scholarly journals Influence of Linker Length and Composition on Enzymatic Activity and Ribosomal Binding of Neomycin Dimers

2015 ◽  
Vol 59 (7) ◽  
pp. 3899-3905 ◽  
Author(s):  
Derrick Watkins ◽  
Sunil Kumar ◽  
Keith D. Green ◽  
Dev P. Arya ◽  
Sylvie Garneau-Tsodikova
Keyword(s):  
Enzymatic Activity ◽  
Aminoglycoside Antibiotics ◽  
Substantial Decrease ◽  
Selective Binding ◽  
Linker Length ◽  
Neomycin B ◽  
A Site ◽  
Site Binding

ABSTRACTThe human and bacterial A site rRNA binding as well as the aminoglycoside-modifying enzyme (AME) activity against a series of neomycin B (NEO) dimers is presented. The data indicate that by simple modifications of linker length and composition, substantial differences in rRNA selectivity and AME activity can be obtained. We tested five different AMEs with dimeric NEO dimers that were tethered via triazole, urea, and thiourea linkages. We show that triazole-linked dimers were the worst substrates for most AMEs, with those containing the longer linkers showing the largest decrease in activity. Thiourea-linked dimers that showed a decrease in activity by AMEs also showed increased bacterial A site binding, with one compound (compound 14) even showing substantially reduced human A site binding. The urea-linked dimers showed a substantial decrease in activity by AMEs when a conformationally restrictive phenyl linker was introduced. The information learned herein advances our understanding of the importance of the linker length and composition for the generation of dimeric aminoglycoside antibiotics capable of avoiding the action of AMEs and selective binding to the bacterial rRNA over binding to the human rRNA.

scholarly journals Singly Modified Amikacin and Tobramycin Derivatives Show Increased rRNA A-Site Binding and Higher Potency against Resistant Bacteria

ChemMedChem ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. 2164-2171 ◽  
Author(s):  
Richard J. Fair ◽  
Lisa S. McCoy ◽  
Mary E. Hensler ◽  
Bernice Aguilar ◽  
Victor Nizet ◽  
...  
Keyword(s):  
Resistant Bacteria ◽  
A Site ◽  
Site Binding

scholarly journals pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

2010 ◽  
Vol 108 (1) ◽  
pp. 79-84 ◽  
Author(s):  
Magnus Johansson ◽  
Ka-Weng Ieong ◽  
Stefan Trobro ◽  
Peter Strazewski ◽  
Johan Åqvist ◽  
...  
Keyword(s):  
Ph Value ◽  
Ph Dependence ◽  
Peptide Bond ◽  
Bulk Solution ◽  
Peptide Bond Formation ◽  
Transfer Rates ◽  
Peptidyl Transfer ◽  
A Site ◽  
Rate Limiting ◽  
Site Binding

We studied the pH-dependence of ribosome catalyzed peptidyl transfer from fMet-tRNAfMet to the aa-tRNAs Phe-tRNAPhe, Ala-tRNAAla, Gly-tRNAGly, Pro-tRNAPro, Asn-tRNAAsn, and Ile-tRNAIle, selected to cover a large range of intrinsic pKa-values for the α-amino group of their amino acids. The peptidyl transfer rates were different at pH 7.5 and displayed different pH-dependence, quantified as the pH-value, , at which the rate was half maximal. The -values were downshifted relative to the intrinsic pKa-value of aa-tRNAs in bulk solution. Gly-tRNAGly had the smallest downshift, while Ile-tRNAIle and Ala-tRNAAla had the largest downshifts. These downshifts correlate strongly with molecular dynamics (MD) estimates of the downshifts in pKa-values of these aa-tRNAs upon A-site binding. Our data show the chemistry of peptide bond formation to be rate limiting for peptidyl transfer at pH 7.5 in the Gly and Pro cases and indicate rate limiting chemistry for all six aa-tRNAs.

scholarly journals Arginine-linked neomycin B dimers: synthesis, rRNA binding, and resistance enzyme activity

MedChemComm ◽  
2016 ◽  
Vol 7 (1) ◽  
pp. 164-169 ◽  
Author(s):  
Yi Jin ◽  
Derrick Watkins ◽  
Natalya N. Degtyareva ◽  
Keith D. Green ◽  
Meredith N. Spano ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Bacterial Rna ◽  
Neomycin B ◽  
A Site

New dimeric aminoglycosides conjugated to arginine were synthesized and found to efficiently bind to human and bacterial RNA A-site and to evade the activity of resistance enzymes.

scholarly journals Antimicrobial Activity, AME Resistance, and A-Site Binding Studies of Anthraquinone–Neomycin Conjugates

2017 ◽  
Vol 3 (3) ◽  
pp. 206-215 ◽  
Author(s):  
Natalya N. Degtyareva ◽  
Changjun Gong ◽  
Sandra Story ◽  
Nathanael S. Levinson ◽  
Adegboyega K. Oyelere ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Binding Studies ◽  
A Site ◽  
Site Binding

scholarly journals Histidine 197 in Release Factor 1 Is Essential for A Site Binding and Peptide Release

Biochemistry ◽  
2010 ◽  
Vol 49 (43) ◽  
pp. 9385-9390 ◽  
Author(s):  
Andrew Field ◽  
Byron Hetrick ◽  
Merrill Mathew ◽  
Simpson Joseph
Keyword(s):  
Release Factor ◽  
Peptide Release ◽  
A Site ◽  
Site Binding

Aminoglycoside antibiotics: Chemical conversion of neomycin B, paromomycin, and lividomycin B into bioactive pseudosaccharides

1978 ◽  
Vol 56 (11) ◽  
pp. 1482-1491 ◽  
Author(s):  
Stephen Hanessian ◽  
Tetsuyoshi Takamoto ◽  
Robert Massé ◽  
Ghanshyam Patil
Keyword(s):  
Chemical Conversion ◽  
Aminoglycoside Antibiotics ◽  
Biological Probes ◽  
Neomycin B ◽  
Vicinal Diols

Pseudosaccharides containing various natural combinations of rings present in aminoglycoside antibiotics were prepared from the parent antibiotics, neomycin B, paromomycin, and lividomycin B, by oxidation of available vicinal diols and β-elimination. Pseudotrisaccharides comprising rings A, B, and C of paromomycin and lividomycin B, a pseudotrisaccharide comprising rings B, C, and D of the three antibiotics, and a 'core' pseudotrisaccharide containing rings B and C were thus prepared. These are valuable biological probes and intermediates for semisynthetic work in this series.

scholarly journals Intramolecular interactions dominate the autoregulation ofEscherichia colistringent factor RelA

2019 ◽  
Author(s):  
Kathryn Jane Turnbull ◽  
Ievgen Dzhygyr ◽  
Søren Lindemose ◽  
Vasili Hauryliuk ◽  
Mohammad Roghanian
Keyword(s):  
Enzymatic Activity ◽  
Ectopic Expression ◽  
Direct Interaction ◽  
Terminal Region ◽  
Intramolecular Interactions ◽  
Synthetic Activity ◽  
Rrm Domain ◽  
The Individual ◽  
High Level ◽  
A Site

AbstractAmino acid starvation inEscherichia coliactivates the enzymatic activity of the stringent factor RelA, leading to accumulation of the alarmone nucleotide (p)ppGpp. The alarmone acts as an intercellular messenger to regulate transcription, translation and metabolism to mediate bacterial stress adaptation. The enzymatic activity of RelA is subject to multi-layered allosteric control executed both by ligands – such as ‘starved’ ribosomal complexes, deacylated tRNA and pppGpp – and by individual RelA domains. The auto-regulation of RelA is proposed to act eitherin cis(inhibition of the enzymatic activity of the N-terminal region, NTD, by regulatory C-terminal region, CTD) orin trans(CTD-mediated dimerization leading to enzyme inhibition). In this report, we probed the regulatory roles of the individual domains ofE. coliRelA and our results are not indicative of RelA dimerization being the key regulatory mechanism. First, at growth-permitting levels, ectopic expression of RelA CTD does not interfere with activation of native RelA, indicating lack of regulationviainhibitory complex formation in the cell. Second, in our biochemical assays, increasing RelA concentration does not decrease the enzyme activity, as would be expected in the case of efficient auto-inhibitionviadimerization. Third, while high-level CTD expression efficiently inhibits the growth, the effect is independent of native RelA and is mediated by direct inhibition of protein synthesis, likelyviadirect interaction with the ribosomal A-site. Finally, deletion of the RRM domain of the CTD region leads to growth inhibition mediated by accumulation of (p)ppGpp, suggesting de-regulation of the synthetic activity in this mutant.

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