Targeting Mycobacterium abscessus Infection in Cystic Fibrosis: A Structure-guided Fragment-based Drug Discovery Approach

Abstract

Recent years have seen the emergence of Mycobacterium abscessus, a highly drug-resistant non-tuberculous mycobacterium, which causes life-threatening infections in people with chronic lung conditions like cystic fibrosis. This opportunistic pathogen is refractory to treatment with standard anti-tuberculosis drugs and most currently available antibiotics, often resulting in accelerated lung function decline. This project aims to use a structure-guided fragment-based drug discovery approach to develop effective drugs to treat M. abscessus infections. During the early stage of the project, three bacterial targets were identified, based on analysis of the structural proteome of M. abscessus and prior knowledge of M. tuberculosis drug targets, followed by gene knockout studies to determine target essentiality for bacterial survival. The three targets from M. abscessus were then cloned, expressed and purified and suitable crystallization conditions were identified leading to the determination of high resolution structures. Further, a large number of starting fragments that hit the three target proteins were determined, using a combination of biophysical screening methods and by defining crystal structures of the complexes. For target 3, PPAT (Phosphopantethiene adenylyl transferase), a chemical linking of two fragments followed by iterative fragment elaboration was carried out to obtain two compounds with low micromolar affinities in vitro. However, these compounds afforded only low inhibitory activity on M. abscessus whole cell. All starting fragments of target 2, PurC (SAICAR synthase), occupied the ATP indole pocket. Efforts were then made to identify further fragment hits by screening diverse libraries. Sub-structure searches of these initial fragment hits and virtual screening helped to identify potential analogues amenable to further medicinal chemistry intervention. While fragment hits of target 1, TrmD (tRNA-(N1G37) methyl transferase), were prioritized, whereby two chemical series were developed using fragment growing and merging approaches. Iterative fragment elaboration cycle, aided by crystallography, biophysical and biochemical assays led to the development of several potential lead candidates having low nano-molar range of in vitro affinities. Two such compounds afforded moderate inhibition of M. abscessus and stronger inhibition of M. tuberculosis and S. aureus cultures. Further chemical modifications of these compounds as well as others are now being done, to optimize cellular and in vivo activities, to be ultimately presented as early stage clinical candidates.