NPASS Compound

Natural Product: NPC252015

Natural Product ID	NPC252015
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ARSZFSLDAVWWJY-OKMFKZBXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	71448934
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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Standard InCHIKey	ARSZFSLDAVWWJY-OKMFKZBXSA-N
Standard InCHI	InChI=1S/C81H122O39/c1-31-46(87)51(92)56(97)68(107-31)116-63-60(101)72(109-33(3)61(63)115-67-55(96)50(91)42(29-106-67)113-70-58(99)53(94)48(89)40(27-82)111-70)118-65-64(117-69-57(98)52(93)47(88)32(2)108-69)62(114-45(86)18-13-35-11-14-36(105-10)15-12-35)34(4)110-73(65)120-75(104)80-22-21-76(5,6)25-38(80)37-16-17-43-77(7)26-39(85)66(119-71-59(100)54(95)49(90)41(28-83)112-71)79(9,74(102)103)44(77)19-20-78(43,8)81(37,30-84)24-23-80/h11-16,18,31-34,38-44,46-73,82-85,87-101H,17,19-30H2,1-10H3,(H,102,103)/b18-13+/t31-,32-,33-,34+,38-,39-,40+,41+,42+,43+,44+,46-,47-,48-,49+,50-,51+,52+,53-,54-,55+,56+,57+,58+,59+,60+,61-,62-,63-,64-,65+,66-,67-,68-,69-,70-,71-,72-,73-,77+,78+,79-,80-,81-/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@H]1[C@H]([C@@H](O[C@@H](C)[C@@H]1O[C@H]1[C@@H]([C@H]([C@@H](CO1)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O)O)O[C@@H]1[C@H]([C@H]([C@@H](C)O[C@H]1OC(=O)[C@@]12CCC(C)(C)C[C@H]2C2=CC[C@@H]3[C@@]4(C)C[C@@H]([C@@H]([C@](C)([C@@H]4CC[C@@]3(C)[C@@]2(CC1)CO)C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)OC(=O)/C=C/c1ccc(cc1)OC)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1718.76	Volume:	1620.024 ? Van der Waals volume.
Dense:	1.061	LogP:	-0.916 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.71 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.817 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	24.0	Rigid Bonds:	78.0
TPSA:	603.49 ? Topological Polar Surface Area.	H-Bond Acceptor:	39.0
H-Bond Donor:	20.0	Rings:	13.0
Heavy Atoms:	39.0

MedChem Properties

QED Drug-Likeness Score:	0.023	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.71	Fsp³:	0.84
MCE-18:	381.302 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.734	Fluc inhibitor:	0.321 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.061 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.132 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.355	Promiscuous compounds:	0.176

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-7.122	MDCK Permeability:	-4.898
Pgp-inhibitor:	0.0	Pgp-substrate:	0.859
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.986
20% Bioavailability (F20%):	0.919	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	64.955%	Volume Distribution (VD):	-0.234
Fu:	18.576% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

-1.587

Half-life (T1/2):

5.324

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.53	Drug-induced Liver Injury (DILI):	0.984
AMES Toxicity:	0.999	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.964	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	0.015	RPMI-8226 Immunitoxicity:	0.687
A549 Cytotoxicity:	0.996	Hek293 Cytotoxicity:	0.506
BCF:	0.324 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.51 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.566 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.425 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	roots	n.a.	n.a.	PMID[16989524]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[22863942]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	aerial parts	n.a.	n.a.	PMID[24042007]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[38838926]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21485	Polygala sibirica	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27260	Polygala tenuifolia	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC252015 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	14644
0.1-0.2	30549
0.2-0.3	3722
0.3-0.4	802
0.4-0.5	122
0.5-0.6	15
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.6275	Remote Similarity	NPC478822
0.6242	Remote Similarity	NPC478823
0.6138	Remote Similarity	NPC487505
0.6122	Remote Similarity	NPC484942
0.5921	Remote Similarity	NPC478824
0.5767	Remote Similarity	NPC485564
0.5742	Remote Similarity	NPC478825
0.5329	Remote Similarity	NPC124828
0.5167	Remote Similarity	NPC469777
0.5141	Remote Similarity	NPC469774
0.5112	Remote Similarity	NPC469778
0.5082	Remote Similarity	NPC469772
0.5064	Remote Similarity	NPC484943
0.5057	Remote Similarity	NPC469775
0.5056	Remote Similarity	NPC32723
0.5056	Remote Similarity	NPC100925
0.5028	Remote Similarity	NPC481323
0.5028	Remote Similarity	NPC481324
0.5027	Remote Similarity	NPC469773

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC252015 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4826
0.1-0.2	4272
0.2-0.3	50
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data