NPASS Compound

Structure

NPC165159 OpenBabel06302215122D 30 33 0 0 1 0 0 0 0 0999 V2000 -3.8895 -1.1602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1986 -0.2092 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5294 0.5340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5513 0.3260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8821 1.0692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1912 2.0202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 2.2282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8384 1.4850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8166 1.6929 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4783 3.1792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4565 3.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9040 0.8613 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4973 -0.0523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7052 -1.0304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1609 -1.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9040 -0.8613 0.0000 C 0 0 3 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 -1.7321 -0.0000 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 -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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 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 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3412 0.8309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4973 0.0523 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7052 1.0304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1609 1.5304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 12 5 1 1 0 0 0 12 13 1 0 0 0 0 12 30 1 0 0 0 0 13 14 1 6 0 0 0 13 28 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 26 1 0 0 0 0 20 21 2 0 0 0 0 20 25 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 26 27 1 0 0 0 0 28 29 1 6 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	504.27
Volume:	521.678
LogP:	3.063
LogD:	2.032
LogS:	-4.157
# Rotatable Bonds:	8
TPSA:	105.2
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.314
Synthetic Accessibility Score:	5.47
Fsp3:	0.714
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.996
MDCK Permeability:	0.00010173242480959743
Pgp-inhibitor:	0.997
Pgp-substrate:	0.961
Human Intestinal Absorption (HIA):	0.7
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.707

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.326
Plasma Protein Binding (PPB):	81.49500274658203%
Volume Distribution (VD):	2.099
Pgp-substrate:	16.076866149902344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.02
CYP1A2-substrate:	0.029
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.236
CYP2C9-inhibitor:	0.159
CYP2C9-substrate:	0.122
CYP2D6-inhibitor:	0.113
CYP2D6-substrate:	0.205
CYP3A4-inhibitor:	0.458
CYP3A4-substrate:	0.435

ADMET: Excretion

Clearance (CL):	3.235
Half-life (T1/2):	0.031

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.967
Drug-inuced Liver Injury (DILI):	0.901
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.045
Maximum Recommended Daily Dose:	0.765
Skin Sensitization:	0.019
Carcinogencity:	0.047
Eye Corrosion:	0.004
Eye Irritation:	0.036
Respiratory Toxicity:	0.768

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

Natural Product: NPC165159

Natural Product ID:	NPC165159
*Common Name:**	KOWMJRJXZMEZLD-VGBAVMOLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KOWMJRJXZMEZLD-VGBAVMOLSA-N
Standard InCHI:	InChI=1S/C22H26O8/c1-25-15-5-11(6-16(26-2)19(15)23)21-13-9-30-22(14(13)10-29-21)12-7-17(27-3)20(24)18(8-12)28-4/h5-8,13-14,21-24H,9-10H2,1-4H3/t13-,14-,21+,22?/m0/s1
SMILES:	COc1cc(cc(c1O)OC)[C@@H]1[C@H]2COC(c3cc(c(c(c3)OC)O)OC)[C@H]2CO1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	332426
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans

*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
NPO12181	Albizia julibrissin	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9051910]
NPO10969	Epimedium sagittatum	Species	Berberidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[8699184]
NPO12773	Stephania tetrandra	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3728032]
NPO25825	Saussurea lappa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572418]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO4554	Isatis tinctoria	Species	Brassicaceae	Eukaryota	Roots	n.a.	n.a.	PMID[32004936]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO865	Dendrobium loddigesii	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31291099]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO22258	Chrysanthemum indicum	Species	Asteraceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[30726671]

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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
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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC165159 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	423
0.1-0.2	1363
0.2-0.3	4042
0.3-0.4	11085
0.4-0.5	7946
0.5-0.6	5196
0.6-0.7	8729
0.7-0.8	2754
0.8-0.85	777
0.85-0.9	300
0.9-0.95	67
0.95-1	15

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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 NPC165159 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	328
0.1-0.2	811
0.2-0.3	1899
0.3-0.4	2884
0.4-0.5	1696
0.5-0.6	1004
0.6-0.7	460
0.7-0.8	61
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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