NPASS Compound

Natural Product: NPC579002

Natural Product ID	NPC579002
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	veprisiniol
IUPAC Name	5-hydroxy-2-(3-hydroxy-4-methoxy-phenyl)-7-(4-hydroxy-3-methyl-butoxy)chroman-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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

Chemical Representations

RDKit 3D 52 54 0 0 0 0 0 0 0 0999 V2000 -7.4429 -3.0726 1.0669 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3826 -1.6859 0.9626 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1925 -1.0621 0.6256 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0643 -1.8190 0.3929 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8704 -1.2205 0.0566 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7955 0.1688 -0.0515 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5333 0.8509 -0.4121 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6705 2.3078 -0.0239 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3651 2.9797 0.0860 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3330 4.2337 0.1209 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0995 2.2611 0.1570 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1227 2.8993 0.1098 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1734 4.2727 -0.0092 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2545 2.1559 0.1820 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2277 0.7894 0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3980 0.0492 0.3727 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6230 0.7463 0.3204 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8074 -0.1912 0.4099 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8346 -1.1954 -0.7126 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5926 -2.0301 -0.6834 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0962 -2.0125 -0.5711 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1716 -2.6920 0.6238 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9770 0.1690 0.3459 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1952 0.8842 0.2759 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4514 0.2844 0.3195 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9324 0.8903 0.1855 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1540 0.3152 0.5273 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3018 1.0469 0.7664 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1222 -3.5523 0.1243 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4951 -3.3569 1.3411 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7317 -3.3796 1.8785 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0740 -2.9021 0.4651 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9626 -1.7925 -0.1329 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3398 0.7188 -1.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3358 2.7988 -0.7752 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1574 2.3137 0.9820 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8920 4.7936 -0.8146 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2086 2.6977 0.1414 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6980 1.4781 1.1322 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7390 1.3114 -0.6372 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7642 0.3625 0.4812 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7382 -0.7806 1.3649 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8785 -0.6812 -1.6943 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7730 -1.5675 -1.2887 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1848 -2.1537 0.3401 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7353 -3.0517 -1.0939 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2384 -2.6769 -1.4593 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9497 -1.2879 -0.6153 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3486 -2.7156 1.1460 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9297 -0.9168 0.4399 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9724 1.9902 0.1240 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3811 2.0269 0.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 15 23 1 0 23 24 2 0 24 25 1 0 6 26 1 0 26 27 2 0 27 28 1 0 27 3 1 0 25 7 1 0 24 11 1 0 1 29 1 0 1 30 1 0 1 31 1 0 4 32 1 0 5 33 1 0 7 34 1 0 8 35 1 0 8 36 1 0 13 37 1 0 14 38 1 0 17 39 1 0 17 40 1 0 18 41 1 0 18 42 1 0 19 43 1 0 20 44 1 0 20 45 1 0 20 46 1 0 21 47 1 0 21 48 1 0 22 49 1 0 23 50 1 0 26 51 1 0 28 52 1 0 M END

Standard InCHIKey	ZCDWJCSNVHLSHS-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C21H24O7/c1-12(11-22)5-6-27-14-8-16(24)21-17(25)10-19(28-20(21)9-14)13-3-4-18(26-2)15(23)7-13/h3-4,7-9,12,19,22-24H,5-6,10-11H2,1-2H3
SMILES	COC1=CC=C(C2CC(=O)C3=C(O)C=C(OCCC(C)CO)C=C3O2)C=C1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	388.15	Volume:	389.179 ? Van der Waals volume.
Dense:	0.997	LogP:	2.818 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.815 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.416 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	18.0
TPSA:	105.45 ? Topological Polar Surface Area.	H-Bond Acceptor:	7.0
H-Bond Donor:	3.0	Rings:	3.0
Heavy Atoms:	7.0

MedChem Properties

QED Drug-Likeness Score:	0.669	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.353	Fsp³:	0.381
MCE-18:	59.621 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	1
Chelating Alert:	1	PAINS Alert:	0
Colloidal aggregators:	0.496	Fluc inhibitor:	0.603 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.228 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.519 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.07	Promiscuous compounds:	0.104

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.966	MDCK Permeability:	-4.754
Pgp-inhibitor:	0.945	Pgp-substrate:	0.051
PAMPA:	0.353 ? 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):	0.146
20% Bioavailability (F20%):	0.014	30% Bioavailability (F30%):	0.728
50% Bioavailability (F50%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.83
Plasma Protein Binding (PPB):	96.634%	Volume Distribution (VD):	-0.108
Fu:	2.558% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.99
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.994
BSEP inhibitor:	0.916

ADMET: Metabolism

CYP1A2-inhibitor:	0.979	CYP1A2-substrate:	0.99
CYP2C19-inhibitor:	0.093	CYP2C19-substrate:	0.909
CYP2C9-inhibitor:	0.996	CYP2C9-substrate:	0.08
CYP2D6-inhibitor:	0.947	CYP2D6-substrate:	0.985
CYP3A4-inhibitor:	0.029	CYP3A4-substrate:	0.994
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.933
HLM stability:	0.98 ? 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):

5.88

Half-life (T1/2):

1.58

ADMET: Toxicity

hERG Blockers:	0.156	hERG Blockers (10um):	0.496
Human Hepatotoxicity (H-HT):	0.737	Drug-induced Liver Injury (DILI):	0.811
AMES Toxicity:	0.546	Rat Oral Acute Toxicity:	0.375
Maximum Recommended Daily Dose:	0.337	Skin Sensitization:	0.564
Carcinogencity:	0.736	Eye Corrosion:	0.0
Eye Irritation:	0.75	Respiratory Toxicity:	0.663
Drug-induced Neurotoxicity:	0.214	Ototoxicity:	0.589
Hematotoxicity:	0.329	Drug-induced Nephrotoxicity:	0.5
Genotoxicity:	0.553	RPMI-8226 Immunitoxicity:	0.19
A549 Cytotoxicity:	0.508	Hek293 Cytotoxicity:	0.7
BCF:	0.925 ? 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:	3.515 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.062 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.172 ? 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
NPO50458	Vepris glomerata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC579002 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	17113
0.1-0.2	28458
0.2-0.3	3797
0.3-0.4	400
0.4-0.5	74
0.5-0.6	15
0.6-0.7	1
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
0.7458	Intermediate Similarity	NPC18727
0.6	Remote Similarity	NPC302950
0.5968	Remote Similarity	NPC6407
0.5968	Remote Similarity	NPC545184
0.5846	Remote Similarity	NPC48208
0.5634	Remote Similarity	NPC480158
0.5625	Remote Similarity	NPC150648
0.5581	Remote Similarity	NPC105095
0.5581	Remote Similarity	NPC177731
0.5581	Remote Similarity	NPC725
0.5538	Remote Similarity	NPC73028
0.5538	Remote Similarity	NPC329203
0.5538	Remote Similarity	NPC222342
0.5465	Remote Similarity	NPC44328
0.5465	Remote Similarity	NPC79056
0.5278	Remote Similarity	NPC477840
0.5156	Remote Similarity	NPC140890

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC579002 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3288
0.1-0.2	5642
0.2-0.3	212
0.3-0.4	4
0.4-0.5	2
0.5-0.6	1
0.6-0.7	1
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
0.6	Remote Similarity	NPD1934	Phase 0
0.5465	Remote Similarity	NPD7074	Phase 3

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