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LC-MS and molecular networking analyses of the extract of the marine sponge Psammocinia sp. indicated the presence of two new compounds with multiple halogens. LC-MS-guided isolation yielded cyclic peptides, cyclopsammocinamides A (1) and B (2), in an enantiomeric relationship to cyclocinamide A (3). Planar structures of 1 and 2 were elucidated by NMR and mass spectroscopic analyses and the absolute configurations of the amino acid residues were determined using Marfey's method with their acid hydrolysates. The sponge extract exhibited cytotoxicity and the bioassay-guided isolation afforded a dimeric dilactone macrolide, swinholide A, as the cytotoxic compound.

A targeted injury to the mouse intervertebral disc (IVD) is often used to recapitulate the degenerative cascade of the human pathology. Since injuries can vary in magnitude and localization, it is critical to examine the effects of different injuries on IVD degeneration. We thus evaluated the degenerative progression resulting from either a partial- or full-width injury to the mouse lumbar IVD using contrast-enhanced micro-computed tomography and histological analyses. A lateral-retroperitoneal surgical approach was used to access the lumbar IVD, and the injuries to the IVD were produced by either incising one side of the annulus fibrosus or puncturing both sides of the annulus fibrosus. Female C57BL/6J mice of 3–4 months age were used in this study. They were divided into three groups to undergo partial-width, full-width, or sham injuries. The L5/6 and L6/S1 lumbar IVDs were surgically exposed, and then the L6/S1 IVDs were injured using either a surgical scalpel (partial-width) or a 33G needle (full-width), with the L5/6 serving as an internal control. These animals recovered and then euthanized at either 2-, 4-, or 8-weeks after surgery for evaluation. The IVDs were assessed for degeneration using contrast-enhanced microCT (CEµCT) and histological analysis. The high-resolution 3D CEµCT evaluation of the IVD confirmed that the respective injuries were localized within one side of the annulus fibrosus or spanned the full width of the IVD. The full-width injury caused significant deteriorations in the nucleus pulposus, annulus fibrous and at the interfaces after 2 weeks, which was sustained through the 8 weeks, while the partial width injury caused localized disruptions that remained limited to the annulus fibrosus. The use of CEµCT revealed distinct IVD degeneration profiles resulting from partial- and full-width injuries. The partial width injury may serve as an alternative model for IVD degeneration resulting from localized annulus fibrosus injuries.

A new rearranged nitrogenous bisabolone-type sesquiterpene, halichonic acid B (1), was isolated from a marine sponge Axinyssa sp. together with halichonic acid (2) and (6R,7S)-7-amino-7,8-dihydro-α-bisabolene (3). The structure of 1 was determined by extensive NMR and MS analyses, revealing an unprecedented carbon framework, and its absolute configuration was elucidated by time-dependent density-functional theory (TDDFT)-based electronic circular dichroism (ECD) spectrum calculation. We propose that 1 and 2 may be biosynthesized in the same pathway, involving the reaction between farnesyl pyrophosphate and glycine, followed by cyclization.

The Janus kinase (JAK) pathway has been shown to play key roles in the growth and resistance to drugs that develop in multiple myeloma (MM) patients. The anti-MM effects of the selective JAK1 inhibitor INCB052793 (INCB) alone and in combination with anti-MM agents were evaluated in vitro and in vivo. Significant inhibition of cell viability of primary MM cells obtained fresh from MM patients, and the MM cell lines RPMI8226 and U266, was observed with single agent INCB and was enhanced in combination with other anti-MM agents including proteasome inhibitors and glucocorticosteroids. Single-agent INCB resulted in decrease in tumor growth of the MM xenograft LAGκ-1A growing in severe combined immunodeficient mice. Mice dosed with INCB (30 mg/kg) showed significant reductions in tumor volume on days 28, 35, 42, 49, 56, and 63. Similarly, INCB at 10 mg/kg showed anti-tumor effects on days 56 and 63. Tumor-bearing mice receiving combinations of INCB with carfilzomib, bortezomib, dexamethasone, or lenalidomide showed significantly smaller tumors when compared to vehicle control and mice treated with single agents. These results provide further support for the clinical evaluation of INCB052793 alone and in combination treatment for MM patients.

Natural products are important sources for drug development. Discovery of natural products that inhibit cell cycle progression significantly contributes to the progress of cancer biology and the development of new antitumor agents. In this study, cell cycle inhibitory activity was evaluated with our extract library of natural resources, including marine invertebrates, fungi, and bacteria, using HeLa/Fucci2 cells which allow classification of the cell cycle phases of living cells. Screening of the extract library revealed that the extract of the marine sponge Dactylospongia metachromia inhibited cell cycle progression at S/G2/M phases. Bioassay-guided fractionation afforded a new sesquiterpene quinone, neoisosmenospongine (1), and four known compounds, nakijiquinone I, N, and Q (2-4) and (-)-dictyoceratin-C (5). The chemical structure of 1 was elucidated by interpretating the NMR and mass spectroscopic data, and the absolute configuration was determined by comparison of the experimental and calculated ECD spectra. Fluorescent imaging of HeLa/Fucci2 cells revealed that 1-4 inhibited the cell cycle progression at S/G2/M phases. This study demonstrated that fluorescent image-based high-content screening using HeLa/Fucci2 cells is an effective approach for isolating cell cycle inhibitors from natural resources.

Natural products that inhibit cell cycle progression show promise as anticancer agents and chemical probes. In our research on biologically active natural products that affect cell cycle progression of HeLa/fluorescent ubiquitination-based cell cycle indicator (Fucci)2 cells, the extract of the marine sponge Neopetrosia chaliniformis was revealed to inhibit cell proliferation. Purification of the extract afforded four new pyridine alkaloids, neopetrosidines A–D (1–4). Their structures were elucidated by the interpretation of spectroscopic data and chemical degradation. Compounds 1–4 were found to inhibit cell proliferation of HeLa/Fucci2 cells, and time-lapse imaging showed that 1 exerts its effect by increasing the duration of the cell cycle. Furthermore, we show that 1 perturbs bioenergetics to exhibit a cytostatic effect by reducing the mitochondrial membrane potential.

Six new spongian diterpene derivatives, ceylonins A–F (1–6), were isolated from the Indonesian marine sponge Spongia ceylonensis along with spongia-13(16),14-dien-19-oic acid (7). They contained three additional carbons in ring D to supply an ether-bridged bicyclic ring system. Their structures were elucidated by analyzing NMR spectroscopic data and calculated ECD spectra in comparison to experimental ECD spectra. The bicyclic ring system may be derived from the major metabolite 7 and a C3 unit (an acrylic acid equivalent) through an intermolecular Diels–Alder reaction, which was experimentally supported by the formation of 1–6 from 7 and acrylic acid. The inhibitory effects of the isolated compounds on the RANKL-induced formation of multinuclear osteoclasts in RAW264 macrophages were examined.

Five new polyketide endoperoxides, manadodioxans A−E, were isolated from the marine sponge Plakortis bergquistae. Manadodioxan E showed antimicrobial activity against Escherichia coli at 10 μg/disk, while its oxo congener, manadodioxan D, was inactive.

Two unique sesterterpenes, hyattellactones A (1) and B (2), together with two known sesterterpenes, phyllofolactones F (3) and G (4), were isolated from the Indonesian marine sponge Hyattella sp. The structures of the two new compounds, 1 and 2 were assigned based on their spectroscopic data. Hyattellactone A (1) was a scalarane sesterterpene with an α,β-unsaturated-γ-lactone ring and C-ethyl group, while B (2) was an epimer of 1 at the C-24 position. Compounds 1 and 3 inhibited PTP1B activity with IC50 values of 7.45 and 7.47 μM, respectively. On the other hand, compounds 2 and 4 (24S-isomers of 1 and 3, respectively) showed much reduced activity than the 24R-isomers.

Salsolinol (1), a tetrahydroisoquinoline alkaloid, was isolated from the marine sponge Xestospongia cf. vansoesti collected in Indonesia as a proteasome inhibitor, along with three salsolinol derivatives, norsalsolinol (2), cis-4-hydroxysalsolinol (3), and trans-4-hydroxysalsolinol (4). Compounds 1 and 2 inhibited the chymotrypsin-like activity of the proteasome with IC(50) values of 50 and 32 µg/ml, respectively, but 3 and 4 showed no inhibitory effect even at 100 µg/ml.

Four new sesquiterpenes, lamellodysidines A and B, O,O-dimethyllingshuiolide A, and 11-epi-O,O-dimethyllingshuiolide A (1–4), were obtained from the marine sponge, Lamellodysidea herbacea, collected in Indonesia. Their planar structures were elucidated by analysis of spectroscopic data. The absolute configurations of the new compounds were determined by the calculated ECD spectra. Compound 1 has a unique carbon framework, and 2 is a new nitrogenous sesquiterpene.

Three new furanosesterterpene tetronic acids, sulawesins A–C (1–3), were isolated from a Psammocinia sp. marine sponge, along with the known compounds ircinins-1 (4) and -2 (5). Although ircinins-1 and -2 were previously isolated as (+)- or (−)-enantiomers from marine sponges, we isolated them as enantiomeric mixtures. Sulawesins A and B possess a new carbon skeleton with a 5-(furan-3-yl)-4-hydroxycyclopent-2-enone moiety and were also found to be diastereomeric mixtures of four isomers by an HPLC analysis with a chiral-phase column. Sulawesin C has a dimeric structure of ircinin-1 and is the first dimer in this family. USP7, a deubiquitinating enzyme, is an emergent target of cancer therapy, and the isolated compounds inhibited USP7 with IC50 values in the range of 2.7–4.6 μM.

The ethanol extract of an Indonesian marine sponge Lamellodysidea herbacea inhibited the activity of protein tyrosine phosphatase 1B (PTP1B), an important target enzyme for the treatment of type II diabetes. Bioassay-guided isolation yielded a known polybromodiphenyl ether (1) as a sole bioactive component. The structure of 1 was confirmed by spectroscopic data for 1 and its methyl ether derivative (2). Compound 1 markedly inhibited the PTP1B activity (IC50 = 0.85 μM) and showed a moderate cytotoxicity against two human cancer cell lines, HCT-15 (colon) and Jurkat (T-cell lymphoma) cells. On the other hand, compound 2 maintained potent inhibitory activity against PTP1B (IC50 = 1.7 μM) but did not show apparent cytotoxicity at 18 μM against these cancer cells. Four ester derivatives [acetyl (3), butyryl (4), hexanoyl (5), and benzoyl (6)] were prepared from 1 and their activities evaluated against PTP1B and two cancer cell lines to investigate the structure–activity relationships. Although compounds 3–6 exhibited potent inhibitory effects against PTP1B activity, cytotoxicity against HCT-15 and Jurkat cells was observed as a similar efficacy to that of 1. From these results, compound 2 was found to be the best inhibitor of PTP1B with no apparent cytotoxicity. Therefore, 2 may be a lead compound for making a new type of PTP1B inhibitor. Moreover, compound 2 did not inhibit the cell growth of Huh-7 cells (hepatoma). Hepatocytes are one of the locations of PTP1B, and Huh-7 cells are used to study the mechanism of action of compound 2.

Siladenoserinols A-L were isolated from a tunicate as inhibitors of p53-Hdm2 interaction, a promising target for cancer chemotherapy. Their structures including the absolute configurations were elucidated to be new sulfonated serinol derivatives, each of which contains a 6,8-dioxabicyclo[3.2.1]octane unit and either glycerophosphocholine or glycerophosphoethanolamine moiety. They inhibited p53-Hdm2 interaction with IC(50) values of 2.0-55 μM. Among them, siladenoserinol A and B exhibited the strongest inhibition with an IC(50) value of 2.0 μM.

Seven new spongian diterpenes, ceylonamides A–F (1–6) and 15α,16-dimethoxyspongi-13-en-19-oic acid (7), were isolated from the Indonesian marine sponge Spongia ceylonensis along with eight known spongian diterpenes, 8–15. Compounds 1–6 were determined to be nitrogenous spongian diterpenes. The isolated compounds were examined for the inhibition of RANKL-induced osteoclastogenesis in RAW264 macrophages. Ceylonamide A (1) exhibited the most potent inhibitory activity with an IC50 value of 13 μM, followed by ceylonamide B (2) (IC50, 18 μM). An examination of the structure–activity relationships of the isolated compounds revealed that the position of the carbonyl group of the γ-lactam ring and bulkiness of the substituent at its nitrogen atom were important for inhibitory activity.

Two new dimeric sterols, manadosterols A (1) and B (2), were isolated from the marine sponge Lissodendryx fibrosa collected in Indonesia. The two compounds are comprised of two sulfonated sterol cores connected through the respective side chains. Manadosterols A (1) and B (2) inhibited the Ubc13-Uev1A interaction with IC(50) values of 0.09 and 0.13 μM, respectively. They are the second and third natural compounds showing inhibitory activities against the Ubc13-Uev1A interaction and are more potent than leucettamol A (IC(50), 106 μM), the first such inhibitor, isolated from another marine sponge.

Hyrtioreticulins A–E (1–5) were isolated from the marine sponge Hyrtios reticulatus, along with a known alkaloid, hyrtioerectine B (6). Structural elucidation on the basis of spectral data showed that 1, 2, and 5 are new tetrahydro-β-carboline alkaloids, while 3 and 4 are new azepinoindole-type alkaloids. Hyrtioreticulins A and B (1 and 2) inhibited ubiquitin-activating enzyme (E1) with IC50 values of 0.75 and 11 μg/mL, respectively, measured by their inhibitory abilities against the formation of an E1-ubiquitin intermediate. So far, only five E1 inhibitors, panapophenanthrine, himeic acid A, largazole, and hyrtioreticulins A and B (1 and 2), have been isolated from natural sources and, among them, 1 is the most potent E1 inhibitor.

Two new tryptamine-derived alkaloids, named as leptoclinidamide (1) and (-)-leptoclinidamine B (2), were isolated from an Indonesian ascidian Leptoclinides dubius together with C2-α-D-mannosylpyranosyl-L-tryptophan (3). The structure of 1 was assigned on the basis of spectroscopic data for 1 and its N-acetyl derivative (4). Compound 1 was an amide of tryptamine with two β-alanine units. Although the planar structure of 2 is identical to that of the known compound (+)-leptoclinidamine B (5), compound 2 was determined to be the enantiomer of 5 based on amino acid analysis using HPLC methods. Compounds 1 to 4 were evaluated for cytotoxicity against two human cancer cell lines, HCT-15 (colon) and Jurkat (T-cell lymphoma) cells, but none of the compounds showed activity.

N,N-Didesmethylgrossularine-1 (DDMG-1), a compound with a rare alpha-carboline structure, was isolated from an Indonesian ascidian Polycarpa aurata as responsible for the observed inhibitory activity against TNF-alpha production in lipopolysaccharide-stimulated murine macrophage-like RAW264.7 cells. DDMG-1 inhibited the mRNA level of mTNF-alpha, IkappaB-alpha degradation, and binding of NF-kappaB to the target DNA site in LPS-stimulated RAW 264.7 cells. Moreover, DDMG-1 had an inhibitory effect on the production of IL-8, which is produced in CD14(+)-THP-1 cells stimulated by LPS. DDMG-1 is thus a promising drug candidate lead compound for the treatment of chronic inflammatory diseases, such as rheumatoid arthritis.

Four new polysulfur aromatic alkaloids, lissoclibadins 4 (1), 5 (2), 6 (3), and 7 (4), were isolated from the ascidian Lissoclinum cf. badium collected in Indonesia, together with seven known alkaloids, lissoclibadins 1 (5), 2 (6), and 3 (7), lissoclinotoxins E (8) and F (9), 3,4-dimethoxy-6-(2'-N,N-dimethylaminoethyl)-5-(methylthio)benzotrithiane (10), and N,N-dimethyl-5-(methylthio)varacin (11). Compounds 1-11 were isolated from the ascidian collected in March (wet season), while 5-11 have been obtained previously from the organism collected in September (dry season) at the same site. The structures of the new compounds were assigned on the basis of their spectroscopic data. Lissoclibadins 4-7 (1-4) inhibited the colony formation of Chinese hamster V79 cells with EC50 values of 0.71, 0.06, 0.06, and 0.17 microM, respectively. Compounds 1-4 showed also weak antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Saccharomyces cerevisiae.

Two new β-carboline alkaloids, variabines A (1) and B (2), were isolated from the Indonesian marine sponge Luffariella variabilis. Their structures were elucidated from spectral data, and 1 was found to be a sulfonated derivative of 2. Although numerous β-carboline alkaloids have been isolated from natural sources to date, 1 is the first β-carboline derivative containing a sulfate group. Compound 2 inhibited chymotrypsin-like activity of the proteasome and Ubc13 (E2)–Uev1A interaction with IC50 values of 4 and 5 μg/mL, respectively, whereas 1 had little effect on the activity or interaction.

Two new merosesquiterpenes, verruculides A ( 1 ) and B ( 2 ), were isolated from a culture broth of the Indonesian ascidian-derived Penicillium verruculosum TPU1311, together with three known congeners, chrodrimanins A ( 3 ), B ( 4 ), and H ( 5 ). The structures of 1 and 2 were assigned on the basis of their spectroscopic data (1D and 2D NMR, HRMS, UV, CD, and IR). Compound 2 had a linear sesquiterpene moiety and was considered to be the derivative of the biosynthetic precursor for 1 and 3 – 5 . Compounds 1 , 3 , and 5 inhibited the activity of protein tyrosine phosphatase 1B (PTP1B) with IC 50 values of 8.4, 8.5, and 14.9 μM, respectively. Compound 2 showed 40% inhibition at 23.1 μM, while 4 was not active at 20.7 μM.

A detection method based on high-performance liquid chromatography coupled with ultraviolet diode-array detection and electrospray ionization ion trap tandem mass spectrometry (HPLC-UV-ESI-MS/MS) was developed to investigate the total alkaloids prepared from the ascidian Lissoclinum cf. badium. The aromatic alkaloids possessing polysulfide structures are the major bioactive constituents isolated from ascidians of the genera Lissoclinum, Eudistoma, and Polycitor. These compounds presented various important biological activities. The ESI-MS fragmentation behavior of this kind of alkaloids was studied, and the fragmentation was characterized by elimination of the NH(CH(3))(2) moiety. The use of reversed-phase HPLC/UV-ESI-MS allowed the online separation and detection of 25 aromatic alkaloids. This approach provided data that can be used for detection of biologically active aromatic alkaloids from marine organisms.

Two new manzamine alkaloids, acantholactam (3) and pre-neo-kauluamine (4), were isolated from the marine sponge Acanthostrongylophora ingens along with manzamine A (1) and neo-kauluamine (2). Acantholactam contains a γ-lactam ring N-substituted with a (Z)-2-hexenoic acid moiety and is proposed to be biosynthetically derived from manzamine A by oxidative cleavage of the eight-membered ring. Compound 4 was converted to the dimer 2 during storage, suggesting nonenzymatic dimer formation. Among the four isolated compounds, 1, 2, and 4 showed proteasome inhibitory activity.

Aaptamine (1), isoaaptamine (2), and demethylaaptamine (3) were isolated from the marine sponge Aaptossuberitoides collected in Indonesia as inhibitors of the proteasome. They inhibited the chymotrypsin-like and caspase-like activities of the proteasome with IC(50) values of 1.6-4.6 microg/mL, while they showed less inhibition of the trypsin-like activity of the proteasome. The three compounds showed cytotoxic activities against HeLa cells, but their cytotoxicity did not correlate with their potency as proteasome inhibitors, strongly suggesting that their proteasomal inhibitory activity is dispensable to their cytotoxicity.

(25 S )-3-Oxocholesta-1,4-dien-26-oic acid ( 1 ) and a new (25 S )-18-acetoxy-3-oxocholesta-1,4-dien-26-oic acid ( 2 ) were isolated from a soft coral Minabea sp. (cf. aldersladei ) collected in North Sulawesi, Indonesia, together with two known cholic-acid-type compounds, 3-oxochol-1,4-dien-24-oic acid ( 3 ) and 3-oxochol-4-en-24-oic acid ( 4 ). The structures of these compounds were determined on the basis of their spectroscopic data. The absolute stereochemistry at C-25 of 2 was determined by comparative 1 H NMR study using chiral anisotropic reagents [( S )- and ( R )-phenylglycine methyl esters]. This is the first to report compound 1 as a natural product.

Two new imidazole alkaloids, naamidines H ( 1) and I ( 2), were isolated from the marine sponge Leucetta chagosensis, collected in North Sulawesi, Indonesia. The compounds ( 1 and 2) showed cytotoxicity against HeLa cells with IC50 values of 5.6 and 15 microg/mL, respectively.

The formation of foam cells in macrophages plays an essential role in the progression of early atherosclerotic lesions and therefore its prevention is considered to be a promising target for the treatment of atherosclerosis. We found that an extract of the marine sponge Acanthostrongylophora ingens inhibited the foam cell formation induced by acetylated low-density lipoprotein (AcLDL) in human monocyte-derived macrophages, as measured based on the accumulation of cholesterol ester (CE). Bioassay-guided purification of inhibitors from the extract afforded manzamines. Manzamine A was the most potent inhibitor of foam cell formation, and also suppressed CE formation in Chinese hamster ovary cells overexpressing acyl-CoA:cholesterol acyl-transferase (ACAT)-1 or ACAT-2. In addition, manzamine A inhibited ACAT activity. Next, we orally administered manzamine A to apolipoprotein E (apoE)-deficient mice for 80 days, and found that total cholesterol, free cholesterol, LDL-cholesterol, and triglyceride levels in serum were significantly reduced and the area of atherosclerotic lesions in the aortic sinus was also substantially diminished. These findings clearly suggest that manzamine A suppresses hyperlipidemia and atherosclerosis in apoE-deficient mice by inhibiting ACAT and is therefore a promising lead compound in the prevention or treatment of atherosclerosis. Although manzamine A has been reported to show several biological activities, this is the first report of a suppressive effect of manzamine A on atherosclerosis in vivo.

The extract of an Indonesian marine sponge Haliclona sp. showed potent cytotoxicity against human solid cancer cell lines, MCF-7 (breast), LNCap (prostate), Caco-2 (colon) and HCT-15 (colon) cells. Study on nuclear morphological changes and flow cytometric analysis suggested that the component(s) in the extract would induce an apoptosis to these cancer cells. Bioassay-guided isolation yielded two pentacyclic alkaloids, papuamine (1) and haliclonadiamine (2), which inhibited cell proliferation of six human cancer cell lines with IC50 values of 0.93–1.50 and 1.00–4.44 µM, respectively. Compounds 1 and 2 accumulated lymphoma U937 cells at sub-G1 phase and induced a condensation of chromatin and fragmentation of nucleus.

Three new sesquiterpenes, 2-deoxy-7-O-methyllemnacarnol (1), 2-deoxy-12 alpha-ethoxy-7-O-methyllemnacarnol (2), and 2-deoxy-12 alpha-methoxy-7-O-methyllemnacarnol (3), were isolated from a soft coral Nephthea sp. collected in Indonesia, together with five known sesquiterpenes. The structures of the new compounds were assigned on the basis of their spectroscopic data.

Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations., We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license.

A compound that inhibits the formation of a complex composed of the ubiquitin E2 enzyme Ubc13 and Uev1A was isolated from the marine sponge Leucetta aff. microrhaphis. The compound was identified as leucettamol A (1) by spectroscopic analysis. Its inhibition of Ubc13-Uev1A interaction was tested by the ELISA method, revealing an IC(50) value of 50 microg/mL. The compound is the first inhibitor of Ubc13-Uev1A interaction, that is, that of the E2 activity of Ubc13. Such inhibitors are presumed to be leads for anti-cancer agents that upregulate activity of the tumor suppressor p53 protein. Interestingly, hydrogenation of 1 increased its inhibitory activity with an IC(50) value of 4 microg/mL, while its tetraacetate derivative was inactive, indicating that the hydroxy and/or amino groups of 1 are required for the inhibition.