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: NPC9290

*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
MIC	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT635	Organism	Botryotinia fuckeliana	Botryotinia fuckeliana	MIC	=	3.0	ug.mL-1	PMID[533891]

☑ 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 NPC9290 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	935
0.1-0.2	21333
0.2-0.3	15223
0.3-0.4	4159
0.4-0.5	858
0.5-0.6	157
0.6-0.7	29
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.7568	Intermediate Similarity	NPC122676
0.725	Intermediate Similarity	NPC147824
0.6667	Remote Similarity	NPC281043
0.6596	Remote Similarity	NPC126184
0.6512	Remote Similarity	NPC159773
0.65	Remote Similarity	NPC308418
0.6471	Remote Similarity	NPC478117
0.6458	Remote Similarity	NPC15789
0.6458	Remote Similarity	NPC236338
0.6429	Remote Similarity	NPC298413
0.64	Remote Similarity	NPC327103
0.6383	Remote Similarity	NPC90490
0.6364	Remote Similarity	NPC41409
0.6364	Remote Similarity	NPC190649
0.6304	Remote Similarity	NPC270706
0.6279	Remote Similarity	NPC250954
0.6279	Remote Similarity	NPC297608
0.625	Remote Similarity	NPC82446
0.625	Remote Similarity	NPC234084
0.6222	Remote Similarity	NPC103560
0.6222	Remote Similarity	NPC40805
0.62	Remote Similarity	NPC191643
0.617	Remote Similarity	NPC128280
0.6111	Remote Similarity	NPC189700
0.6098	Remote Similarity	NPC65353
0.6087	Remote Similarity	NPC312547
0.6087	Remote Similarity	NPC51329
0.6	Remote Similarity	NPC63354
0.6	Remote Similarity	NPC286189
0.6	Remote Similarity	NPC133600
0.6	Remote Similarity	NPC217161
0.5962	Remote Similarity	NPC218486
0.5957	Remote Similarity	NPC26600
0.5957	Remote Similarity	NPC47946
0.5918	Remote Similarity	NPC135698
0.5893	Remote Similarity	NPC130953
0.5882	Remote Similarity	NPC203105
0.5854	Remote Similarity	NPC297363
0.5854	Remote Similarity	NPC60675
0.5849	Remote Similarity	NPC173157
0.5833	Remote Similarity	NPC197467
0.5833	Remote Similarity	NPC211250
0.5789	Remote Similarity	NPC151648
0.5789	Remote Similarity	NPC217537
0.5789	Remote Similarity	NPC323552
0.5741	Remote Similarity	NPC221763
0.5741	Remote Similarity	NPC150717
0.5741	Remote Similarity	NPC230296
0.5714	Remote Similarity	NPC68577
0.5714	Remote Similarity	NPC128520
0.569	Remote Similarity	NPC44343
0.569	Remote Similarity	NPC68110
0.569	Remote Similarity	NPC210303
0.569	Remote Similarity	NPC179087
0.569	Remote Similarity	NPC473737
0.569	Remote Similarity	NPC132243
0.5682	Remote Similarity	NPC200147
0.566	Remote Similarity	NPC159535
0.566	Remote Similarity	NPC478120
0.566	Remote Similarity	NPC151761
0.5652	Remote Similarity	NPC57923
0.5636	Remote Similarity	NPC249850
0.5636	Remote Similarity	NPC135863
0.5636	Remote Similarity	NPC293437
0.5614	Remote Similarity	NPC98519
0.561	Remote Similarity	NPC224651
0.561	Remote Similarity	NPC98098
0.56	Remote Similarity	NPC223675

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 NPC9290 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1166
0.1-0.2	6357
0.2-0.3	1358
0.3-0.4	211
0.4-0.5	44
0.5-0.6	10
0.6-0.7	3
0.7-0.8	1
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
0.7941	Intermediate Similarity	NPD9114	Clinical (unspecified phase)
0.675	Remote Similarity	NPD9115	Approved
0.6279	Remote Similarity	NPD8839	Phase 3
0.5957	Remote Similarity	NPD9378	Approved
0.587	Remote Similarity	NPD9411	Phase 1
0.5686	Remote Similarity	NPD6927	Phase 3
0.561	Remote Similarity	NPD8573	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