NPASS Compound

Natural Product: NPC252572

Natural Product ID	NPC252572
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5H-Indolo[3,2-B]Quinolin-11(10H)-One
IUPAC Name	5,10-dihydroindolo[3,2-b]quinolin-11-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1256564
PubChem CID	337827
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001253] Quinolines and derivatives [CHEMONTID:0000061] Indoloquinolines

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 28 31 0 0 0 0 0 0 0 0999 V2000 1.4125 -2.8190 -0.3493 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1259 -1.5858 -0.1998 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1577 -0.6705 -0.0523 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4863 -1.0997 -0.0683 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4773 -0.1539 0.0819 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1900 1.1835 0.2447 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8808 1.6046 0.2602 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8700 0.6660 0.1104 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5665 1.0386 0.1199 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.4519 0.1761 -0.0204 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1880 -1.1691 -0.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3724 -1.8323 -0.3047 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.3948 -0.9660 -0.2237 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8301 0.2898 -0.0463 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6362 1.3938 0.0714 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0172 1.3131 0.0206 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5688 0.0494 -0.1575 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7521 -1.0545 -0.2749 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7253 -2.1518 -0.1960 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5373 -0.4371 0.0767 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0033 1.9170 0.3625 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6138 2.6291 0.3836 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3683 2.0551 0.2442 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4633 -2.8653 -0.4396 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2330 2.3969 0.2117 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6591 2.1779 0.1125 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6422 -0.0637 -0.2034 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2060 -2.0221 -0.4121 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 11 2 1 0 18 13 1 0 8 3 1 0 14 10 1 0 4 19 1 0 5 20 1 0 6 21 1 0 7 22 1 0 9 23 1 0 12 24 1 0 15 25 1 0 16 26 1 0 17 27 1 0 18 28 1 0 M END

Standard InCHIKey	AETJISOJRRTLLJ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H10N2O/c18-15-10-6-2-4-8-12(10)16-13-9-5-1-3-7-11(9)17-14(13)15/h1-8,17H,(H,16,18)
SMILES	O=c1c2ccccc2[nH]c2c1[nH]c1c2cccc1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	234.08	Volume:	243.462 ? Van der Waals volume.
Dense:	0.961	LogP:	2.724 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.375 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.849 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	0.0	Rigid Bonds:	21.0
TPSA:	48.65 ? Topological Polar Surface Area.	H-Bond Acceptor:	3.0
H-Bond Donor:	2.0	Rings:	4.0
Heavy Atoms:	3.0

MedChem Properties

QED Drug-Likeness Score:	0.482	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.077	Fsp³:	0.0
MCE-18:	19.0 ? 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:	0.582	Fluc inhibitor:	0.901 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.931 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.543 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.321	Promiscuous compounds:	0.979

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.002	MDCK Permeability:	-4.646
Pgp-inhibitor:	0.834	Pgp-substrate:	0.008
PAMPA:	0.349 ? 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):	0.007
20% Bioavailability (F20%):	0.004	30% Bioavailability (F30%):	0.132
50% Bioavailability (F50%):	0.386

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.148	MRP1:	0.284
Plasma Protein Binding (PPB):	96.661%	Volume Distribution (VD):	0.072
Fu:	4.016% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.974
OATP1B3 inhibitor:	0.998	BCRP inhibitor:	0.316
BSEP inhibitor:	0.992

ADMET: Metabolism

CYP1A2-inhibitor:	0.996	CYP1A2-substrate:	0.02
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.023
CYP2C9-inhibitor:	0.055	CYP2C9-substrate:	0.116
CYP2D6-inhibitor:	0.003	CYP2D6-substrate:	0.092
CYP3A4-inhibitor:	0.034	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.786 ? 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):

7.476

Half-life (T1/2):

1.278

ADMET: Toxicity

hERG Blockers:	0.291	hERG Blockers (10um):	0.624
Human Hepatotoxicity (H-HT):	0.659	Drug-induced Liver Injury (DILI):	0.768
AMES Toxicity:	0.787	Rat Oral Acute Toxicity:	0.702
Maximum Recommended Daily Dose:	0.673	Skin Sensitization:	0.589
Carcinogencity:	0.712	Eye Corrosion:	0.012
Eye Irritation:	0.981	Respiratory Toxicity:	0.916
Drug-induced Neurotoxicity:	0.792	Ototoxicity:	0.418
Hematotoxicity:	0.521	Drug-induced Nephrotoxicity:	0.76
Genotoxicity:	0.683	RPMI-8226 Immunitoxicity:	0.07
A549 Cytotoxicity:	0.33	Hek293 Cytotoxicity:	0.496
BCF:	1.472 ? 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:	4.296 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.278 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.306 ? 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
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	PMID[14640526]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	depth of 25 m off the shore of Keomun Island, Korea	2004-AUG	PMID[18407691]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2853205]
NPO20169	Alseodaphne perakensis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31266357]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32998509]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20912	Wisteria brachybotrys	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14826	Streptomyces mobaraensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO20169	Alseodaphne perakensis	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20989	Calea integrifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11155	Ambrosia maritima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24783	Erysimum diffusum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20237	Poecillastra wondoensis	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21890	Epidendrum moseni	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18755	Fumaria judaica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20299	Strongylophora durissima	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO17131	Yucca periculosa	Species	Asparagaceae	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	1

Activity Type	# Activity
Organism	1

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
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	10000.0	nM	PMID[20801652]

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 NPC252572 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	46633
0.1-0.2	2771
0.2-0.3	430
0.3-0.4	23
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	Natural Product ID
		NPC

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC252572 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8518
0.1-0.2	604
0.2-0.3	27
0.3-0.4	1
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