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: NPC223893

*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
IC50	4

Activity Type	# Activity
Individual Protein	1
Others	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT5276	Individual Protein	Mannosyl-oligosaccharide alpha-1,2-mannosidase isoform B	Drosophila melanogaster	IC50	=	150.0	nM	PMID[476393]
NPT2	Others	Unspecified		IC50	=	240.0	nM	PMID[476391]
NPT2	Others	Unspecified		IC50	=	350.0	nM	PMID[476392]
NPT2	Others	Unspecified		IC50	=	3000.0	nM	PMID[476393]

☑ 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 NPC223893 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	711
0.1-0.2	27932
0.2-0.3	12489
0.3-0.4	1242
0.4-0.5	222
0.5-0.6	83
0.6-0.7	17
0.7-0.8	0
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
0.6197	Remote Similarity	NPC65832
0.6197	Remote Similarity	NPC10262
0.6197	Remote Similarity	NPC311668
0.6081	Remote Similarity	NPC30126
0.6081	Remote Similarity	NPC474014
0.6081	Remote Similarity	NPC57846
0.5972	Remote Similarity	NPC8979
0.589	Remote Similarity	NPC204709
0.5867	Remote Similarity	NPC8087
0.5867	Remote Similarity	NPC62507
0.5844	Remote Similarity	NPC474928
0.5811	Remote Similarity	NPC193593
0.5811	Remote Similarity	NPC76726
0.5811	Remote Similarity	NPC290106
0.5811	Remote Similarity	NPC143809
0.5789	Remote Similarity	NPC150680
0.5789	Remote Similarity	NPC306462
0.5789	Remote Similarity	NPC69669
0.5789	Remote Similarity	NPC22774
0.5789	Remote Similarity	NPC2432
0.5789	Remote Similarity	NPC218150
0.5775	Remote Similarity	NPC272396
0.5769	Remote Similarity	NPC69798
0.5769	Remote Similarity	NPC473952
0.5769	Remote Similarity	NPC77191
0.5769	Remote Similarity	NPC315980
0.5769	Remote Similarity	NPC116377
0.5769	Remote Similarity	NPC303798
0.5769	Remote Similarity	NPC101746
0.5769	Remote Similarity	NPC286851
0.5696	Remote Similarity	NPC129100
0.5696	Remote Similarity	NPC322801
0.5696	Remote Similarity	NPC291650
0.5679	Remote Similarity	NPC473710
0.5679	Remote Similarity	NPC475694
0.5641	Remote Similarity	NPC471780
0.5641	Remote Similarity	NPC471892
0.5641	Remote Similarity	NPC223386
0.5641	Remote Similarity	NPC198341
0.5641	Remote Similarity	NPC142290
0.5641	Remote Similarity	NPC75435
0.561	Remote Similarity	NPC255535
0.561	Remote Similarity	NPC299603
0.561	Remote Similarity	NPC28959
0.561	Remote Similarity	NPC137554
0.561	Remote Similarity	NPC285014

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 NPC223893 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	262
0.1-0.2	5984
0.2-0.3	2300
0.3-0.4	477
0.4-0.5	104
0.5-0.6	23
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
0.5946	Remote Similarity	NPD9239	Approved
0.5946	Remote Similarity	NPD9240	Approved
0.5789	Remote Similarity	NPD9026	Phase 2
0.5789	Remote Similarity	NPD9029	Phase 3
0.5789	Remote Similarity	NPD9027	Phase 3
0.5789	Remote Similarity	NPD9028	Phase 2
0.5696	Remote Similarity	NPD9033	Approved
0.5696	Remote Similarity	NPD9031	Approved
0.5696	Remote Similarity	NPD9032	Approved
0.5696	Remote Similarity	NPD9030	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