Design, Synthesis, and Biological Evaluation of Pyrimido[4,5‑b]indole Derivatives with Potent Activity against Multidrug-Resistant Gram-Negative Bacteria

The escalating crisis of antimicrobial resistance (AMR),
particularly
multidrug-resistant (MDR) Gram-negative bacterial infections, presents
a grave threat to global public health. This urgent unmet medical
need underscores the demand for novel antibiotics capable of overcoming
existing resistance mechanisms. The ATP-binding sites of bacterial
type II topoisomerases represent promising therapeutic targets against
MDR Gram-negative pathogens. Pyrimido[4,5-b]indole-based
compounds (GP-1) are the first reported ATPase inhibitors of DNA gyrase
with potent and broad-spectrum antibacterial activity against both
MDR Gram-positive and Gram-negative pathogens; however, they are associated
with hERG inhibition and suboptimal pharmacokinetic profiles. To overcome
these limitations, we designed a new series of pyrimido[4,5-b]indole-based derivatives using structure-based scaffold
modification and CADD-guided optimization. This campaign culminated
in the discovery of compound 65, which exhibited potent
broad-spectrum antibacterial activity against MDR Gram-negative bacteria
without detectable hERG liability. Moreover, 65 demonstrated
improved pharmacokinetic properties, leading to enhanced in
vivo efficacy compared to levofloxacin in a murine infection
model.