CellSTAR: a comprehensive resource for single-cell transcriptomic annotation.

Large-scale studies of single-cell sequencing and biological experiments have successfully revealed expression patterns that distinguish different cell types in tissues, emphasizing the importance of studying cellular heterogeneity and accurately annotating cell types. Analysis of gene expression profiles in these experiments provides two essential types of data for cell type annotation: annotated references and canonical markers. In this study, the first comprehensive database of single-cell transcriptomic annotation resource (CellSTAR) was thus developed. It is unique in (a) offering the comprehensive expertly annotated reference data for annotating hundreds of cell types for the first time and (b) enabling the collective consideration of reference data and marker genes by incorporating tens of thousands of markers. Given its unique features, CellSTAR is expected to attract broad research interests from the technological innovations in single-cell transcriptomics, the studies of cellular heterogeneity & dynamics, and so on. It is now publicly accessible without any login requirement at: https://idrblab.org/cellstar.

MolBiC: the cell-based landscape illustrating molecular bioactivities.

The measurement of cell-based molecular bioactivity (CMB) is critical for almost every step of drug development. With the booming application of AI in biomedicine, it is essential to have the CMB data to promote the learning of cell-based patterns for guiding modern drug discovery, but no database providing such information has been constructed yet. In this study, we introduce MolBiC, a knowledge base designed to describe valuable data on molecular bioactivity measured within a cellular context. MolBiC features 550 093 experimentally validated CMBs, encompassing 321 086 molecules and 2666 targets across 988 cell lines. Our MolBiC database is unique in describing the valuable data of CMB, which meets the critical demands for CMB-based big data promoting the learning of cell-based molecular/pharmaceutical pattern in drug discovery and development. MolBiC is now freely accessible without any login requirement at: https://idrblab.org/MolBiC/.

PDCdb: the biological activity and pharmaceutical information of peptide-drug conjugate (PDC).

Peptide-drug conjugates (PDCs) have emerged as a promising class of targeted therapeutics with substantial pharmaceutical advantages and market potentials, which is a combination of a peptide (selective to the disease-relevant target), a linker (stable in circulation but cleavable at target site) and a cytotoxic/radioactive drug (efficacious/traceable for disease). Among existing PDCs, those based on radiopharmaceuticals (a.k.a. radioactive drugs) are valued due to their accurate imaging and targeted destruction of disease sites. It's demanded to accumulate the biological activity and pharmaceutical information of PDCs. Herein, a database PDCdb was thus constructed to systematically describe these valuable data. Particularly, biological activities for 2036 PDCs were retrieved from literatures, which resulted in 1684, 613 and 2753 activity data generated based on clinical trial, animal model and cell line, respectively. Furthermore, the pharmaceutical information for all 2036 PDCs was collected, which gave the diverse data of (a) ADME property, plasma half-life and administration approach of a PDC and (b) chemical modification, primary target, mode of action, conjugating feature of the constituent peptide/linker/drug. In sum, PDCdb systematically provided the biological activities and pharmaceutical information for the most comprehensive list of PDCs among the available databases, which was expected to attract broad interest from related communities and could be freely accessible at: https://idrblab.org/PDCdb/.

Advancing Natural Product Discovery: A Structure-Oriented Fractions Screening Platform for Compound Annotation and Isolation.

Natural product discovery is hindered by the lack of tools that integrate untargeted nuclear magnetic resonance and mass spectrometry data on a library scale. This article describes the first application of the innovative NMR/MS-based machine learning tool, the "Structure-Oriented Fractions Screening Platform (SFSP)", enabling functional-group-guided fractionation and accelerating the discovery and characterization of undescribed natural products. The concept was applied to the extract of a marine fungus known to be a prolific producer of diverse natural products. With the assistance of SFSP, we isolated 24 flavipidin derivatives and five phenalenone analogues from Aspergillus sp. GE2-6, revealing 27 undescribed compounds. Compounds 7-22 were proposed as isomeric derivatives featuring a 5/6-ring fusion, formed by the dimerization of flavipidin E (5). Compounds 23 and 24 were envisaged as isomeric derivatives with a 6/5/6-ring fusion, generated through the degradation of two flavipidin E molecules. Furthermore, flavipidin A (1) and asperphenalenone E (28) exhibited potent anti-influenza (PR8) activities, with IC50 values of 21.9 ± 0.2 and 12.9 ± 0.1 µM, respectively. Meanwhile, asperphenalenone (26) and asperphenalenone P (27) treatments exhibited significant inhibition of HIV pseudovirus infection in 293FT cells, boasting IC50 values of 6.1 ± 0.9 and 4.6 ± 1.1 µM, respectively. Overall, SFSP streamlines natural product isolation through NMR and MS data integration, as showcased by the discovery of numerous undescribed flavipidins and phenalenones based on NMR olefinic signals and low-field hydroxy signals.

Kueishanamides A and B from the Hydrothermal Vent Sediment Derived Streptomyces sp. WU20.

Marine actinomycetes are known for their production of remarkable organic molecules, particularly those featuring polyoxygenated long-chain backbones. Determining the absolute configurations of these compounds remains a challenging task even today. In this study, we successfully established the planar structures and absolute configurations of two highly flexible amide alkaloids from Streptomyces sp. WU20: kueishanamides A (1) and B (2). These compounds possess a C13 linear backbone and each contains five stereogenic carbon centers. Our approach involved a combination of spectroscopic and computational methods, including J-based configurational analysis and VCD calculations, ensuring the unambiguous determination of their configurations. Kueishanamide A (1) and kueishanamide B (2) showed moderate antifungal activity against pathogenic fungus Crytococcus neoformans, with MIC values of 25 µg/mL each.

Citrinin Monomer, Trimer, and Tetracyclic Alkaloid Derivatives from the Hydrothermal Vent-Associated Fungus Penicillium citrinum TW132-59.

Five new unusual citrinin-derived alkaloids with a tetracyclic core, citrinidines A-E (1-5), two new amide alkaloids, methyl (2S,8E)-1'-(2-methyl-3-oxodec-8-enamido) butanoate (6) and (2S,8E)-2-methyl-3-oxodec-8-enamide (7), a new unusual citrinin trimer, tricitrinol C (8), a new citrinin acetal-ketal derivative, citrininol (9), together with four known citrinin monomers (10-13), and three known citrinin dimers (14-16), were isolated from the fermentation of hydrothermal vent-associated fungus Penicillium citrinum TW132-59. Their structures were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, Mosher's method, 13C NMR calculation in combination with DP4+, and ECD calculations. A plausible biosynthetic pathway of all new compounds (1-9) was proposed. Citrinin trimer (8) exhibited potent cytotoxicity activity with an IC50 value of 1.34 ± 0.11 µM, and compounds 1 and 15 showed moderate cytotoxicity with IC50 values of 17.50 ± 1.43 and 9.45 ± 0.55 µM, respectively, against A549 cell line.

Talaropeptins A and B, Tripeptides with an N-trans-Cinnamoyl Moiety from the Marine-Derived Fungus Talaromyces purpureogenus CX11.

We report the discovery of talaropeptins A (1) and B (2), tripeptides with an unusual 5/6/5 heterocyclic scaffold and an N-trans-cinnamoyl moiety, which were identified from the marine-derived fungus Talaromyces purpureogenus CX11. A bioinformatic analysis of the genome of T. purpureogenus CX11 and gene inactivation revealed that the biosynthesis of talaropeptins involves a nonribosomal peptide synthase gene cluster. Their chemical structures were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The absolute configurations of 1 and 2 were established by electronic circular dichroism calculations and Marfey's method. The plausible biosynthesis of 1 and 2 is also proposed on the basis of gene deletion, substrate feeding, and heterologous expression. Compounds 1 and 2 showed moderate antifungal activity against phytopathogenic fungus Fusarium oxysporum with MIC values of 12.5 and 25 µg/mL, respectively.

New Cytotoxic Secondary Metabolites from Two Deep-Sea-Derived Fungi and the Co-Culture Impact on the Secondary Metabolic Patterns.

In this study, chemical profiles for two co-existing deep-sea-derived Penicillium fungal strains were thoroughly investigated. Two new compounds and 11 known compounds were identified from Penicillium sp. LXY140-R, while one new compound and 12 known compounds were isolated from Penicillium sp. LXY140-3. Their structures were elucidated by extensive 1D and 2D NMR experiments, which were supported by HR-ESI-MS data. The antiproliferative activities of all isolates against HCT-116, A549 and Bel-7402 cell lines were also evaluated. Compounds 2, 5, 6, 10 and 13 showed potent antiproliferative activity. To reveal the metabolic relationship of the two strains, we conducted co-culture experiments to discover cross-talk molecules by a device that allows only small molecule to communicate. Extensive HPLC/MS2 experiments were applied to identify the disturbance of the chemical profiles within the synthetic Penicillium-Penicillium community. The fungal strain LXY140-R was found to accumulate mono or multiple-acetylation derivatives of deoxynivalenol (DON) sesquiterpenes as responsible molecules by the disturbance of the metabolites produced by the LXY140-3 strain.

Comparative Metabolomics Reveals Fungal Conversion of Co-Existing Bacterial Metabolites within a Synthetic Aspergillus-Streptomyces Community.

In nature, secondary metabolites have been proven to be the essential communication media between co-occurring microorganisms and to influence their relationship with each other. In this study, we conducted a metabolomics survey of the secondary metabolites of an artificial co-culture related to a hydrothermal vent fungal-bacterial community comprising Aspergillus sclerotiorum and Streptomyces and their reciprocal relationship. The fungal strain was found to increase the secretion of notoamides and the compound cyclo(Pro-Trp) produced by the actinomycetes strain was discovered to be the responsible molecule. This led to the hypothesis that the fungi transformed cyclo(Pro-Trp) synthesized by the actinomycetes as the biosynthetic precursors of notoamides in the chemical communication. Further analysis showed Streptomyces sp. WU20 was efficient in transforming amino acids into cyclo(Pro-Trp) and adding tryptophan as well as proline into the chemical communication enhanced the induction of the notoamide accumulation. Thus, we propose that the microbial transformation during the synthetic metabolically-mediated chemical communication might be a promising means of speeding up the discovery of novel bioactive molecules. The objective of this research was to clarify the mechanism of microbial transformation for the chemical communication. Besides, this research also highlights the utility of mass spectrometry-based metabolomics as an effective tool in the direct biochemical analysis of community metabolites.

Harzianolides B-G: Undescribed Butenolides isolated from the fungus Trichoderma harzianum ZN-4.

Five undescribed γ-butyrolactones harzianolides BF (1-5), one precursor harzianolide G (6) along with two known analogues, were isolated and identified from the EtOAc extract of the liquid fermentation of Trichoderma harzianum ZN-4, which was obtained from the sediment of Zhoushan coastal area. Notably, compound 1 featured an unusual carbon skeleton with methylene-bridged furan rings system. Their structures were determined by detailed interpretation of NMR and mass spectroscopic data, and the absolute configurations were unambiguously established based on ECD quantum chemical calculations. In bioassay, 1 and 7 showed inhibitory activity against Pestalotiopsis theae, with MIC values of 25 and 50 µg/mL, respectively.

Antimicrobial spiroketal macrolides and dichloro-diketopiperazine from Micromonospora sp. FIMYZ51.

Four compounds (1-4) featuring with an L-rhodinose and spiroketal, possess uncommon continuous hydroxy groups in the macrolide skeleton, and a dichloro-diketopiperazine (5) were isolated from a marine derived Micromonospora sp. FIMYZ51. The determination of the relative and absolute configurations of all isolates was achieved by extensive spectroscopic analyses, single-crystal X-ray diffraction analysis, and ECD calculations. According to structural characteristic and genomic sequences, a plausible biosynthetic pathway for compound 1-4 was proposed and a spirocyclase was inferred to be responsible for the formation of the rare spirocyclic moiety. Compounds 1-4 exhibited potent antifungal activities which is equal to itraconazole against Aspergillus niger. Compounds 1-5 exhibited different degree of inhibitory activities against opportunistic pathogenic bacteria of endocarditis (Micrococcus luteus) with MIC values ranging from 0.0625 µg/mL to 32 µg/mL. Compounds 2 and 3 showed moderate cytotoxicity against drug-resistant tumor cell lines (Namalwa and U266). The result not only provides active lead-compounds, but also reveal the potential of the spirocyclase gene resources from Micromonospora sp., which highlights the promising potential of the strain for biomedical applications.

Spirocyclic polyketides from the marine fungus Talaromyces sp. CX11.

Three new spirocyclic polyketides, talaromyacins A - C, were identified from the endophytic fungus Talaromyces sp. CX11. Their structures including absolute configurations were determined by extensive spectroscopic analysis, Snatzke's method and quantum chemical calculations. Talaromyacin A is identical to the known sequoiamonascin A, for which a structural revision is required.

Specialized metabolites of the fungal genus Phomopsis: Structures, bioactivities and biosynthesis.

Fungi are important resources of novel bioactive compounds which have a high potential to be drug leads or candidates for further pharmacological applications. Phomopsis, a genus widely distributed in the environment, can produce various types of compounds including polyketides, alkaloids, terpenoids, cytochalasins, steroids and flavonoids. The metabolites of Phomopsis sp. showed diverse bioactivities such as antibacterial, anti-inflammatory, antimalarial, and so on, many of which may influence the physiological behaviour of the host plants. In this review, we focus on the chemical structures and biological activities of 183 specialized metabolites isolated from Phomopsis sp. in the decade (2013-2022). Moreover, the biosynthetic pathways of some typical components are summarized.

Antifungal polyketides from the marine-derived fungus Nigrospora sp. MG36-1.

Three new polyketides, a griseofulvin derivative 1, a hydroanthraquinone derivative 8 and a pyranolactone derivative 10, together with eight known compounds (2-7, 9 and 11), were isolated from the marine-derived fungus Nigrospora sp. MG36-1. The structures of the three new compounds were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, 13C NMR calculation in combination with DP4+ and ECD calculations. The antitumor, antibacterial and antifungal activities of the compounds 1-9 were evaluated in vitro. Compound 1 showed antibacterial activity against Acinetobacter baumannii with MIC 42.5 µg/mL. Compounds 1 and 8 exhibited antifungal activity against Candida albicans with MICs 21.5 µg/mL and 17.5 µg/mL, respectively.

Cytotoxic shornephines and asterresins from the hydrothermal vent associated fungus Aspergillus terreus CXX-158-20.

A previously unreported alkaloid, bearing an undescribed 5/7/8 tricyclic heterocyclic skeleton, shornephine D, an undescribed diketomorpholine (DKM) shornephine B, two undescribed diketomorpholine derivatives shornephine C and seco-shornephine B methyl ester, an undescribed indole-isoquinoline alkaloid asterresin C, three undescribed indole alkaloids asterresins A-B and D, together with five known compounds, were isolated from the culture of hydrothermal vent associated fungus Aspergillus terreus CXX-158-20. Their structures were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry, Mosher's method, 13C NMR calculation in combination with DP4+, and ECD calculations. Shornephine D and asterresin C represent two undescribed heterocyclic skeletons. Asterresin D and giluterrin exhibited cytotoxicity activities with IC50 values of 3.96 µM and 7.97 µM against A549 cell line. Asterresin D exhibited cytotoxicity activities with IC50 values of 12.36 µM and 12.48 µM against Namalwa and U266 cell lines. Asterresin A and giluterrin exhibited synergistic effect with adriamycin against MCF-7 cell line.

Exploring gabosine and chlorogentisyl alcohol derivatives from a marine-derived fungus as EcGUS inhibitors with informatic assisted approaches.

ß-Glucuronidase catalyzes the cleavage of glucuronosyl-O-bonds, whose inhibitors reduce the level of toxic substances present in the intestine caused by anti-cancer and anti-inflammatory therapies. Herein, we presented a new tool, Bioactive Fractions Filtering Platform (BFFP), which is able to reliably discern active candidate node from crude extracts. The source code for the BFFP is available on GitHub (https://github.com/BioGavin/msbff). With the assistant of BFFP, 25 gabosine and chlorogentisyl alcohol derivatives including 19 new compounds were isolated from a marine-derived fungus Epicoccum sp. GST-5. Compounds 7, 9-15 possessed an unusual hybrid skeleton of gabosine and chlorogentisyl alcohol units. Compounds 9-12, 16 and 17 possessed a novel three-membered spiral ring skeleton with one/two gabosine and one/two chlorogentisyl alcohol units. Compound 25 represented new gabosine-derived skeleton possessing an unusual 6/6/6/5/6 condensed ring system. All isolates were evaluated for in vitro E. coli ß-glucuronidase (EcGUS) inhibitory activity. 14 Compounds demonstrated superior inhibitory activity (IC50 = 0.24-4.61 µM) to that of standard d-saccharic acid 1,4-lactone (DSL, IC50 = 56.74 ± 4.01 µM). Compounds with chlorogentisyl alcohol moiety, such as 17 (IC50 = 0.24 ± 0.02 µM) and 1 (IC50 = 0.74 ± 0.03 µM), exhibited the most potent inhibitory activity. Furthermore, literature based QSAR profiling by applying PCA and OPLS analysis was carried out to analyze the features of compounds against EcGUS, revealing that the introduction of substituents able to form polar interactions with binding sites of receptor would lead to more active structures.

A new antibacterial 3,5-dimethylorsellinic acid-based meroterpene from the marine fungus Aspergillus sp. CSYZ-1.

Chemical investigation of the extracts of Aspergillus sp. CSYZ-1 resulted in the identification of compound 1, aspergillactone, a new 3,5-dimethylorsellinic acid-based meroterpenoid, together with four known metabolites (2-5). The structure and relative configuration of 1 were unambiguously determined by nuclear magnetic resonance (NMR), mass spectrometry. The absolute configuration of 1 was defined by quantum chemical TDDFT calculated and the experimental ECD spectra. The possible biosynthetic pathway of compound 1 was also proposed. The new compound exhibited potent antimicrobial activity against Helicobacter pylori and Staphylococcus aureus with MIC values of around 1-4 and 2-16 µg/mL, respectively.

New Analogues of Aporphine Alkaloids.

Aporphine alkaloids, characterized by a heterocyclic aromatic basic skeleton, are known from different organisms and exhibit various biological activities: anti-tumor, anti-viral, anti-microbial, anti-inflammatory etc. The review gives information which provides an overview of the latest progress in the structural diversity and the biological activity of the aporphine alkaloids with their derivatives isolated from natural resource in recent years. Additionally, the synthetic approaches of aporphine alkaloids have also been reviewed.

Aporphine Alkaloids from Illigera aromatica from Guangxi Province, China.

Three undescribed aporphine alkaloids laurodionine B (1), illigerine A (2), and N-formyl-laurolitsine (3) were isolated from the methanolic extracts of the Chinese medicinal plant, Illigera aromatica, together with three known analogues (4-6). The chemical structures of 1-6 were identified by spectroscopic methods including 1D and 2D NMR (1H, 13C, COSY, HSQC, and HMBC) and high resolution mass spectrometry (HRESIMS). Compounds 1-3 showed moderate inhibitory activities in vitro against two cultured tumor cell lines, Hela and SMMC7721, with IC50 values of 32.42-62.90 µM. Only compound 1 had in vitro cytotoxic activity against Bcap37 cells, with the IC50 value of 90.61 µM.