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Specialty Journal of Pharmacognosy, Phytochemistry, and Biotechnology

Volume 5, Issue 2 (2025)

Inferring Medicinal-Plant Biosynthetic Pathways Without a Single Omics Layer Dominating the Answer: A Multi-Omics Evidence Architecture for Gene–Metabolite Assignment
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Views: 170
Written by Wouter De Smet   Published on Vol 5 Issue 2, 2025
Medicinal-plant pathway discovery increasingly combines genome assemblies, gene-expression profiles, metabolite measurements, spatial information, and functional assays, yet the presence of multiple data layers does not itself resolve which gene produces, modifies, transports, or regulates a given metabolite. This article develops an original, evidence-bounded multi-omics architecture for gene–metabolite assignment in specialized metabolism. The analysis separates candidate nomination from biolo

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Prioritizing Biosynthetic Gene Clusters When Genomes Overpredict Chemistry: Coupling Genomic Novelty, Metabolite Evidence, Ecological Context, and Chemical Tractability in Microbial Natural-Product Discovery
Downloads: 26
Views: 197
Written by Ana Rodrigues   Published on Vol 5 Issue 2, 2025
Microbial genome mining routinely identifies far more biosynthetic gene clusters (BGCs) than can be experimentally characterized, creating a prioritization problem rather than a simple detection problem. Sequence novelty is frequently treated as the principal triage signal, yet sequence divergence does not guarantee production, structural novelty, ecological relevance, or practical chemical access. This article develops an original computational prioritization model that integrates four non-equi

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Unknown Peaks Should Carry Uncertainty, Not Forced Identities: A Confidence-Aware Computational Scheme for Annotating Plant LC–MS/MS Features Across Libraries and In-Silico Predictions
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Views: 205
Written by Krzysztof Wiśniewski   Published on Vol 5 Issue 2, 2025
Untargeted plant LC–MS/MS routinely produces far more reproducible spectral features than can be assigned to authenticated molecular structures. The resulting gap between detection and identification is increasingly filled by spectral-library search, molecular networking, formula inference, class prediction, candidate ranking, predicted spectra, retention modeling, and de novo structure generation. These tools expand chemical coverage, but their outputs are often reported at a level of structura

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Poorly Soluble Phytochemicals Change Rank After Formulation: A Developability Model Connecting Solid State, Dissolution, Biorelevant Exposure, and Delivery-Strategy Selection
Downloads: 20
Views: 223
Written by Ahmed Ben Ali   Published on Vol 5 Issue 2, 2025
Poor aqueous solubility frequently lowers the apparent developability of phytochemical candidates, yet that judgment is often made before formulation has revealed whether the limitation is intrinsic, state-dependent, or technologically tractable. This article develops an original formulation-aware developability model in which candidate quality is treated as conditional on material state, gastrointestinal dissolution behavior, exposure-relevant solution state, and the suitability of the selected

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Extract Activity, Compound Activity, and Target Activity Are Different Claims: An Evidence-Translation Model for Preventing Mechanistic Overstatement in Pharmacognosy
Downloads: 23
Views: 229
Written by Peter Nilsson   Published on Vol 5 Issue 2, 2025
Pharmacognosy frequently moves across materials and levels of inference: a botanical extract produces a phenotype, chemical analysis detects candidate constituents, an isolated compound shows activity, and computational or experimental work nominates a molecular target. These observations are scientifically valuable but do not represent equivalent claims. Mechanistic overstatement arises when evidence supporting one level is silently transferred to another—for example, when extract activity is a

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Plant Pathways Do Not Become Microbial Pathways by Gene Transfer Alone: A Compatibility Model for Cofactors, Compartmentation, Toxicity, Flux, and Product Export
Downloads: 24
Views: 220
Written by James O'Leary   Published on Vol 5 Issue 2, 2025
Transferring plant biosynthetic genes into a microbial chassis can reproduce enzyme inventories without reproducing the cellular conditions that made the pathway functional in its native organism. This distinction becomes increasingly consequential as heterologous routes incorporate membrane-associated enzymes, redox-intensive reactions, spatially separated intermediates, toxic metabolites, competing precursor demands, and products that require active removal. This article develops an original p

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Scale-Up Can Reverse a Promising Fermentation Route: A Decision Model Linking Oxygen Transfer, Precursor Supply, Morphology, Product Toxicity, and Recovery Economics
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Views: 221
Written by Lukas Weber   Published on Vol 5 Issue 2, 2025
Industrial fermentation routes are commonly ranked from laboratory performance, yet scale-up changes the physical environment, the temporal exposure history of cells, and the economic consequences of upstream choices. This article develops an original, evidence-bounded bioprocess decision model for assessing when a route that appears superior at small scale may become less attractive after scale-dependent biological, engineering, and recovery constraints are considered. The analysis separates ab

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Endophyte–Host Chemical Ecology as a Discovery Engine: An Integrative Review of Signaling, Silent Biosynthetic Pathways, Co-Culture, and Natural-Product Expression
Downloads: 24
Views: 272
Written by Maria Gonzales   Published on Vol 5 Issue 2, 2025
Endophytic fungi can harbor extensive biosynthetic capacity, yet natural-product discovery commonly interrogates them after removal from the host and transfer to simplified culture. This creates a central uncertainty: chemistry observed ex planta may represent only one state within a larger, interaction-dependent chemical repertoire. This integrative review synthesized ecological, metabolomic, genomic, regulatory, co-culture, and pathway-activation evidence relevant to endophyte chemical express

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Ginsenoside Rk3 Inhibits Human Platelet Activation via cAMP Elevation and PI3K/MAPK Pathway Suppression
Downloads: 25
Views: 120
Written by Rafael Mendoza   Published on Vol 5 Issue 2, 2025
Previous studies have established the aggregation-inhibitory properties of synthetic ginsenoside derivatives, such as G-Rp (1, 3, and 4), as well as natural ginsenosides isolated from Panax ginseng, including 20(S)-Rg3, Rg6, F4, and Ro. However, the specific inhibitory mechanisms of G-Rk3, another bioactive compound derived from Panax ginseng, require further detailed investigation. This research aimed to evaluate the effects of G-Rk3 on agonist-induced human platelet aggregation. We assessed th

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Regulation of Lipid Metabolism and Cholesterol Homeostasis Genes Underlies the Anti-Obesity Effects of Centella asiatica in Mice
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Views: 187
Written by Wouter De Smet   Published on Vol 5 Issue 2, 2025
To elucidate the mechanisms underlying the anti-obesity properties of Centella asiatica (CA), this study evaluated body weight, serum profiles, white adipose tissue (WAT) mass, histological characteristics, and the expression of genes associated with cholesterol homeostasis and lipid metabolism. These parameters were assessed in mice with obesity induced by a high-fat, high-sugar diet (HFHSD) following oral administration of CA for 12 weeks. Male C57BL/6J mice, aged eight weeks, were divided int

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p38MAPK- and Akt/mTOR-Mediated Signaling Underlies the Pro-Myogenic Effects of Ginsenoside Rg5
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Views: 188
Written by Ana Rodrigues   Published on Vol 5 Issue 2, 2025
Skeletal muscles are essential for both energy metabolism and physical movement. A reduction in skeletal muscle mass can lead to functional and metabolic complications. Ongoing research aims to avert these conditions by enhancing muscle mass and regenerative potential. While Ginsenoside Rg5 is known for its diverse pharmacological properties, research specifically addressing its impact on muscle development and differentiation remains limited. To explore the influence of Rg5 on myogenesis, C2C12

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γ-Mangostin Induces Immunogenic Cell Death and Activates cGAS Signaling in Acute Myeloid Leukemia
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Views: 168
Written by Krzysztof Wiśniewski   Published on Vol 5 Issue 2, 2025
Conventional treatments like chemotherapy and radiotherapy frequently provoke anti-tumor immunity by initiating immunogenic cell death (ICD), a process where expiring cancer cells extrude damage-associated molecular patterns to stimulate targeted immune reactions. Despite this, the capacity of natural compounds to precipitate ICD within leukemic contexts remains largely unexplored. The present investigation demonstrates that the dietary compound γ-mangostin successfully eliminates primary murine

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Activation of the AKT/GSK-3β/β-Catenin Axis Underlies the Pro-Osteogenic Effects of Penicopeptide A from Deep-Sea-Derived Fungusa
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Views: 183
Written by Ahmed Ben Ali   Published on Vol 5 Issue 2, 2025
Despite their pharmacological promise, marine-derived compounds remain largely unexplored in the context of osteoporosis therapeutics. To address this gap, the present investigation evaluated whether primary isolates sourced from the deep-marine fungus Penicillium solitum MCCC 3A00215 could stimulate osteogenesis utilizing both living subjects and controlled laboratory environments. Initial assessments revealed that bone marrow mesenchymal stem cells (BMSCs) exhibited increased osteoblastic mine

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Suppression of SLC7A11-Mediated Inhibition of Dendritic Cell Efferocytosis Underlies the Wound-Healing Effects of Ginsenoside Rg5
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Views: 201
Written by Peter Nilsson   Published on Vol 5 Issue 2, 2025
Ginsenoside Rg5 represents a scarce ginsenoside recognized for its ability to lower blood glucose levels in diabetic mice. The present investigation aimed to examine the influence of ginsenoside Rg5 on cutaneous wound repair in Lepr<sup>db/db</sup> mutant (db/db) mice on a C57BL/KsJ genetic background and to clarify the associated molecular pathways. Experiments were conducted using seven-week-old male C57BL/6J mice, SLC7A11-knockout (KO) animals, their corresponding littermate wild-type (WT) co

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Endoplasmic Reticulum Protein Processing Is a Molecular Target of Ginsenoside Rk1 in Cervical Cancer Cells
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Views: 172
Written by James O'Leary   Published on Vol 5 Issue 2, 2025
Modifications in work-life balance have contributed to higher rates of cervical cancer in younger adults. Ginsenoside Rk1, a low-abundance saponin component of ginseng, is recognized for its capacity to restrain growth and survival across multiple human cancer cell types. Nonetheless, its influence on the proliferative capacity of HeLa cells has not been established. Exposure to ginsenoside Rk1 caused HeLa cells to arrest in the G0/G1 phase in a manner dependent on concentration, while also supp

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