Synthesis and Characterization of Functionalized Amino Dihydropyrimidines Toward the Analysis of their Antibacterial Structure–Activity Relationships and Mechanism of Action

Abstract

Antibiotic resistance among bacteria puts immense strain on public health. The discovery of new antibiotics that work through unique mechanisms is one important pillar toward combating this threat of resistance. A functionalized amino dihydropyrimidine was reported to exhibit antibacterial activity via the inhibition of dihydrofolate reductase, an underexploited antibacterial target. Despite this promise, little is known about its structure–activity relationships (SAR) and mechanism of activity. Toward this goal, the aza-Biginelli reaction was optimized to allow for the preparation of focused libraries of functionalized amino dihydropyridines, which in some cases required the use of variable temperature NMR analysis for the conclusive assignment of compound identity and purity. Antibacterial activity was examined using microdilution assays, and compound interactions with dihydrofolate reductase were assessed using antimicrobial synergy studies alongside in vitro enzyme kinetics, differential scanning fluorimetry, and protein crystallography. Clear antibacterial SAR trends were unveiled (MIC values from >64 to 4 μg/mL), indicating that this compound class has promise for future development as an antibacterial agent. Despite this, the in vitro biochemical and biophysical studies performed alongside the synergy assays call the antibacterial mechanism into question, indicating that further studies will be required to fully evaluate the antibacterial potential of this compound class.

Diastereoselective synthesis of cyclic tetrapeptide pseudoxylallemycin A illuminates the impact of base during macrolactamization

“…30 As the spectral ambiguity from signal broadening in both the 1 H and 13 C NMR spectra were expected to be derived from slow conformational interconversions, we postulated that acquiring the spectra at an increased temperature would result in an increased rate of equilibrium between the various conformational isomers, and this may cause signal averaging, making individual signals more pronounced. 48 To examine this, 1 H NMR was acquired at room temperature, 45 °C, and 85 °C, and immense peak sharpening was achieved at higher temperature (Fig. 3a).…”

Catalytic role in Biginelli reaction: Synthesis and biological property studies of 2‐oxo/thioxo‐1,2,3,4‐tetrahydropyrimidines

“…Compound 11 was an antibacterial substance that functions by inhibiting DHFR. [ 76 ] Using nickel nitrate hexahydrate as the catalyst, Akhter et al developed a simple, versatile, high‐yielding method for the synthesis of 1‐phenyl‐2‐thioxo‐1,2,3,4‐tetrahydropyrimidines. Most of the produced compounds showed good to moderate antibacterial activity against Bacillus cereus using the Kirby‐Bauer disc‐diffusion method.…”

“…[75] The possible biological that functions by inhibiting DHFR. [76] versatile, high-yielding method for the synthesis of 1-phenyl-2thioxo-1,2,3,4-tetrahydropyrimidines. Most of the produced compounds showed good to moderate antibacterial activity against Bacillus cereus using the Kirby-Bauer disc-diffusion method.…”

Scalable and Chromatography‐Free Synthesis of Efflux Pump Inhibitor Phenylalanine Arginine β‐Naphthylamide for Its Validation in Wild‐Type Bacterial Strains

“…While a full literature review of its use is beyond the scope of this report, we would like to highlight PAβN's recent use cases where it has been employed to inhibit efflux while other disease relevant parameters are investigated including virulence phenotypes, [16][17][18] biofilm formation and disruption, [19] the development of antibiotic resistance, [20][21][22][23] and quorum sensing; [24] it is also used as a standard for benchmarking newly developed EPIs. [25][26][27] Further, it is commonly used during the development process of new antibiotics; [28][29][30][31][32][33] indeed, our laboratory's interest in PAβN originated during our investigations of antibacterial compounds [34] and natural products [35] that lacked activity against P. aeruginosa. Additional studies show that nonspecific membrane permeabilization may be another pathway by which PAβN potentiates antibiotics, independent of their efflux inhibition, further lending credibility to its broad application as a tool compound.…”