Identification of chemical features that influence mycomembrane permeation and antitubercular activity

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is the deadliest single-agent infection worldwide. Current antibiotic treatment for TB takes a minimum of four months, underscoring the need for better therapeutics. The unique mycobacterial cell envelope, particularly the outermost mycomembrane, has long been thought to promote intrinsic antibiotic resistance by limiting compound entry into Mtb. Understanding chemical features that influence permeation across the mycomembrane may enable more accurate predictions of whole cell anti-Mtb activity, leading to development of more effective antibacterials. Here we query the mycomembrane permeation of over 1500 azide-tagged compounds in live Mtb with the bioorthogonal click chemistry-based assay PAC-MAN. We use cheminformatics and machine learning to identify chemical features associated with mycomembrane permeation and show that they have predictive value via systematic modification of two small molecule series. Additionally, we find that chemical features that influence mycomembrane permeation correlate with anti-Mtb activity in large compound libraries. These findings suggest that the mycomembrane is indeed a significant barrier to whole cell activity in Mtb and provide a rational framework for designing or modifying compounds to overcome this barrier.