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Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers.

ABSTRACT: The 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.

SUBMITTER: Watkins D

PROVIDER: S-EPMC4468663 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

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Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers.

Watkins Derrick D Kumar Sunil S Green Keith D KD Arya Dev P DP Garneau-Tsodikova Sylvie S

Antimicrobial agents and chemotherapy 20150420 7

The 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 ...[more]

PMID: 25896697

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Project description:Perylenediimide (PDI) derivatives have been widely studied as electron acceptor alternatives to fullerenes in organic photovoltaics (OPVs) because of their tunable absorption in the visible range, inexpensive synthesis, and photochemical stability. A common motif for improving device efficiency involves joining multiple PDIs together through electron-rich linkers to form a twisted acceptor-donor-acceptor molecule. Molecular features such as ring fusion are further employed to modify the structure locally and in films. These synthetic efforts have greatly enhanced OPV device efficiencies, however it remains unclear how the increasingly elaborate structural modifications affect the photophysical processes integral to efficient photon-to-charge conversion. Here we carry out a systematic study of a series of PDI dimers with thienoacene linkers in which the twist angle, linker length, and degree of ring fusion are varied to investigate the effects of these structural features on the molecular excited states and exciton recombination dynamics. Spectroscopic characterization of the dimers suggest that ring fusion causes greater coupling between the donor and acceptor components and greatly enhances the lifetime of a thienoacene to PDI charge transfer state. The lifetime of this CT state also correlates well with the linker-PDI dihedral angle, with smaller dihedral angle resulting in longer lifetime. DFT and two-photon absorption TDDFT calculations were developed in-house to model the ground state and excited transitions, providing theoretical insight into the reasons for the observed photophysical properties and identifying the charge transfer state in the excited state absorption spectra. These results highlight how the longevity of the excited state species, important for the efficient conversion of excitons to free carriers in OPV devices, can be chemically tuned by controlling ring fusion and by using steric effects to control the relative orientations of the molecular fragments. The results provide a successful rationalization of the behavior of solar cells involving these acceptor molecules.

Project description:The antibacterial effects of aminoglycosides are based on their association with the A-site of bacterial rRNA and interference with the translational process in the bacterial cell, causing cell death. The clinical use of aminoglycosides is complicated by resistance and side effects, some of which arise from their interactions with the human mitochondrial 12S rRNA and its deafness-associated mutations, C1494U and A1555G. We report a rapid assay that allows screening of aminoglycoside compounds to these classes of rRNAs. These screening tools are important to find antibiotics that selectively bind to the bacterial A-site rather than human, mitochondrial A-sites and its mutant homologues. Herein, we report our preliminary work on the optimization of this screen using 12 anthraquinone-neomycin (AMA-NEO) conjugates against molecular constructs representing five A-site homologues, Escherichia coli, human cytosolic, mitochondrial, C1494U, and A1555G, using a fluorescent displacement screening assay. These conjugates were also tested for inhibition of protein synthesis, antibacterial activity against 14 clinically relevant bacterial strains, and the effect on enzymes that inactivate aminoglycosides. The AMA-NEO conjugates demonstrated significantly improved resistance against aminoglycoside-modifying enzymes (AMEs), as compared with NEO. Several compounds exhibited significantly greater inhibition of prokaryotic protein synthesis as compared to NEO and were extremely poor inhibitors of eukaryotic translation. There was significant variation in antibacterial activity and MIC of selected compounds between bacterial strains, with Escherichia coli, Enteroccocus faecalis, Citrobacter freundii, Shigella flexneri, Serratia marcescens, Proteus mirabilis, Enterobacter cloacae, Staphylococcus epidermidis, and Listeria monocytogenes exhibiting moderate to high sensitivity (50-100% growth inhibition) whereas Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiellla pneumoniae, and MRSA strains expressed low sensitivity, as compared to the parent aminoglycoside NEO.

Dataset Information

Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers.

Publications

Influence of linker length and composition on enzymatic activity and ribosomal binding of neomycin dimers.

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