx.doi.org/10.1039/C9CC00414A] [PMID: 30714603]
[32]
Sato, Y.; Rokugawa, M.; Ito, S.; Yajima, S.; Sugawara, H.; Teramae, N.; Nishizawa, S. Fluorescent trimethylated naphthyridine derivative with an aminoalkyl side chain as the tightest non‐aminoglycoside ligand for the bacterial A‐site RNA. ‎. Chemistry, 2018, 24(52), 13862-13870.
[http://dx.doi.org/10.1002/chem.201802320] [PMID: 29971862]
[33]
Katsoulis, I.A.; Kythreoti, G.; Papakyriakou, A.; Koltsida, K.; Anastasopoulou, P.; Stathakis, C.I.; Mavridis, I.; Cottin, T.; Saridakis, E.; Vourloumis, D. Synthesis of 5,6-spiroethers and evaluation of their affinities for the bacterial A site. ChemBioChem, 2011, 12(8), 1188-1192.
[http://dx.doi.org/10.1002/cbic.201100076] [PMID: 21557427]
[34]
Gupta, P.; Muse, O.; Rozners, E. Recognition of double-stranded RNA by guanidine-modified peptide nucleic acids. Biochemistry, 2012, 51(1), 63-73.
[http://dx.doi.org/10.1021/bi201570a] [PMID: 22146072]
[35]
Zhou, P.; Dragulescu-Andrasi, A.; Bhattacharya, B.; O’Keefe, H.; Vatta, P.; Hyldig-Nielsen, J.J.; Ly, D.H. Synthesis of cell-permeable peptide nucleic acids and characterization of their hybridization and uptake properties. Bioorg. Med. Chem. Lett., 2006, 16(18), 4931-4935.
[http://dx.doi.org/10.1016/j.bmcl.2006.06.052] [PMID: 16809033]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy