Selection of Small Peptides, Inhibitors of Translation

Llano-Sotelo, Beatriz; Klepacki, Dorota; Mankin, Alexander S.

doi:10.1016/j.jmb.2009.06.069

Cited by 19 publications

(29 citation statements)

References 35 publications

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“…Related studies that were reported recently reveal similar results (52). The limitation of using phage display to screen peptides that specifically interfere with protein synthesis of bacteria is that the strongest binders may not actually be selected because the host E. coli would not survive, therefore failing to amplify the phage bearing the infused peptide.…”

Section: Discussionsupporting

confidence: 87%

Selection of Peptides That Target the Aminoacyl-tRNA Site of Bacterial 16S Ribosomal RNA

Duc

Klosi

et al. 2009

Biochemistry

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For almost five decades, antibiotics have been used successfully to control infectious diseases caused by bacterial pathogens. More recently, however, two-thirds of bacterial pathogens exhibit resistance and are continually evolving new resistance mechanisms against almost every clinically used antibiotic. Novel efforts are required for the development of new drugs or drug leads to combat these infectious diseases. A number of antibiotics target the bacterial aminoacyl-tRNA site (A site) of 16S ribosomal RNA (rRNA). Mutations in the A-site region are known to cause antibiotic resistance. In this study, a bacterial (E. coli) A-site rRNA model was chosen as a target to screen for peptide binders. Two heptapeptides, HPVHHYQ and LPLTPLP, were selected through M13 phage display. Both peptides display selective binding to the A-site 16S rRNA with on-bead fluorescence assays. Dissociation constants (K d s) of the amidated peptide HPVHHYQ-NH 2 to various A-site RNA constructs were determined by using enzymatic footprinting, electrospray ionization mass spectrometry (ESI-MS), and isothermal titration calorimetry (ITC) under a variety of buffer and solution conditions. HPVHHYQ-NH 2 exhibits moderate affinity for the A-site RNA, with an average K d value of 16 μM. In addition, enzymatic footprinting assays and competition ESI-MS with a known A-site binder (paromomycin) revealed that peptide binding occurs near the asymmetric bulge at positions U1495 and G1494 and leads to increased exposure of residues A1492 and A1493.It has been half a century since the first antibiotic penicillin was discovered and successfully applied to the treatment of infectious diseases; however, infectious diseases still remain the third-leading cause of death in the United States and the second-leading cause of death worldwide (1). Widespread and intensive use of antibiotics in hospitals and agriculture has led to significant levels of resistance (2,3). The emergence of antibiotic resistance, especially multidrug resistance, is a growing threat to human health (4). Therefore, a significant driving force exists for the development of new antimicrobial agents, especially those to combat multidrug-resistant pathogens.The majority of antibiotics used in the clinic target protein synthesis, which occurs at the core of the ribosome (5). High-resolution X-ray crystal structures of rRNA fragments, 30S and 50S subunits, and whole ribosomes, either free or complexed with antibiotics, have provided important information that will help in the design of new anti-infective compounds (6-10). † This work was supported by NIH grant AI061192. SUPPORTING INFORMATION AVAILABLEFigures S1-S4 show MALDI-TOF characterization of HPVHHYQ-NH 2 , ESI-MS data (salt dependence), and binding curve for RNase footprinting data (A1493). This material is available free of charge via the Internet at http://pubs.acs.org. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2010 September 8. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH...

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Section: Discussionsupporting

confidence: 87%

Selection of Peptides That Target the Aminoacyl-tRNA Site of Bacterial 16S Ribosomal RNA

Duc

Klosi

et al. 2009

Biochemistry

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“…Importantly, macrolide binding seems to be involved in cellular processes. Thus, stalling by specific nascent peptides, a cellular mechanism used for regulation of expression of several bacterial and eukaryotic genes, is sensitive to signals connected with macrolide binding (73)(74)(75)(76)(77)(78)(79)(80)(81)(82)(83).…”

Section: Figurementioning

confidence: 99%

“…Examples are those used recently to target Helix 69 (111), the first 16 residues of the proline-rich antimicrobial peptide mammalian Bac7 (112), the thiazolyl peptide antibiotics (113), and the small peptides that were shown to inhibit translation in prokaryotes (75,114).…”

Section: Figurementioning

confidence: 99%

A Bright Future for Antibiotics?

Matzov

Bashan²,

Yonath³

2017

Annu. Rev. Biochem.

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Multidrug resistance is a global threat as the clinically available potent antibiotic drugs are becoming exceedingly scarce. For example, increasing drug resistance among gram-positive bacteria is responsible for approximately one-third of nosocomial infections. As ribosomes are a major target for these drugs, they may serve as suitable objects for novel development of next-generation antibiotics. Three-dimensional structures of ribosomal particles from Staphylococcus aureus obtained by X-ray crystallography have shed light on fine details of drug binding sites and have revealed unique structural motifs specific for this pathogenic strain, which may be used for the design of novel degradable pathogen-specific, and hence, environmentally friendly drugs.

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“…This seemingly simple process could be assisted by other molecules acting as small chaperones [35] offering stabilization. Additional structural support could be obtained from short peptides that have high affinity for RNA [36], or from longer poly-amino acids, similar to protein-RNA interactions within the contemporary ribosome, or from interactions of low-molecular-mass compounds with exposed regions of RNA. These short peptides could have been produced by uncoded elongation by early versions of the proto-ribosome or by other means.…”

Section: Emergence Of the Proto-ribosomementioning

confidence: 99%

Ancient machinery embedded in the contemporary ribosome

Belousoff

Davidovich

Zimmerman

et al. 2010

Biochemical Society Transactions

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Structural analysis, supported by biochemical, mutagenesis and computational evidence, indicates that the peptidyltransferase centre of the contemporary ribosome is a universal symmetrical pocket composed solely of rRNA. This pocket seems to be a relic of the proto-ribosome, an ancient ribozyme, which was a dimeric RNA assembly formed from self-folded RNA chains of identical, similar or different sequences. This could have occurred spontaneously by gene duplication or gene fusion. This pocket-like entity was capable of autonomously catalysing various reactions, including peptide bond formation and non-coded or semi-coded amino acid polymerization. Efforts toward the structural definition of the early entity capable of genetic decoding involve the crystallization of the small ribosomal subunit of a bacterial organism harbouring a single functional rRNA operon.

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Selection of Small Peptides, Inhibitors of Translation

Cited by 19 publications

References 35 publications

Selection of Peptides That Target the Aminoacyl-tRNA Site of Bacterial 16S Ribosomal RNA

Selection of Peptides That Target the Aminoacyl-tRNA Site of Bacterial 16S Ribosomal RNA

A Bright Future for Antibiotics?

Ancient machinery embedded in the contemporary ribosome

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