Identification of cellular targets of a series of boron heterocycles using TIPA II-A sensitive target identification platform.

One of the hurdles in the discovery of antibiotics is the difficulty of linking antibacterial compounds to their cellular targets. Our laboratory has employed a genome-wide approach of over-expressing essential genes in order to identify cellular targets of antibacterial inhibitors. Our objective in this project was to develop and validate a more sensitive disk diffusion based platform of target identification (Target Identification Platform for Antibacterials version 2; TIPA II) using a collection of cell clones in an Escherichia coli mutant (AS19) host with increased outer membrane permeability. Five known antibiotics/inhibitors and 28 boron heterocycles were tested by TIPA II assay, in conjunction with the original assay TIPA. The TIPA II was more sensitive than TIPA because eight boron heterocycles previously found to be inactive to AG1 cells in TIPA assays exhibited activity to AS19 cells. For 15 boron heterocycles, resistant colonies were observed within the zones of inhibition only on the inducing plates in TIPA II assays. DNA sequencing confirmed that resistant clones harbor plasmids with fabI gene as insert, indicating that these boron heterocycles all target enoyl ACP reductase. Additionally, cell-based assays and dose response curved obtained indicated that for two boron heterocycle inhibitors, the fabI cell clone in AG1 (wild-type) host cells exhibited at least 11 fold more resistance under induced conditions than under non-induced conditions. Moreover, TIPA II also identified cellular targets of known antibacterial inhibitors triclosan, phosphomycin, trimethoprim, diazaborine and thiolactomycin, further validating the utility of the new system.

Synthesis, characterization, and antibacterial activity of structurally complex 2-acylated 2,3,1-benzodiazaborines and related compounds.

A set of 2-acylated 2,3,1-benzodiazaborines and some related boron heterocycles were synthesized, characterized, and tested for antibacterial activity against Escherichia coli and Mycobacterium smegmatis. By high-field solution NMR, the heretofore unknown class of 2-acyl-1-hydroxy-2,3,1-diazaborines has been found to be able to exist in several interconvertable structural forms along a continuum comprised of an open hydrazone a, a monomeric B-hydroxy diazaborine b, and an anhydro dimer c. X-Ray crystallography of one of the anhydro dimers, 17c, revealed it to have an unprecedented structure featuring a double intramolecular O→B chelation. The crystal structure of another compound, 37, showed it to be based on a new pentacyclic B heterocycle framework. Nine compounds were found to possess activities against E. coli, and two others were active against M. smegmatis. The finding that these two contain isoniazid covalently embedded in their structures suggests that they might possibly be acting as prodrugs of this well-known antituberculosis agent in vivo.

A disk-diffusion-based target identification platform for antibacterials (TIPA): an inducible assay for profiling MOAs of antibacterial compounds.

One of the challenges in antibiotic lead discovery is the difficulty and time-consuming task of determining the mechanism of action (MOA) of antibacterial compounds. In this report, we describe the development and validation of a facile and inexpensive assay system utilizing disk diffusion of inhibitors on solid agar medium embedded with mixed pools of a comprehensive collection of Escherichia coli clones each containing a plasmid-borne inducible essential gene from E. coli. From individual clones, pilot small-scale (48 or 50 clones) assays, to full-scale target identification platform for antibacterials (TIPA) system, involving a variety of assay formats (liquid vs solid media, individual vs mix clones), we demonstrate that elevated resistance phenotypes of relevant cell clones were highly specific. In particular, the TIPA system was able to reveal cellular targets of several known antibacterial inhibitors: cerulenin, diazaborine, indolmycin, phosphomycin, and triclosan. Complementary to several existing MOA profiling schemes, the TIPA system offers a simple and low-cost method for elucidating the target proteins of antibacterial inhibitors, thus will facilitate discovery and development of novel antibacterial compounds to combat multidrug-resistant bacterial pathogens.

Phenotypic and molecular characterization of Acinetobacter clinical isolates obtained from inmates of California correctional facilities.

Acinetobacter spp. increasingly have been wreaking havoc in hospitals and communities worldwide. Although much has been reported regarding Acinetobacter isolates responsible for nosocomial infections, little is known about these organisms in correctional facilities. In this study, we performed species identification, examined the antibiotic resistance profiles, and determined the mechanisms of resistance and clonal relationships of 123 Acinetobacter isolates obtained from inmates of 20 California correctional facilities (CCFs). We found that 57.7% of the isolates belong to A. baumannii, followed by isolates of Acinetobacter genomic species 3 (gen. sp. 3; 23.6%) and of Acinetobacter gen. sp. 13TU (10.6%). Multidrug-resistant (MDR) CCF isolates were found in only six CCFs. Additionally, DNA sequences of gyrA and parC genes were consistent with fluoroquinolone (FQ) susceptibility phenotypes. Furthermore, the presence of class 1 integrons was detected in 15 CCF isolates, all of which are MDR. Integron-associated gene cassettes encode several aminoglycoside modification enzymes, which correlate with most of the aminoglycoside-resistant phenotypes. Antimicrobial susceptibility testing in the presence of Phe-Arg-ß-naphthylamide dihydrochloride and 1-(1-naphthylmethyl)-piperazine indicated the involvement of efflux pumps in the FQ resistance of only a few CCF isolates. Finally, genetic profiling showed that there was no evidence of A. baumannii outbreaks in CCFs. Instead, our analyses revealed only limited clonal dissemination of mostly non-MDR A. baumannii strains in a few facilities. This study represents the first report to characterize phenotypic and molecular features of Acinetobacter isolates in correctional facilities, which provides a baseline for monitoring the antimicrobial resistance changes and dissemination patterns of these organisms in such specialized institutions.

Estimation of binding constants between ristocetin and teicoplanin and peptides using on-column ligand derivatization coupled to affinity capillary electrophoresis.

This work utilizes on-column ligand synthesis and affinity capillary electrophoresis (ACE) to determine binding constants ( K(b)) of 9-flourenylmethyloxy carbonyl (Fmoc)-amino acid derivatives to the glycopeptide antibiotics ristocetin (Rist) and teicoplanin (Teic). In this technique, two separate plugs of sample are injected on to the capillary column and electrophoresed. The initial sample plug contains a D-Ala- D-Ala terminus peptide and either one or two non-interacting standard(s). The second plug contains a Fmoc-amino acid- N-hydroxysuccinimide (NHS) ester. The electrophoresis is then carried out with an increasing concentration of Rist or Teic in the running buffer. Upon electrophoresis the initial D-Ala- D-Ala peptide reacts with the Fmoc-amino acid yielding a new Fmoc-amino acid- D-Ala- D-Ala peptide derivative. Continued electrophoresis results in the binding of Rist or Teic to the Fmoc-amino acid- D-Ala- D-Ala peptide derivatives. Analysis of the change in the relative migration time ratio ( RMTR) or electrophoretic mobility (mu) of the Fmoc-amino acid- D-Ala- D-Ala peptide derivatives relative to the non-interacting standards, as a function of the concentration of Rist and Teic, yields a value for K(b). These findings demonstrate the advantage of coupling on-column ligand synthesis to ACE for estimating binding parameters between antibiotics and ligands.

Partial-filling affinity capillary electrophoresis.

Partial-filling affinity capillary electrophoresis (PFACE) is used to examine the binding interactions between two model biological systems: D-Ala-D-Ala terminus peptides to the glycopeptide antibiotic vancomycin (Van) from Streptomyces orientalis, and arylsulfonamides to carbonic anhydrase B (CAB, EC 4.2.1.1, bovine erythrocytes). Using these two systems, modifications in the PFACE technique are demonstrated including flow-through PFACE (FTPFACE), competitive flow-through PFACE (CFTPFACE), on-column ligand synthesis PFACE (OCLSPFACE), and multiple-step ligand injection PFACE (MSLIPFACE). In PFACE small plugs of sample are injected into the capillary column and an equilibrium is established between receptor and ligand during electrophoresis. Binding constants are then obtained by Scatchard analysis using changes in the migration time of the receptor/ligand on changing the concentration of the ligand/receptor. Data demonstrating the quantitative potential of these methods are presented. This review focuses on the unique capabilities of the different PFACE techniques as applied to two model biological systems.