A potent, non-cytotoxic indazole sulfonamide was identified by
high-throughput screening of >100,000 synthetic compounds for activity
against Mycobacterium tuberculosis (Mtb). This
non-cytotoxic compound did not directly inhibit cell wall biogenesis but
triggered a slow lysis of Mtb cells as measured by release of
intracellular green fluorescent protein (GFP). Isolation of resistant mutants
followed by whole-genome sequencing showed an unusual gene amplification of a 40
gene region spanning Rv3371 to Rv3411c and in
one case a potential promoter mutation upstream of guaB2
(Rv3411c) encoding inosine monophosphate dehydrogenase
(IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH
by an uncompetitive mode of inhibition and growth inhibition could be rescued by
supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads
containing immobilized indazole sulfonamides specifically interacted with IMPDH
in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex
revealed that the primary interactions of these compounds with IMPDH were direct
pi-pi interactions with the IMP substrate. Advanced lead compounds in this
series with acceptable pharmacokinetic properties failed to show efficacy in
acute or chronic murine models of tuberculosis (TB). Time-kill experiments
in vitro suggest that sustained exposure to drug
concentrations above MIC for 24 hours were required for a cidal effect, levels
that have been difficult to achieve in vivo. Direct measurement
of guanine levels in resected lung tissue from tuberculosis infected animals and
patients revealed 0.5–2 mM concentrations in caseum and normal lung
tissue. The high lesional levels of guanine and the slow lytic, growth-rate
dependent, effect of IMPDH inhibition pose challenges to developing drugs
against this target for use in treating TB.
With
the emergence of multidrug-resistant strains of Mycobacterium
tuberculosis there is a pressing need for new oral drugs
with novel mechanisms of action. Herein, we describe the identification
of a novel morpholino–thiophenes (MOT) series following phenotypic
screening of the Eli Lilly corporate library against M. tuberculosis strain H37Rv. The design, synthesis, and structure–activity
relationships of a range of analogues around the confirmed actives
are described. Optimized leads with potent whole cell activity against
H37Rv, no cytotoxicity flags, and in vivo efficacy in an acute murine
model of infection are described. Mode-of-action studies suggest that
the novel scaffold targets QcrB, a subunit of the menaquinol cytochrome c oxidoreductase, part of the bc1-aa3-type cytochrome c oxidase complex that is responsible for driving oxygen-dependent
respiration.
The availability of suitable diverse fragment- and lead-oriented screening compounds is key for the identification of suitable chemical starting points for drug discovery programs. The physicochemical properties of molecules are crucial in determining the success of small molecules in clinical development, yet reports suggest that pharmaceutical and academic sectors often produce molecules with poor drug-like properties. We present a platform to design novel, high quality and diverse fragment- and lead-oriented libraries with appropriate physicochemical properties in a cost-efficient manner. This approach has the potential to assist the way libraries are constructed by significantly addressing the historical uneven exploration of chemical space for drug discovery. Additionally, this platform can teach undergraduates and graduates about compound library design.
With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
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