C3 Marfey Research Articles

Marine Depsipeptide Nobilamide I Inhibits Cancer Cell Motility and Tumorigenicity via Suppressing Epithelial-Mesenchymal Transition and MMP2/9 Expression.

A cyclic depsipeptide, nobilamide I (1), along with the known peptide A-3302-B/TL-119 (2), was isolated from the saline cultivation of the marine-derived bacterium Saccharomonospora sp., strain CNQ-490. The planar structure of 1 was elucidated by interpretation of 1D and 2D NMR and MS spectroscopic data. The absolute configurations of the amino acids in 1 were assigned by using the C3 Marfey’s analysis and comparing them with those of 2 based on their biosynthetic pathways. Nobilamide I (1) decreased cell motility by inhibiting epithelial–mesenchymal transition markers in A549 (lung cancer), AGS (gastric cancer), and Caco2 (colorectal cancer) cell lines. In addition, 1 modulated the expression of the matrix metalloproteinase (MMP) family (MMP2 and MMP9) in the three cell lines.

Cyclopeptides from the Mushroom Pathogen Fungus Cladobotryum varium.

Three new cyclopeptides with serial Phe residues were identified with the aid of HPLC-DAD analysis, from the culture broth of Cladobotryum varium, a fungal pathogen causing mushroom cobweb disease. Cladoamides A (1) and B (2) have two consecutive N-methylphenylalanine units in the destruxin class cyclic depsipentapeptide framework, while cladoamide C (3) has a three consecutive Phe motif in a cyclopentapeptide structure. Of these three cyclopeptides, 1 showed potent autophagy-inducing activity at 10 μg/mL, comparable to a positive control, rapamycin. For the determination of the absolute configurations of the Ile residues in 1 and 3, new conditions for separating Ile and allo-Ile, using a pentafluorophenyl-bonded solid phase and methanolic solvent, were established within the analytical scheme of the advanced Marfey's method, thus offering a convenient alternative to the C3 Marfey's method, which requires elution with a three-solvent mixture. The sequence of two d-Phe and one l-Phe in 3 was determined through NMR chemical shift prediction by DFT-based calculations and chemical synthesis, which demonstrated the significance of noncovalent interactions in the accurate calculation of stable conformers for peptides with multiple aromatic rings.

Suntamide A, a neuroprotective cyclic peptide from Cicadidae Periostracum

Suntamide A (1), a new cyclic peptide, was isolated from Cicadidae Periostracum. The gross structure of 1 was elucidated by detailed analysis of HRMS and 1D/2D NMR spectra, and the absolute configuration was established by C3 Marfey’s method. We extended our study to examine biological activity of 1, and found that 1 protected SH-SY5Y cells against rotenone-induced neurotoxicity. This effect of 1 seemed to be attributed to antioxidant induction and protection of mitochondria from rotenone-caused injury. Along with augmentation of the antioxidant system by 1, there was an evident activation of Nrf2, a transcription factor involved in the activation of the antioxidant system. These results indicate that 1 rescued the cells from rotenone-mediated neurotoxicity by enhancing antioxidant capacity via induction of Nrf2, suggesting that the compound could be used as a therapeutic intervention in neurodegenerative diseases such as Parkinson’s disease.

New chloptosins B and C from an Embleya strain exhibit synergistic activity against methicillin-resistant Staphylococcus aureus when combined with co-producing compound L-156,602.

Two new dimeric cyclohexapeptides, chloptosins B and C, were discovered from the culture broth of Embleya sp. MM621-AF10 together with the known compounds chloptosin and L-156,602. The structures of the new chloptosins were determined by spectroscopic studies and advanced Marfey's methods. The stereo structure of the constituent isoleucine was determined by C3 Marfey's analysis. Chloptosins demonstrated potent antimicrobial activity against Gram-positive bacteria including drug-resistant strains of methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci with MICs of 0.5-2 µg ml-1. The antimicrobial activities of chloptosins were enhanced by addition of co-producing compound L-156,602, as shown by checkerboard analysis.

Potashchelins, a Suite of Lipid Siderophores Bearing Both L-threo and L-erythro Beta-Hydroxyaspartic Acids, Acquired From the Potash-Salt-Ore-Derived Extremophile Halomonas sp. MG34.

Four new lipid siderophores bearing both L-threo- and L-erythro-β-hydroxyaspartic acids, potashchelins A-D (1-4), were isolated from the potash-salt-ore-derived extremophile Halomonas sp. MG34. The planar structures of 1-4 were elucidated on the basis of extensive 1D and 2D NMR studies and MS/MS data. Potashchelins 1-4 contain a hydrophilic nonapeptide headgroup sequentially consisting of β-hydroxyaspartic acid, serine, glycine, serine, serine, β-hydroxyaspartic acid, threonine, serine, and cyclic N(δ)-hydroxy-ornithine, which is appended by one of a series of fatty acids ranging from dodecanoic acid to tetradecanoic acid. The absolute configurations of the amino acids of potashchelins 1-4 were determined by C3 and advanced Marfey's reaction, partial hydrolysis, and bioinformatics analysis, which revealed that potashchelins 1-4 bear both L-threo- and L-erythro-β-hydroxyaspartic acid. Phylogenetic analysis showed that the stand-alone β-hydroxylase, PtcA, and the fused domain with β-hydroxylase activity in PtcB are expected to be responsible for the formation of L-erythro and L-threo diastereomers, respectively. Additionally, utilizing a comparative genomics approach, we revealed an evolutionary mechanism for lipid siderophores in Halomonas involving horizontal transfer. Bioassays showed that potashchelin A and D had weak antibacterial activity against B. subtilis CPCC 100029 with an MIC value of 64 μg/mL.

Scopularides Revisited: Molecular Networking Guided Exploration of Lipodepsipeptides in Australian Marine Fish Gastrointestinal Tract-Derived Fungi.

Chemical analysis of a cultivation of an Australian Mugil mullet gastrointestinal tract (GIT) derived fungus, Scopulariopsis sp. CMB-F458, yielded the known lipodepsipeptides scopularides A (1) and B (2). A comparative global natural product social (GNPS) molecular networking analysis of ×63 co-isolated fungi, detected two additional fungi producing new scopularides, with Beauveria sp. CMB-F585 yielding scopularides C–G (3–7) and Scopulariopsis sp. CMB-F115 yielding scopularide H (8). Structures inclusive of absolute configurations were assigned by detailed spectroscopic and C3 Marfey’s analysis, together with X-ray analyses of 3 and 8, and biosynthetic considerations. Scopularides A–H (1–8) did not exhibit significant growth inhibitory activity against a selection of Gram positive (+ve) and negative (−ve) bacteria, a fungus, or a panel of three human carcinoma cell lines.

Geninthiocins C and D from Streptomyces as 35-membered macrocyclic thiopeptides with modified tail moiety.

Geninthiocin is a thiopeptide with 35-membered macrocyclic core moiety. It has potent anti-Gram-positive (G+) bacteria activity. Herein, we reported two new congeners (2-3) of geninthiocin (geninthiocin A, 1) from Streptomyces sp. CPCC 200267, and designated them as geninthiocins C and D, whose structures were determined by NMR. Geninthiocins A, C and D had the same 35-membered macrocyclic core moiety, but possessed a -Dha-Dha-NH2, -Dha-Ala-NH2, and -NH2 tail, respectively. Besides, the Ala residue in geninthiocin C was determined as L- configuration by C3 Marfey's method. In vitro assays indicated that geninthiocins C-D showed no antibacterial activity, in contrast to the potent anti-G+ bacteria activity displayed by geninthiocin A. Therefore, the -Dha-Dha-NH2 tail of geninthiocin A played an important role in its potent activity against G+ bacteria.

Trichodermides A-E: New Peptaibols Isolated from the Australian Termite Nest-Derived Fungus Trichoderma virens CMB-TN16.

Chemical analysis of a fermentation of the Australian termite nest-derived fungus Trichoderma virens CMB-TN16 yielded five new acyclic nonapeptides, trichodermides A-E (1-5). Amino acid residues, configurations, and sequences were determined by a combination of spectroscopic (NMR and MS-MS) and chemical (C3 Marfey's) methods. The trichodermides adhere to the sequence homology pattern common to Trichoderma 11 amino acid residue peptaibols; however, unlike other peptaibols the trichodermides do not exhibit antibacterial or antifungal activity and exhibit low to no cytotoxicity against mammalian cells. This variability in biological activity highlights the importance of knowing both planar structures and absolute configurations when interpreting structure-activity relationships.

Prolinimines: N-Amino-l-Pro-methyl Ester (Hydrazine) Schiff Bases from a Fish Gastrointestinal Tract-Derived Fungus, Trichoderma sp. CMB-F563.

A rice cultivation of a fish gastrointestinal tract-derived fungus, Trichoderma sp. CMB-F563, yielded natural products incorporating a rare hydrazine moiety, embedded within a Schiff base. Structures inclusive of absolute configurations were assigned to prolinimines A-D (1-4) on the basis of detailed spectroscopic and C3 Marfey's analysis, as well as biosynthetic considerations, biomimetic total synthesis, and chemical transformations. Of note, monomeric 1 proved to be acid labile and, during isolation, underwent quantitative transformation to dimeric 3 and trimeric 4. Prolinimines are only the second reported natural products incorporating an N-amino-Pro residue, the first to include l-Pro, the first to occur as Schiff bases, and the first to be isolated from a microorganism.

Talarolide A, a Cyclic Heptapeptide Hydroxamate from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. (CMB-TU011).

A miniaturized 24-well plate microbioreactor approach was used to explore secondary metabolite media dependence in an Australian marine tunicate-associated fungus, Talaromyces sp. (CMB TU011). Detailed chemical investigations of an antifungal M1-saline cultivation yielded talarolide A (1), only the second reported natural cyclic peptide hydroxamate, and the first from a fungus. The antifungal properties of the M1-saline extract were attributed to the known diterpene glycoside sordarin (2). Structure elucidation of 1 and 2 was achieved by detailed spectroscopic analysis, with amino acid configurations in 1 assigned by the C3 and C18 Marfey's methods, and l-Ala and d-Ala regiochemistry by the recently reported 2D C3 Marfey's method.

Talarazines A-E: Noncytotoxic Iron(III) Chelators from an Australian Mud Dauber Wasp-Associated Fungus, Talaromyces sp. (CMB-W045).

Chemical analysis of an Australian mud dauber wasp-associated fungus, Talaromyces sp. (CMB-W045), yielded five new coprogen siderophores, talarazines A-E (1-5), together with dimerumic acid (6), desferricoprogen (7), and elutherazine B (8). Structures inclusive of absolute configuration were assigned on the basis of detailed spectroscopic analysis and application of the C3 Marfey's method. We report on the noncytotoxic Fe(III) chelation properties of 1-8 and demonstrate that biosynthesis is regulated by available Fe(III) in culture media. We demonstrate a magnetic nanoparticule approach to extracting high-affinity Fe(III) binding metabolites (i.e., 8) from complex extracts.

Structure revision of the Penicillium alkaloids haenamindole and citreoindole

Herein, we describe the isolation of rare alkaloids, haenamindole and citreoindole, from a South China Sea deep-sea fungus, Penicillium citrinum (MF006), and their structure revision based on detailed spectroscopic and C3 Marfey’s analysis.

C3 and 2D C3 Marfey's Methods for Amino Acid Analysis in Natural Products.

We validate the improved resolution and sensitivity of the C3 Marfey's method, including an ability to resolve all Ile isomers, against an array of amino acids commonly encountered in natural products and by comparison to an existing Marfey's method. We also describe an innovative 2D C3 Marfey's method as an analytical approach for determining the regiochemistry of enantiomeric amino acid residues in natural products. The C3 and 2D C3 Marfey's methods represent valuable tools for probing and defining the stereocomplexity of hydrolytically accessible amino acid residues in natural products.

Rare Streptomyces N-formyl amino-salicylamides inhibit oncogenic K-Ras.

During a search for inhibitors of oncogenic K-Ras, we detected two known and two new examples of the rare neoantimycin structure class from a liquid cultivation of Streptomyces orinoci, and reassigned/assigned structures to all based on detailed spectroscopic analysis and microscale C3 Marfey's and C3 Mosher chemical degradation/derivatization/analysis. SAR investigations inclusive of the biosynthetically related antimycins and respirantin, and synthetic benzoxazolone, documented a unique N-formyl amino-salicylamide pharmacophore as a potent inhibitor of oncogenic K-Ras.

Wollamides: Antimycobacterial Cyclic Hexapeptides from an Australian Soil Streptomyces

A soil Streptomyces nov. sp. (MST-115088) isolated from semiarid terrain near Wollogorang Station, Queensland, returned two known and two new examples of a rare class of cyclic hexapeptide, desotamides A and B (1 and 2) and E and F (3 and 4), respectively, together with two new d-Orn homologues, wollamides A and B (5 and 6). Structures were assigned by detailed spectroscopic and C3 Marfey's analysis. The desotamides/wollamides exhibit growth inhibitory activity against Gram-positive bacteria (IC50 0.6-7 μM) and are noncytotoxic to mammalian cells (IC50 >30 μM). The wollamides exhibit antimycobacterial activity (IC50 2.8 and 3.1 μM), including reduction in the intracellular mycobacterial survival in murine bone marrow-derived macrophages.

Mollemycin A: An Antimalarial and Antibacterial Glyco-hexadepsipeptide-polyketide from an Australian Marine-Derived Streptomyces sp. (CMB-M0244)

A marine-derived Streptomyces sp. (CMB-M0244) isolated from a sediment collected off South Molle Island, Queensland, produced mollemycin A (1) as a new first in class glyco-hexadepsipeptide-polyketide. The structure of 1 was assigned by detailed spectroscopic analysis, supported by chemical derivatization and degradation, and C3 Marfey's analysis. Mollemycin A (1) exhibits exceptionally potent and selective growth inhibitory activity against Gram-positive and Gram-negative bacteria (IC50 10-50 nM) and drug-sensitive (3D7; IC50 7 nM) and multidrug-resistant (Dd2; IC50 9 nM) clones of the malaria parasite Plasmodium falciparum.

Diketopiperazine Derivatives from the Marine-Derived Actinomycete Streptomyces sp. FXJ7.328

Five new diketopiperazine derivatives, (3Z,6E)-1-N-methyl-3-benzylidene-6-(2S-methyl-3-hydroxypropylidene)piperazine-2,5-dione (1), (3Z,6E)-1-N-methyl-3-benzylidene-6-(2R-methyl-3-hydroxypropylidene)piperazine-2,5-dione (2), (3Z,6Z)-3-(4-hydroxybenzylidene)-6-isobutylidenepiperazine-2,5-dione (3), (3Z,6Z)-3-((1H-imidazol-5-yl)-methylene)-6-isobutylidenepiperazine-2,5-dione (4), and (3Z,6S)-3-benzylidene-6-(2S-but-2-yl)piperazine-2,5-dione (5), were isolated from the marine-derived actinomycete Streptomyces sp. FXJ7.328. The structures of 1–5 were determined by spectroscopic analysis, CD exciton chirality, the modified Mosher’s, Marfey’s and the C3 Marfey’s methods. Compound 3 showed modest antivirus activity against influenza A (H1N1) virus with an IC50 value of 41.5 ± 4.5 μM. In addition, compound 6 and 7 displayed potent anti-H1N1 activity with IC50 value of 28.9 ± 2.2 and 6.8 ± 1.5 μM, respectively. Due to the lack of corresponding data in the literature, the 13C NMR data of (3Z,6S)-3-benzylidene-6-isobutylpiperazine-2,5-dione (6) were also reported here for the first time.

Acremolides A−D, Lipodepsipeptides from an Australian Marine-Derived Fungus, Acremonium sp.

An Australian estuarine isolate of an Acremonium sp. (MST-MF588a) yielded the two known compounds 19- O-acetylchaetoglobosin D ( 1) and 19- O-acetylchaetoglobosin B ( 2), as the sole cytotoxic principles, along with the known aromatic metabolite RKB 3564S ( 3), and a novel family of lipodepsipeptides, acremolides A-D ( 4- 7). Structures were assigned to 4- 7 on the basis of detailed spectroscopic analysis and chemical derivatization and by application of a new C 3 Marfey's method for amino acid analysis.