Asperdichrome, an unusual dimer of tetrahydroxanthone through an ether bond, with protein tyrosine phosphatase 1B inhibitory activity, from the Okinawan freshwater Aspergillus sp. TPU1343

Lead optimization of Allium sativum L. compounds for PTP1B inhibition in diabetes treatment: in silico molecular docking and dynamics simulation

Protein tyrosine phosphatase 1B (PTP1B) has been identified as a promising drug target for the development of diabetes medications via an inhibition mechanism. Using a computational approach, this study investigates the binding mechanism of lead optimized natural compounds from Allium sativum against the human PTP1B. The molecular docking, induced-fit docking, and binding free energy calculations were analyzed using Schrödinger Suite 2021-2. MD simulation, and gene enrichment analysis was achieved via the Desmond module of Schrödinger to identify best compounds as inhibitors against PTP1B in diabetes management. The docking scores of the lead optimized compounds were good; 5280443_121 from apigenin had the best binding score of -9.345 kcal/mol, followed by 5280443_129 with a binding score of -9.200 kcal/mol, and 5280863_177 from kaempferol had a binding score of -8.528 kcal/mol, followed by 5280863_462 with a binding score of -8.338 kcal/mol. The top two lead optimized compounds, docked better than the standard PTP1B inhibitor (-7.155 kcal/mol), suggesting them as potent inhibitors than the standard PTP1B inhibitor. The outcomes of the induced-fit docking were consistent with the increased binding affinity used in the Glide computation of the five conformed poses between the derivatives (5280443_121, 5280443_129, 5280863_177, and 5280863_462) and the protein (PTP1B). Based on the binding fee energies (MM-GBSA), the lead optimized compounds from kaempferol exhibited more stability than those from apigenin. In the pharmacophore development, all the models exhibit good results across the different metrics. The best performing model with five of five matches on a 1.34 and 1.33 phase score was DDRRR_1, DDRRR_2, and DDDRR_1. The average BEDROC value (= 160.9) was 1, while the average EF 1% value across all models was 101. There were no substantial conformational modifications during the MD simulation process, indicating that the apigenin derivatives (5280443_121) was stable in the protein's active site in 100 ns. IGF1R, EGFR, INSR, PTPN1, SRC, JAK2, GRB2, BCAR1, and IRS1 are among the 11 potential targets found in the protein-protein interaction (PPI) of A. sativum against PTP1B that may be important in A. sativum's defense against PTP1B. Sixty-four (64) pathways were found by KEGG pathway enrichment analysis to be potentially involved in the anti-PTP1B of A. sativum. Consequently, data obtained indicates the effectiveness of the in silico studies in identifying potential lead compounds in A. sativum against PTP1B target.

Xanthone Dimers in Angiosperms, Fungi, Lichens: Comprehensive Review of Their Sources, Structures, and Pharmacological Properties

Xanthone dimers, a distinctive class of natural metabolites renowned for their unique structures, are abundantly present in a diverse array of angiosperms, fungi, and lichens. These compounds not only exhibit remarkable diversity but also possess a broad spectrum of biological activities. In this comprehensive review spanning from 1966 to 2024, we synthesized the relevant literature to delve into the natural occurrence, biological potency, molecular structure and chemical diversity of xanthone dimers. The aim of this review is to serve as an insightful reference point for future scientific inquiries into xanthone dimers and their potential applications.

Structurally Diverse New Metabolites from Three Hadal Trench-Derived Microorganisms

Two new tetraene lactone derivatives (1 and 2), two new α-pyrone derivatives (3 and 4), three compounds reported as natural products for the first time [an α-pyrone derivative (5), an indole-diketopiperazine alkaloid (6), and a β-amino acid derivative (8)], and 11 known compounds (7, 9-18), were obtained from microorganisms isolated from hadal trench sediments in the Pacific Ocean. Their structures were determined using NMR, HRESIMS, optical rotatory dispersion (ORD) spectra, NMR calculations followed by DP4+ analysis, electronic circular dichroism (ECD) calculations, X-ray crystallography analysis, and advanced Marfey's and modified Mosher eater methods. Microbial broth dilution assay suggested that compounds 6-11 and 15 had weak antibacterial effects.

Investigation on the chemical constituents of the marine-derived fungus strain Aspergillus brunneoviolaceus MF180246

Aspergillus have been proven to be excellent resources for new natural products. During our systematic biodiversifying new compounds from marine derived fungi, one novel compound, asperbrunneo acid (1), along with seven bistetrahydroxanthone analogues, secalonic acid D (2), secalonic acid F (3), secalonic acid F1 (4), secalonic acid H (5), penicillixanthone A (6), chrysoxanthone C (7), and asperdichrome (8), one ketodivinyllactonic steroid, herbarulide (9), as well as one tyrosine-derived compound, aspergillusol A (10), were isolated from the marine-derived fungus Aspergillus brunneoviolaceus MF180246. These structures were elucidated by HRMS, 1 D and 2 D NMR analysis. Compound 1 possessed the first reported new carbon skeleton natural product. Compounds 1, 4, 5, 6, 7 and 8 showed antibacterial activity against Staphylococcus aureus with minimum inhibitory concentration values of 200, 25, 50, 6.25, 50, and 25 µg/ml, respectively.

Structure-Guided Discovery of Diverse Cytotoxic Dimeric Xanthones/Chromanones from Penicillium chrysogenum C-7-2-1 and Their Interconversion Properties

Xanthone-chromanone homo- or heterodimers are regarded as a novel class of topoisomerase (Topo) inhibitors; however, limited information about these compounds is currently available. Here, 14 new (1-14) and 6 known tetrahydroxanthone chromanone homo- and heterodimers (15-20) are reported as isolated from Penicillium chrysogenum C-7-2-1. Their structures and absolute configurations were unambiguously demonstrated by a combination of spectroscopic data, single-crystal X-ray diffraction, modified Mosher's method, and electronic circular dichroism analyses. Plausible biosynthetic pathways are proposed. For the first time, it was discovered that tetrahydroxanthones can convert to chromanones in water, whereas chromone dimerization does not show this property. Among them, compounds 5, 7, 8, and 16 exhibited significant cytotoxicity against H23 cell line with IC50 values of 6.9, 6.4, 3.9, and 2.6 μM, respectively.

Two Antimicrobial Heterodimeric Tetrahydroxanthones with a 7,7'-Linkage from Mangrove Endophytic Fungus Aspergillus flavus QQYZ

Mangrove endophytic fungi represent significant and sustainable sources of novel metabolites with unique structures and excellent biological activities, attracting extensive chemical investigations. In this research, two novel heterodimeric tetrahydroxanthones, aflaxanthones A (1) and B (2), dimerized via an unprecedented 7,7′-linkage, a sp³-sp³ dimeric manner, were isolated from the mangrove endophytic fungus Aspergillus flavus QQYZ. Their structures were elucidated through high resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR) spectroscopy, the absolute configurations of them were determined by a single-crystal X-ray diffraction combined with calculated electronic circular dichroism (ECD) spectra and a 1D potential energy scan. These compounds were evaluated for antifungal activities in vitro and exhibited broad-spectrum and potential antifungal activities against several pathogenic fungi with minimum inhibitory concentration (MIC) values in the range of 3.13–50 μM. They also performed moderate antibacterial activities against several bacteria with MIC values in the range of 12.5–25 μM. This research enriched the resources of lead compounds and templates for marine-derived antimicrobial drugs.

Exploration of marine natural resources in Indonesia and development of efficient strategies for the production of microbial halogenated metabolites

Nature is a prolific source of organic products with diverse scaffolds and biological activities. The process of natural product discovery has gradually become more challenging, and advances in novel strategic approaches are essential to evolve natural product chemistry. Our focus has been on surveying untouched marine resources and fermentation to enhance microbial productive performance. The first topic is the screening of marine natural products isolated from Indonesian marine organisms for new types of bioactive compounds, such as antineoplastics, antimycobacterium substances, and inhibitors of protein tyrosine phosphatase 1B, sterol O-acyl-transferase, and bone morphogenetic protein-induced osteoblastic differentiation. The unique biological properties of marine organohalides are discussed herein and attempts to efficiently produce fungal halogenated metabolites are documented. This review presents an overview of our recent work accomplishments based on the MONOTORI study.

Dimeric Drugs

This review intends to summarize the structures of an extensive number of symmetrical-dimeric drugs, having two monomers linked via a bridging entity while emphasizing the large versatility of biologically active substances reported to possess dimeric structures. The largest number of classes of these compounds consist of anticancer agents, antibiotics/antimicrobials, and anti-AIDS drugs. Other symmetrical-dimeric drugs include antidiabetics, antidepressants, analgesics, anti-inflammatories, drugs for the treatment of Alzheimer's disease, anticholesterolemics, estrogenics, antioxidants, enzyme inhibitors, anti-Parkisonians, laxatives, antiallergy compounds, cannabinoids, etc. Most of the articles reviewed do not compare the activity/potency of the dimers to that of their corresponding monomers. Only in limited cases, various suggestions have been made to justify unexpected higher activity of the dimers vs. the corresponding monomers. These suggestions include statistical effects, the presence of dimeric receptors, binding of a dimer to two receptors simultaneously, and others. It is virtually impossible to predict which dimers will be preferable to their respective monomers, or which linking bridges will lead to the most active compounds. It is expected that the extensive number of articles summarized, and the large variety of substances mentioned, which display various biological activities, should be of interest to many academic and industrial medicinal chemists.

Freshwater Fungi as a Source of Chemical Diversity: A Review

As their name indicates, freshwater fungi occur on submerged substrates in fresh water habitats. This review brings together the chemical diversity and biological activity of 199 of the 280 known freshwater fungal metabolites published from 1992 to 2020, representing at least seven structural classes, including polyketides, phenylpropanoids, terpenoids, meroterpenoids, alkaloids, polypeptides, and monosaccharides. In addition to describing what they are, where they are found, and what they do, we also discuss strategies for the collection, isolation, and identification of fungi from freshwater habitats, with the goal of enhancing chemists' knowledge of several mycological principles. We anticipate that this review will provide a springboard for future natural products studies from this fascinating but underexplored group of Ascomycota.

Integrating Molecular Networking and 1H NMR To Target the Isolation of Chrysogeamides from a Library of Marine-Derived Penicillium Fungi

A challenging problem in natural product discovery is to rapidly dereplicate known compounds and expose novel ones from complicated components. Herein, integrating the LC-MS/MS-dependent molecular networking and ¹H NMR techniques efficiently and successfully enabled the targeted identification of seven new cyclohexadepsipeptides, chrysogeamides A-G (1-7), from the coral-derived fungus Penicillium chrysogenum (CHNSCLM-0003) which was targeted from a library of marine-derived Penicillium fungi. Compound 4 features a rare 3-hydroxy-4-methylhexanoic acid (HMHA) moiety which was first discovered from marine-derived organisms. Interestingly, isotope-labeling feeding experiments confirmed that ¹³C₁-l-Leu was transformed into ¹³C₁-d-Leu moiety, indicating that d-Leu could be isomerized from l-Leu. Compounds 1 and 2 obviously promoted angiogenesis in zebrafish at 1.0 μg/mL with nontoxic to embryonic zebrafish at 100 μg/mL. Combining molecular networking with ¹H NMR as a discovery tool will be implemented as a systematic strategy, not only for known compounds dereplication but also for untapped reservoir discovery.

Cytotoxic Tetrahydroxanthone Dimers from the Mangrove-Associated Fungus Aspergillus versicolor HDN1009

Three new tetrahydroxanthone dimers, 5-epi-asperdichrome (1), versixanthones N (2), and O (3), were isolated from the mangrove-derived fungus Aspergillus versicolor HDN1009. Their structures, including the absolute configurations, were elucidated by NMR, HRMS, and circular dichroism (CD) experiments. Among them, compound 1 was the second example of tetrahydroxanthone dimers, which dimerized by a rare diaryl ether linkage and showed promising antibacterial activities against Vibrio parahemolyticus, Bacillus subtilis, Mycobacterium phlei, and Pseudomonas aeruginosa, with MIC values ranging from 100 μM to 200 μM; whilst compounds 2 and 3 exhibited extensive cytotoxicities against five cancer cell lines (HL-60, K562, H1975, MGC803, and HO-8910), with IC₅₀ values ranging from 1.7 μM to 16.1 μM.

Absolute Structures of Wedelolide Derivatives and Structure-Activity Relationships of Protein Tyrosine Phosphatase 1B Inhibitory ent-Kaurene Diterpenes from Aerial Parts of Wedelia spp. Collected in Indonesia and Japan

Two sesquiterpene lactones with the (9R)-eudesman-9,12-olide framework, wedelolides I and J, have been isolated together with five eudesmanolide sesquiterpenes and twelve ent-kaurene diterpenes from the aerial parts of Indonesian Wedelia prostrata. The absolute configurations of wedelolides I and J, proposed in the previous communication, were proven by comparing their experimental Electronic Circular Dichroism (ECD) spectra with the calculated ECD spectrum of wedelolide I. The phytochemical study on the aerial parts of Okinawan Wedelia chinensis led to the isolation of three other eudesmanolide sesquiterpenes in addition to the three sesquiterpenes and eleven diterpenes isolated from the Indonesian W. prostrata as above. However, the wedelolide derivatives found in the Indonesian plant were not detected. Among these compounds, most of the diterpenes inhibited protein tyrosine phosphatase (PTP) 1B activity, and a structure-activity relationship study revealed that the cinnamoyl group enhanced inhibitory activity. Therefore, two ent-kaurene derivatives with and without a cinnamoyl group were examined for the ability to accumulate phosphorylated-Akt (p-Akt) because PTP1B dephosphorylates signal transduction from the insulin receptor such as phosphorylated Akt, a key downstream effector. However, neither compound enhanced insulin-stimulated p-Akt levels in two human hepatoma cell lines (Huh-7 and HepG2) at non-cytotoxic doses.

Substituted l-tryptophan-l-phenyllactic acid conjugates produced by an endophytic fungus Aspergillus aculeatus using an OSMAC approach

The endophytic fungus Aspergillus aculeatus isolated from leaves of the papaya plant Carica papaya was fermented on solid rice medium, yielding a new l-tryptophan-l-phenyllactic acid conjugate (1) and thirteen known compounds (11, 14-25). In addition, an OSMAC approach was employed by adding eight different sodium or ammonium salts to the rice medium. Addition of 3.5% NaNO3 caused a significant change of the metabolite pattern of the fungus as indicated by HPLC analysis. Subsequent isolation yielded several new substituted l-tryptophan-l-phenyllactic acid conjugates (1-10) in addition to three known compounds (11-13), among which compounds 2-10, 12-13 were not detected in the rice control culture. All structures were unambiguously elucidated by one and two dimensional NMR spectroscopy and by mass spectrometry. The absolute configuration of the new compounds was determined by Marfey's reaction and X-ray single crystal diffraction. Compounds 19-22 showed cytotoxicity against the L5178Y mouse lymphoma cell line with IC50 values of 3.4, 1.4, 7.3 and 23.7 μM, respectively.

Computational Insight into Protein Tyrosine Phosphatase 1B Inhibition: A Case Study of the Combined Ligand- and Structure-Based Approach

Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. Firstly, the pharmacophore model of PTP1B inhibitors was built based on the common feature of sixteen compounds. It was found that the pharmacophore model consisted of five chemical features: one aromatic ring (R) region, two hydrophobic (H) groups, and two hydrogen bond acceptors (A). To further elucidate the binding modes of these inhibitors with PTP1B active sites, four docking programs (AutoDock 4.0, AutoDock Vina 1.0, standard precision (SP) Glide 9.7, and extra precision (XP) Glide 9.7) were used. The characteristics of the active sites were then described by the conformations of the docking results. In conclusion, a combination of various pharmacophore features and the integration information of structure activity relationship (SAR) can be used to design novel potent PTP1B inhibitors.

Oleanane triterpenes with protein tyrosine phosphatase 1B inhibitory activity from aerial parts of Lantana camara collected in Indonesia and Japan

During the search for new protein tyrosine phosphatase (PTP) 1B inhibitors, EtOH extracts from the aerial parts of Lantana camara L. (lantana) collected at Manado (Indonesia) and two subtropical islands in Japan (Ishigaki and Iriomote Islands, Okinawa) exhibited potent inhibitory activities against PTP1B in an enzyme assay. Four previously undescribed oleanane triterpenes were isolated together with known triterpenes and flavones from the Indonesian lantana. The EtOH extracts of lantana collected in Ishigaki and Iriomote Islands exhibited different phytochemical profiles from each other and the Indonesian lantana. Triterpenes with a 24-OH group were isolated from the Indonesian lantana only. Five known triterpene compounds were detected in the Ishigaki lantana, and two oleanane triterpenes with an ether linkage between 3β and 25 were the main components together with five known triterpenes as minor components in the Iriomote lantana. The structures of previously undescribed compounds were assigned on the basis of their spectroscopic data. Among the compounds obtained in this study, oleanolic acid exhibited the most potent activity against PTP1B, and is used as a positive control in studies on PTP1B.

Aspergchromones A and B, two new polyketides from the marine sponge-associated fungus Aspergillus sp. SCSIO XWS03F03

Two new polyketides, aspergchromones A (1) and B (2), together with five known compounds, secalonic acid D (3), noreugenin (4), (3S)-5-hydroxymellein (5), (4S)-6-hydroxyisosclerone (6), and (-)-regiolone (7), were isolated from the ethyl acetate extract of marine sponge-derived fungus Aspergillus sp. SCSIO XWS03F03. Their structures were elucidated by means of spectroscopic techniques (1D and 2D NMR, MS, UV, and IR). The absolute configurations of the new compounds were established by ECD calculations. Compound 3 showed moderate antimicrobial activity.