Potentiation of rifampin activity in a mouse model of tuberculosis by activation of host transcription factor EB.

Author summary Tuberculosis (TB) is now the leading cause of death from a single infection. Effective TB treatments take months, are toxic and lead to the development of multidrug- (MDR) and extensively drug-resistant (XDR) TB. Host-directed therapies (HDT) are being explored for their potential to enhance the efficacy of anti-mycobacterial agents and reduce lung pathology. Rifampin is one of the most important TB drugs but many patients taking the standard dose have suboptimal plasma levels. We discovered an aminopyrimidine compound with no direct antimycobacterial activity that enhanced control ofMycobacterium tuberculosis(Mtb) in combination with low-dose rifampin in macrophages and in mice. Beneficial effects correlated with the activation of the host transcription factor EB, a master regulator of lysosomal biogenesis and lysosomal activation. Selective activators of host TFEB may aid in the management of TB in patients with suboptimal plasma levels of rifampin. Efforts at host-directed therapy of tuberculosis have produced little control of the disease in experimental animals to date. This is not surprising, given that few specific host targets have been validated, and reciprocally, many of the compounds tested potentially impact multiple targets with both beneficial and detrimental consequences. This puts a premium on identifying appropriate molecular targets and subjecting them to more selective modulation. We discovered an aminopyrimidine small molecule, 2062, that had no direct antimycobacterial activity, but synergized with rifampin to reduce bacterial burden in Mtb infected macrophages and mice and also dampened lung immunopathology. We used 2062 and its inactive congeners as tool compounds to identify host targets. By biochemical, pharmacologic, transcriptomic and genetic approaches, we found that 2062's beneficial effects on Mtb control and clearance in macrophages and in mice are associated with activation of transcription factor EB via an organellar stress response. 2062-dependent TFEB activation led to improved autophagy, lysosomal acidification and lysosomal degradation, promoting bacterial clearance in macrophages. Deletion of TFEB resulted in the loss of IFN gamma-dependent control of Mtb replication in macrophages. 2062 also targeted multiple kinases, such as PIKfyve, VPS34, JAKs and Tyk2, whose inhibition likely limited 2062's efficacy in vivo. These findings support a search for selective activators of TFEB for HDT of TB.