Fragment-based development of small molecule inhibitors targeting <em>Mycobacterium tuberculosis</em> cholesterol metabolism
bioRxiv [Preprint]. 2024 Dec 3:2024.10.28.620643. doi: 10.1101/2024.10.28.620643.
ABSTRACT
Mycobacterium tuberculosis (Mtb) is the world's most deadly infectious pathogen and new drugs are urgently required to combat the emergence of multi- (MDR) and extensively- (XDR) drug resistant strains. The bacterium specifically upregulates sterol uptake pathways in infected macrophages and the metabolism of host-derived cholesterol is essential for Mtb's long-term survival in vivo. Here, we report the development of antitubercular small molecules that inhibit the Mtb cholesterol oxidases CYP125 and CYP142, which catalyze the initial step of cholesterol metabolism. An efficient biophysical fragment screen was used to characterize the structure-activity relationships of CYP125 and CYP142, and identify a non-azole small molecule 1a that can bind to the heme cofactor of both enzymes. A structure-guided fragment-linking strategy was used to optimize the binding affinity of 1a, yielding a potent dual CYP125/142 inhibitor 5m (KD CYP125/CYP142 = 0.04/0.16 μM). Compound 5m potently inhibits the catalytic activity of CYP125 and CYP142 in vitro (KI values < 0.1 μM), and rapidly depletes Mtb intracellular ATP (IC50 = 0.15 μM). The compound has antimicrobial activity against both drug susceptible and MDR Mtb (MIC99 values 0.4 - 1.5 μM) in extracellular assays, and inhibits the growth of Mtb in human macrophages (MIC = 1.7 μM) with good selectivity over mammalian cytotoxicity (LD50 ≥ 50 μM). The combination of small molecule inhibitors and structural data reported here provide useful tools to study the role of cholesterol metabolism in Mtb and are a promising step towards novel antibiotics targeting bioenergetic pathways, which could be used to help combat MDR-TB.
PMID:39803573 | PMC:PMC11722527 | DOI:10.1101/2024.10.28.620643
The mutational landscape of Staphylococcus aureus during colonisation
Nat Commun. 2025 Jan 13;16(1):302. doi: 10.1038/s41467-024-55186-x.
ABSTRACT
Staphylococcus aureus is an important human pathogen and a commensal of the human nose and skin. Survival and persistence during colonisation are likely major drivers of S. aureus evolution. Here we applied a genome-wide mutation enrichment approach to a genomic dataset of 3060 S. aureus colonization isolates from 791 individuals. Despite limited within-host genetic diversity, we observed an excess of protein-altering mutations in metabolic genes, in regulators of quorum-sensing (agrA and agrC) and in known antibiotic targets (fusA, pbp2, dfrA and ileS). We demonstrated the phenotypic effect of multiple adaptive mutations in vitro, including changes in haemolytic activity, antibiotic susceptibility, and metabolite utilisation. Nitrogen metabolism showed the strongest evidence of adaptation, with the assimilatory nitrite reductase (nasD) and urease (ureG) showing the highest mutational enrichment. We identified a nasD natural mutant with enhanced growth under urea as the sole nitrogen source. Inclusion of 4090 additional isolate genomes from 731 individuals revealed eight more genes including sasA/sraP, darA/pstA, and rsbU with signals of adaptive variation that warrant further characterisation. Our study provides a comprehensive picture of the heterogeneity of S. aureus adaptive changes during colonisation, and a robust methodological approach applicable to study in host adaptive evolution in other bacterial pathogens.
PMID:39805814 | DOI:10.1038/s41467-024-55186-x