Rifamycin W Analogues from Amycolatopsis mediterranei S699 Δrif-orf5 Strain.

Rifamycin W, the most predominant intermediate in the biosynthesis of rifamycin, needs to undergo polyketide backbone rearrangement to produce rifamycin B via an oxidative cleavage of the C-12/C-29 double bond. However, the mechanism of this putative oxidative cleavage has not been characterized yet. Rif-Orf5 (a putative cytochrome P450 monooxygenase) was proposed to be involved in the cleavage of this olefinic moiety of rifamycin W. In this study, the mutant strain Amycolatopsis mediterranei S699 Δrif-orf5 was constructed by in-frame deleting the rif-orf5 gene to afford thirteen rifamycin W congeners (1-13) including seven new ones (1-7). Their structures were elucidated by extensive analysis of 1D and 2D NMR spectroscopic data and high-resolution ESI mass spectra. Presumably, compounds 1-4 were derivatized from rifamycin W via C-5/C-11 retro-Claisen cleavage, and compounds 1-3, 9 and 10 featured a hemiacetal. Compounds 5-7 and 11 showed oxygenations at various sites of the ansa chain. In addition, compounds 1-3 exhibited antibacterial activity against Staphylococcus aureus with minimal inhibitory concentration (MIC) values of 5, 40 and 0.5 µg/mL, respectively. Compounds 1 and 3 showed modest antiproliferative activity against HeLa and Caco-2 cells with half maximal inhibitory concentration (IC50) values of about 50 µM.

8-Deoxy-Rifamycin Derivatives from Amycolatopsis mediterranei S699 ΔrifT Strain.

Proansamycin X, a hypothetical earliest macrocyclic precursor in the biosynthesis of rifamycin, had never been isolated and identified. According to bioinformatics analysis, it was proposed that RifT (a putative NADH-dependent dehydrogenase) may be a candidate target responsible for the dehydrogenation of proansamycin X. In this study, the mutant strain Amycolatopsis mediterranei S699 ΔrifT was constructed by deleting the rifT gene. From this strain, eleven 8-deoxy-rifamycin derivatives (1-11) and seven known analogues (12-18) were isolated. Their structures were elucidated by extensive analysis of 1D and 2D NMR spectroscopic data and high-resolution ESI mass spectra. Compound 1 is a novel amide N-glycoside of seco-rifamycin. Compounds 2 and 3 feature conserved 11,12-seco-rifamycin W skeleton. The diverse post-modifications in the polyketide chain led to the production of 4-11. Compounds 2, 3, 5, 6, 13 and 15 exhibited antibacterial activity against Staphylococcus aureus (MIC (minimal inhibitory concentration) values of 10, 20, 20, 20, 40 and 20 µg/mL, respectively). Compounds 14, 15, 16, 17 and 18 showed potent antiproliferative activity against KG1 cells with IC50 (half maximal inhibitory concentration) values of 14.91, 44.78, 2.16, 18.67 and 8.07 µM, respectively.

Isolation of 11,12- seco-Rifamycin W Derivatives Reveals a Cleavage Pattern of the Rifamycin Ansa Chain.

This study reported the isolation and characterization of 11 rifamycin congeners including six new ones (1-6) from the agar fermentation extract of Amycolatopsis mediterranei S699. Compounds 1 and 2 are rifamycin glycosides named as rifamycinosides A and B, respectively. Their polyketide skeleton represents a novel cleavage pattern of the rifamycin ansa chain. Compounds 6 and 8 showed potential T3SS inhibitory activity, and 6 induced G2/M phase arrest and caused DNA damage in HCT116 cells.

Bacterial Transcription as a Target for Antibacterial Drug Development.

Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.

LC-MS-based metabolomics study of marine bacterial secondary metabolite and antibiotic production in Salinispora arenicola.

An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A "chemical profile" link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time.

Juanlimycins A and B, ansamycin macrodilactams from Streptomyces sp.

Ansamycins are a family of macrolactams characterized by an aromatic chromophore with an aliphatic chain (ansa chain) connected back to a nonadjacent position through an amide bond. This family has shown a high degree of druggability exemplified by rifamycins, maytansinoids, and geldanamycins. In this study, the isolation of two novel ansamycin macrodilactams with unprecedented features, juanlimycins A (1) and B (2), from Streptomyces sp. LC6 were reported. The structures of 1 and 2 were assigned on the basis of analysis of NMR spectroscopic data and X-ray single crystal diffraction.

Determination of rifaximin in rat serum by ionic liquid based dispersive liquid-liquid microextraction combined with RP-HPLC.

An efficient and environmental friendly ionic liquid based dispersive liquid-liquid microextraction procedure was optimized for determination of rifaximin in rat serum by reverse phase high-performance liquid chromatography. The effect of ionic liquids, dispersive solvents, extractant/disperser ratio, and salt concentrations on sample recovery and enrichment factors were studied. Among the five ionic liquids studied in the present investigation, 1-butyl-3-methylimidazolium hexafluorophosphate was found to be most effective for extraction of rifaximin. The recovery was found to be more than 98% using 1-butyl-3-methylimidazolium hexafluorophosphate and methanol as extraction and dispersive solvents, at an extractant/disperser ratio of 0.43. The recovery was further enhanced to 99.5% by the addition of 5.0% NaCl solution. A threefold enhancement in detection limit was achieved when compared to protein precipitation. The ionic liquid containing the extracted rifaximin was directly injected into HPLC system. The linear relationship was observed in the range of 0.03-10.0 µg/mL with the correlation coefficient (r(2)) 0.9998. Limits of detection and quantification were found to be 0.01 and 0.03 µg/mL, respectively. The relative standard deviation was 2.5%. The method was validated and applied to study pharmacokinetics of rifaxmin in rat serum.

Determination of rifalazil, a potent antibacterial agent, in human plasma by liquid-liquid extraction and LC-MS/MS.

A sensitive assay for determination of rifalazil (also known as ABI-1648 and KRM-1648) in human plasma is described. The analytical method utilizes liquid-liquid extraction of plasma with methyl tert-butyl ether, followed by reversed-phase liquid chromatography with a C18 column and a mobile phase gradient utilizing 0.1% formic acid in water and acetonitrile, respectively. Electrospray mass spectrometry in the positive ion mode with selected reaction monitoring of rifalazil and an isotope labeled internal standard, 13C4-rifalazil (ABI-9901) was used for selective and sensitive detection. The calibration range was 0.050-50 ng/mL plasma using 200 microL plasma sample volume. The absolute extraction recovery of rifalazil from K2-EDTA plasma, evaluated at three concentration levels, was 88.6-97.3%, and the recovery for the internal standard was 96.8%. A study of plasma matrix effects showed a peak area response at 90-99% compared to neat solutions for both rifalazil and the internal standard. Stability evaluation of rifalazil in plasma, whole blood and methanol showed that the analyte stability was adequate when stored under study conditions. The precision, as evaluated in three validation batches, was consistent for fortified plasma quality control (QC) samples at four concentration levels, with < or =6% R.S.D. except for at the lowest quality control level where it was 10.7% R.S.D. The accuracy for QC samples (difference between found and nominal concentration) ranged from -2.3% to 5.1%. Similar precision and accuracy values were obtained over 6 months of routine application of this method. It was concluded that the performance improved markedly during routine operation by replacing a closely related structural analog internal standard with the stable isotope internal standard.

Biosynthesis of rifamycin SV by Amycolatopsis mediterranei MTCC17 in solid cultures.

Studies were performed on the production of rifamycin SV, an ansamycin compound, extensively used for curing tuberculosis, leprosy and several other mycobacterial infections, using a strain of Amycolatopsis mediterranei MTCC17 in solid cultures. Wheat bran was employed as a solid substrate. The culture produced 4 g of rifamycin SV/kg of substrate. Pre-treatment of the substrate with dilute HCl was found to increase the yield of rifamycin SV by 300% (from 4 to 12 g x kg of substrate(-1)). Various process parameters were tested to establish the best conditions for the maximum production of the compound and a initial moisture level of 80%, inoculum size of 40%, initial substrate pH of 7.0, incubation temperature of 26 degrees C and a 7 day fermentation period were found to be optimal. Different solvents were used for the extraction of rifamycin SV from the fermented matter and methanol was found to be most suitable. Under optimized conditions, the yield of rifamycin SV further increased from 12 to 32 g x kg of substrate(-1), showing an 8-fold increase from the initial value.

New insights into rifamycin B biosynthesis: isolation of proansamycin B and 34a-deoxy-rifamycin W as early macrocyclic intermediates indicating two separated biosynthetic pathways.

Proansamycin B, the formerly postulated intermediate of rifamycin B biosynthesis, was isolated from cultures of the Amycolatopsis mediterranei mutant F1/24. The structure was determined using UV, IR, NMR and MS techniques. Biotransformation studies demonstrate that proansamycin B is an intermediate of a shunt pathway, a 8-deoxy variant, of rifamycin B biosynthesis leading to 8-deoxy-rifamycin B as the final product. In addition, 34a-deoxy-rifamycin W, the direct precursor of rifamycin W, could be isolated representing the earliest macrocyclic intermediate obtained so far in the biosynthetic route to rifamycin B. Furthermore, the new rifamycin W-28-desmethyl-28-carboxy and rifamycin W-hemiacetal, intermediates in the transformation sequence of rifamycin W to rifamycin S, were isolated. Application of proton NMR measurements (double resonance and ROESY experiments) on the latter compound indicated that the stereochemistry at the chiral center C-28 is R.

Cloning and partial characterization of the putative rifamycin biosynthetic gene cluster from the actinomycete Amycolatopsis mediterranei DSM 46095.

The actinomycete Amycolatopsis mediterranei produces the commercially and medically important polyketide antibiotic rifamycin, which is widely used against mycobacterial infections. The rifamycin biosynthetic (rif) gene cluster has been isolated, cloned and characterized from A. mediterranei S699 and A. mediterranei LBGA 3136. However, there are several other strains of A. mediterranei which also produce rifamycins. In order to detect the variability in the rif gene cluster among these strains, several strains were screened by PCR amplification using oligonucleotide primers based on the published DNA sequence of the rif gene cluster and by using dEBS II (second component of deoxy-erythronolide biosynthase gene) as a gene probe. Out of eight strains of A. mediterranei selected for the study, seven of them showed the expected amplification of the DNA fragments whereas the amplified DNA pattern was different in strain A. mediterranei DSM 46095. This strain also showed striking differences in the banding pattern obtained after hybridization of its genomic DNA against the dEBS II probe. Initial cloning and characterization of the 4-kb DNA fragment from the strain DSM 46095, representing a part of the putative rifamycin biosynthetic cluster, revealed nearly 10% and 8% differences in the DNA and amino acid sequence, respectively, as compared to that of A. mediterranei S699 and A. mediterranei LBGA 3136. The entire rif gene cluster was later cloned on two cosmids from A. mediterranei DSM 46095. Based on the partial sequence analysis of the cluster and sequence comparison with the published sequence, it was deduced that among eight strains of A. mediterranei, only A. mediterranei DSM 46095 carries a novel rifamycin biosynthetic gene cluster.

Enantiomeric resolution using the macrocyclic antibiotics rifamycin B and rifamycin SV as chiral selectors for capillary electrophoresis.

Rifamycin B and rifamycin SV belong to the class of macrocyclic antibiotics known as ansamycins. These macrocyclic antibiotics were used as chiral selectors in capillary electrophoresis to enantioselectively resolve a number of chiral compounds. They contain groups capable of providing the types of multiple interactions necessary to achieve chiral recognition between enantiomers. In fact, they appear to be complimentary in the types of compounds they can enantiomerically resolve. Rifamycin B is shown to be enantioselective towards positively charged compounds, while rifamycin SV was enantioselective towards negatively charged solutes. The choice of wavelength for detection significantly affects sensitivity. Monitoring one of the wavelengths which coincide with the absorption minima of the chiral selector enhances sensitivity. Resolution is enhanced by keeping the amount of analyte injected on column as low as possible and it is demonstrated that it is possible to detect as little as 0.1% of one enantiomer in the presence of the other enantiomer using indirect detection.

New rifamycins produced by a recombinant strain of Nocardia mediterranei.

A recombinant strain of Nocardia mediterranei was found to produce a number of new rifamycins which are structurally related to rifamycin S, rifamycin W and rifamycin G. This strain was derived from two Nocardia mediterranei mutants by intraspecific recombination.

3-Hydroxyrifamycin S and further novel ansamycins from a recombinant strain R-21 of Nocardia mediterranei.

The structures of 3-hydroxyrifamycin S and six further novel ansamycins isolated from the recombinant strain R-21 of Nocardia mediterranei were identified by spectroscopic methods. Three types of structure were distinguished: Type 1: Ansamycins of the rifamycin S type Type 2: Ansamycins of the rifamycin G type Type 3: Ansamycins of the rifamycin W type.