Abstract
Reactive multi-target ‘fragment drugs’ represent critical components of current tuberculosis regimens. These compounds, such as pyrazinamide, are old synthetic antimycobacterials that are activated inside Mycobacterium tuberculosis bacilli and are smaller than the usual drug-like, single-target molecules. Based on the success of small ‘dirty’ drugs in the chemotherapy of tuberculosis, we suggested previously that fragment-based whole cell screens should be introduced in our current antimycobacterial drug discovery efforts. Here, we carried out such a screen and characterized bactericidal activity, selectivity and spectrum of hits we obtained. A library of 1725 fragments was tested at a single concentration for growth inhibitory activity against M. bovis BCG as screening strain and 38 of 116 primary hits were confirmed in dose response analyses to be active against virulent M. tuberculosis. Bacterial kill experiments showed that most hits displayed bactericidal activity at their minimal inhibitory concentration. Cytotoxicity assays established that a large proportion of hits displayed a favorable selectivity index for mammalian cells. Importantly, one third of M. tuberculosis active fragments were also active against M. abscessus and M. avium, two emerging non-tuberculous mycobacterial (NTM) pathogens, opening the opportunity to develop broad spectrum antimycobacterials. Activity determination against Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa) bacteria, as well as fungi (Candida albicans, Cryptococcus neoformans) showed only a small overlap indicating a generally narrow spectrum of these novel antimicrobial hits for mycobacteria. In conclusion, we carried out the first fragment-based whole cell screen against bacteria and identified a substantial number of hits with excellent physicochemical properties and dual activity against M. tuberculosis and NTM pathogens. These hits will now be evaluated in animal models of mycobacterial infection to determine whether any of them can be moved forward as a new antimycobacterial fragment drug candidate.
Highlights
Mycobacterium tuberculosis remains the most deadly bacterial pathogen globally and acquired resistance to current antimycobacterials threatens global tuberculosis control efforts (WHO, 2015)
Based on the success of small ‘dirty’ drugs in the chemotherapy of tuberculosis, we suggested previously that fragment-based whole cell screens should be introduced in our current antimycobacterial drug discovery efforts
While prolonged chemotherapies are required for treating M. avium infections, lung disease caused by M. abscessus is considered incurable (Griffith et al, 2007; Nessar et al, 2012; Aksamit et al, 2014; Park and Olivier, 2015)
Summary
Mycobacterium tuberculosis remains the most deadly bacterial pathogen globally and acquired resistance to current antimycobacterials threatens global tuberculosis control efforts (WHO, 2015). After a decade of high throughput screening against isolated biochemical targets the antimycobacterial discovery field largely moved back to phenotypic whole cell screens to identify compounds with antimicrobial activity first, deconvolute the target via selection of spontaneous resistance mutants and whole genome sequencing. This strategic shift is due to the large scale failure of target-based approaches. The low permeability of the mycobacterial cell envelope affects the productivity of phenotypic whole cell screens which use the same standard pharmaceutical chemical libraries employed for targetbased screens Screening those drug-like, rule-of-five compliant (Lipinski, 2000) archives has resulted in very low hit rates (Barry et al, 2009; Campbell, 2011)
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