NPASS Compound

Natural Product: NPC131766

Natural Product ID	NPC131766
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3,8-Dihydroxybenzo[C]Chromen-6-One
IUPAC Name	3,8-dihydroxybenzo[c]chromen-6-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1836264
PubChem CID	5488186
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives

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 25 27 0 0 0 0 0 0 0 0999 V2000 4.8049 0.2514 0.7517 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4203 0.2071 0.5948 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6124 0.5887 1.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2254 0.5410 1.4647 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7194 0.1163 0.2768 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5323 -0.2744 -0.7844 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9019 -0.2209 -0.6026 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0375 -0.6849 -1.9328 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2535 -0.7349 -2.1033 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7638 -1.1283 -3.2045 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1472 -0.3721 -1.1210 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6740 0.0706 0.1157 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5343 0.4397 1.1161 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8921 0.3765 0.9077 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3552 -0.0561 -0.3012 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5109 -0.4308 -1.3174 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7302 -0.1383 -0.5627 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4420 -0.1013 0.0515 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0640 0.9204 2.5600 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6474 0.8487 2.3020 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5613 -0.5248 -1.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2018 0.7749 2.0520 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6243 0.6553 1.6612 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8566 -0.7760 -2.2812 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4249 0.0068 0.1532 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 15 17 1 0 7 2 1 0 16 11 1 0 12 5 1 0 1 18 1 0 3 19 1 0 4 20 1 0 7 21 1 0 13 22 1 0 14 23 1 0 16 24 1 0 17 25 1 0 M END

Standard InCHIKey	RIUPLDUFZCXCHM-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C13H8O4/c14-7-1-3-9-10-4-2-8(15)6-12(10)17-13(16)11(9)5-7/h1-6,14-15H
SMILES	Oc1ccc2c(c1)oc(=O)c1c2ccc(c1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	228.04	Volume:	224.441 ? Van der Waals volume.
Dense:	1.016	LogP:	2.309 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.429 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.156 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	17.0
TPSA:	70.67 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	3.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.457	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.123	Fsp³:	0.0
MCE-18:	16.0 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.645	Fluc inhibitor:	0.624 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.924 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.457 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.867	Promiscuous compounds:	0.666

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.987	MDCK Permeability:	-4.748
Pgp-inhibitor:	0.001	Pgp-substrate:	0.039
PAMPA:	0.927 ? 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):	0.002
20% Bioavailability (F20%):	0.422	30% Bioavailability (F30%):	0.234
50% Bioavailability (F50%):	0.322

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	0.983
Plasma Protein Binding (PPB):	84.799%	Volume Distribution (VD):	-0.285
Fu:	18.405% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.061
OATP1B3 inhibitor:	0.042	BCRP inhibitor:	0.002
BSEP inhibitor:	0.362

ADMET: Metabolism

CYP1A2-inhibitor:	0.312	CYP1A2-substrate:	0.01
CYP2C19-inhibitor:	0.168	CYP2C19-substrate:	0.333
CYP2C9-inhibitor:	0.967	CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.983	CYP2D6-substrate:	0.031
CYP3A4-inhibitor:	0.175	CYP3A4-substrate:	0.008
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.998
HLM stability:	0.622 ? 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):

6.848

Half-life (T1/2):

1.161

ADMET: Toxicity

hERG Blockers:	0.102	hERG Blockers (10um):	0.426
Human Hepatotoxicity (H-HT):	0.495	Drug-induced Liver Injury (DILI):	0.651
AMES Toxicity:	0.629	Rat Oral Acute Toxicity:	0.498
Maximum Recommended Daily Dose:	0.726	Skin Sensitization:	0.658
Carcinogencity:	0.864	Eye Corrosion:	0.654
Eye Irritation:	0.997	Respiratory Toxicity:	0.653
Drug-induced Neurotoxicity:	0.139	Ototoxicity:	0.145
Hematotoxicity:	0.09	Drug-induced Nephrotoxicity:	0.041
Genotoxicity:	0.909	RPMI-8226 Immunitoxicity:	0.039
A549 Cytotoxicity:	0.124	Hek293 Cytotoxicity:	0.636
BCF:	1.124 ? 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:	3.676 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.394 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.002 ? 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
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1007/s00217-007-0799-1]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1016/j.foodchem.2011.01.077]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520216]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15620261]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[36560643]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39138188]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39527985]
NPO10597	Fructus syzygii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Twig	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Stem Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Root Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO10597	Fructus syzygii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO10597	Fructus syzygii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21349	Punica granatum	Species	Lythraceae	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

Activity Type	# Activity
IC50	2
Activity	7

Activity Type	# Activity
Organism	9

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
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	20000.0	nM	DOI[10.6019/CHEMBL4651402]
NPT20555	Organism	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	IC50	>	19952.62	nM	DOI[10.6019/CHEMBL4651402]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	35.0	%	PMID[21843938]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	26.0	%	PMID[21843938]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	34.0	%	PMID[21843938]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	142.0	%	PMID[21843938]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	118.0	%	PMID[21843938]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	42.7	%	PMID[35489224]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	30.8	%	PMID[35489224]

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 NPC131766 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	38613
0.1-0.2	10210
0.2-0.3	945
0.3-0.4	79
0.4-0.5	9
0.5-0.6	1
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	Natural Product ID
0.775	Intermediate Similarity	NPC254994
0.5208	Remote Similarity	NPC41326

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC131766 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7438
0.1-0.2	1672
0.2-0.3	38
0.3-0.4	1
0.4-0.5	1
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