NPASS Compound

Structure

CID243528 OpenBabel06191716042D 29 31 0 0 0 0 0 0 0 0999 V2000 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 15 1 0 0 0 0 2 29 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 4 8 1 0 0 0 0 5 9 2 0 0 0 0 6 7 2 0 0 0 0 6 10 1 0 0 0 0 7 11 1 0 0 0 0 8 16 2 0 0 0 0 9 16 1 0 0 0 0 10 17 2 0 0 0 0 11 19 2 0 0 0 0 12 13 1 0 0 0 0 12 16 1 0 0 0 0 13 20 1 0 0 0 0 14 17 1 0 0 0 0 14 18 1 0 0 0 0 15 22 2 0 0 0 0 15 24 1 0 0 0 0 17 19 1 0 0 0 0 18 22 1 0 0 0 0 18 23 2 0 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 20 26 2 0 0 0 0 21 23 1 0 0 0 0 21 24 2 0 0 0 0 22 27 1 0 0 0 0 23 28 1 0 0 0 0 24 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	392.16
Volume:	415.577
LogP:	4.898
LogD:	3.45
LogS:	-4.503
# Rotatable Bonds:	7
TPSA:	86.99
# H-Bond Aceptor:	5
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.515
Synthetic Accessibility Score:	2.428
Fsp3:	0.208
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.064
MDCK Permeability:	2.676424992387183e-05
Pgp-inhibitor:	0.309
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.818
30% Bioavailability (F30%):	0.233

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022
Plasma Protein Binding (PPB):	99.95012664794922%
Volume Distribution (VD):	0.439
Pgp-substrate:	0.8692669868469238%

ADMET: Metabolism

CYP1A2-inhibitor:	0.677
CYP1A2-substrate:	0.839
CYP2C19-inhibitor:	0.922
CYP2C19-substrate:	0.131
CYP2C9-inhibitor:	0.867
CYP2C9-substrate:	0.909
CYP2D6-inhibitor:	0.635
CYP2D6-substrate:	0.615
CYP3A4-inhibitor:	0.492
CYP3A4-substrate:	0.51

ADMET: Excretion

Clearance (CL):	10.322
Half-life (T1/2):	0.748

ADMET: Toxicity

hERG Blockers:	0.075
Human Hepatotoxicity (H-HT):	0.121
Drug-inuced Liver Injury (DILI):	0.698
AMES Toxicity:	0.13
Rat Oral Acute Toxicity:	0.3
Maximum Recommended Daily Dose:	0.051
Skin Sensitization:	0.941
Carcinogencity:	0.099
Eye Corrosion:	0.003
Eye Irritation:	0.898
Respiratory Toxicity:	0.028

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC243528

Natural Product ID:	NPC243528
*Common Name:**	Anguvetin
IUPAC Name:	1-[2,4-dihydroxy-3-[(2-hydroxyphenyl)methyl]-6-methoxy-5-methylphenyl]-3-phenylpropan-1-one
Synonyms:	Anguvetin
Standard InCHIKey:	AJLNIEILVUYJPG-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C24H24O5/c1-15-22(27)18(14-17-10-6-7-11-19(17)25)23(28)21(24(15)29-2)20(26)13-12-16-8-4-3-5-9-16/h3-11,25,27-28H,12-14H2,1-2H3
SMILES:	COc1c(C(=O)CCc2ccccc2)c(O)c(c(c1C)O)Cc1ccccc1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL452756
PubChem CID:	158308
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO8708	Vibrio cholerae	Species	Vibrionaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12116	Anabasis brevifolia	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18174	Rinodina lepida	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15901	Pentanema indicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17722	Athroisma gracile	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
Others	3

Activity Type	# Activity
Organism	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	Activity	=	1.5	ug ml-1	PMID[505586]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	Activity	=	0.2	ug ml-1	PMID[505586]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	Activity	=	1.5	ug ml-1	PMID[505586]

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC243528 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	358
0.1-0.2	1650
0.2-0.3	4124
0.3-0.4	11390
0.4-0.5	6739
0.5-0.6	3902
0.6-0.7	5874
0.7-0.8	5184
0.8-0.85	1997
0.85-0.9	944
0.9-0.95	489
0.95-1	46

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC251681
0.9778	High Similarity	NPC26238
0.9773	High Similarity	NPC13575
0.9699	High Similarity	NPC186838
0.9699	High Similarity	NPC1486

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC243528 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	339
0.1-0.2	973
0.2-0.3	1408
0.3-0.4	2671
0.4-0.5	1913
0.5-0.6	1235
0.6-0.7	425
0.7-0.8	132
0.8-0.85	37
0.85-0.9	10
0.9-0.95	7
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9323	High Similarity	NPD1240	Approved
0.9286	High Similarity	NPD4378	Clinical (unspecified phase)
0.9286	High Similarity	NPD7410	Clinical (unspecified phase)
0.9191	High Similarity	NPD1510	Phase 2
0.9185	High Similarity	NPD1607	Approved

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Bioactivity similarity: Similar Natural Products in NPASS

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