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Biomedical subjects

John F Barrett

Publications and source records attributed to John F Barrett.

At least 19 recordsLinked to original sources
PubMed2006

Antibacterial drug discovery--then, now and the genomics future.

Drug discovery research in the area of infectious diseases, in particular that dealing with antibacterial/antibiotic susceptibility and resistance, is in a process of continuing evolution. Steeped in the history of the highly successful intervention with chemotherapeutic agents to treat human infections, the emergence of drug-resistant pathogens worldwide presents a serious unmet medical need, if not a pending catastrophe. Research in both academia and industry over the past 30 years using molecular biology, genetics and more recently--bacterial genomics--has assembled key enabling technologies to increase productivity and success rates in the discovery and development of novel antibacterial agents. However genomics is not limited only to antibacterial target selection but provides the opportunity to further understand key interactions in the use of antibacterial compounds as therapeutic agents (such as resistance emergence, susceptibility, efflux, interactions between compound and pathogen, etc.). Genomics also offers the potential for insights into: bacterial niche adaptation, host susceptibility, treatment regimens, antibiotic resistance, pharmacokinetics (e.g., host metabolism differences), safety and the microbial genesis of chronic diseases (e.g., gastric ulceration).

Anti-Bacterial Agents↗
PubMed2006

Empirical antibacterial drug discovery--foundation in natural products.

Natural products have been a rich source in providing leads for the development of drugs for the treatment of bacterial infections. However, beyond the discovery of the natural product, thienamycin and the synthetic lead, oxazolidinone in the 1970s, there has been a dearth of new compounds. This commentary provides an overview of current antibiotic leads and their mechanism of action, and highlights tools that can be applied to the discovery of new antibiotics.

Anti-Bacterial Agents↗
PubMed2006

Discovery of FabH/FabF inhibitors from natural products.

Condensing enzymes are essential in type II fatty acid synthesis and are promising targets for antibacterial drug discovery. Recently, a new approach using a xylose-inducible plasmid to express antisense RNA in Staphylococcus aureus has been described; however, the actual mechanism was not delineated. In this paper, the mechanism of decreased target protein production by expression of antisense RNA was investigated using Northern blotting. This revealed that the antisense RNA acts posttranscriptionally by targeting mRNA, leading to 5' mRNA degradation. Using this technology, a two-plate assay was developed in order to identify FabF/FabH target-specific cell-permeable inhibitors by screening of natural product extracts. Over 250,000 natural product fermentation broths were screened and then confirmed in biochemical assays, yielding a hit rate of 0.1%. All known natural product FabH and FabF inhibitors, including cerulenin, thiolactomycin, thiotetromycin, and Tü3010, were discovered using this whole-cell mechanism-based screening approach. Phomallenic acids, which are new inhibitors of FabF, were also discovered. These new inhibitors exhibited target selectivity in the gel elongation assay and in the whole-cell-based two-plate assay. Phomallenic acid C showed good antibacterial activity, about 20-fold better than that of thiolactomycin and cerulenin, against S. aureus. It exhibited a spectrum of antibacterial activity against clinically important pathogens including methicillin-resistant Staphylococcus aureus, Bacillus subtilis, and Haemophilus influenzae.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed2006

Conserved fungal genes as potential targets for broad-spectrum antifungal drug discovery.

The discovery of novel classes of antifungal drugs depends to a certain extent on the identification of new, unexplored targets that are essential for growth of fungal pathogens. Likewise, the broad-spectrum capacity of future antifungals requires the target gene(s) to be conserved among key fungal pathogens. Using a genome comparison (or concordance) tool, we identified 240 conserved genes as candidates for potential antifungal targets in 10 fungal genomes. To facilitate the identification of essential genes in Candida albicans, we developed a repressible C. albicans MET3 (CaMET3) promoter system capable of evaluating gene essentiality on a genome-wide scale. The CaMET3 promoter was found to be highly amenable to controlled gene expression, a prerequisite for use in target-based whole-cell screening. When the expression of the known antifungal target C. albicans ERG1 was reduced via down-regulation of the CaMET3 promoter, the CaERG1 conditional mutant strain became hypersensitive, specifically to its inhibitor, terbinafine. Furthermore, parallel screening against a small compound library using the CaERG1 conditional mutant under normal and repressed conditions uncovered several hypersensitive compound hits. This work therefore demonstrates a streamlined process for proceeding from selection and validation of candidate antifungal targets to screening for specific inhibitors.

Antifungal Agents↗
PubMed2006

What are we looking for in new antibacterials and how do we design it?

The need for new antibacterial agents is a pressing, unmet medical need, but success has been limited, resulting in decreased business interest. Part of the problem is the lack of clarity regarding what would make a new-generation 'blockbuster' antibacterial and how this agent could be designed. To this end, the authors outline a few ideas regarding the changes in approach in order to accomplish these needs, including a fundamental change in the drug discovery process.

Animals↗
PubMed2006

Pharmacoeconomics of treatment with the newer anti-Gram-positive agents.

The unmet medical need of emerging resistance among Gram-positive pathogens, such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and penicillin-resistant Streptococcus pneumoniae, has driven industry towards the identification and development of novel anti-Gram-positive agents. Among the newer agents are improved quinolones, a lipopeptide, an oxazolidinone and novel glycopeptides. Scientific distinctions between these drugs, which impact on the placement, usage and, ultimately, the pharmacoeconomics of several of these new agents, may lead to further consideration despite poor initial observations of minimal improvement. Key differences in the characteristics of these drugs (i.e., spectrum, activity, resistance emergence, efficacy, target, safety) provide a basis for an emerging pharmacoeconomic-based distinction between these newer anti-Gram-positive agents.

Animals↗
PubMed2005

Biaryl isoxazolinone antibacterial agents.

In an era of increasing resistance to classical antibacterial agents, the synthetic oxazolidinone series of antibiotics has attracted much interest. Zyvoxtrade mark was the first oxazolidinone to be approved for clinical use against infections caused by multi-drug resistant Gram-positive bacteria. In the course of studies directed toward the discovery of novel antibacterial agents, a new series of synthetic phenyl-isoxazolinone agents that displayed potent activity against Gram-positive bacterial strains was recently discovered at Bristol-Myers Squibb. Extensive investigation of various substitutions on the phenyl ring was then undertaken. We report here, the synthesis and antibacterial activity of a series of biaryl isoxazolinone compounds.

Animals↗
PubMed2005

Stimulation of Myc transactivation by the TATA binding protein in promoter-reporter assays.

BACKGROUND: The c-Myc oncogenic transcription factor heterodimerizes with Max, binds specific DNA sites and regulates transcription. The role of Myc in transcriptional activation involves its binding to TRRAP and histone acetylases; however, Myc's ability to activate transcription in transient transfection assays is remarkably weak (2 to 5 fold) when compared to other transcription factors. Since a deletion Myc mutant D106-143 and a substitution mutant W135E that weakly binds TRRAP are still fully active in transient transfection reporter assays and the TATA binding protein (TBP) has been reported to directly bind Myc, we sought to determine the effect of TBP on Myc transactivation. RESULTS: We report here a potent stimulation of Myc transactivation by TBP, allowing up to 35-fold transactivation of reporter constructs. Although promoters with an initiator (InR) element briskly responded to Myc transactivation, the presence of an InR significantly diminished the response to increasing amounts of TBP. We surmise from these findings that promoters containing both TATA and InR elements may control Myc responsive genes that require brisk increased expression within a narrow window of Myc levels, independent of TBP. In contrast, promoters driven by the TATA element only, may also respond to modulation of TBP activity or levels. CONCLUSION: Our observations not only demonstrate that TBP is limiting for Myc transactivation in transient transfection experiments, but they also suggest that the inclusion of TBP in Myc transactivation assays may further improve the characterization of c-Myc target genes.

Animals↗
PubMed2005

Antibiotics: where did we go wrong?

In the late 1960s, the medical need for new antibiotics began to be questioned, and the pharmaceutical industry shifted its emphasis of antibacterials from that of a therapeutic leader to a low-priority research area. Although infectious diseases, in particular those caused by bacterial infections, are still among the top causes of mortality in the world, industrial support continues to wane. The shift from this important area of antimicrobial research has been attributed to a combination of science, medical, marketing and business reasons. This decline in antibacterial drug discovery, coupled with increasing risk as a result of infections caused by drug-resistant bacterial pathogens, represents a clear public health threat.

Anti-Bacterial Agents↗
PubMed2005

Can biotech deliver new antibiotics?

The evolution of support for the discovery and development of antibacterial (or antibiotic) agents from the larger pharmaceutical companies to the entrepreneur-like small biotechnology companies has been an experiment in the making for the past 15 years. The word 'experiment' is precisely chosen as the outcome is not certain. Many of the antibiotic biotech organizations that were most likely to undertake the task of picking up where large pharmaceutical companies left off have failed to survive, despite their use of outstanding science and their novel approaches to the development of discovery platforms. So this leaves one with the question of 'can biotech deliver the new antibiotics?'.

Anti-Bacterial Agents↗
PubMed2005

MRSA--what is it, and how do we deal with the problem?

Methicillin-resistant Staphylococcus aureus (MRSA) has become a serious nosocomial pathogen, and more recent reports in the scientific literature underscore the potential issues with emerging community-MRSA. MRSA is reported to be involved in > 50% of hospital S. aureus infections, more in the intensive care unit (ICU) than the non-ICU, and increases in multi-drug resistant MRSA and increasingly virulent MRSA have been reported. Together with its broad-based beta-lactam resistance, MRSA often possesses a multi-drug resistance genotype, including cephalosporins, aminoglycosides, fluoroquinolones, and macrolide resistances. MRSA has now emerged as the predominant nosocomial Gram-positive pathogen, and it has a high rate of morbidity and mortality. Action must be taken to contain and eradicate MRSA through a combination of infection control, the development of novel anti-MRSA agents, development of vaccines and other non-traditional approaches of intervention.

Animals↗
PubMed2005

Recent developments in glycopeptide antibacterials.

The glycopeptide class of antibiotics, namely vancomycin and teicoplanin, are intravenously administered in the hospital setting for the treatment of the most severe of Gram-positive infections. Although a mainstay of the hospital formulary for over four decades, the rise of increasingly frequent high-level vancomycin resistance in enterococci and low-level resistance in staphylococci (as well as a few high-level vancomycin resistance cases) has highlighted the need for the identification of naturally occurring and semi-synthetically modified glycopeptide derivatives that have antibacterial activity against these resistant strains. Among the leading development candidates are dalbavancin, oritavancin, telavancin and ramoplanin, each of which provides a unique microbiological and pharmacological profile to fill an important unmet medical need.

Animals↗
PubMed2004

Determination of selectivity and efficacy of fatty acid synthesis inhibitors.

Type II fatty acid synthesis (FASII) is essential to bacterial cell viability and is a promising target for the development of novel antibiotics. In the past decade, a few inhibitors have been identified for this pathway, but none of them lend themselves to drug development. To find better inhibitors that are potential drug candidates, we developed a high throughput assay that identifies inhibitors simultaneously against multiple targets within the FASII pathway of most bacterial pathogens. We demonstrated that the inverse t(1/2) value of the FASII enzyme-catalyzed reaction gives a measure of FASII activity. The Km values of octanoyl-CoA and lauroyl-CoA were determined to be 1.1 +/- 0.3 and 10 +/- 2.7 microM in Staphylococcus aureus and Bacillus subtilis, respectively. The effects of free metals and reducing agents on enzyme activity showed an inhibition hierarchy of Zn2+ > Ca2+ > Mn2+ > Mg2+; no inhibition was found with beta-mercaptoethanol or dithiothreitol. We used this assay to screen the natural product libraries and isolated an inhibitor, bischloroanthrabenzoxocinone (BABX) with a new structure. BABX showed IC50 values of 11.4 and 35.3 microg/ml in the S. aureus and Escherichia coli FASII assays, respectively, and good antibacterial activities against S. aureus and permeable E. coli strains with minimum inhibitory concentrations ranging from 0.2 to 0.4 microg/ml. Furthermore, the effectiveness, selectivity, and the in vitro and in vivo correlations of BABX as well as other fatty acid inhibitors were elucidated, which will aid in future drug discovery.

Anti-Bacterial Agents↗
PubMed2004

Discovery of isoxazolinone antibacterial agents. Nitrogen as a replacement for the stereogenic center found in oxazolidinone antibacterials.

A series of potential antimicrobial derivatives possessing bioisosteric replacements for the central oxazolidinone ring found in oxazolidinone antibacterials have been prepared. The design concept involved replacement of the requisite sp(3)-hybridized stereogenic center found at the 5-position of the oxazolidinone with a nitrogen atom. The synthesis and antibacterial activity of three such ring systems, the benzisoxazolinones, pyrroles, and isoxazolinones is described.

Anti-Bacterial Agents↗
PubMed2004

Antimicrobial evaluation of nocathiacins, a thiazole peptide class of antibiotics.

Nocathiacins are cyclic thiazolyl peptides with inhibitory activity against gram-positive bacteria. BMS-249524 (nocathiacin I), identified from screening a library of compounds against a multiply antibiotic-resistant Enterococcus faecium strain, was used as a lead chemotype to obtain additional structurally related compounds. The MIC assay results of BMS-249524 and two more water-soluble derivatives, BMS-411886 and BMS-461996, revealed potent in vitro activities against a variety of gram-positive pathogens including methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, vancomycin intermediate-resistant S. aureus, vancomycin-resistant enterococci, Mycobacterium tuberculosis and Mycobacterium avium. Analysis of killing kinetics revealed that these compounds are bactericidal for S. aureus with at least a 3-log(10) reduction of bacterial growth within 6 h of exposure to four times the MICs. Nocathiacin-resistant mutants were characterized by DNA sequence analyses. The mutations mapped to the rplK gene encoding the L11 ribosomal protein in the 50S subunit in a region previously shown to be involved in the binding of related thiazolyl peptide antibiotics. These compounds demonstrated potential for further development as a new class of antibacterial agents with activity against key antibiotic-resistant gram-positive bacterial pathogens.

Anti-Bacterial Agents↗
PubMed2004

Antibacterial drug discovery & development summit.

Over 100 senior researchers and managers from academic and industrial research organisations attended this 2-day annual international discovery summit on antibacterial R&D. A number of firms, particularly biotechnology firms, presented compounds that are advancing through clinical development. In addition, areas for basic research and development included metallo-beta-lactamases, ribosomal structural studies and phage-selected targets were described.

Anti-Bacterial Agents↗