Discovery of Phospopantetheinyl Transferse Inhibitors Against Mycobacterium tuberculosis

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Abstract Tuberculosis (TB) presents an ongoing global challenge to medical science that will only be met by multiple approaches. Due to the length of even “routine” TB therapy and the age of existing drugs – which contributes to the emergence of devastating resistant forms of the disease – the discovery of new drugs, especially those that function by new mechanisms of action, has become critical. In early 2019, a team including the present laboratory reported AU 8918 as the first high-quality inhibitor of 4'-phosphopantetheinyl transferase (PptT). PptT, which catalyzes the placement of a 4'-phosphopantetheinyl moiety onto a client carrier protein, is essential for the biosynthesis of mycobacterial fatty acids and virulence factors. PptT represents a valuable anti-TB target because (1) it is essential for mycobacterial tuberculosis (Mtb) survival in vitro and in mice, (2) it is divergent from the closest host ortholog, and (3) it is distinct from all targets of established TB drugs. In addition, its inhibition has been shown (4) to effectively kill Mtb including multi- and extensively-drug-resistant variants and (5) to block Mtb growth in mice, while (6) sparing other bacterial or mammalian cells. The primary hit compound, AU 8918, has an IC50 of 2.3 M in biochemical assays of PptT inhibition, a MIC90 of 3.1 M against Mtb in vitro, and has some physical properties features consistent with advancement as a drug candidate, but suffers from off-target cardiotoxicity likely associated with sodium channel blockade. The present proposal seeks to support an ongoing collaboration between three laboratories that share the common goal to design, synthesize, and characterize PptT inhibitors suitable for pre-clinical development. The availability of five high resolution co-crystal structures of AU 8918 and analogs bound to Mtb PptT has been leveraged to establish a robust in silico modeling protocol for the preliminary assessment of analogs. Several avenues to create novel PptT inhibitors are proposed, including (1) SAR exploration of AU 8918, (2) discovery and exploration of new scaffolds arising from bioisosteric replacements of the amidinourea subunit of AU 8918, and (3) new hits arising from an ongoing screen against PptT. We will characterize inhibitors by (1) biochemical PptT inhibition, (2) X-ray crystallography of inhibitor•PptT co-crystals, and (3) advanced biochemical characterization (including intracellular macrophage activity measurements, verification of on-target activity by knockdown/knockout studies, safety profiling against off-target liabilities, pharmacokinetic and metabolic characterization, metabolomics, and synergy studies). The final goal of the project is to identify 1–2 advanced compounds for advancement to in vivo studies in Mtb infected mice, having the following properties: (<0.1 M potency against PptT, <1 M MIC90 against Mtb, retention of positive physical properties, and lacking cardiotoxicity or activity (>30 M inhibition) at relevant Ca and Na channels.