Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses

Domingo-Fernández, Daniel; Gadiya, Yojana; Mubeen, Sarah; Bollerman, Thomas Joseph; Healy, Matthew D.; Chanana, Shaurya; Sadovsky, Rotem Gura; Healey, David; Colluru, Viswa

doi:10.1016/j.isci.2023.107729

Cited by 12 publications

(6 citation statements)

References 61 publications

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“…Natural product-derived compounds have always been considered of great importance for drug discovery [31], and ethnobotanical knowledge has often contributed to laying the basis for finding natural molecules and extracts endowed with specific bioactivity [32][33][34].…”

Section: Discussionmentioning

confidence: 99%

Exploring the Anti-Inflammatory and Antioxidant Potential, Metabolite Composition and Inorganic Profile of Cistus monspeliensis L. Aerial Parts and Roots

Mac Sweeney,

Chiocchio,

Mandrone

et al. 2024

Antioxidants

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This work focuses on Cistus monspeliensis L. aerial parts (AP) and roots (R) extracts, investigating the anti-inflammatory and antioxidant potential of the two organs in comparison. At dosages between 1.56 and 6.25 µg/mL, both extracts showed a protective effect against LPS inflammatory stimulus on a macrophage cell line (RAW 264.7). Interestingly, only R was able to significantly reduce both IL-1β and IL-6 mRNA gene expression in the presence of LPS. Moreover, the treatment of a neuroblastoma cell line (SH-SY5Y) with AP and R at 6.25 µg/mL increased the cell survival rate by nearly 20% after H2O2 insult. However, only R promoted mitochondria survival, exhibited a significantly higher production of ATP and a higher activity of the enzyme catalase than the control. Both AP and R had similar primary metabolites; in particular, they both contained 1-O-methyl-epi-inositol. Labdane and methoxylated flavonoids were the most characteristic compounds of AP, while R contained mainly catechins, gallic acid, and pyrogallol derivatives. Considering the importance of elemental composition in plants, the inorganic profile of AP and R was also investigated and compared. No potentially toxic elements, such as Pb, were detected in any sample.

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Section: Discussionmentioning

confidence: 99%

Exploring the Anti-Inflammatory and Antioxidant Potential, Metabolite Composition and Inorganic Profile of Cistus monspeliensis L. Aerial Parts and Roots

Mac Sweeney,

Chiocchio,

Mandrone

et al. 2024

Antioxidants

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“…In two out of the three in vitro toxicity studies (hepatotoxicity and CYP450), NPs appear to be less toxic compared to synthetics. One possible explanation for this observation could be the presence of ethnobotanical priors (i.e., plants with known uses in treating certain indications by specific cultures) with documented hepatoprotective properties among the set of investigated NPs. , As an example, ethnomedicinal data from Egypt cites a compound from Silybum marianum known for its effectiveness in treating liver pathologies. , Similarly, traditional Chinese medicine demonstrates the hepatoprotective activity of puerarin, a compound derived from the root of Pueraria lobata . Such historical uses of medicinal plants suggest a preselection for safety and efficacy, possibly contributing to the lower toxicity profiles observed in NP and hybrid compounds in our study.…”

Section: Discussionmentioning

confidence: 99%

Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process

Domingo-Fernández,

Gadiya,

Preto

et al. 2024

J. Nat. Prod.

Self Cite

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Natural products (NPs) or their derivatives represent a large proportion of drugs that successfully progress through clinical trials to approval. This study explores the presence of NPs in both early-and late-stage drug discovery to determine their success rate, and the factors or features of natural products that contribute to such success. As a proxy for early drug development stages, we analyzed patent applications over several decades, finding a consistent proportion of NP, NP-derived, and synthetic-compoundbased patent documents, with the latter group outnumbering NP and NPderived ones (approximately 77% vs 23%). We next assessed clinical trial data, where we observed a steady increase in NP and NP-derived compounds from clinical trial phases I to III (from approximately 35% in phase I to 45% in phase III), with an inverse trend observed in synthetics (from approximately 65% in phase I to 55% in phase III). Finally, in vitro and in silico toxicity studies revealed that NPs and their derivatives were less toxic alternatives to their synthetic counterparts. These discoveries offer valuable insights for successful NP-based drug development, highlighting the potential benefits of prioritizing NPs and their derivatives as starting points.

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“…In order to construct relevant hypergraphs and evaluate the performance of the HGHDA model, we adopt two benchmark datasets, one is collected from the TCM-suite database [ 41 ], and the other is curated from taxonomically related plants [ 42 ]. Specifically, the first benchmark dataset, namely TCM-suite, is composed of herb–component associations, component–target protein associations and target protein–disease associations collected from two sub-databases: Holmes-Suite focusing on herb ingredient identification, and Watson-Suite facilitating pharmacological network analysis.…”

Section: Methodsmentioning

confidence: 99%

“…The second benchmark dataset, Ethnobotany, is derived from a comprehensive cross-cultural analysis of traditional medicine, focusing on assessing the empirical and non-random nature of the traditional use of plants for medicinal purposes [ 42 ]. However, given that the original dataset lacks associations between diseases and target proteins, we integrate these associations from the Comparative Toxicogenomics Database [ 43 ], enabling the construction of a comprehensive hypergraph for the Ethnobotany dataset.…”

Section: Methodsmentioning

confidence: 99%

Dual-channel hypergraph convolutional network for predicting herb–disease associations

Hu,

Zhang,

et al. 2024

Briefings in Bioinformatics

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Herbs applicability in disease treatment has been verified through experiences over thousands of years. The understanding of herb–disease associations (HDAs) is yet far from complete due to the complicated mechanism inherent in multi-target and multi-component (MTMC) botanical therapeutics. Most of the existing prediction models fail to incorporate the MTMC mechanism. To overcome this problem, we propose a novel dual-channel hypergraph convolutional network, namely HGHDA, for HDA prediction. Technically, HGHDA first adopts an autoencoder to project components and target protein onto a low-dimensional latent space so as to obtain their embeddings by preserving similarity characteristics in their original feature spaces. To model the high-order relations between herbs and their components, we design a channel in HGHDA to encode a hypergraph that describes the high-order patterns of herb-component relations via hypergraph convolution. The other channel in HGHDA is also established in the same way to model the high-order relations between diseases and target proteins. The embeddings of drugs and diseases are then aggregated through our dual-channel network to obtain the prediction results with a scoring function. To evaluate the performance of HGHDA, a series of extensive experiments have been conducted on two benchmark datasets, and the results demonstrate the superiority of HGHDA over the state-of-the-art algorithms proposed for HDA prediction. Besides, our case study on Chuan Xiong and Astragalus membranaceus is a strong indicator to verify the effectiveness of HGHDA, as seven and eight out of the top 10 diseases predicted by HGHDA for Chuan-Xiong and Astragalus-membranaceus, respectively, have been reported in literature.

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Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses

Cited by 12 publications

References 61 publications

Exploring the Anti-Inflammatory and Antioxidant Potential, Metabolite Composition and Inorganic Profile of Cistus monspeliensis L. Aerial Parts and Roots

Exploring the Anti-Inflammatory and Antioxidant Potential, Metabolite Composition and Inorganic Profile of Cistus monspeliensis L. Aerial Parts and Roots

Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process

Dual-channel hypergraph convolutional network for predicting herb–disease associations

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