Bioguided Isolation of Cyclopenin Analogues as Potential SARS-CoV-2 Mpro Inhibitors from Penicillium citrinum TDPEF34.

SARS-CoV-2 virus mutations might increase its virulence, and thus the severity and duration of the ongoing pandemic. Global drug discovery campaigns have successfully developed several vaccines to reduce the number of infections by the virus. However, finding a small molecule pharmaceutical that is effective in inhibiting SARS-CoV-2 remains a challenge. Natural products are the origin of many currently used pharmaceuticals and, for this reason, a library of in-house fungal extracts were screened to assess their potential to inhibit the main viral protease Mpro in vitro. The extract of Penicillium citrinum, TDPEF34, showed potential inhibition and was further analysed to identify potential Mpro inhibitors. Following bio-guided isolation, a series of benzodiazepine alkaloids cyclopenins with good-to-moderate activity against SARS-CoV-2 Mpro were identified. The mode of enzyme inhibition of these compounds was predicted by docking and molecular dynamic simulation. Compounds 1 (isolated as two conformers of S- and R-isomers), 2, and 4 were found to have promising in vitro inhibitory activity towards Mpro, with an IC50 values range of 0.36-0.89 µM comparable to the positive control GC376. The in silico investigation revealed compounds to achieve stable binding with the enzyme active site through multiple H-bonding and hydrophobic interactions. Additionally, the isolated compounds showed very good drug-likeness and ADMET properties. Our findings could be utilized in further in vitro and in vivo investigations to produce anti-SARS-CoV-2 drug candidates. These findings also provide critical structural information that could be used in the future for designing potent Mpro inhibitors.

New compounds from a hydrothermal vent crab-associated fungus Aspergillus versicolor XZ-4.

Three new quinazoline derivatives (1-3), one new oxepin-containing natural product (4) and four new cyclopenin derivatives (5-7 and 9) have been isolated from an EtOAc extract of the Taiwan Kueishantao hydrothermal vent crab-associated fungus Aspergillus versicolor XZ-4. Their planar structures were established by HRMS, 1D and 2D NMR spectroscopic data analyses. The absolute configurations for compounds 1 and 4 were determined by chiral phase HPLC analysis of their hydrolysis products. The absolute configurations of 2, 3 and 7 were defined mainly by comparison of the quantum chemical TDDFT calculated and the experimental ECD spectra, and the absolute configuration of 5 was deduced from comparison of the optical rotation values reported in the literature. The presence of two atropisomers of 5 was established by NOE analyses. The Ile & Val units in compounds 1-3 allowed the assignment of a new quinazoline skeleton and it's the first time the configuration of isoleucine in the quinazoline skeleton was defined. A series of 7-methoxy cyclopenin derivatives were reported for the first time in this study. The bioevaluation of compounds 5, 7, 8 and 9 revealed inhibitory activities against E. coli at MIC values around 32 µg mL-1.

The Toxin-Producing Pathobiont Klebsiella oxytoca Is Not Associated with Flares of Inflammatory Bowel Diseases.

BACKGROUND: Alterations in the intestinal microbiota are thought to be involved in the pathogenesis of inflammatory bowel diseases (IBD). Klebsiella oxytoca is an intestinal pathobiont that can produce a cytotoxin (tillivaline). AIM: We aimed to elucidate the pathogenetic relevance of toxin-producing K. oxytoca in patients with IBD flares and investigated the clonal relationship of K. oxytoca isolates from IBD patients using multilocus sequence typing (MLST). METHODS: Fecal samples of 235 adult IBD patients were collected from January 2008 to May 2009 and were tested for K. oxytoca, C. difficile toxin, and other pathogens by standard microbiological methods. Clinical data and disease activity scores were collected. K. oxytoca isolates were tested for toxin production using cell culture assays. A total of 45 K. oxytoca isolates from IBD patients, healthy, asymptomatic carriers and from patients with antibiotic-associated hemorrhagic colitis in part from our strain collection were tested for their clonal relationship using MLST. RESULTS: The prevalence of K. oxytoca in IBD overall was 4.7%. Eleven K. oxytoca isolates were detected. Two of 11 isolates were tested positive for toxin production. There was no significant difference in the distribution of K. oxytoca isolates between the groups (active vs. remission in UC and CD). MLST yielded 33 sequence types. K. oxytoca isolates from IBD did not cluster separately from isolates from asymptomatic carriers. CONCLUSIONS: Our data demonstrate that toxin (tilivalline)-producing K. oxytoca is not associated with IBD flares.

A New Meroditerpene and a New Tryptoquivaline Analog from the Algicolous Fungus Neosartorya takakii KUFC 7898.

A new meroditerpene sartorenol (1), a new natural product takakiamide (2) and a new tryptoquivaline analog (3) were isolated, together with nine known compounds, including aszonapyrone A, chevalone B, aszonalenin, acetylaszonalenin, 3'-(4-oxoquinazolin-3-yl) spiro[1H-indole-3,5'-oxolane]-2,2'-dione, tryptoquivalines L, F and H, and the isocoumarin derivative, 6-hydroxymellein, from the ethyl acetate extract of the culture of the algicolous fungus Neosartorya takakii KUFC 7898. The structures of the new compounds were established based on 1D and 2D NMR spectral analysis, and, in the case of sartorenol (1) and tryptoquivaline U (3), X-ray analysis was used to confirm their structures and to determine the absolute configuration of their stereogenic carbons. Compounds 1, 2 and 3 were evaluated for their antimicrobial activity against Gram-positive and Gram-negative bacteria, and multidrug-resistant isolates from the environment; however, none exhibited antibacterial activity (MIC ˃ 256 mg/mL). The three new compounds did not show any quorum sensing inhibition in the screening protocol based on the pigment production by Chromobacterium violaceum (ATCC 31532).

Synthesis, Chiral Separation, Absolute Configuration Assignment, and Biological Activity of Enantiomers of Retro-1 as Potent Inhibitors of Shiga Toxin.

The Shiga toxin (Stx) family is composed of related protein toxins produced by the bacteria Shigella dysenteriae and certain pathogenic strains of E. coli. No effective therapies for Stx intoxication have been developed yet. However, inhibitors that act on the intracellular trafficking of these toxins may provide new options for the development of therapeutic strategies. This study reports the synthesis, chromatographic separation, and pharmacological evaluation of the two enantiomers of Retro-1, a compound active against Stx and other such protein toxins. Retro-1 works by inhibiting retrograde transport of these toxins inside cells. In vitro experiments proved that the configuration of the stereocenter at position 5 is not crucial for the activity of this compound. X-ray diffraction data revealed (S)-Retro-1 to be slightly more active than (R)-Retro-1.

Cytotoxic and pathogenic properties of Klebsiella oxytoca isolated from laboratory animals.

Klebsiella oxytoca is an opportunistic pathogen implicated in various clinical diseases in animals and humans. Studies suggest that in humans K. oxytoca exerts its pathogenicity in part through a cytotoxin. However, cytotoxin production in animal isolates of K. oxytoca and its pathogenic properties have not been characterized. Furthermore, neither the identity of the toxin nor a complete repertoire of genes involved in K. oxytoca pathogenesis have been fully elucidated. Here, we showed that several animal isolates of K. oxytoca, including the clinical isolates, produced secreted products in bacterial culture supernatant that display cytotoxicity on HEp-2 and HeLa cells, indicating the ability to produce cytotoxin. Cytotoxin production appears to be regulated by the environment, and soy based product was found to have a strong toxin induction property. The toxin was identified, by liquid chromatography-mass spectrometry and NMR spectroscopy, as low molecular weight heat labile benzodiazepine, tilivalline, previously shown to cause cytotoxicity in several cell lines, including mouse L1210 leukemic cells. Genome sequencing and analyses of a cytotoxin positive K. oxytoca strain isolated from an abscess of a mouse, identified genes previously shown to promote pathogenesis in other enteric bacterial pathogens including ecotin, several genes encoding for type IV and type VI secretion systems, and proteins that show sequence similarity to known bacterial toxins including cholera toxin. To our knowledge, these results demonstrate for the first time, that animal isolates of K. oxytoca, produces a cytotoxin, and that cytotoxin production is under strict environmental regulation. We also confirmed tilivalline as the cytotoxin present in animal K. oxytoca strains. These findings, along with the discovery of a repertoire of genes with virulence potential, provide important insights into the pathogenesis of K. oxytoca. As a novel diagnostic tool, tilivalline may serve as a biomarker for K oxytoca-induced cytotoxicity in humans and animals through detection in various samples from food to diseased samples using LC-MS/MS. Induction of K. oxytoca cytotoxin by consumption of soy may be in part involved in the pathogenesis of gastrointestinal disease.

(+)-Cyclopenol, a new naturally occurring 7-membered 2,5-dioxopiperazine alkaloid from the fungus Penicillium sclerotiorum endogenous with the Chinese mangrove Bruguiera gymnorrhiza.

One new naturally occurring 7-membered 2,5-dioxopiperazine alkaloid named (+)-cyclopenol (1), along with nine known compounds including viridicatol (2), 3-(dimethylaminomethyl)-1-(1,1-dimethyl-2-propenyl)indole (3), anacine (4), aurantiomide C (5), viridicatin (6), 3-O-methylviridicatin (7), verrucosidin (8), ergosterol (9), and ergosterol peroxide (10), was isolated from the EtOAc extract of fungus Penicillium sclerotiorum, an endophytic fungal strain isolated from Chinese mangrove Bruguiera gymnorrhiza. The chemical structure of the new compound 1 was elucidated on the basis of detailed spectroscopic analysis. The absolute configuration of 1 was determined by single-crystal X-ray analysis with Cu Kα radiation (λ = 1.54178 Å). To our knowledge, (+)-cyclopenol (1) represents the first example of 7-membered 2,5-dioxopiperazine isolated from mangrove endophytic fungus.

[Identification of tetracenomycin X from a marine-derived Saccharothrix sp. guided by genes sequence analysis].

The crude extracts of the fermentation broth from a marine sediment-derived actinomycete strain, Saccharothrix sp. 10-10, showed significant antibacterial activities against drug-resistant pathogens. A genome-mining PCR-based experiment targeting the genes encoding key enzymes involved in the biosynthesis of secondary metabolites indicated that the strain 10-10 showed the potential to produce tetracenomycin-like compounds. Further chemical investigation of the cultures of this strain led to the identification of two antibiotics, including a tetracenomycin (Tcm) analogs, Tcm X (1), and a tomaymycin derivative, oxotomaymycin (2). Their structures were identified by spectroscopic data analysis, including UV, 1D-NMR, 2D-NMR and MS spectra. Tcm X (1) showed moderate antibacterial activities against a number of drug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE) pathogens, with the MIC values in the range of 32-64 microg x mL(-1). In addition, 1 also displayed significant cytotoxic activities against human cancer cell lines, including HL60 (leukemia), HepG2 (liver), and MCF-7 (breast) with the IC 50 values of 5.1, 9.7 and 18.0 micromol x L(-1), respectively. Guided by the PCR-based gene sequence analysis, Tcm X (1) and oxotomaymycin (2) were identified from the genus of Saccharothrix and their 13C NMR data were correctly assigned on the basis of 2D NMR spectroscopic data analysis for the first time.

Boseongazepines A-C, pyrrolobenzodiazepine derivatives from a Streptomyces sp. 11A057.

Three new pyrrolobenzodiazepine derivatives, boseongazepines A-C (1-3), were isolated from a culture broth of Streptomyces sp. 11A057, together with the known compound usabamycin B (4). The structures of 1-4 were determined through the analysis of spectroscopic data including extensive 1D-, 2D-NMR, and MS techniques. Cell growth inhibition effects of these compounds were evaluated against Jurkat, K-562, HL-60, and HepG2 cell lines.

Optimization of 12 chiral analytes with 8 polymeric surfactants.

This manuscript discusses the results of studies that were performed to determine optimum capillary electrophoresis (CE) conditions for the enantiomeric resolution of twelve chiral analytes with eight amino acid based polymeric surfactants. The parameters that were optimized include pH, buffer type, and concentration of surfactant. The results indicated that the optimum conditions for enantiomeric separations with the amino acid based polymeric surfactants examined in this study using CE were analyte dependent, not surfactant dependent. In other words, the optimum conditions for a particular analyte were the same for all the amino acid based polymeric surfactants examined in this study. The results of these studies indicate that when using a large group of related amino acid based polymeric surfactants only a few surfactants need to be optimized for each analyte under study. These studies were limited to anionic surfactants that contain the amino acids glycine, L-alanine, L-valine, and L-leucine only. No inference can be necessarily drawn about surfactants containing other types of amino acids such as threonine and serine, which contain extra heteroatoms, or phenylalanine that has an aromatic moiety.

Circumdatin I, a new ultraviolet-A protecting benzodiazepine alkaloid from a marine isolate of the fungus Exophiala.

A new ultraviolet-A (UV-A) protecting benzodiazepine alkaloid, circumdatin I (1), along with the previously described circumdatin C (2) and circumdatin G (3), have been isolated from the mycelium of a marine-derived fungus of the genus Exophiala. The structures of the three circumdatins were assigned on the basis of physicochemical evidence. The absolute stereochemistry of 1 was determined by comparison of optical rotation and CD experiments with those of 2 and 3.

Circumdatin H, a new inhibitor of mitochondrial NADH oxidase, from Aspergillus ochraceus.

Circumdatin H (1), a new alkaloid from the culture broth of Aspergillus ochraceus, has been isolated, together with a known circumdatin, circumdatin E (2) and other known compounds: flavacol (3) and stephacidin A (4). The structure of 1 was established on the basis of chemical and spectral evidence. All of these alkaloids showed biological activity as inhibitors of the mammalian mitochondrial respiratory chain.

Separation of oxazepam, lorazepam, and temazepam enantiomers by HPLC on a derivatized cyclodextrin-bonded phase: application to the determination of oxazepam in plasma.

The enantioselective high-performance liquid chromatography (HPLC) of three racemic 3-hydroxybenzodiazepines, oxazepam (Oxa), lorazepam (Lor), and temazepam (Tem), is a difficult operation because of the spontaneous chiral inversion in polar solvent. To solve this problem, we have developed an HPLC method based on a chiral Cyclobond I-2000 RSP column, maintained at 12 degrees C, and a reversed mobile phase (acetonitrile in 1% triethylamine acetate buffer, TEAA) at a flow rate of 0.4 ml/min. Peaks were detected by a photodiode-array detector at 230 nm for quantification and by an optical rotation detector for identification of (+) and (-) enantiomers. The results showed that peak resolutions of Oxa, Lor, and Tem enantiomers, analyzed under the same conditions, were 3.2, 2.0, and 1.8, respectively. For the determination of Oxa enantiomers in plasma of rabbits, extraction with diethyl ether at pH 1.5, a polar organic mobile phase, and a Cyclobond I-2000 SP column were used. Other analytical conditions were the same as previously described. Blood samples were immediately cooled at 4 degrees C and centrifuged at 0 degrees C for the collection of plasma. The results showed a difference in plasma S(+)- and R(-)-oxazepam concentrations in rabbits. No racemization of S(+)- or R(-)-Oxa enantiomers, added alone to blank plasma, was observed after extraction and enantioselective HPLC analysis.

Overpressured layer chromatographic study of retention behaviour of various benzodiazepine derivatives on layers impregnated with tricaprylmethylammonium chloride.

The retention behaviour of various benzodiazepine derivatives was investigated on silica gel layers impregnated with tricaprylmethylammonium chloride (TCMA). The chromatograms were developed by means of overpressured layer chromatography (OPLC). As for the case of amino- and nitrosalicylic acids, pyrimidine derivatives, barbiturates, penicillins, cephalosporins and tetracyclines, the retention of benzodiazepine derivatives increased with increasing layer TCMA concentration with eluents containing methanol and water, but not TCMA. On increase of the methanol content of the eluent, a retention-decreasing effect was observed. On layers impregnated with TCMA, a linear relationship existed between the RM values of the benzodiazepines and the methanol content of the eluent. A similar relationship held for silica gel layers impregnated with paraffin oil (traditional reversed-phase). There was no correlation between the results obtained on layers treated with TCMA or with paraffin oil. On TCMA-impregnated layers, the retention of compounds having different chemical structures showed no dependence on the pH of the eluent. There were two reasons for this. Firstly, as it was established, above a certain RF value, the pH of the layer in the presence of TCMA was almost identical irrespective of the original pH of the buffer. Secondly, below this RF value, the actual pH of the layer did not have a strong enough effect to cause appreciable differences between the retentions of the dissociated and undissociated species of the analytes. The conditions for optimum separation are given.

Direct liquid chromatographic separation of enantiomers on immobilized protein stationary phases. IX. Influence of the cross-linking reagent on the retentive and enantioselective properties of chiral sorbents based on bovine serum albumin.

Three modifications of silica-bound, cross-linked bovine serum albumin (BSA) were evaluated as chiral sorbents for use in the liquid chromatographic separation of enantiomers. Glutaraldehyde, formaldehyde and di-(N-succinimidyl) carbonate were used as bifunctional reagents for the immobilization of BSA. The sorbents all contain the same loading of BSA (14.4 +/- 0.1%, w/w) and differ only with respect to the cross-linker used for immobilization. Despite their apparent similarity, the sorbents show very different chromatographic properties, not only with respect to retention of analyte enantiomers (k' and alpha), but also with respect to column efficiency (affecting Rs values). The data obtained indicate that the chemical structure of the cross-linking reagent affects to a large extent the accessibility of important chiral binding sites. Although the data obtained are difficult to interpret in any detail, certain generalizations concerning the different behaviour of the sorbents can be made.

Isolation of clobazam-orosomucoid complexes from patients' sera.

Orosomucoid, a member of the lipocalin family, may function in the in vivo transport of lipophilic compounds such as basic and neutral drugs. We describe the identification of 7-chloro-1-methyl-1,5-benzodiazepine-2,4-dione (clobazam) bound to the serum orosomucoid from individuals actively taking this tranquillizer. This suggests not only that other endogenous factors limit access to the benzodiazepine binding site on human serum albumin, but also that the differential binding of benzodiazepines and their metabolites by orosomucoid should be considered in determining therapeutic doses, particularly in the acute phase response.

Application of preparative liquid chromatography to the isolation of enantiomers of a benzodiazepinone derivative.

The isolation of milligram amounts of the enantiomers of a benzodiazepinone derivative was performed on an analytical cellulose tribenzoate-based column by multiple repetitive injections. An enantiomeric purity greater than 98% was required. First, an analytical method was developed to maximize the resolution by adjusting the mobile phase composition, flow-rate and most importantly the column temperature. Then the preparative separation was optimized by adjusting the sample size and detecting the sample where its UV absorbance was low. The locations of the cut points were determined by use of detector response levels. The method development, preparative separations and analytical assays of the fractions obtained were all performed on analytical columns.

New pyrrolobenzodiazepine antibiotics, RK-1441A and B. II. Isolation and structure.

Antibacteriophage antibiotics, RK-1441A and B, related to neothramycin were isolated from the culture broth of Streptomyces sp. and their structures were deduced from spectroscopic analyses. The structure of RK-1441A was 8,11-dihydroxy-3,7-dimethoxy-5-oxo-1H-pyrrolo[2,1-c:1,4]benzodiazepine. RK-1441B is a tautomeric mixture at C-3 of the structure, 3,8,11-trihydroxy-7-methoxy-5-oxo-1H-pyrrolo[2,1-c:1,4]benzodiazepine.

Porothramycin, a new antibiotic of the anthramycin group: production, isolation, structure and biological activity.

A new antitumor antibiotic porothramycin was produced by a new strain of Streptomyces albus. The antibiotic was isolated in two active forms, the natural free hydroxyl form (porothramycin A) or the crystalline methyl ether form (porothramycin B) depending upon the isolation process used. Structural studies established that porothramycin is a new member of the pyrrolo[1,4]benzodiazepine group antibiotics having only one substituent on the benzene ring. The antibiotic exhibited antimicrobial activity against Gram-positive bacteria and anaerobes and significantly prolonged the survival times of mice implanted with experimental tumors.

Novel cholecystokinin antagonists from Aspergillus alliaceus. I. Fermentation, isolation, and biological properties.

The discovery and biological properties of four novel cholecystokinin antagonists produced by Aspergillus alliaceus is described. One of these was seven times more potent than the previously reported asperlicin.