The concept of “pharmacophylogeny” was proposed by Professor Peigen Xiao in the 1980s based on long-term studies of Chinese researchers especially since the 1950s and is embedded in a wider global development of molecular phylogeny and pharmacology globally. The complicated systematic relationships and connectivity between medicinal plants, their chemical profiles and therapeutic utilities are consistent goals in pharmacophylogenetic studies, which benefit innovative plant-based drug R&D. More recently, the concept of “pharmacophylogenomics” has been of importance in botanical drug R&D and over the last decades has seen an gradual increase in its importance. Pharmacophylogeny and pharmacophylogenomics are truly transdisciplinary i.e. the synthesis of multiple disciplines, such as molecular phylogeny/chemotaxonomy, plant morphology, plant biochemistry/molecular biology and the various omics approaches, ethnobotany/ethnopharmacology, and the like. Medicinal plants within the same phylogenetic groups may have the same or similar therapeutically active metabolites and consequently effects, thus forming the core of pharmacophylogeny. In the past, pharmacophylogeny has played a major role in the search for alternative resources for imported drugs globally including in China. At present, it continues to play an active role in expanding medicinal plant resources, quality control/identification of herbal medicines, as well as predicting the chemical constituents or active ingredients of herbal medicine and the identification/determination of active metabolites. In the future, it will play an important role in the search for new drugs, enabling a scientific understanding of and improving herbal medicines and their use. This will form a core basis for the sustainable use, conservation and future utilization of traditional/natural medicinal resources.

Relationships between species may be cryptic due to genetic factors or they may be morphologically and biochemically distinct. Biologically active compounds are mostly secondary metabolites, and the systematic distribution of these metabolites is a core area of deeper phylogenetic research. This includes potentially ‘inactive’ isomers based on biosynthetic pathways in plants. During the past two decades, various omics techniques have continued to evolve towards elucidating the cryptic relationships between plant phylogeny, secondary metabolites and their biosynthesis/biological activities, which promisingly provide lead entities to develop novel plant-derived drugs.

The goal of this Research Topic is to gain novel insights into the newly mined, cryptic and/or close relationships between plant phylogeny/phylogenomics, chemical composition/metabolomics and biological activity (including traditional efficacy and pharmacological activities). A triple helix systems perspective would be preferred to illustrate the latest awareness and prospects of pharmacophylogeny, pharmacophylogenomics and related concepts, as well as their expanding utility in botanical drug R&D. Such studies need to be developed within the context of deeper investigations of molecular biology and genomics of medicinal plants, their metabolites and metabolomics, and ethnopharmacology-based assessments with the wider aim of enabling the sustainable conservation and utilization of botanical resources.

We welcome submissions of different types of manuscripts including original research papers, reviews, and methods, including but not limited to:

1. Phylogenetic relationships of medicinal plants and relevant taxonomic groups based on molecular markers and omics big data;
2. Biosynthesis pathways of phytometabolites and their regulatory mechanisms in wild or cultivated medicinal plants, their evolutionary and ecological/geographical implications;
3. Phytochemical and metabolomic analyses of medicinal plants, with plant pharmacophylogeny consequences;
4. Association between plant physiology/pathology of specialized metabolites and their bioactivity/pharmacological activity;
5. Mining local plant resources and expanding plant chemodiversity resources in the context of pharmacophylogeny/pharmacophylogenomics;
6. Utility of genomics/epigenomics, transcriptomics, proteomics and bioinformatics in the identification/determination and analysis of medicinal plants and varieties;
7. Technical advances in all aspects of medicinal plants, e.g. predicting metabolite distribution on the phylogenetic tree, identifying low abundance phytometabolites, improving ethnobotany experiences.

Studies need to comply with the best practice guidelines of the leading journals for pharmacological studies on plant extract / natural products including the Four Pillars of Best Practice in Ethnopharmacology including a detailed description of the material studied, its extraction and processing. (you can freely download the full version here).

Disclaimer: We welcome submissions of different types of related manuscripts, but descriptive studies lacking a testable research question and which do not offer significant advances in plant biology/biochemistry, plant evolution/ecology or studies only focusing on pharmacological function but without phylogenetic framework are rejected without peer review.

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