ABSTRACT
Non-tuberculosis mycobacteria (NTM) are ubiquitous environmental bacteria comprising rapid- and slow-
growing (RGM and SGM) opportunistic pathogens and causing tuberculosis (TB)-like lung disease in patients
with pre-existing lung conditions or compromised immunity. The most frequently encountered RGM and SGM
are Mycobacterium abscessus and the M. avium complex (MAC), respectively. Other clinically important NTM
include M. fortuitum and M. chelonae (RGM), and M. kansasii, M. genavense, M. xenopi, and M. simiae (SGM).
The often multiyear-long treatment consists of mostly repurposed and underperforming antibiotic combinations.
For many NTM diseases, there is no reliable curative regimen and mortality is high Our overarching goal is to
optimize rifamycins to overcome intrinsic resistance and improve treatment of NTM lung disease.
Rifampicin (RIF) is the pillar of TB therapy owing to its exquisite potency against the obligate pathogen M.
tuberculosis (Mtb), favorable pharmacokinetics and excellent penetration to the sites of disease. Although RIF
is recommended for the treatment of all SGM pulmonary diseases but M. simiae, its therapeutic utility has not
been established except for M. kansasii disease, in line with RIF being similarly potent against M. kansasii and
Mtb but poorly active against all other NTMs. Rifamycins do not achieve acceptable efficacy against most NTM
diseases due to intrinsic bacterial resistance not associated with polymorphisms or mutations in their target, the
RpoB subunit of the RNA polymerase. Rather, we have shown that M. abscessus undergoes intrabacterial
metabolism by rifamycin monooxygenase(s) (ROX) and ADP-ribosylase (Arr). Through systematic genomics
searches, we have identified these metabolic enzymes in all major RGM and several SGM. M. kansassii, in line
with its favorable response to rifampicin treatment, is Arr-negative. Rifamycin glycosylases and phosphorylases,
discovered in other bacteria, are potential additional candidates contributing to intrinsic resistance in some NTM.
We propose to characterize the species-specific rifamycin resistome of NTMs and exploit this knowledge to
overcome intrinsic resistance and rationally optimize the rifamycin class to improve the treatment of NTM lung
disease. Using ROX-resistant rifabutin (RBT) as chemical starting point in preliminary studies, we have blocked
ADP-ribosylation, resulting in a dramatic potency improvement against M. abscessus, similar to that of RIF
against Mtb (which does not harbor ROX or Arr). We will expand this approach to appropriate RGM and SGM
species as guided by resistome findings. To deliver a preclinical development candidate for the treatment of M.
abscessus and other Arr-positive NTM lung diseases, medicinal chemistry efforts will focus on reducing plasma
protein binding and removing drug-drug interactions due to cytochrome P450 induction, while maintaining
potency and favorable penetration into lung lesions. Through combination studies in vitro and in mouse models,
we will identify best partner drugs to deliver all-oral bactericidal rifamycin-based combinations that can improve
cure rates and shorten treatment duration.
