Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fungal Depsides-Naturally Inspiring Molecules: Biosynthesis, Structural Characterization, and Biological Activities.

ABSTRACT: Fungi represent a huge reservoir of structurally diverse bio-metabolites. Although there has been a marked increase in the number of isolated fungal metabolites over the past years, many hidden metabolites still need to be discovered. Depsides are a group of polyketides consisting of two or more ester-linked hydroxybenzoic acid moieties. They possess valuable bioactive properties, such as anticancer, antidiabetic, antibacterial, antiviral, anti-inflammatory, antifungal, antifouling, and antioxidant qualities, as well as various human enzyme-inhibitory activities. This review provides an overview of the reported data on fungal depsides, including their sources, biosynthesis, physical and spectral data, and bioactivities in the period from 1975 to 2020. Overall, 110 metabolites and more than 122 references are confirmed. This is the first review of these multi-faceted metabolites from fungi.

SUBMITTER: Ibrahim SRM

PROVIDER: S-EPMC8540757 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Fungal Depsides-Naturally Inspiring Molecules: Biosynthesis, Structural Characterization, and Biological Activities.

Ibrahim Sabrin R M SRM Sirwi Alaa A Eid Basma G BG Mohamed Shaimaa G A SGA Mohamed Gamal A GA

Metabolites 20211005 10

Fungi represent a huge reservoir of structurally diverse bio-metabolites. Although there has been a marked increase in the number of isolated fungal metabolites over the past years, many hidden metabolites still need to be discovered. Depsides are a group of polyketides consisting of two or more ester-linked hydroxybenzoic acid moieties. They possess valuable bioactive properties, such as anticancer, antidiabetic, antibacterial, antiviral, anti-inflammatory, antifungal, antifouling, and antioxid ...[more]

PMID: 34677398

Similar Datasets

Biosynthesis, Characterization, and Biological Activities of Procyanidin Capped Silver Nanoparticles.

Project description:In this study, procyanidin dimers and Leucosidea sericea total extract (LSTE) were employed in the synthesis of silver nanoparticles (AgNPs) and characterized by ultraviolet-visible (UV-Visible) spectroscopy, high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED), X-ray diffraction (XRD), and dynamic light scattering (DLS) techniques. AgNPs of about 2-7 nm were obtained. DLS and stability evaluations confirmed that the AgNPs/procyanidins conjugates were stable. The formed nanoparticles exhibited good inhibitory activities against the two enzymes studied. The IC50 values against the amylase enzyme were 14.92 ± 1.0, 13.24 ± 0.2, and 19.13 ± 0.8 µg/mL for AgNPs coordinated with LSTE, F1, and F2, respectively. The corresponding values for the glucosidase enzyme were 21.48 ± 0.9, 18.76 ± 1.0, and 8.75 ± 0.7 µg/mL. The antioxidant activities were comparable to those of the intact fractions. The AgNPs also demonstrated bacterial inhibitory activities against six bacterial species. While the minimum inhibitory concentrations (MIC) of F1-AgNPs against Pseudomonas aeruginosa and Staphylococcus aureus were 31.25 and 15.63 µg/mL respectively, those of LSTE-AgNPs and F2-AgNPs against these organisms were both 62.50 µg/mL. The F1-AgNPs demonstrated a better bactericidal effect and may be useful in food packaging. This research also showed the involvement of the procyanidins as reducing and capping agents in the formation of stable AgNPs with potential biological applications.

| S-EPMC7564108 | biostudies-literature

Characterization of a fungal thioesterase having Claisen cyclase and deacetylase activities in melanin biosynthesis.

Project description:Melanins are a broad class of darkly pigmented macromolecules formed by oxidative polymerization of phenolic monomers. In fungi, melanins are known virulence factors that contribute to pathogenicity. Their biosynthesis generally involves polymerization of 1,8-dihydroxynaphthalene via a 1,3,6,8-tetrahydroxynaphthalene (THN) precursor assembled by multidomain, nonreducing polyketide synthases. Convergent routes to THN have evolved in fungi. Parallel heptaketide and hexaketide pathways exist that utilize conventional C-terminal thioesterase/Claisen cyclase domains and separate side-chain deacylases. Here, in vitro characterization of Pks1 from Colletotrichum lagenarium establishes a true THN synthase with a bifunctional thioesterase (TE) catalyzing both cyclization and deacetylation of an enzyme-bound hexaketide substrate. Chimeric TE domains were generated by swapping lid regions of active sites between classes of melanin TEs to gain insight into this unprecedented catalysis of carbon-carbon bond making and breaking by an α/β-hydrolase fold enzyme.

| S-EPMC3530136 | biostudies-literature

Biosynthesis of Silver Nanoparticles by <i>Aspergillus terreus</i>: Characterization, Optimization, and Biological Activities.

Project description:In this study, mycelial filtrate of Aspergillus terreus BA6 was used to reduce AgNO3 to form silver nanoparticles (AgNPs). The effect of seven independent variables on the diameter of AgNPs was studied by applying design of experiments (DOE). At optimal conditions, the diameter of AgNPs was reduced by approximately 26.7% compared to the basal culture condition and AgNO3 concentration was found to be the most significant factor affecting the diameter of AgNPs. A. terreus nano-Ag was characterized using UV-visible spectroscopy, transmission electron microscopy, energy dispersive X-ray (EDX), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Zeta potential. The maximum UV absorption was obtained at 420 nm and the microscopic results showed particles with narrow size distribution ranging from 7 to 23 nm. XRD pattern of AgNPs revealed four diffraction peaks of metallic silver and the EDX spectrum showed a strong signal attributed to Ag nano-crystals. AgNPs mycofabricated by A. terreus showed potent minimum inhibitory concentration (MIC) and broad minimum bactericidal/fungicidal concentration (MBC/MFC) against 12 reference microorganisms. The MIC and MBC/MFC values of AgNPs were 0.312 to 1.25 μg/ml and 0.625 to 10 μg/ml, respectively. Nevertheless, AgNPs did not demonstrate any antagonistic activity against Coxsackie B virus. The in vitro cytotoxicity of the mycosynthesized AgNPs showed significant antitumor activity against adenocarcinoma epithelial cells from human breast cancer (Mcf-7) cell line with an inhibitory concentration (IC50) of 87.5 μg/ml.

| S-EPMC8081910 | biostudies-literature

Pyrimidine Schiff Bases: Synthesis, Structural Characterization and Recent Studies on Biological Activities.

Project description:Recently, 5-[(4-ethoxyphenyl)imino]methyl-N-(4-fluorophenyl)-6-methyl-2-phenylpyrimidin-4-amine has been synthesized, characterized, and evaluated for its antibacterial activity against Enterococcus faecalis in combination with antineoplastic activity against gastric adenocarcinoma. In this study, new 5-iminomethylpyrimidine compounds were synthesized which differ in the substituent(s) of the aromatic ring attached to the imine group. The structures of newly obtained pyrimidine Schiff bases were established by spectroscopy techniques (ESI-MS, FTIR and 1H NMR). To extend the current knowledge about the features responsible for the biological activity of the new 5-iminomethylpyrimidine derivatives, low-temperature single-crystal X-ray analyses were carried out. For all studied crystals, intramolecular N-H∙∙∙N hydrogen bonds and intermolecular C-H∙∙∙F interactions were observed and seemed to play an essential role in the formation of the structures. Simultaneously, their biological properties based on their cytotoxic features were compared with the activities of the Schiff base (III) published previously. Moreover, computational investigations, such as ADME prediction analysis and molecular docking, were also performed on the most active new Schiff base (compound 4b). These results were compared with the highest active compound III.

| S-EPMC10889512 | biostudies-literature

Biosynthesis, synthesis, and biological activities of pyrrolobenzodiazepines.

Project description:Pyrrolobenzodiazepines (PBDs) are sequence selective DNA alkylating agents with remarkable antineoplastic activity. They are either naturally produced by actinomycetes or synthetically produced. The remarkable broad spectrum of activities of the naturally produced PBDs encouraged the synthesis of several PBDs, including dimeric and hybrid PBDs yielding to an improvement in the DNA-binding sequence specificity and in the potency of this class of compounds. However, limitation in the chemical synthesis prevented the testing of one of the most potent PBDs, sibiromycin, a naturally produced glycosylated PBDs. Only recently, the biosynthetic gene clusters for PBDs have been identified opening the doors to the production of glycosylated PBDs by mutasynthesis and biosynthetic engineering. This review describes the recent studies on the biosynthesis of naturally produced pyrrolobenzodiazepines. In addition, it provides an overview on the isolation and characterization of naturally produced PBDs, chemical synthesis of PBDs, mechanism of DNA alkylation, and DNA-binding affinity and cytotoxic properties of both naturally produced and synthetic pyrrolobenzodiazepines.

| S-EPMC4127195 | biostudies-literature

Extraction, structural characterization, and biological activities of a new glucan from Codonopsis pilosula.

Project description:In this study, a powerful and rapid aqueous two-phase system (ATPS) method was used to extract polysaccharides from Codonopsis pilosula. The ATPS process was investigated with response surface methodology (RSM). At an ammonium sulfate concentration of 17%, ethanol concentration of 30%, and extraction temperature of 40 °C at pH 6, the total extraction yield of polysaccharides reached (31.57 ± 1.28)%. After separation and purification, a homogenized polysaccharide CPP 2-4 with molecular weight of 3.9 × 104 kDa was obtained from the bottom phase. The physicochemical properties and structural features confirmed that CPP 2-4 was an α-1,6-glucan. Activity studies showed that the IC50 of CPP 2-4 for DPPH radical scavenging was 0.105 mg/mL. The FRAP and ABTS assays showed that CPP 2-4 had strong antioxidant activity in a dose-dependent manner. Furthermore, CPP 2-4 inhibited NO release in RAW264.7 cells induced by lipopolysaccharide, which indicated a certain anti-inflammatory effect. This study improved the extraction rate of polysaccharides from C. pilosula and identified a glucan for the first time, that can contribute to a better understanding of the composition and structure of polysaccharides from C. pilosula and provide data support for the medicine and food homology of C. pilosula.

| S-EPMC10024767 | biostudies-literature

Structural and spectroscopic characterization of RufO indicates a new biological role in rufomycin biosynthesis.

Project description:Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting a novel drug target. Several nonproteinogenic amino acids are integrated into rufomycins, including a conserved 3-nitro-tyrosine. RufO, a cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation of 3-nitro-tyrosine in the presence of O2 and NO. To define its biological function, the interaction between RufO and the proposed substrate tyrosine is investigated using various spectroscopic methods that are sensitive to the structural change of a heme center. However, a low- to high-spin state transition and a dramatic increase in the redox potential that are commonly found in CYPs upon ligand binding have not been observed. Furthermore, a 1.89-Å crystal structure of RufO shows that the enzyme has flexible surface regions, a wide-open substrate access tunnel, and the heme center is largely exposed to solvent. Comparison with a closely related nitrating CYP reveals a spacious and hydrophobic distal pocket in RufO, which is incapable of stabilizing a free amino acid. Molecular docking validates the experimental data and proposes a possible substrate. Collectively, our results disfavor tyrosine as the substrate of RufO and point to the possibility that the nitration occurs during or after the assembly of the peptides. This study indicates a new function of the unique nitrating enzyme and provides insights into the biosynthesis of nonribosomal peptides.

| S-EPMC10424215 | biostudies-literature

Structural characterization of naturally occurring RNA single mismatches.

Project description:RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence-structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.

| S-EPMC3035445 | biostudies-literature

Four New Depsides Isolated from Salvia miltiorrhiza and Their Significant Nerve-Protective Activities.

Project description:By investigating of the roots of Salvia miltiorrhiza, which is one of the most widely used Chinese herbs, we used phytochemical methods successfully to obtain twelve depsides: four depsides (1⁻4) that were previously undescribed, along with eight known ones (5⁻12). Their structure characteristics were assessed by HR-ESIMS, CD, NMR (¹H, 13C, HSQC, HMBC) data analyses. These four newly isolated compounds (1⁻4), as well as the other eight compounds (5⁻12), show extraordinary protective effects on hydrogen peroxide-induced apoptosis in HS-SY5Y cells. Among them, depside 4 and depside 6 displayed more obviously protective effects than others.

| S-EPMC6320994 | biostudies-literature

Glucosinolates: Natural Occurrence, Biosynthesis, Accessibility, Isolation, Structures, and Biological Activities.

Project description:Glucosinolates (GSLs) are secondary plant metabolites abundantly found in plant order Brassicales. GSLs are constituted by an S-β-d-glucopyrano unit anomerically connected to O-sulfated (Z)-thiohydroximate moiety. The side-chain of the O-sulfate thiohydroximate moiety, which is derived from a different amino acid, contributes to the diversity of natural GSL, with more than 130 structures identified and validated to this day. Both the structural diversity of GSL and their biological implication in plants have been biochemically studied. Although chemical syntheses of GSL have been devised to give access to these secondary metabolites, direct extraction from biomass remains the conventional method to isolate natural GSL. While intact GSLs are biologically inactive, various products, including isothiocyanates, nitriles, epithionitriles, and cyanides obtained through their hydrolysis of GSLs, exhibit many different biological activities, among which several therapeutic benefits have been suggested. This article reviews natural occurrence, accessibility via chemical, synthetic biochemical pathways of GSL, and the current methodology of extraction, purification, and characterization. Structural information, including the most recent classification of GSL, and their stability and storage conditions will also be discussed. The biological perspective will also be explored to demonstrate the importance of these prominent metabolites.

| S-EPMC7582585 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data