Structure determination of oligomycins A and C

Antimicrobial Natural Products Derived from Microorganisms Inhabiting the MENA Region

Objective/Background

Natural products (NPs) derived from microorganisms are the basis of a plethora of clinically utilized medications, namely, antimicrobial remedies. Although these secondary metabolites have been extensively explored all over the planet, they remain understudied in the Middle East and North Africa (MENA) region.

Methods

A literature search was conducted to first find NPs that were isolated from environmental fungi and bacteria that inhabit the soils and seawater of the MENA region. Then, purified molecules with biological activity against pathogenic bacteria, biofilms, fungi, and parasites were described in terms of structure, function, and location. Moreover, the methods that could be used to ameliorate the discovery of novel NPs from this region were investigated.

Results

A multitude of antimicrobial molecules from various chemical classes were found to be derived from the environmental microbes of MENA. Although many were rediscovered, some represented novel structural scaffolds for novel families of antimicrobial agents. Additionally, the geographical distribution showed a high number of these NPs were unraveled in a restricted area leaving much of MENA untapped. Furthermore, as relatively traditional and low-efficiency methods were typically used in the discovery process, advanced high-throughput techniques were suggested to enhance this practice at the regional level.

Conclusion

MENA represents a fairly unexploited region where antimicrobial drug discovery could be performed comprehensively through the concomitant exploration of untouched geographical locations and advanced molecular techniques.

Dunaimycin C3, a new GRP78 downregulator from Streptomyces sp. RAN389

A new member of the dunaimycin family, dunaimycin C3 (2), was isolated from a fermented broth of Streptomyces sp. RAN389. The molecular formula of 2 was established as C₄₂H₇₀O₁₀ by high-resolution FAB-MS, and the structure was elucidated by NMR spectroscopic analyses. Dunaimycin C3 inhibited the expression of the molecular chaperone GRP78 in HT1080 G-L cells in the presence of 10 mM of 2-deoxyglucose with an IC₅₀ of 8.4 nM.

YO-001A, a new antifungal agent produced by Streptomyces sp. YO15-A001

A new antifungal compound YO-001A was found from the culture broth of Streptomyces sp. YO15-A001, which was isolated from a soil sample collected in Toyama Prefecture. YO-001A was identified through morphological changes-based screening of the rice blast fungus, Pyricularia oryzae (P. oryzae). YO-001A is a new 26-membered macrolide of the oligomycin family, which exhibits potent antifungal activity against P. oryzae with an IC₅₀ of 0.012 µM by disrupting mitochondrial respiration via inhibition of the F_OF₁-ATPase activity.

Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora

The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.

Verification of oligomycin A structure: synthesis and biological evaluation of 33-dehydrooligomycin A

Although, the structure of oligomycin A (1) was confirmed by spectroscopic and chemical evaluations, some crystallographic data cast doubt on the originally adopted structure of the side 2-hydroxypropyl moiety of this antibiotic. It was suggested that the side chain of the oligomycin is enol-related (2-hydroxy-1-propenyl). To clarify this matter we synthesized and evaluated 33-dehydrooligomycin A (2) prepared by the Kornblum oxidation of 33-O-mesyloligomycin A (3) by dimethyl sulfoxide. NMR data for 33-dehydrooligomycin (2) and results of quantum chemical calculations have shown that this derivative exists in the keto rather than in the enol tautomer 2a. The in vitro antimicrobial activity of 2 was approximately two times weaker in comparison with oligomycin A against Streptomyces fradiae ATCC-19609 and reference Candida spp. strains and similar activity against certain filamentous fungi. The docking binding estimate of 2 with F_OF₁ATP synthase showed a slight decrease in binding affinity for 2 when compared with oligomycin A; that correlated with its activity against S. fradiae ATCC 19609 that is supersensitive to oligomycin A. The in vitro antiproliferative activities of 2 are also discussed.

Oligomycins as inhibitors of K-Ras plasma membrane localisation

Frequently present in pancreatic, colorectal and non-small cell lung carcinomas, oncogenic mutant K-Ras must be localised to the plasma membrane (PM) to be functional. Inhibitors of K-Ras PM localisation are therefore putative cancer chemotherapeutics. By screening a microbial extract library in a high content cell-based assay we detected the rare oligomycin class of Streptomyces polyketides as inhibitors of K-Ras PM localisation. Cultivation and fractionation of three unique oligomycin producing Streptomyces strains yielded oligomycins A-E (1-5) and 21-hydroxy-oligomycin A (6), together with the new 21-hydroxy-oligomycin C (7) and 40-hydroxy-oligomycin B (8). Structures for 1-8 were assigned by detailed spectroscopic analysis. Cancer cell viability screening confirmed 1-8 were cytotoxic to human colorectal carcinoma cells (IC50 > 3 μM), and were inhibitors of the ABC transporter efflux pump P-glycoprotein (P-gp), with 5 being comparable in potency to the positive control verapamil. Significantly, oligomycins 1-8 proved to be exceptionally potent inhibitors of K-Ras PM localisation (Emax 0.67-0.75 with an IC50 ~ 1.5-14 nM).

Study on retroaldol degradation products of antibiotic oligomycin A

Studies of reactivity of antibiotic oligomycin A in various alkaline conditions showed that the compound easily undergoes retroaldol degradation in β-hydroxy ketone fragments positioned in the C7-C13 moiety of the antibiotic molecule. Depending on reaction conditions, the retroaldol fragmentation of the 8,9 or 12,13 bonds or formation of a product through double retroaldol degradation, when the fragment C9-C12 was detached, took place followed by further transformations of the intermediate aldehydes formed. The structures of the obtained non-cyclic derivatives of oligomycin A were supported by NMR and MS methods. NMR parameters demonstrate the striking similarity of the geometry (conformation) of the fragment C20-C34 in the non-cyclic products of retroaldol degradation and the starting antibiotic 1. The compounds obtained had lower cytototoxic properties than oligomycin A for human leukemia cells K-562 and colon cancer cells HCT-116 and lower activity against growth inhibition of model object Streptomyces fradiae. It cannot be excluded that the products of retroaldol degradation participate in the biological effects of antibiotic oligomycin A.

A novel acyclic oligomycin A derivative formed via retro-aldol rearrangement of oligomycin A

The antibiotic oligomycin A in the presence of K(2)CO(3) and n-Bu(4)NHSO(4) in chloroform in phase-transfer conditions afforded a novel derivative through the initial retro-aldol fragmentation of the 8,9 bond, followed by further transformation of the intermediate aldehyde. NMR, MS and quantum chemical calculations showed that the novel compound is the acyclic oligomycin A derivative, in which the 8,9 carbon bond is disrupted and two polyfunctional branches are connected with spiroketal moiety in positions C-23 and C-25. The tri-O-acetyl derivative of the novel derivative was prepared. The acyclic oligomycin A derivative retained the ability to induce apoptosis in tumor cells at low micromolar concentrations, whereas its antimicrobial potencies decreased substantially. The derivative virtually lost the inhibitory activity against F(0)F(1) ATP synthase-containing proteoliposomes, strongly suggesting the existence of the target(s) beyond F(0)F(1) ATP synthase that is important for the antitumor potency of oligomycin A.

Structure and absolute stereochemistry of 21-hydroxyoligomycin A

21-Hydroxyoligomycin A (1) was isolated from Streptomyces cyaneogriseus ssp. noncyanogenus (LL-F28249) and fully characterized by NMR and single-crystal X-ray diffraction methods. The complete 1H and 13C NMR chemical shift assignments for 1 were made using 2D NMR experiments, and the chirality at C-21 was deduced to be R from a J-based configuration analysis. The absolute configuration at C-21 and at the other 18 chiral centers in the molecule were independently confirmed by anomalous dispersion measurements on a crystal of the chloroform methanol solvate of 21-hydroxyoligomycin A (1).

On the Susceptibility of Organic Peroxy Bonds to Hydride Reduction

Reduction of organic molecules that contain a peroxy bond is broadly considered as a "risky" and uncertain operation when cleavage of the peroxy linkage is not desired. For this reason, such reduction steps are normally avoided at the planning stage of the synthesis when possible. As a natural consequence, the information in the literature about the susceptibility of organic peroxy bonds to reducing species is scant. In this work the tolerance of organic peroxy bonds to some common hydride reductants was examined systematically for the first time. Using reduction of ester group to alcohol as a probe, LiAlH(4), LiAlH(O(t)()Bu)(3), LiBHEt(3), and LiBH(4) were found to be significantly better than other reductants examined when taking into consideration both the completeness of the reduction of ester groups and the peroxy bond survival rate. LiBH(4) appeared to be the most suitable reductant for the reduction under discussion, not only because of the high reduction yields/excellent compatibility with peroxy bonds, but also because of the advantages in practical aspects. The results disclosed herein may (hopefully) provide a handy reference for dealing with reduction of other peroxy bond-containing molecules in the future.

An MS/MS library on an ion-trap instrument for efficient dereplication of natural products. Different fragmentation patterns for [M + H]+ and [M + Na]+ ions

The structural novelty of lead compounds is very important in the agrochemical and pharmaceutical industries, and as such, natural products can be an important source. Taking into account that the isolation of lead compounds is very time-consuming, the efficient and safe identification of compounds in microorganism and plant extracts isolated previously is essential. A suitable procedure for this task based on an HPLC system interfaced with an electrospray (ESI) source and a Thermo Finnigan LCQ deca XP plus ion-trap mass spectrometer was developed, and an extensive MS/MS spectral library of characterized natural products was built up. This report summarizes the parameters used for acquiring the library spectra and discusses current limitations of the NIST library and search algorithm. The advantages of the newly introduced Mass Frontier 4.0 for the search of MS/MS product-ion spectra are discussed. Different mechanisms for fragmentation of some [M + H](+) and [M + Na](+) ions that were found are proposed. Oligomycin A, a macrolide antibiotic, exhibits different fragmentation mechanisms in positive and negative ion modes. The cleavage of the ester bond is the preferred mechanism in the positive ion mode, whereas two different pathways-one showing a rare retro-Michael-addition-are observed in the negative ion mode.

Total synthesis of rutamycin B and oligomycin C

The asymmetric synthesis of the macrolide antibiotics (+)-rutamycin B (1) and (+)-oligomycin C (2) is described. The approach relied on the synthesis and coupling of the individual spiroketal fragments 3a and 3b with the C1-C17 polyproprionate fragment 4. The preparation of the spiroketal fragments was achieved using chiral (E)-crotylsilane bond construction methodology, which allowed the introduction of the stereogenic centers prior to spiroketalization. The present work details the synthesis of the C19-C28 and C29-C34 subunits as well as their convergent assembly through an alkylation reaction of the lithiated N,N-dimethylhydrazones 6 and 8 to afford the individual linear spiroketal intermediates 5a and 5b, respectively. After functional group adjustment, these advanced intermediates were cyclized to their respective spiroketal-coupling partners 40 and 41. The requisite polypropionate fragment was assembled in a convergent manner using asymmetric crotylation methodology for the introduction of six of the nine-stereogenic centers. The use of three consecutive crotylation reactions was used for the construction of the C3-C12 subunit 32. A Mukaiyama-type aldol reaction of 35 with the chiral alpha-methyl aldehyde 39 was used for the introduction of the C12-C13 stereocenters. This anti aldol finished the construction of the C3-C17 advanced intermediate 36. A two-carbon homologation completed the construction of the polypropionate fragment 38. The completion of the synthesis of the two macrolide antibiotics was accomplished by the union of two principal fragments that was achieved with an intermolecular palladium-(0) catalyzed cross-coupling reaction between the terminal vinylstannanes of the individual spiroketals 3a and 3b and the polypropionate fragment 4. The individual carboxylic acids 46 and 47 were cyclized to their respective macrocyclic lactones 48 and 49 under Yamaguchi reaction conditions. Deprotection of these macrolides completed the synthesis of the rutamycin B and oligomycin C.

Three new furan derivatives and a new fatty acid from a Taiwanese marine sponge Plakortis simplex

Three new furan derivatives, plakorsins A-C (6-8), together with a new fatty acid, plakortic acid (9), have been isolated from the Taiwanese marine sponge Plakortis simplex in addition to the known metabolites chondrillin (1), 6-epi-chondrillin (2), 2-oxo-2,5-dihydrofuran-5-acetic acid methyl ester (methyl 1,4-epoxy-1-oxo-2-hexenoate) (3), dimethyl beta-ketoadipate (4), and the monomethyl ester of cis,cis-muconic acid (5). The structures of these compounds were established mainly on the basis of spectral data and chemical methods. Biological studies revealed that compound 7 exhibited cytotoxic activity against COLO-250 and KB-16 cells, and compound 1 is active against KB-16 cells.

Binding domain of oligomycin on Na(+),K(+)-ATPase

Oligomycin inhibits Na(+),K(+)-ATPase activity by stabilizing the Na(+) occlusion but not the K(+) occlusion. To locate the binding domain of oligomycin on Na(+),K(+)-ATPase, the tryptic-digestion profile of Na(+),K(+)-ATPase was compared with the profile of Na(+) occlusion within the digested Na(+),K(+)-ATPase in the presence of oligomycin. The Na(+) occlusion profile is responsible for the digestion profile of the alpha-subunit, which is the catalytic subunit of the ATPase. The effect of oligomycin on chimeric Ca(2+)-ATPase activity was examined. The chimera used, in which the 163 N-terminal amino acids of chicken sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPase 1 were replaced with the 200 N-terminal amino acids of the chicken Na(+),K(+)-ATPase alpha1-subunit, partially retains the Na(+)-dependent characteristics of Na(+), K(+)-ATPase, because the chimeric Ca(2+)-ATPase activity is activated by Na(+) but inhibited by ouabain, a specific inhibitor of Na(+),K(+)-ATPase (Ishii, T., Lemas, M.V., Takeyasu, K., 1994, Proc. Natl. Acad. Sci. U. S. A., 91, 6103-6107). Oligomycin depressed the activation by Na(+) of the chimeric Ca(2+)-ATPase activity. These findings suggest that the 200 N-terminal amino acids of the Na(+), K(+)-ATPase alpha-subunit include a binding domain for oligomycin.

Isolation, identification, and antifungal activity of a macrolide antibiotic, oligomycin A, produced by Streptomyces libani

The antibiotic As1A, strongly inhibitory to Phytophthora capsici Leonian in vitro and in vivo, was isolated from the broth culture of Streptomyces libani Baldacci & Grein using various chromatographic procedures. The molecular formula of the antibiotic As1A was deduced to be C45H74O11 (M+H, m/z 791.5307) by high resolution fast atom bombardment - mass spectroscopy. The analysis of 1H-NMR (nuclear magnetic resonance) and 13C-NMR spectroscopy, DEPT experiment, and two-dimensional NMR spectral data revealed that the antibiotic is a macrolide antibiotic having a 26-membered alpha, beta-unsaturated macrolactone ring with a conjugated diene fused to a bicyclic spiroketal. Based on the comparison of NMR data and other chemical properties, the antibiotic As1A turned out to have the same structure as oligomycin A. The antibiotic As1A showed a high level of inhibitory activity against Botrytis cinerea Pers.: Pers., Cladosporium cucumerinum Ellis & Arthur, Colletotrichum lagenarium (C.P. Robin) Berkhout, Magnaporthe grisea (Herb.) Barr, and P. capsici, ranging from 3 to 5 µg·mL-1 of MICs. However, no antimicrobial activity was found against yeasts and bacteria. In further evaluation under greenhouse conditions, developments of the Phytophthora disease, anthracnose, and leaf blast were markedly inhibited on pepper (Capsicum annuum L. cv. Hanbyul), cucumber (Cucumis sativus L. cv. Baekrokdadaki), and rice (Oryza sativa L. cv. Nakdong) plants by treatments with the antibiotic As1A, respectively. Control efficacies of the antibiotic As1A against these plant diseases were in general similar to those of metalaxyl, chlorothalonil, and tricyclazole. The antibiotic As1A did not show any phytotoxicity on pepper, cucumber, and rice plants even at 500 µg·mL-1.Key words: Streptomyces libani, oligomycin A, antifungal activity, plant disease control.

Recent advances in immunosuppressants

In recent years, a large number of structurally diverse immunosuppressants have been discovered that are effective for the treatment of organ transplantation. Some of them are undergoing clinical trials and may soon enter into routine clinical practice. These compounds are either chemical entities obtained from natural sources/synthetic means or biomaterials such as monoclonal antibodies/gene products/proteins. They have been found to interfere at different stages of T cell activation and proliferation, and can be identified as inhibitors of nucleotide synthesis, growth factor signal transduction and differentiation. Newer strategies involving combination of new agents with traditional immunosuppressants, monoclonal antibodies and gene therapy offer enormous potential, not only for the investigation of mechanisms pertaining to graft rejection, but also for its therapeutic prevention.

Total Synthesis of the Alkoxydioxines (+)- and (-)-Chondrillin and (+)- and (-)-Plakorin via Singlet Oxygenation/Radical Rearrangement

The sequential application of singlet oxygenation and peroxyl radical rearrangement provides an asymmetric entry to 4-peroxy-2-enols and 4-peroxy-2-enones. Enantiomerically enriched 2-hydroperoxy-3-alkenols, obtained via hydroxyl-directed addition of (1)O(2) to Z-allylic alcohols, undergo stereospecific radical rearrangement to form 4-hydroperoxy-2-alkenols. The yields of the rearrangement are improved in the presence of excess tert-butyl hydroperoxide, which limits dimerization of the substrate peroxyl radicals. However, the rearrangement equilibrium is unaffected by the presence of polar co-solvents or by the incorporation of a group able to selectively hydrogen bond to the product hydroperoxide. Photoisomerization of the (E)-4-hydroperoxy-2-enone rearrangement products results in irreversible ring closure to furnish diastereomeric mixtures of enantiomerically enriched dioxinols. The strategy is applied to the total synthesis of the alkoxydioxine natural products chondrillin and plakorin. Comparison of the optical rotation of the synthetic material against literature reports indicates that the natural products are either enantiomerically pure or highly enriched in one enantiomer. In addition, our results conclusively demonstrate that the reported configuration of chondrillin is in error.

Isolation and cytotoxic evaluation of marine sponge-derived norterpene peroxides

The marine sponge Diacarnus cf. spinopoculum has provided a series of norterpenes, including five new compounds (7-11), two new ent-compounds [(-)-1a and (+)-1b], and three known compounds (2a, 2b, and 12). Eight of these compounds represent additional examples of the muqubilin/sigmosceptrellin classes (norsesterterpene peroxides) or the nuapapuin class (norditerpene peroxides). Also isolated were dinorditerpenones 11 and 12, which are biosynthetically related to the muqubilin/sigmosceptrellin structure classes. In all, 11 compounds were evaluated for their cytotoxic properties using a soft agar assay system and the NCI's 60 cell-line screen. Compounds without peroxide functionality were inactive. Overall, the norsesterterpene peroxides were less selective as cytotoxins than norditerpene peroxide analogues. Two compounds, nuapapuin A methyl ester (3) and nuapapuin B (7), which were somewhat selective in their cytotoxic behavior, were selected for further in vivo evaluation.