polyphyllin H   Click here for help

GtoPdb Ligand ID: 13592

Compound class: Natural product
Comment: Polyphyllin H is a plant-derived saponin. Its chemical structure is taken from [2]. Polyphyllin H is reported as a bioactive component of the traditional Chinese herbal medicine Rhizoma Paridis (ChongLou in the Chinese Pharmacopeia) that is used to treat treat inflammation, infection, and bleeding. Studies have demonstrated a variety of Polyphyllin H-mediated pharmacological activities [1,3,5]. Most recently (2024), polyphyllin H was reported as an inhibitor of select Cytochrome P450 enzymes (CYPs) [4], behaving as a competitive inhibitor of CYPs 1A2 and 2D6 and a non-competitive inhibitor of CYP3A4. It is suggested that this mechanism may contribute to the hepatic toxicity of R. paridis extracts.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 17
Hydrogen bond donors 9
Rotatable bonds 8
Topological polar surface area 255.91
Molecular weight 871.02
XLogP 1.04
No. Lipinski's rules broken 3

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@]3([C@]([H])(C[C@@]4([H])[C@]5([H])CC=C6C[C@H](CC[C@]6(C)[C@@]5([H])CC[C@@]43C)O[C@H]7[C@@H]([C@H]([C@@H]([C@@H](CO)O7)O[C@H]8[C@@H]([C@H]([C@H](CO)O8)O)O)O)O[C@H]9[C@@H]([C@@H]([C@H]([C@H](C)O9)O)O)O)O2)O)OC1
Isomeric SMILES O[C@@]12[C@](O[C@@]3(OC[C@@H](CC3)C)[C@H]1C)([H])C[C@@]4([H])[C@@]5(CC=C6C[C@H](CC[C@]6(C)[C@@]5([H])CC[C@]24C)O[C@@H]7O[C@H](CO)[C@H]([C@@H]([C@H]7O[C@@H]8O[C@@H](C)[C@@H]([C@H]([C@H]8O)O)O)O)O[C@H]9[C@@H]([C@@H](O)[C@@H](O9)CO)O)[H]
InChI InChI=1S/C44H70O17/c1-19-8-13-43(54-18-19)21(3)44(53)29(61-43)15-26-24-7-6-22-14-23(9-11-41(22,4)25(24)10-12-42(26,44)5)56-40-37(60-38-34(51)32(49)30(47)20(2)55-38)35(52)36(28(17-46)58-40)59-39-33(50)31(48)27(16-45)57-39/h6,19-21,23-40,45-53H,7-18H2,1-5H3/t19-,20+,21-,23+,24-,25+,26+,27+,28-,29+,30+,31+,32-,33-,34-,35+,36-,37-,38+,39+,40-,41+,42+,43-,44-/m1/s1
InChI Key DEUSODBYLVUUQI-CRUCUECZSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Li J, Jia J, Zhu W, Chen J, Zheng Q, Li D. (2023)
Therapeutic effects on cancer of the active ingredients in rhizoma paridis.
Front Pharmacol, 14: 1095786. [PMID:36895945]
2. Lu W, Pan M, Zhang P, Zheng T, Huang L, Ye F, Lei P. (2020)
The Pharmacokinetics and Tissue Distributions of Nine Steroidal Saponins from Paris polyphylla in Rats.
Eur J Drug Metab Pharmacokinet, 45 (5): 665-673. [PMID:32661907]
3. Quan Q, Weng D, Li X, An Q, Yang Y, Yu B, Ma Y, Wang J. (2022)
Analysis of drug efficacy for inflammatory skin on an organ-chip system.
Front Bioeng Biotechnol, 10: 939629. [PMID:36118585]
4. Wang E, Wang M, Gao M. (2024)
Probe substrates assay estimates the effect of polyphyllin H on the activity of cytochrome P450 enzymes in human liver microsomes.
Pharmacol Res Perspect, 12 (5): e70002. [PMID:39210686]
5. Yang Y, Wang C, Wang J, Yang L, Lv Z, An Q, Wang Y, Shao X, Wang F, Huo T et al.. (2024)
Rhizoma Paridis saponins attenuate Gram-negative bacteria-induced inflammatory acne by binding to KEAP1 and modulating Nrf2 and MAPK pathways.
J Cell Mol Med, 28 (6): e18146. [PMID:38426932]