Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

被引:10
作者
Chaudhury, Sidhartha [1 ]
Abdulhameed, Mohamed Diwan M. [1 ]
Singh, Narender [1 ]
Tawa, Gregory J. [1 ]
D'haeseleer, Patrik M. [2 ]
Zemla, Adam T. [2 ]
Navid, Ali [2 ]
Zhou, Carol E. [2 ]
Franklin, Matthew C. [3 ]
Cheung, Jonah [3 ]
Rudolph, Michael J. [3 ]
Love, James [3 ]
Graf, John F. [4 ]
Rozak, David A. [5 ]
Dankmeyer, Jennifer L. [5 ]
Amemiya, Kei [5 ]
Daefler, Simon [6 ]
Wallqvist, Anders [1 ]
机构
[1] USA, Dept Def Biotechnol, High Performance Comp Software Applicat Inst, Telemed & Adv Technol Res Ctr,Med Res & Mat Comma, Ft Detrick, MD USA
[2] Lawrence Livermore Natl Lab, Livermore, CA USA
[3] New York Struct Biol Ctr, New York, NY USA
[4] GE Co, GE Global Res, Diagnost & Biomed Technol, Computat Biol & Biostat Lab, Niskayuna, NY USA
[5] USA, Bacteriol Div, Med Res Inst Infect Dis, Ft Detrick, MD USA
[6] Mt Sinai Sch Med, New York, NY USA
来源
PLOS ONE | 2013年 / 8卷 / 05期
关键词
FLUX BALANCE ANALYSIS; MYCOBACTERIUM-TUBERCULOSIS; ACCURATE DOCKING; SYSTEMS BIOLOGY; DRUG DISCOVERY; INHIBITORS; DATABASE; ENZYME; PREDICTION; TULAREMIA;
D O I
10.1371/journal.pone.0063369
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited efficacy or availability. To prepare for this eventuality, our objective was to use a metabolic network-based approach to rapidly identify potential drug targets and prospectively screen and validate novel small-molecule antimicrobials. Our target organism was the fully virulent Francisella tularensis subspecies tularensis Schu S4 strain, a highly infectious intracellular pathogen that is the causative agent of tularemia and is classified as a category A biological agent by the Centers for Disease Control and Prevention. We proceeded with a staggered computational and experimental workflow that used a strain-specific metabolic network model, homology modeling and X-ray crystallography of protein targets, and ligand- and structure-based drug design. Selected compounds were subsequently filtered based on physiological-based pharmacokinetic modeling, and we selected a final set of 40 compounds for experimental validation of antimicrobial activity. We began screening these compounds in whole bacterial cell-based assays in biosafety level 3 facilities in the 20th week of the study and completed the screens within 12 weeks. Six compounds showed significant growth inhibition of F. tularensis, and we determined their respective minimum inhibitory concentrations and mammalian cell cytotoxicities. The most promising compound had a low molecular weight, was non-toxic, and abolished bacterial growth at 13 mu M, with putative activity against pantetheine-phosphate adenylyltransferase, an enzyme involved in the biosynthesis of coenzyme A, encoded by gene coaD. The novel antimicrobial compounds identified in this study serve as starting points for lead optimization, animal testing, and drug development against tularemia. Our integrated in silico/in vitro approach had an overall 15% success rate in terms of active versus tested compounds over an elapsed time period of 32 weeks, from pathogen strain identification to selection and validation of novel antimicrobial compounds.
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页数:13
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