Bisubstrate Adenylation Inhibitors of Biotin Protein Ligase from Mycobacterium tuberculosis

Abstract

SUMMARY The mycobacterial biotin protein ligase (MtBPL) globally regulates lipid metabolism in Mtb through the posttranslational biotinylation of acyl coenzyme A carboxylases involved in lipid biosynthesis that catalyze the first step in fatty acid biosynthesis and pyruvate coenzyme A carboxylase, a gluconeogenic enzyme vital for lipid catabolism. Here we describe the design, development and evaluation of a rationally designed bisubstrate inhibitor of MtBPL. This inhibitor displays potent sub-nanomolar enzyme inhibition and antitubercular activity against multi- and extensively drug resistant Mtb strains. We show that the inhibitor decreases in vivo protein biotinylation of key enzymes involved in fatty acid biosynthesis and that the anti-bacterial activity is MtBPL-dependent. Additionally, the gene encoding BPL was found to be essential in M. smegmatis. Finally, the X-ray co-crystal structure of inhibitor bound MtBPL was solved providing detailed insight for further structure-activity analysis. Collectively, these data suggest that MtBPL is a promising target for further antitubercular therapeutic development.

Targeting protein biotinylation enhances tuberculosis chemotherapy

“…This led to 5′-[N-(d-biotinoyl)sulfamoyl]amino-5′-deoxyadenosine (Bio-AMS), a BPL inhibitor with potent on-target whole-cell activity against drugsensitive and drug-resistant Mtb (17). Nevertheless, several important questions remained concerning its mechanism of action, mechanism of resistance in Mtb, pharmacokinetic (PK) properties, synergy with other antitubercular drugs, and, importantly, consequences of BPL inhibition in vivo.…”

“…We previously reported the design and characterization of potent inhibitors of biotin protein ligase (BPL), the enzyme responsible for covalently ligating biotin onto the ACCs (12)(13)(14)(15)(16)(17)(18)(19). This led to 5′-[N-(d-biotinoyl)sulfamoyl]amino-5′-deoxyadenosine (Bio-AMS), a BPL inhibitor with potent on-target whole-cell activity against drugsensitive and drug-resistant Mtb (17).…”

Genetic Approaches to Facilitate Antibacterial Drug Development

“…As expected, the activity of BioAMS (but not of INH or ethambutol) against Mtb and M. smegmatis directly correlated with expression of BirA, and growth inhibition coincided with the depletion of biotinylated proteins. Together, these straightforward observations confirmed BirA as the primary target of BioAMS (Duckworth et al 2011). The second main advantage of target-based approaches is that they can survey a much larger chemical space than what can be covered in phenotypic screens, especially if fragment-based approaches are included (Scott et al 2012).…”

“…For example, a bisubstrate inhibitor (Bio-AMS) designed to inactivate the protein biotin ligase (BirA) was recently found to inhibit the growth of Mtb. The study conducted by Duckworth et al (2011) examined the impact of Bio-AMS on growth and biotinylation of proteins in M. smegmatis and Mtb. As expected, the activity of BioAMS (but not of INH or ethambutol) against Mtb and M. smegmatis directly correlated with expression of BirA, and growth inhibition coincided with the depletion of biotinylated proteins.…”

“…This was indeed observed for several conditional M. smegmatis knockdown mutants described recently. Underexpression of gyrase subunit A (GyrA, target of quinolones [Sugino et al 1977], Alr [Caceres et al 1997 (Duckworth et al 2011;Kim et al 2010;Wei et al 2011). Similar observations were made with Mtb, in which partial genetic inactivation of the biotin synthesis enzyme BioA or DHFR increased its susceptibility toward the novel inhibitors of these enzymes (Shi et al 2011;Kumar et al 2012).…”