Additional file 1 of Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions
Creators: name: Domingo-Fernández, Daniel
name: Gadiya, Yojana
name: Mubeen, Sarah
name: Healey, David
name: Norman, Bryan H.
name: Colluru, Viswa
Publisher: name: figshare
Year: 2024
Subjects: subject: Organic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Comparison of the original Newman dataset and the dataset used in this work after normalization and filtering. Table S2. List of plants containing phytochemicals that are now approved-drugs. The last column indicates whether the plant is considered a medicinal plant (e.g., has been traditionally used to treat indications). Figure S1. Number of species (plants) and their corresponding genera and families after each filtering step for the showcase of the chemotaxonomy. Figure S2. A) Correlation between the observed chemicals specific to the family against the expected chemicals specific to the same family, corrected by the total number of species in the family. B) Correlation between the observed number of medicinal plants found in the family against the expected number of medicinal plants belonging to the same family, corrected by the total number of species in the family. C) Correlation between the observed number of chemicals found in the family against the expected number of chemicals belonging to the same family, corrected by the total number of species in the family. The y-axis range is set to 1,000, although a few families have over 2,000 chemicals. Figure S3. A) Proportion of plant-specific compounds present in the NP approved-drugs curated by Newman and Cragg [2]. B) Overlap of the matching phytochemicals of the two datasets: Newman and Cragg [2] and Wishart et al. [24]. C) Number of plant-specific compounds present in the dataset curated by Wishart et al. [24]. D) Number of plant-specific compounds present in the FDA orange book. Figure 4. t-SNE of the relative abundance of the chemical classes from NP-classifier. Figure S5. Distribution of four chemical properties between ChEMBL compounds (version 32) and all phytochemicals in medicinal and non-medicinal plants used in our work. A) Distribution of the molecular weights (MW), B) Distribution of the LogP. C) Distribution of the topological polar surface area (TPSA) D) Distribution of the fraction of sp3 hybridized carbon atoms (Fsp3). Figure S6. Comparison of the log distributions of NP approved drugs versus phytochemicals and their corresponding bioassays over time. The plots highlight a decline in NP approved drugs around the late 1980s. At the same time, the plots indicate an increase in the number of phytochemicals being tested for bioactivity, especially in the last 15 years. Figure S7. Distribution of the number of bioactive compounds in medicinal (inner circle) and non-medicinal (outer circle) plants across plant families. Due to a few families having a disproportionately large number of bioactive compounds compared to the rest, we set their values to white any family with more than 150 bioactive compounds in both medicinal and non-medicinal plants to able to spot easier the differences between the two groups for the rest with a smaller range in the color palette (intensity). Figure S8. Distribution of the number of observed and expected bioactive compounds across the plant families with the highest expected values. The expected number of bioactive compounds is calculated by multiplying the average number of bioactive compounds per plant by the number of species in a family. The plot shows that a very low percentage of bioactive compounds have been identified in plant families such as Asreraceae and Fabaceae, unlike Pinaceae where the number of bioactive compounds identified is relatively similar to the number expected for this plant family. Figure S9. Overlap between the DrugBank, FDA orange book and Newman and Cragg datasets.