Discovery and development of new antibiotics is a widely recognized, urgent medical need. However, over the past decades, very few new antibiotics have been approved for clinical use and the antibiotic drug pipeline is alarmingly scarce. One of the major factors contributing to the dismal productivity is the lack of technologies that quickly link potent antibacterial compounds to their cellular targets, limiting further development of many compounds. Without a rapid way to make such a link, it is very difficult to advance antibacterial compounds through the lead-development process. Our long-term goal is to discover novel antibiotics employing bacterial functional genomics, molecular biology, bacterial physiology, novel assay development and high throughput approaches. With the current SCORE funding support, we have obtained proof-of-concept for a strategy of target identification using a collection of Escherichia coli cell clones each over-expressing one particular essential gene. In addition, a prototype target identification assay involving 50 cell clones each over-expressing one essential gene was established and validated against three known antibacterial compounds. We expect that a complete over-expression target identification assay will be developed by the end of the current funding period. We propose here to create a complementary target identification technique employing a comprehensive collection of E. coli cell clones each under-expressing one particular essential gene via controlled antisense RNA expression. Specifically, we will construct antisense clones in E. coli cells targeting approximately 250 essential genes and determine optimal induction conditions for sensitization of each cell clone. Subsequently, these antisense clones will be employed to develop a target identification assay which will be validated by using known antibiotics and newly identified antibacterial compounds discovered from a natural product compound library. The E. coli over-expression and under-expression assays, when used in parallel, will provide corroborating as well as complementary results to accelerate the discovery of novel drug candidates with new mechanisms of action to combat multi-drug resistant pathogens.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Continuance Award (SC3)
Project #
3SC3GM083686-02S1
Application #
7933109
Study Section
Special Emphasis Panel (ZGM1-MBRS-8 (MV))
Program Officer
Singh, Shiva P
Project Start
2009-09-30
Project End
2011-09-29
Budget Start
2009-09-30
Budget End
2011-09-29
Support Year
2
Fiscal Year
2009
Total Cost
$106,194
Indirect Cost
Name
California State University Los Angeles
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
066697590
City
Los Angeles
State
CA
Country
United States
Zip Code
90032
Ward, Matthew S; Silva, Isba; Martinez, Walfre et al. (2016) Identification of cellular targets of a series of boron heterocycles using TIPA II-A sensitive target identification platform. Bioorg Med Chem 24:3267-75
Silva, Isba; Real, Lilian J; Ward, Matthew S et al. (2014) A disk-diffusion-based target identification platform for antibacterials (TIPA): an inducible assay for profiling MOAs of antibacterial compounds. Appl Microbiol Biotechnol 98:5551-66
Kanichar, Divya; Roppiyakuda, Lance; Kosmowska, Ewa et al. (2014) Synthesis, characterization, and antibacterial activity of structurally complex 2-acylated 2,3,1-benzodiazaborines and related compounds. Chem Biodivers 11:1381-97
Meng, Jia; Kanzaki, Gregory; Meas, Diane et al. (2012) A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes. FEMS Microbiol Lett 329:45-53
Golanbar, Galarah D; Lam, Christopher K; Chu, Yi-Ming et al. (2011) Phenotypic and molecular characterization of Acinetobacter clinical isolates obtained from inmates of California correctional facilities. J Clin Microbiol 49:2121-31
Yuan, Hai; Chai, Sergio C; Lam, Christopher K et al. (2011) Two methionine aminopeptidases from Acinetobacter baumannii are functional enzymes. Bioorg Med Chem Lett 21:3395-8