Synthesis, evaluation, and CoMFA study of fluoroquinophenoxazine derivatives as bacterial topoisomerase IA inhibitors

Abstract

New antibacterial agents with novel target and mechanism of action are urgently needed to combat problematic bacterial infections and mounting antibiotic resistances. Topoisomerase IA represents an attractive and underexplored antibacterial target, as such, there is a growing interest in developing selective and potent topoisomerase I inhibitors for antibacterial therapy. Based on our initial biological screening, fluoroquinophenoxazine 1 was discovered as a low micromolar inhibitor against E. coli topoisomerase IA. In the literature, fluoroquinophenoxazine analogs have been investigated as antibacterial and anticancer agents, however, their topoisomerase I inhibition was relatively underexplored and there is little structure-activity relationship (SAR) available. The good topoisomerase I inhibitory activity of 1 and the lack of SAR prompted us to design and synthesize a series of fluoroquinophenoxazine analogs to systematically evaluate the SAR and to probe the structural elements of the fluoroquinophenoxazine core toward topoisomerase I enzyme target recognition. In this study, a series of fluoroquinophenoxazine analogs was designed, synthesized, and evaluated as topoisomerase I inhibitors and antibacterial agents. Target-based assays revealed that the fluoroquinophenoxazine derivatives with 9-NH2 and/or 6-substituted amine functionalities generally exhibited good to excellent inhibitory activities against topoisomerase I with IC50s ranging from 0.24–3.9 µM. Notably, 11a bearing the 6-methylpiperazinyl and 9-amino motifs was identified as one of the most potent topoisomerase I inhibitors (IC50 = 0.48 µM), and showed broad spectrum antibacterial activity (MICs = 0.78–7.6 µM) against all the bacteria strains tested. Compound 11g with the 6-bipiperidinyl lipophilic side chain exhibited the most potent antituberculosis activity (MIC = 2.5 µM, SI = 9.8). In addition, CoMFA analysis was performed to investigate the 3D-QSAR of this class of fluoroquinophenoxazine derivatives. The constructed CoMFA model produced reasonable statistics (q2 = 0.688 and r2 = 0.806). The predictive power of the developed model was obtained using a test set of 7 compounds, giving a predictive correlation coefficient r2pred of 0.767. Collectively, these promising data demonstrated that fluoroquinophenoxazine derivatives have the potential to be developed as a new chemotype of potent topoisomerase IA inhibitors with antibacterial therapeutic potential.

Mechanism and resistance for antimycobacterial activity of a fluoroquinophenoxazine compound

“…In previous studies, the FP-11g compound has been proposed as an antimycobacterial agent active against M. tuberculosis (MIC = 2.5 μM) [11]. Here we demonstrate its activity against the pathogenic NTM M. abscessus.…”

“…FP-11g (Scheme 1) was synthesized using our previously reported procedure [11]. The structure was confirmed by 1 H NMR, and high-resolution mass spectrometry (HRMS).…”

“…We have previously shown [11] that a fluoroquinophenoxazine compound (FP-11g, shown in Scheme 1) with a 6-bipiperidinyl lipophilic side chain inhibited the catalytic activity of Escherichia coli topoisomerase I (IC 50 = 0.48 μM), and showed promising antituberculosis activity (MIC = 2.5 μM against Mtb H37Rv, SI = 9.8 for Vero cell cytotoxicity). In this study, we followed up on the antimycobacterial activity of this compound to further explore its therapeutic potential.…”

4‐Quinolone Derivatives and Their Activities Against Gram‐negative Pathogens

“…The difluoroquinolone derivative NSC648059 bearing a six‐membered ring linked N‐1 and C‐8 positions was found with low micromolar inhibitory activity (IC 50 : 0.8–2.0 μM) against E . coli topoisomerase I by Yu et al . Further modification indicated that the substituents at both N‐1 phenyl group and C‐7 position significantly influenced the activity and the SAR outlined in Figure .…”

“…coli topoisomerase I by Yu et al . Further modification indicated that the substituents at both N‐1 phenyl group and C‐7 position significantly influenced the activity and the SAR outlined in Figure . For the N‐1 phenyl groups, 4‐NH 2 was most favorable against both E .…”