Fluorine-substituted dihydrobicyclomycins: Synthesis and biochemical and biological properties

Bicyclomycin generates ROS and blocks cell division in Escherichia coli

The role of reactive oxygen species (ROS) in the killing exerted by antibiotics on bacteria is debated. Evidence attributes part of toxicity of many antibiotics to their ability to generate ROS by interfering with cellular metabolism, but some studies dismiss the role of ROS. Bicyclomycin (BCM) is a broad-spectrum antibiotic that is the only known compound to inhibit E. coli transcription terminator factor Rho with no known other cellular targets. In the present study, we addressed this question by checking whether the induction of oxidative stress could explain the increased sensitivity to Bicyclomycin in the hns deleted strain even in Δkil background in E. coli. BCM evoked the generation of ROS in E. coli cells. BCM is known to cause the cell filamentation phenotype in E. coli. Performing fluorescence microscopic analysis, we show that bicyclomycin-dependent cell filamentation is associated with SOS response. RecA-GFP filaments were found to colocalize with the damaged DNA sites in the cell. Further analysis revealed that the genomic DNA was partitioned but the cell septum formation was severely affected under BCM treatment. Furthermore, we observed biofilm formation by E. coli after BCM treatment. We hypothesize that ROS production after BCM treatment could lead to cell filamentation in bacteria. A better understanding of the mode of toxicity of BCM will help us design better antibiotic treatment regimes for clinical practices, including combinatorial drug therapies. The cell filamentation phenotype observed after BCM treatment makes this antibiotic a promising drug for phage-antibiotic synergy (PAS) therapy.

New Protocol for the Synthesis of S-Thioesters from Benzylic, Allylic and Tertiary Alcohols with Thioacetic Acid

A new one-pot solvent-less reaction to convert benzylic, allylic, ferrocenyl or tertiary alcohols into S-thioesters, bench-stable and less odorous precursors of the corresponding thiols, which is based on reactions in neat thioacetic acid in the presence of tetrafluoroboric acid, is presented. Reaction monitoring by NMR and GC of the benzyl alcohol conversion indicated the intermediate formation of benzyl acetate and benzyl thionoacetate (PhCH2 OC(S)CH3 ) prior to the slower conversion to the final S-benzyl thioacetate product. Increasing the HBF4 concentration enhanced the reaction rate, giving good to excellent yield (up to 99 %) for a large scope of alcohols. Control experiments, with support of DFT calculations, have revealed a thermodynamically favorable, though requiring HBF4 -activation, disproportionation of CH3 C(O)SH to CH3 C(O)OH and CH3 C(S)SH, the latter immediately decomposing to H2 S and (MeC)4 S6 but also generating the hitherto unreported [MeC(O)C(Me)S]2 (μ-S)2 . Kinetic investigations demonstrated that the rate of benzyl alcohol conversion is second-order in [PhCH2 OH] and second order in [HBF4 ], while the rate of conversion of the benzyl acetate intermediate to S-benzyl thioacetate is second order in [PhCOOMe] and fourth order in [HBF4 ]. The DFT calculations rationalize the need to two alcohol molecules and two protons to generate the reactive benzyl cation.

Cyclic Dipeptide: A Privileged Molecular Scaffold to Derive Structural Diversity and Functional Utility

Cyclic dipeptides (CDPs) are the simplest form of cyclic peptides with a wide range of applications from therapeutics to biomaterials. CDP is a versatile molecular platform endowed with unique properties such as conformational rigidity, intermolecular interactions, structural diversification through chemical synthesis, bioavailability and biocompatibility. A variety of natural products with the CDP core exhibit anticancer, antifungal, antibacterial, and antiviral activities. The inherent bioactivities have inspired the development of synthetic analogues as drug candidates and drug delivery systems. CDP plays a crucial role as conformation and molecular assembly directing core in the design of molecular receptors, peptidomimetics and fabrication of functional material architectures. In recent years, CDP has rapidly become a privileged scaffold for the design of advanced drug candidates, drug delivery agents, bioimaging, and biomaterials to mitigate numerous disease conditions. This review describes the structural diversification and multifarious biomedical applications of the CDP scaffold, discusses challenges, and provides future directions for the emerging field.

Easy Access to Novel Tetrahydro-1-benzazepine-2-carboxylic Acids and Tetrahydro-1-benzazepines Carrying [a]-Fused Heterocyclic Units from 2-(Allylaryl)glycinates

A concise, efficient, and versatile approach to access novel tetrahydro-1H-benzo[b]azepine-2-carboxylic acids and tricyclic tetra­hydro-1-benzazepines carrying [a]-fused heterocyclic units is reported. The easily accessible 2-(allylaryl)glycinates were used as starting material to synthesize, via the corresponding 1,4-epoxycycloadducts, the required key intermediate benzo[b]azepine-2-carboxylates. Hydrolysis of the latter afforded the targeted benzo[b]azepine-2-carboxylic acids. The key intermediate was also converted into N-2-chloroacetyl derivatives which, in turn, were transformed into the corresponding tricyclic target hexahydrobenzo[f]pyrazino[1,2-a]azepine-1,4-diones by reaction with benzylamine or aminoethanol. The reaction of the common intermediate with hydrazine gave the corresponding intermediate carbohydrazides, which, by reaction with trimethoxymethane, were transformed into another tricyclic target tetrahydrobenzo[f][1,2,4]tri­azino[4,5-a]azepin-4(3H)-ones. Full spectroscopic characterization (IR, HRMS, and 1H and 13C NMR) is also reported for each compound.

New Indole Diketopiperazine Alkaloids from Soft Coral-Associated Epiphytic Fungus Aspergillus sp. EGF 15-0-3

Three new indole diketopiperazine alkaloids, 11-methylneoechinulin E and variecolorin M, and (+)-variecolorin G, along with 12 known analogs, were isolated from a soft coral-associated epiphytic fungus Aspergillus sp. EGF 15-0-3. The structures of the new compounds were unambiguously established by extensive spectroscopic analyses including HR-ESI-MS, 1D and 2D NMR spectroscopy and optical rotation measurements. The absolute configurations of (+)- and (-)-variecolorin G were determined by experimental and quantum-chemical ECD investigations and single-crystal X-ray diffraction analysis. Variecolorin G is a pair of enantiomeric mixtures with a ratio of 1 : 2. Moreover, (+)-neoechinulin A is firstly reported as a natural product. The cytotoxic activities of all the isolated compounds against NCI-H1975 gefitinib resistance (NCI-H1975/GR) cell lines were preliminarily evaluated by MTT method.

Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes

Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesized by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo(l-Ile-l-Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesized by a cyclodipeptide synthase, and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded by the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus. Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements.

IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known bicyclomycin-producing organism Streptomyces cinnamoneus, which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including in the opportunistic pathogen Pseudomonas aeruginosa. This wide distribution of a complex biosynthetic pathway is very unusual and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.

A versatile synthesis of cyclic dipeptides using the stepwise construction of the piperazine-2,5-dione ring from simple precursors: synthetic sequence and the structure of a representative product, (3RS)-4-(2-allyl-3,5-dimethylphenyl)-1-benzyl-3-phenylpiperazine-2,5-dione

A versatile synthesis of multiply substituted cyclic dipeptides has been designed, based on the stepwise construction of the piperazine-2,5-dione ring using molecular fragments from four different precursor molecules. Starting from substituted 2-allylanilines, reaction with methyl 2-bromo-2-phenylacetate yields the corresponding methyl 2-(2-allylanilino)-2-phenylacetates, which react with haloacetyl chlorides to give methyl 2-[N-(2-allylphenyl)-2-haloacetamido]-2-phenylacetates, which then undergo ring closure with benzylamine to yield the corresponding cyclic dipeptides of type 4-(2-allylphenyl)-1-benzyl-3-phenylpiperazine-2,5-dione. (3RS)-4-(2-Allyl-3,5-dimethylphenyl)-1-benzyl-3-phenylpiperazine-2,5-dione, C28H28N2O2, (IIId), crystallizes with Z′ = 2 in the space group P21/c; the allyl groups in the two independent molecules adopt different conformations and, in one of them, the allyl group is disordered over two sets of atomic sites having occupancies of 0.534 (4) and 0.466 (4). In both molecules, the piperazine-2,5-dione ring adopts a boat conformation, with the 3-phenyl ring in a quasi-axial site. The molecules of (IIId) are linked into a three-dimensional framework structure by a combination of three C—H...O hydrogen bonds and three C—H...π(arene) hydrogen bonds. Comparisons are made with some related structures.

Novel Potent and Selective Acetylcholinesterase Inhibitors as Potential Drugs for the Treatment of Alzheimer's Disease: Synthesis, Pharmacological Evaluation, and Molecular Modeling of Amino-Alkyl-Substituted Fluoro-Chalcones Derivatives

A new series of-fluoro chalcones-substituted amino-alkyl derivatives (3a˜3l) were designed, synthesized, characterized and evaluated for the inhibitory activity against acetylcholinesterase and butyrylcholinesterase. The results showed that the alteration of fluorine atom position and amino-alkyl groups markedly influenced the activity and the selectivity of chalcone derivates in inhibiting acetylcholinesterase and butyrylcholinesterase. Among them, compound 3l possesses the most potent inhibitory against acetylcholinesterase (IC50  = 0.21 ± 0.03 μmol/L), and the highest selectivity for acetylcholinesterase over butyrylcholinesterase (IC50 (BuChE)/IC50 (AChE) = 65.0). Molecular modeling and enzyme kinetic study on compound 3l supported its dual acetylcholinesterase inhibitory profile, simultaneously binding at the catalytic active and peripheral anionic site of the enzyme.

Lethal synergy involving bicyclomycin: an approach for reviving old antibiotics

BACKGROUND

One way to address the growing problem of antimicrobial resistance is to revive old compounds that may have intrinsic lethal activity that is obscured by protective factors. Bicyclomycin is an old inhibitor of the Rho transcription terminator that by itself shows little rapid lethal activity. However, bicyclomycin participates in bacteriostatic synergy, which raises the possibility that conditions for lethal synergy may exist, perhaps through a suppression of protective factors.

METHODS

Bicyclomycin was combined with bacteriostatic inhibitors of gene expression, and bactericidal activity was measured with several cultured Gram-negative pathogens.

RESULTS

When used alone, bicyclomycin failed to rapidly kill growing cultures of Escherichia coli; however, the additional presence of bacteriostatic concentrations of tetracycline, chloramphenicol or rifampicin led to rapid killing. Four other pathogen species, Acinetobacter baumannii, Klebsiella pneumoniae, Salmonella enterica serotype Typhimurium and Shigella dysenteriae, also exhibited enhanced killing when bicyclomycin was combined with tetracycline or rifampicin. This lethal synergy was achieved at low concentrations (slightly above the MIC) for all agents tested in combinations. Follow-up work with E. coli indicated that lethal synergy arose from a blockage of transcription elongation. Moreover, lethal synergy was reduced when bicyclomycin was added 60 min before tetracycline, suggesting that bicyclomycin induces a protective factor.

CONCLUSIONS

The action of bicyclomycin illustrates the potential present in a largely abandoned antibacterial agent; it exhibits lethal synergy when coadministered with known, bacteriostatic inhibitors of gene expression. The identification of protective factors, which are currently uncharacterized, may reveal new ways to promote the lethal action of some old antibiotics.

Unsaturated fluoro-ketopyranosyl nucleosides: Synthesis and biological evaluation of 3-fluoro-4-keto-β-d-glucopyranosyl derivatives of N4-benzoyl cytosine and N6-benzoyl adenine

The protected beta-nucleosides 1-(2,4,6-tri-O-acetyl-3-deoxy-3-fluoro-beta-d-glucopyranosyl)-N(4)-benzoyl cytosine (2a) and 9-(2,4,6-tri-O-acetyl-3-deoxy-3-fluoro-beta-d-glucopyranosyl)-N(6)-benzoyl adenine (2b), were synthesized by the coupling of peracetylated 3-deoxy-3-fluoro-d-glucopyranose (1) with silylated N(4)-benzoyl cytosine and N(6)-benzoyl adenine, respectively. The nucleosides were deacetylated and several subsequent protection and deprotection steps afforded the partially acetylated nucleosides of cytosine 7a and adenine 7b, respectively. Finally, direct oxidation of the free hydroxyl group at 4'-position of 7a and 7b, and simultaneous elimination reaction of the beta-acetoxyl group, afforded the desired unsaturated 3-fluoro-4-keto-beta-d-glucopyranosyl derivatives. These newly synthesized compounds were evaluated for their potential antitumor and antiviral activities. Compared to 5FU, the newly synthesized derivatives showed to be more efficient as antitumor growth inhibitors and they exhibited direct antiviral effect toward rotavirus.