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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

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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.

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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.

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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.

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Insights into the Composition and Antibacterial Activity of Amomum tsao-ko Essential Oils from Different Regions Based on GC-MS and GC-IMS.

Project description:Chemical components are one of the most significant traits and attributes of plant tissues, and lead to their different functions. In this study, the composition of Amomun tsao-ko essential oils (AEOs) from different regions was first determined by a combination of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). In total, 141 compounds were identified, of which terpenes and aldehydes were the main groups. Orthogonal partial least square discriminant analysis (OPLS-DA) distinguished the samples from different regions clearly, and the main differences were terpenes, aldehydes, and esters. Meanwhile, AEOs showed strong antibacterial activity against Staphylococcus aureus (S. aureus), and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) reached 0.20 mg/mL and 0.39-0.78 mg/mL, respectively. From correlation analysis, 1,8-cineole, (E)-dec-2-enal, citral, α-pinene, and α-terpineol were determined to be the potential antibacterial compounds. This study provides the basis for the variety optimization of A. tsao-ko and its application as a natural food preservative.

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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.

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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.

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