title: Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs.
abstract: Riboswitches are messenger RNA (mRNA) domains that regulate gene function in response to the intracellular concentration of a variety of metabolites and second messengers. They control essential genes in many pathogenic bacteria, thus representing an inviting new class of biomolecular target for the development of antibiotics and chemical-biological tools. In this Account, we briefly review the discovery of riboswitches in the first years of the 21st century and their ensuing characterization over the past decade. We then discuss the progress achieved so far in using riboswitches as a focus for drug discovery, considering both the value of past serendipity and the particular challenges that confront current researchers.  Five mechanisms of gene regulation have been determined for riboswitches. Most bacterial riboswitches modulate either transcription termination or translation initiation in response to ligand binding. All known examples of eukaryotic riboswitches, and some bacterial riboswitches, control gene expression by alternative splicing. The glmS riboswitch, which is widespread in Gram-positive bacteria, is a catalytic RNA activated by ligand binding: its self-cleavage destabilizes the mRNA of which it is part. Finally, one example of a trans-acting riboswitch is known.  Three-dimensional structures have been determined for representatives of 13 structurally distinct riboswitch classes, providing atomic-level insight into their mechanisms of ligand recognition. While cellular and viral RNAs have attracted widespread interest as potential drug targets, riboswitches show special promise due to the diversity of small-molecule recognition strategies that are on display in their ligand-binding pockets. Moreover, riboswitches have evolved to recognize small-molecule ligands, which is unique among known structured RNA domains.  Structural and biochemical advances in the study of riboswitches provide an impetus for the development of methods for the discovery of novel riboswitch activators and inhibitors. Recent rational drug design efforts focused on select riboswitch classes have yielded a small number of candidate antibiotic compounds, including one active in a mouse model of  Staphylococcus aureus  infection. The development of high-throughput methods suitable for riboswitch-specific drug discovery is ongoing. A fragment-based screening approach employing equilibrium dialysis that may be generically useful has demonstrated early success. Riboswitch-mediated gene regulation is widely employed by bacteria; however, only the thiamine pyrophosphate-responsive riboswitch has thus far been found in eukaryotes. Thus, riboswitches are particularly attractive as targets for antibacterials. Indeed, antimicrobials with previously unknown mechanisms have been found to function by binding riboswitches and causing aberrant gene expression.
authors: Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors: Katherine E
authors: KE
authors: Deigan
authors: Adrian R
authors: AR
authors: Ferré-D'Amaré
references: Chem Biol. 2005 Dec;12(12):1325-35
references: 16356850
references: Bioorg Chem. 2005 Aug;33(4):338-44
references: 15967475
references: Science. 2006 May 26;312(5777):1208-11
references: 16675665
references: Biochemistry. 2010 Nov 2;49(43):9123-31
references: 20931966
references: J Mol Biol. 2010 Feb 12;396(1):153-65
references: 19925806
references: Nat Struct Mol Biol. 2008 Feb;15(2):177-82
references: 18204466
references: Chem Rev. 2008 Apr;108(4):1171-224
references: 18361529
references: J Biol Chem. 2008 Aug 15;283(33):22347-51
references: 18593706
references: Science. 2000 Sep 15;289(5486):1938-42
references: 10988075
references: Mol Cell. 2006 Nov 17;24(4):535-45
references: 17188032
references: Bioorg Med Chem Lett. 2008 Jun 15;18(12):3541-4
references: 18502126
references: Nature. 2006 Jun 29;441(7097):1172-5
references: 16810258
references: Nat Struct Mol Biol. 2009 Mar;16(3):343-4
references: 19234468
references: Genome Biol. 2007;8(11):R239
references: 17997835
references: Nature. 2008 Jul 17;454(7202):358-61
references: 18548004
references: J Am Chem Soc. 2007 Dec 5;129(48):14858-9
references: 17990888
references: J Mol Biol. 1996 Jun 28;259(5):916-25
references: 8683594
references: RNA. 2010 Nov;16(11):2144-55
references: 20864509
references: Nat Chem Biol. 2007 Jan;3(1):44-9
references: 17143270
references: Chem Biol. 2007 Jan;14(1):97-105
references: 17196404
references: Cell. 2009 Nov 13;139(4):770-9
references: 19914169
references: Nat Struct Mol Biol. 2009 Dec;16(12):1212-7
references: 19898478
references: J Antibiot (Tokyo). 1974 Jan;27(1):86-7
references: 4843053
references: Physiol Chem Phys Med NMR. 1986;18(3):159-64
references: 3588693
references: Angew Chem Int Ed Engl. 2007;46(34):6420-36
references: 17634987
references: Nature. 2004 Nov 18;432(7015):411-5
references: 15549109
references: Science. 2006 Sep 22;313(5794):1752-6
references: 16990543
references: Nature. 1991 Sep 26;353(6342):368-70
references: 1922343
references: ACS Chem Biol. 2007 Dec 21;2(12):819-27
references: 18154269
references: J Am Chem Soc. 2008 Jul 2;130(26):8116-7
references: 18533652
references: Curr Opin Microbiol. 2005 Oct;8(5):534-42
references: 16111914
references: J Biochem. 1976 Apr;79(4):845-7
references: 179991
references: Chembiochem. 2006 Sep;7(9):1451-6
references: 16871614
references: Trends Genet. 1999 Nov;15(11):439-42
references: 10529804
references: Chem Biol. 2004 Dec;11(12):1729-41
references: 15610857
references: Proc Natl Acad Sci U S A. 1999 May 25;96(11):6155-60
references: 10339557
references: Curr Opin Struct Biol. 2003 Feb;13(1):49-55
references: 12581659
references: Biopolymers. 2004 Jan;73(1):71-8
references: 14691941
references: Appl Environ Microbiol. 2004 Oct;70(10):5769-77
references: 15466513
references: PLoS Pathog. 2010 Apr 22;6(4):e1000865
references: 20421948
references: Structure. 2006 Sep;14(9):1459-68
references: 16962976
references: Nat Struct Biol. 2001 Jun;8(6):510-4
references: 11373618
references: Structure. 2010 Jul 14;18(7):787-97
references: 20637415
references: Bioorg Med Chem Lett. 2006 Jul 1;16(13):3600-4
references: 16603349
references: FEMS Microbiol Lett. 1998 Dec 1;169(1):165-70
references: 9851048
references: RNA. 1995 Mar;1(1):95-101
references: 7489494
references: Nature. 2008 Oct 30;455(7217):1263-7
references: 18784651
references: Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2830-5
references: 20133756
references: Cell. 2007 Sep 7;130(5):878-92
references: 17803910
references: EMBO J. 2002 Feb 15;21(4):760-8
references: 11847123
references: RNA Biol. 2008 Jan-Mar;5(1):24-9
references: 18388492
references: Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10804-9
references: 20534493
references: Microbiol Mol Biol Rev. 2009 Mar;73(1):36-61
references: 19258532
references: RNA. 2010 Mar;16(3):598-609
references: 20106958
references: Nature. 2009 Mar 12;458(7235):233-7
references: 19169240
references: RNA Biol. 2009 Jul-Aug;6(3):276-80
references: 19333008
references: Nat Struct Mol Biol. 2009 Dec;16(12):1218-23
references: 19898477
references: RNA Biol. 2009 Apr-Jun;6(2):187-94
references: 19246992
references: J Mol Biol. 2011 Jan 28;405(4):926-38
references: 21075119
references: J Biol Chem. 2009 Apr 24;284(17):11012-6
references: 19261617
references: J Gen Microbiol. 1991 May;137(5):1135-43
references: 1907638
references: Chem Biol. 2008 Oct 20;15(10):1125-37
references: 18940672
references: Nucleic Acids Res. 2007;35(15):5262-73
references: 17686787
references: J Mol Biol. 2009 Jan 23;385(3):938-48
references: 19007790
references: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15908-13
references: 12456892
references: Nat Struct Mol Biol. 2008 Oct;15(10):1076-83
references: 18806797
references: J Chem Inf Comput Sci. 2001 May-Jun;41(3):856-64
references: 11410068
references: Nature. 2006 Jun 29;441(7097):1167-71
references: 16728979
references: J Mol Biol. 2007 Feb 2;365(5):1393-406
references: 17118400
references: Mol Cell. 2009 Mar 27;33(6):784-90
references: 19285444
references: J Biol Chem. 2000 Jul 7;275(27):20660-6
references: 10747964
references: Proc Natl Acad Sci U S A. 1941 Sep 15;27(9):419-22
references: 16578020
references: Mol Cell. 2010 Dec 10;40(5):774-86
references: 21145485
references: Chembiochem. 2006 Apr;7(4):602-4
references: 16485317
references: RNA Biol. 2006 Apr;3(2):77-81
references: 17114942
references: Genes Dev. 2003 Nov 1;17(21):2688-97
references: 14597663
references: Nature. 2009 Feb 12;457(7231):915-9
references: 19098893
references: Nat Biotechnol. 2006 Dec;24(12):1558-64
references: 17160062
references: Biochim Biophys Acta. 1958 Aug;29(2):333-44
references: 13572351
references: ACS Chem Biol. 2009 Nov 20;4(11):915-27
references: 19739679
references: J Mol Biol. 2007 Oct 12;373(1):178-89
references: 17804015
references: Q Rev Biophys. 2010 Nov;43(4):423-47
references: 20822574
references: ACS Chem Biol. 2010 Apr 16;5(4):355-8
references: 20158266