Molecular Simulation-based Combinatorial Modeling and Antioxidant Activities of Zingiberaceae Family Rhizomes

Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour

Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat-retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.

Gas chromatography-mass spectrometry metabolic profiling, molecular simulation and dynamics of diverse phytochemicals of Punica granatum L. leaves against estrogen receptor

Introduction: Breast cancer is the most common type of cancer globally and its treatment with many FDA-approved synthetic drugs manifests various side effects. Alternatively, phytochemicals are natural reserves of novel drugs for cancer therapy. Punica granatum commonly known as pomegranate is a rich source of phytopharmaceuticals. Methods: The phytoconstituents of Punica granatum leaves were profiled using GC-MS/MS in the present work. Cytoscape-assisted network pharmacology of principal and prognostic biomarkers, which are immunohistochemically tested in breast cancer tissue, was carried out for the identification of protein target. Followed by, rigorous virtual screening of 145 phytoconstituents against the three ER isoforms (α, β and γ) was performed using Discovery Studio. The docked complexes were further evaluated for their flexibility and stability using GROMACS2016 through 50 ns long molecular dynamic simulations. Results: In the current study, we report the precise and systematic GC-MS/MS profiling of phytoconstituents (19 novel metabolites out of 145) of hydromethanolic extract of Punica granatum L. (pomegranate) leaves. These phytocompounds are various types of fatty acids, terpenes, heterocyclic compounds and flavonoids. 4-coumaric acid methyl ester was identified as the best inhibitor of ER isoforms with drug-likeness and no toxicity from ADMET screening. γ-ligand binding domain complex showed the best interactions with minimum RMSD, constant Rg, and the maximum number of hydrogen bonds. Conclusion: We conclude that 4-coumaric acid methyl ester exhibits favourable drug-like properties comparable to tamoxifen, an FDA-approved breast cancer drug and can be tested further in preclinical studies.

Uncharted Source of Medicinal Products: The Case of the Hedychium Genus

A current research topic of great interest is the study of the therapeutic properties of plants and of their bioactive secondary metabolites. Plants have been used to treat all types of health problems from allergies to cancer, in addition to their use in the perfumery industry and as food. Hedychium species are among those plants used in folk medicine in several countries and several works have been reported to verify if and how effectively these plants exert the effects reported in folk medicine, studying their essential oils, extracts and pure secondary metabolites. Hedychium coronarium and Hedychium spicatum are the most studied species. Interesting compounds have been identified like coronarin D, which possesses antibacterial, antifungal and antitumor activities, as well as isocoronarin D, linalool and villosin that exhibit better cytotoxicity towards tumor cell lines than the reference compounds used, with villosin not affecting the non-tumor cell line. Linalool and α-pinene are the most active compounds found in Hedychium essential oils, while β-pinene is identified as the most widespread compound, being reported in 12 different Hedychium species. Since only some Hedychium species have been investigated, this review hopes to shed some light on the uncharted territory that is the Hedychium genus.