NPASS Compound

Structure

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

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

Natural Product: NPC173862

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference

☑ 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	NP ID	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
Others	3

Activity Type	# Activity
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT27	Others	Unspecified		Log C	=	-1.111	n.a.	PMID[502477]
NPT2	Others	Unspecified		Inhibition	<	8.0	%	PMID[502478]

☑ 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 NPC173862 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	17373
0.1-0.2	22588
0.2-0.3	2153
0.3-0.4	391
0.4-0.5	119
0.5-0.6	46
0.6-0.7	18
0.7-0.8	5
0.8-0.85	1
0.85-0.9	2
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.8571	High Similarity	NPC208021
0.8182	Intermediate Similarity	NPC8368
0.7826	Intermediate Similarity	NPC35155
0.7778	Intermediate Similarity	NPC117411
0.75	Intermediate Similarity	NPC137050
0.6957	Remote Similarity	NPC23508
0.6957	Remote Similarity	NPC2419
0.6923	Remote Similarity	NPC159398
0.6667	Remote Similarity	NPC110107
0.6522	Remote Similarity	NPC308490
0.65	Remote Similarity	NPC146289
0.64	Remote Similarity	NPC41485
0.64	Remote Similarity	NPC3693
0.64	Remote Similarity	NPC32280
0.6364	Remote Similarity	NPC37493
0.625	Remote Similarity	NPC8187
0.625	Remote Similarity	NPC30787
0.6154	Remote Similarity	NPC127134
0.6154	Remote Similarity	NPC201132
0.6154	Remote Similarity	NPC166804
0.6071	Remote Similarity	NPC312003
0.6	Remote Similarity	NPC114586
0.6	Remote Similarity	NPC184593
0.6	Remote Similarity	NPC147054
0.5926	Remote Similarity	NPC143211
0.5926	Remote Similarity	NPC248233
0.5909	Remote Similarity	NPC68873
0.5909	Remote Similarity	NPC283245
0.5909	Remote Similarity	NPC1502
0.5769	Remote Similarity	NPC28246
0.5714	Remote Similarity	NPC231957
0.5714	Remote Similarity	NPC317739
0.5714	Remote Similarity	NPC88135
0.5714	Remote Similarity	NPC316272
0.5714	Remote Similarity	NPC281943
0.5652	Remote Similarity	NPC237869
0.5652	Remote Similarity	NPC43196
0.56	Remote Similarity	NPC307812
0.56	Remote Similarity	NPC203105
0.56	Remote Similarity	NPC7459

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 NPC173862 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	6497
0.1-0.2	2083
0.2-0.3	375
0.3-0.4	140
0.4-0.5	32
0.5-0.6	19
0.6-0.7	4
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
0.6154	Remote Similarity	NPD8989	Approved
0.6	Remote Similarity	NPD47	Approved
0.6	Remote Similarity	NPD50	Approved
0.6	Remote Similarity	NPD105	Approved
0.6	Remote Similarity	NPD7363	Approved
0.6	Remote Similarity	NPD48	Approved
0.6	Remote Similarity	NPD7365	Approved
0.6	Remote Similarity	NPD7362	Approved
0.6	Remote Similarity	NPD49	Approved
0.5909	Remote Similarity	NPD7364	Approved
0.5909	Remote Similarity	NPD8200	Phase 2
0.5769	Remote Similarity	NPD8188	Approved
0.5714	Remote Similarity	NPD8547	Phase 2
0.5652	Remote Similarity	NPD7356	Approved
0.5652	Remote Similarity	NPD7357	Approved

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