A new class of penicillin-binding protein inhibitors to address drug-resistant Neisseria gonorrhoeae

Abstract

β-Lactams are the most widely used antibiotics for the treatment of bacterial infections because of their proven track record of safety and efficacy. However, susceptibility to β-lactam antibiotics is continually eroded by resistance mechanisms. Emerging multidrug-resistant (MDR) Neisseria gonorrhoeae strains possessing altered penA alleles (encoding PBP2) pose a global health emergency as they threaten the utility of ceftriaxone, the last remaining outpatient antibiotic. Here we disclose a novel benzoxaborinine-based penicillin-binding protein inhibitor series (boro-PBPi) that is envisioned to address penA-mediated resistance while offering protection against evolution and expansion of β-lactamases. Optimization of boro-PBPi led to the identification of compound 21 (VNRX-14079) that exhibits potent antibacterial activity against MDR N. gonorrhoeae achieved by high affinity binding to the PBP2 target. Boro-PBPi/PBP2 complex structures confirmed covalent interaction of the boron atom with Ser310 and the importance of the β₃-β₄ loop for improved affinity. 21 elicits bactericidal activity, a low frequency of resistance, a good safety profile, suitable pharmacokinetic properties, and in vivo efficacy in a murine infection model against ceftriaxone-resistant N. gonorrhoeae. 21 is a promising anti-gonorrhea agent poised for further advancement.

Keywords: PBP inhibitor; antibiotic; boron; gonorrhea; non-β-lactam; penicillin-binding protein.

Figure 1.. Evolution of boro-PBPi from BLI-containing benzoxaborinine core to ureido-containing lead compound 21 (VNRX-14079).

The table shows PBP2 binding and MIC data for ceftriaxone, cefoperazone, and selected boro-PBPi.

Figure 2.. Crystal structures of tPBP2^35/2 in complex with boro-PBPi 12 and 15.

A and B) The crystal structures of mosaic Ng tPBP2^35/2 bound to R,R-12 and R,R-15, respectively. Right hand panels show the interactions made by the para-carboxylate in 12 and phosphonate of 15. C) Superimposition of the crystal structures of Ng tPBP2^35/2 in complex with 15 and apo Ng tPBP2^35/2 (PDB: 6VBL) showing the movement of the β₃-β₄ loop toward the active site in the complex (arrow).

Figure 3.. In vivo efficacy of boro-PBPi 21 in the murine vaginal infection model with ceftriaxone-resistant Neisseria gonorrhoeae H041.

A) The dosing scheme to examine in vivo efficacy of 21 against the ceftriaxone-resistant H041-STM^R strain in the murine vaginal infection model is shown with predicted % fT/MIC. 21 was dosed only on day 1. Vaginal swab samples from infected mice were cultured to confirm H041 infection on day 0 prior to administration of test compound or controls on day 0 (green box). Vaginal cultures were collected on days 1–8 post treatment to determine the bacterial burden (CFU/mL). B) The percentage of mice infected over time with H041, and the average bacterial burden recovered over the course of the experiment. Over 85% of vehicle control mice remained colonized through day 5, with 60% colonized by day 8. SC-administered CRO, used as a positive control, yielded unanticipated underperformance relative to traditional intraperitoneal (IP) injection. The horizontal dashed line denotes the limit of detection (20 CFU/mL). C) The average bacterial burden recovered over the course of the experiment. Error bars indicate standard error of the mean. All bacterial burden data are presented in Table S5.