Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives

Kamal El-sagheir, Ahmed M.; Abdelmesseh Nekhala, Ireny; Abd El-Gaber, Mohammed K.; Aboraia, Ahmed S.; Persson, Jonatan; Schäfer, Ann-Britt; Wenzel, Michaela; Omar, Farghaly A.

doi:10.1039/d3md00309d

Cited by 2 publications

(4 citation statements)

References 55 publications

(71 reference statements)

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“…Stalled MreB movement was also observed with tunicamycin and D-cycloserine (Fig. S14) as well as with all previously tested cell wall synthesis inhibitors ( 61 – 63 ). Membrane-active compounds may detach MreB from the cell membrane (see gramicidin and CCCP; Fig.…”

Section: Resultssupporting

confidence: 58%

“…Membrane-active compounds may detach MreB from the cell membrane (see gramicidin and CCCP; Fig. S14) or induce distinct, static clusters, yet as long as non-clustered MreB remains at the cell membrane, it retains its mobility ( 61 – 63 ). None of the other test compounds affected MreB mobility either (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The promoter may also react to indirect inhibition of the lipid II cycle, e.g., by clustering of RIFs or dissociation of MurG ( 24 , 34 ). Therefore, it can be a valuable complementation of the MreB mobility assay, which reacts to all types of direct cell wall synthesis inhibition but not to membrane-mediated, indirect effects on this pathway ( 61 – 63 ). Together, these two assays allow reliable identification of cell wall synthesis inhibitors as well as narrowing down of the target to the membrane-bound lipid II cycle as opposed to intracellular and extracellular steps of cell wall synthesis.…”

Section: Resultsmentioning

confidence: 99%

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Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit

Schäfer,

Sidarta,

Abdelmesseh Nekhala

et al. 2024

Microbiol Spectr

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Phenotypic analysis assays such as bacterial cytological profiling (BCP) have become increasingly popular for antibiotic mode of action analysis. A plethora of dyes, protein fusions, and reporter strains are available and have been used for this purpose, enabling both rapid mode of action categorization and in-depth analysis of antibiotic mechanisms. However, non-expert researchers may struggle choosing suitable assays and interpreting results. This is a particular problem for antibiotics that have multiple or complex targets, such as the bacterial cell envelope. Here, we set out to curate a minimal set of accessible and affordable phenotypic assays that allow distinction between membrane and cell wall targets, can identify dual-action inhibitors, and can be implemented in most research environments. To this end, we employed BCP, membrane potential, fluidity, and cell wall synthesis assays. To assess specificity and ease of interpretation, we tested three well-characterized and commercially available reference antibiotics: the potassium ionophore valinomycin, the lipid II-binding glycopeptide vancomycin, and the dual-action lantibiotic nisin, which binds lipid II and forms a membrane pore. Based on our experiments, we suggest a minimal set of BCP, a membrane-potentiometric probe, and fluorescent protein fusions to MinD and MreB as basic assay set and recommend complementing these assays with Laurdan-based fluidity measurements and a PliaI reporter fusion, where indicated. We believe that our results can provide guidance for researchers who wish to use phenotypic analysis for mode of action studies but do not possess the specialized equipment or expert knowledge to employ the full breadth of possible techniques. IMPORTANCE Phenotypic analysis assays using specialized fluorescence fusions and dyes have become increasingly popular in antibiotic mode of action analysis. However, it can be difficult to implement these methods due to the need for specialized equipment and/or the complexity of bacterial cell biology and physiology, making the interpretation of results difficult for non-experts. This is especially problematic for compounds that have multiple or pleiotropic effects, such as inhibitors of the bacterial cell envelope. In order to make phenotypic analysis assays accessible to labs, whose primary expertise is not bacterial cell biology, or with limited equipment and resources, a set of simple and broadly accessible assays is needed that is easy to implement, execute, and interpret. Here, we have curated a set of assays and strains that does not need highly specialized equipment, can be performed in most labs, and is straightforward to interpret without knowing the intricacies of bacterial cell biology.

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Section: Resultssupporting

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit

Schäfer,

Sidarta,

Abdelmesseh Nekhala

et al. 2024

Microbiol Spectr

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“…Mp 93 °C. 78 2-Bromo-1-(4-methoxyphenyl)ethan-1-one (3d). It was attained according to steps implemented in 3a, occupying 4-methoxyacetophenone.…”

Section: ■ Rationalementioning

confidence: 99%

Discovery and Mechanistic Studies of Dual-Target Hits for Carbonic Anhydrase IX and VEGFR-2 as Potential Agents for Solid Tumors: X-ray, In Vitro, In Vivo, and In Silico Investigations of Coumarin-Based Thiazoles

Hefny,

El-Moselhy,

El-Din

et al. 2024

J. Med. Chem.

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A dual-targeting approach is predicted to yield better cancer therapy outcomes. Consequently, a series of coumarin-based thiazoles (5a−h, 6, and 7a−e) were designed and constructed as potential carbonic anhydrase (CA) and VEGFR-2 suppressors. The inhibitory actions of the target compounds were assessed against CA isoforms IX and VEGFR-2. The assay results showed that coumarin-based thiazoles 5a, 5d, and 5e can effectively inhibit both targets. 5a, 5d, and 5e cytotoxic effects were tested on pancreatic, breast, and prostate cancer cells (PANC1, MCF7, and PC3). Further mechanistic investigation disclosed the ability of 5e to interrupt the PANC1 cell progression in the S stage by triggering the apoptotic cascade, as seen by increased levels of caspases 3, 9, and BAX, alongside the Bcl-2 decline. Moreover, the in vivo efficacy of compound 5e as an antitumor agent was evaluated. Also, molecular docking and dynamics displayed distinctive interactions between 5e and CA IX and VEGFR-2 binding pockets.

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Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives

Abstract: Fluoroquinolones are broad-spectrum antibiotics that target gyrase and topoisomerase IV, involved in DNA compaction and segregation. We synthesized 28 novel norfloxacin hydroxamic acid derivatives with additional metal-chelating and hydrophobic pharmacophores,...

Cited by 2 publications

References 55 publications

Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit

Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit

Discovery and Mechanistic Studies of Dual-Target Hits for Carbonic Anhydrase IX and VEGFR-2 as Potential Agents for Solid Tumors: X-ray, In Vitro, In Vivo, and In Silico Investigations of Coumarin-Based Thiazoles

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