Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Amomum tsao-ko essential oil, a novel anti-COVID-19 Omicron spike protein natural products: A computational study.

ABSTRACT: Since the outbreak of COVID-19, this virus has been constantly mutating. The latest mutant Omicron has been identified as VOC by WHO. The main reason for its concern is the mutation of 46 amino acids in spike protein, which has brought the global epidemic prevention into another difficulty. Herbal aromatic plant Amomum tsao-ko was excavated from formula 1 and 2 for the treatment of COVID-19 in China, and its active components were extracted and identified. Molecular dynamics simulation and Fpocket were applied to find the key sites on RBD_Omicron, and molecular docking was also used to reveal the interaction between A. tsao-ko essential oil (AEO) and RBD_Omicron. The AEO components were analyzed and identified by GC/Q-TOF MS. There were 20 kinds of AEO with a relative area percentage of more than 1%, and they were related to the three active centres of RBD_Omicron. In this study, virtual screening was used to mine the essential oil components of medicinal plants, and it was found that the components could interact with the spike protein RBD in aerosol to block the interaction of RBD and hACE2, thus cutting off the transmission route and protecting the host. This study has certain guiding significance in the modernization of Traditional Chinese medicine and the prevention of COVID-19.

SUBMITTER: Liu JZ

PROVIDER: S-EPMC9014638 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Amomum tsao-ko.

Project description:Amomum tsao-ko (Zingiberaceae) is an important edible and medicinal crop. The complete chloroplast (cp) genome of A. tsao-ko was determined using Illumina sequencing platform. The size of whole cp genome was 163,648 bp, containing a small single copy (SSC) region of 15,355 bp and a large single copy (LSC) region of 88,741 bp, which were separated by a pair of inverted repeat (IRs) regions (29,776 bp). The A. tsao-ko cp genome contained 133 genes, including eight ribosomal RNA genes (4 rRNA species), 38 transfer RNA genes (30 tRNA species) and 87 protein-coding genes (79 PCG species). The overall GC content of A. tsao-ko cp genome is 36.02%. To investigate the evolution status of A. tsao-ko, as well as Zingiberales, a phylogenetic tree with A. tsao-ko and other 16 species was constructed based on their complete chloroplast genomes. Phylogenetic analysis revealed that A. tsao-ko was closely related to Alpinia zerumbet.

| S-EPMC7748665 | biostudies-literature

Comparison of metabolites and variety authentication of Amomum tsao-ko and Amomum paratsao-ko using GC-MS and NIR spectroscopy.

Project description:Amomum tsao-ko, as an edible and medicinal variety, has been cultivated for more than 600 years in China. Recently, two cultivars, A. tsao-ko and Amomum paratsao-ko, were found in A. tsao-ko planting area. The two cultivars are often confused because of the similar phenotype and difficult to distinguish through sensory judgment. In this study, the non-targeted gas chromatography-mass spectrometry (GC-MS) metabolomics combined with near-infrared spectroscopy (NIRS) were used for dissecting the two cultivars with phenotypic differences. According to principal component analysis (PCA) loading diagram and orthogonal partial least squares discriminant analysis (OPLS-DA) S-plot of the metabolites, the accumulation of major components including 1,8-cineole, α-phellandrene, (E)-2-decenal, (-)-β-pinene, (E)-2-octenal, 1-octanal, D-limonene, and decanal, were present differences between the two cultivars. Seven metabolites potential differentiated biomarkers as β-selinene, decamethylcyclopentasiloxane, (E,Z)-2,6-dodecadienal, (E)-2-hexenal, (E)-2-decenal, isogeranial, 1,8-cineole and β-cubebene were determined. Although A. tsao-ko and A. paratsao-ko belong to the same genera and are similar in plant and fruit morphology, the composition and content of the main components were exposed significant discrepancy, so it is necessary to distinguish them. In this study, the discriminant model established by GC-MS or NIRS combined with multivariate analysis has achieved a good classification effect. NIRS has the advantages of simple, fast and nondestructive and can be used for rapid identification of varieties and fruit tissues.

| S-EPMC8313684 | biostudies-literature

Monoterpenoids from the Fruits of Amomum tsao-ko Have Inhibitory Effects on Nitric Oxide Production.

Project description:In our search for novel plant-derived inhibitors of nitric oxide (NO) with potential for treating inflammatory diseases, the phytochemicals of Amomum tsao-ko fruits were investigated, leading to the isolation of one bicyclic nonane (1), three menthene skeleton monoterpenoids (2-4), and two acyclic monoterpenoids (5 and 6). Their structures were identified using one- and two-dimensional nuclear magnetic resonance spectroscopy, and mass spectrometry. To the best of our knowledge, compounds 2-5 were obtained from the genus Amomum for the first time. All isolates were tested for their ability to inhibit lipopolysaccharide-stimulated NO overproduction in RAW264.7 cells. Compound 4 was found to inhibit NO production. Western blotting analysis indicated that active compound 4 can regulate inducible NO synthase expression. In addition, lipopolysaccharide-induced interleukin 1 beta and interleukin-6 overproduction was reduced in a concentration-dependent manner.

| S-EPMC7911220 | biostudies-literature

Genome Sequencing of Amomum tsao-ko Provides Novel Insight Into Its Volatile Component Biosynthesis.

Project description:As an important economic and medicinal crop, Amomum tsao-ko is rich in volatile oils and widely used in food additives, essential oils, and traditional Chinese medicine. However, the lack of the genome remains a limiting factor for understanding its medicinal properties at the molecular level. Here, based on 288.72 Gb of PacBio long reads and 105.45 Gb of Illumina paired-end short reads, we assembled a draft genome for A. tsao-ko (2.70 Gb in size, contig N50 of 2.45 Mb). Approximately 90.07% of the predicted genes were annotated in public databases. Based on comparative genomic analysis, genes involved in secondary metabolite biosynthesis, flavonoid metabolism, and terpenoid biosynthesis showed significant expansion. Notably, the DXS, GGPPS, and CYP450 genes, which participate in rate-limiting steps for terpenoid backbone biosynthesis and modification, may form the genetic basis for essential oil formation in A. tsao-ko. The assembled A. tsao-ko draft genome provides a valuable genetic resource for understanding the unique features of this plant and for further evolutionary and agronomic studies of Zingiberaceae species.

| S-EPMC9198571 | biostudies-literature

Amomum tsao-ko Crevost & Lemarie: a comprehensive review on traditional uses, botany, phytochemistry, and pharmacology.

Project description:Tsaoko Fructus, the dried ripe fruit of Amomum tsao-ko Crevost & Lemarié, is used as both medicinal material and food additive. This review summarized the traditional uses, botany, phytochemistry, and pharmacological progress on Tsaoko Fructus. One classical prescription and the other 11 representative prescriptions containing Tsaoko Fructus were reviewed. The indications of these prescriptions are major in treating spleen and stomach disorders and epidemic febrile diseases including malaria. At least 209 compounds have been isolated and identified from Tsaoko Fructus, most of which belong to terpenoids, phenylpropanoids, and organic acids. Essential oil, crude extract, and some compounds were observed to have pharmacological activities such as anti-biotics, anti-inflammation, antioxidant, mostly via in vitro experiments. However, the mechanism of its medicinal uses remains unclear. This review provides a comprehensive understanding of Tsaoko Fructus, which will be beneficial to exploring the mechanism and potential medicinal applications of Tsaoko Fructus, as well as developing a rational quality control system for Tsaoko Fructus as a medicinal material in the future.Supplementary informationThe online version contains supplementary material available at 10.1007/s11101-021-09793-x.

| S-EPMC8743105 | biostudies-literature

Development of 23 novel microsatellite markers of Amomum tsao-ko (Zingiberaceae) based on restriction-site-associated DNA sequencing.

Project description:Amomum tsao-ko (Zingiberaceae) is a traditional Chinese medicine and condiment, and an important economic crop in the tropical forest of southwest China. However, few simple sequence repeat (SSR) markers are available in A. tsao-ko, which is hindering genetic research in this species. The aim of this study was to develop and characterize microsatellite markers for A. tsao-ko using restriction-site-associated DNA sequencing. A total of 115,482 microsatellites were identified using MISA software, and 13,411 SSR primer pairs were designed. 100 pairs of SSR primers were selected at random and used to evaluate polymorphisms among 4 A. tsao-ko samples. Finally, 23 pairs of SSR primers with clear bands and obvious polymorphism were selected for genetic diversity analysis of 72 A. tsao-ko accessions. The number of alleles and effective number of alleles per locus ranged from 2 to 6 and from 1.315 to 3.776, respectively. The observed heterozygosity ranged from 0.208 to 0.779, and the expected heterozygosity was from 0.239 to 0.735. The average values of the polymorphic information content were 0.454. Hardy-Weinberg equilibrium (HWE) analysis showed that 10 loci significantly deviated from HWE (P < 0.05). The pairwise FST and genetic distance values revealed low levels of genetic differentiation and high genetic similarity among six A. tsao-ko populations. These microsatellite markers developed will provide a valuable tool for further germplasm characterization, genetic diversity, and breeding studies in A. tsao-ko.

| S-EPMC7811684 | biostudies-literature

Chromosome-level genome assembly of Amomum tsao-ko provides insights into the biosynthesis of flavor compounds.

Project description:Amomum tsao-ko is an economically important spice plant in the ginger family (Zingiberaceae). The dried ripe fruit has been widely used as spice and medicine in Southeast Asia due to its distinct flavor metabolites. However, there is little genomic information available to understand the biosynthesis of its characteristic flavor compounds. Here, we present a high-quality chromosome-level genome of A. tsao-ko with a total length of 2.08 Gb assembled into 24 chromosomes. Potential relationships between genetic variation and chemical constituents were analyzed by a genome-wide association study of 119 representative A. tsao-ko specimens in China. Metabolome and transcriptome correlation analysis of different plant organs and fruit developmental stages revealed the proposed biosynthesis of the characteristic bicyclononane aldehydes and aromatic metabolites in A. tsao-ko fruit. Transcription factors of 20 families may be involved in the regulatory network of terpenoids. This study provides genomic and chemical insights into the biosynthesis of characteristic aroma and flavor constituents, which can be used to improve the quality of A. tsao-ko as food and medicine.

| S-EPMC9719038 | biostudies-literature

Improvement of Obesity and Dyslipidemic Activity of Amomum tsao-ko in C57BL/6 Mice Fed a High-Carbohydrate Diet.

Project description:Amomum tsao-ko Crevost et Lemaire (Zingiberaceae) is a medicinal herb found in Southeast Asia that is used for the treatment of malaria, abdominal pain, dyspepsia, etc. The aim of this study was to investigate the effect of an ethanol extract of Amomum tsao-ko (EAT) on obesity and hyperlipidemia in C57BL/6 mice fed a high-carbohydrate diet (HCD). First, the mice were divided into five groups (n = 6/group) as follows: normal diet, HCD, and HCD+EAT (100, 200, and 400 mg/kg/day), which were orally administered with EAT daily for 84 days. Using microcomputed tomography (micro-CT) analysis, we found that EAT inhibited not only body-weight gain, but also visceral fat and subcutaneous fat accumulation. Histological analysis confirmed that EAT decreased the size of fat tissues. EAT consistently improved various indices, including plasma levels of total cholesterol (TC), triglyceride (TG), low-density lipoprotein, high-density lipoprotein, atherogenic index, and cardiac risk factors, which are related to dyslipidemia-a major risk factor for heart disease. The contents of TC and TG, as well as the lipid droplets of HCD-induced hepatic accumulation in the liver tissue, were suppressed by EAT. Taken together, these findings suggest the possibility of developing EAT as a therapeutic agent for improving HCD-induced obesity and hyperlipidemia.

| S-EPMC7998585 | biostudies-literature

Tsaokoic Acid: A New Bicyclic Nonene from the Fruits of Amomum tsao-ko with Acetylcholinesterase Inhibitory Activity.

Project description:A new bicyclic nonene, tsaokoic acid (1), was isolated from the fruits of Amomum tsao-ko, together with three known compounds (2-4). The structure of 1 was elucidated by analyzing spectroscopic data including 1D and 2D NMR spectra and compounds 2-4 were identified as tsaokoin, vanillin, and tsaokoarylone, respectively, by comparing their NMR spectra with previously reported data. Compounds 1-4 showed possible inhibitory activity against acetylcholinesterase (AChE) in silico molecular docking simulations. They were submitted to in vitro assay system and exhibited moderate inhibitory activity with IC50 values of 32.78, 41.70, 39.25, and 31.13 μM, respectively.

| S-EPMC10059965 | biostudies-literature

Effects of Different Pre-drying and Drying Methods on Volatile Compounds in the Pericarp and Kernel of Amomum tsao-ko.

Project description:The effects of twelve different pre-drying and drying methods on the chemical composition in the pericarp and kernel of Amomum tsao-ko were studied. The volatile components were isolated from the samples by simultaneous distillation and extraction and analyzed by gas chromatography-mass spectrometry (GC-MS). Sixty and thirty-eight compounds were identified from pericarp and kernel, respectively, and the main constituents were oxygenated monoterpenes. These compounds were not only significantly affected by pre-drying and drying methods but also varied in content due to different tissue locations. The total volatile content of pericarp varied from 0.70 to 1.55%, with the highest obtained by microwave-dried samples (150 W) and the lowest in freeze-dried samples. The total volatile content of the kernel varied from 6.11 to 10.69%, with the highest content obtained during sun drying (SD) and the lowest content in samples treated with boiling water for 2 min. Oxygenated monoterpenes were the highest compounds in pericarp and kernel, which were also the most affected by drying methods. The highest content of oxygenated monoterpenes in the pericarp (0.77%) could be obtained by boiling water treatment for 5 min, and the highest content of oxygenated monoterpenes in the kernel (7.48%) could be obtained by SD. Additionally, the main components such as 1,8-cineole, 2-carene, (Z)-citral, nerolidol, (Z)-2-decenal, (E)-2-dodecenal, citral, (E)-2-octenal, 4-propylbenzaldehyde, and phthalan showed remarkable variations in pre-drying and drying methods.

| S-EPMC8914167 | 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