Abstract
Genomic studies and experiments with permeability-deficient strains have revealed a variety of biological targets that can be engaged to kill Gram-negative bacteria. However, the formidable outer membrane and promiscuous efflux pumps of these pathogens prevent many candidate antibiotics from reaching these targets. One such promising target is the enzyme FabI, which catalyzes the rate-determining step in bacterial fatty acid biosynthesis. Notably, FabI inhibitors have advanced to clinical trials for Staphylococcus aureus infections but not for infections caused by Gram-negative bacteria. Here, we synthesize a suite of FabI inhibitors whose structures fit permeation rules for Gram-negative bacteria and leverage activity against a challenging panel of Gram-negative clinical isolates as a filter for advancement. The compound to emerge, called fabimycin, has impressive activity against >200 clinical isolates of Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, and does not kill commensal bacteria. X-ray structures of fabimycin in complex with FabI provide molecular insights into the inhibition. Fabimycin demonstrates activity in multiple mouse models of infection caused by Gram-negative bacteria, including a challenging urinary tract infection model. Fabimycin has translational promise, and its discovery provides additional evidence that antibiotics can be systematically modified to accumulate in Gram-negative bacteria and kill these problematic pathogens.
Synopsis
Fabimycin is a bacterial FabI inhibitor that possesses potent antibiotic activity against multiple ESKAPE pathogens and efficacy in several mouse infection models, while largely sparing human commensal bacteria.
Introduction
Novel antibiotic classes for infections caused by Gram-positive pathogens have been a success story over the last 20 years, with drugs in the oxazolidinone, mutilin, and lipopeptide classes all having notable clinical or veterinary impact. (1−3) Further, there are additional antibiotics moving through clinical trials for Gram-positive infections, including new compound classes and antibiotics that engage unexploited biological targets. (4) In contrast, there has not been a novel class of antibiotics FDA approved for treatment of Gram-negative pathogens contained within the group of high-priority antibiotic-resistant, nosocomoial pathogens (ESKAPE pathogens (5,6)) in over 50 years; this situation has led to increased mortality, with these Gram-negative bacteria representing four of the top six pathogens causing antibiotic-associated deaths, and some studies showing that 75% of deaths from drug-resistant pathogens are now caused by Gram-negative bacteria. (7,8) This discovery void is largely due to the low likelihood that a given compound will accumulate inside Gram-negative bacteria, as their dense lipopolysaccharide outer membrane and promiscuous efflux pumps work in concert to prevent candidate antibiotics from reaching their target. Recent studies reveal that compounds capable of accumulating inside Gram-negative bacteria often possess certain physicochemical properties, (9−11) explaining why high-throughput screens of millions of compounds have failed to identify Gram-negative active antibiotics. (12,13)
Encouragingly, the same biological processes that are exploited through antibiotic intervention against Gram-positive bacteria can typically be leveraged to kill Gram-negative bacteria; inhibitors of protein translation, DNA replication, and cell wall biosynthesis have broad-spectrum activity (Gram-positive and Gram-negative) provided they can enter the cell and reach their target. However, many other promising biological targets have not yet been leveraged to kill Gram-negative organisms, as the antibiotics that engage these targets do not accumulate in Gram-negative bacteria. One such outstanding target is the enoyl-acyl carrier protein reductase enzyme FabI, which catalyzes the rate-determining step in bacterial fatty acid biosynthesis. (14) A lead compound (15,16) identified from a biochemical high-throughput screen for FabI inhibition was optimized into Debio-1452 (Figure 1A), the phosphonoxy methyl prodrug version of which (called afabicin) is in Phase 2 clinical trials for infections caused by Staphylococcus aureus. (17) While FabI is a promising exploitable target for problematic Gram-negative ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, Debio-1452 does not accumulate inside these cells and is consequently inactive against these bacteria. (18)….
