NPASS Compound

Structure

CID263548 OpenBabel06191716062D 35 39 0 0 1 0 0 0 0 0999 V2000 5.0662 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3775 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5081 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 0.9750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8444 1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 -0.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3775 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8444 -1.4625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 -1.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0206 0.6181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2219 -0.4875 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3775 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6887 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 2.9250 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6887 0.9750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9750 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5331 -0.4875 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5331 2.4375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5331 -2.4375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8444 1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5331 1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8444 -0.4875 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5331 -1.4625 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9956 0.6181 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6887 3.9000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3775 2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6887 -2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3775 -2.9250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5 28 1 0 0 0 0 7 8 1 0 0 0 0 7 19 2 0 0 0 0 8 22 1 0 0 0 0 9 12 1 0 0 0 0 9 17 1 0 0 0 0 10 11 1 0 0 0 0 10 21 1 0 0 0 0 11 29 1 0 0 0 0 12 30 1 0 0 0 0 13 14 1 0 0 0 0 13 28 1 0 0 0 0 14 30 1 0 0 0 0 15 20 1 0 0 0 0 15 26 1 0 0 0 0 16 27 1 0 0 0 0 16 31 1 0 0 0 0 17 1 1 6 0 0 0 17 18 1 0 0 0 0 18 2 1 1 0 0 0 18 23 1 0 0 0 0 19 23 1 0 0 0 0 19 28 1 0 0 0 0 20 24 1 0 0 0 0 20 32 1 6 0 0 0 21 26 1 1 0 0 0 21 27 1 0 0 0 0 22 26 1 1 0 0 0 22 29 1 0 0 0 0 23 30 1 6 0 0 0 24 27 1 1 0 0 0 24 33 1 0 0 0 0 25 34 2 0 0 0 0 25 35 1 0 0 0 0 26 3 1 1 0 0 0 27 4 1 1 0 0 0 28 29 1 1 0 0 0 29 6 1 1 0 0 0 30 25 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	488.35
Volume:	523.332
LogP:	4.262
LogD:	3.805
LogS:	-4.058
# Rotatable Bonds:	2
TPSA:	97.99
# H-Bond Aceptor:	5
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.409
Synthetic Accessibility Score:	5.037
Fsp3:	0.9
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:	-5.604
MDCK Permeability:	8.888201591616962e-06
Pgp-inhibitor:	0.002
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.305

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.18
Plasma Protein Binding (PPB):	96.09085083007812%
Volume Distribution (VD):	0.53
Pgp-substrate:	2.6491856575012207%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.542
CYP2C19-inhibitor:	0.005
CYP2C19-substrate:	0.859
CYP2C9-inhibitor:	0.056
CYP2C9-substrate:	0.165
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.407
CYP3A4-substrate:	0.217

ADMET: Excretion

Clearance (CL):	2.206
Half-life (T1/2):	0.416

ADMET: Toxicity

hERG Blockers:	0.015
Human Hepatotoxicity (H-HT):	0.342
Drug-inuced Liver Injury (DILI):	0.031
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.759
Maximum Recommended Daily Dose:	0.422
Skin Sensitization:	0.079
Carcinogencity:	0.033
Eye Corrosion:	0.151
Eye Irritation:	0.12
Respiratory Toxicity:	0.979

Download Data

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

Natural Product: NPC263548

Natural Product ID:	NPC263548
*Common Name:**	Asiatic Acid
IUPAC Name:	(1S,2R,4aS,6aR,6aS,6bR,8aR,9R,10R,11R,12aR,14bS)-10,11-dihydroxy-9-(hydroxymethyl)-1,2,6a,6b,9,12a-hexamethyl-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydro-1H-picene-4a-carboxylic acid
Synonyms:	NSC-88135
Standard InCHIKey:	JXSVIVRDWWRQRT-UYDOISQJSA-N
Standard InCHI:	InChI=1S/C30H48O5/c1-17-9-12-30(25(34)35)14-13-28(5)19(23(30)18(17)2)7-8-22-26(3)15-20(32)24(33)27(4,16-31)21(26)10-11-29(22,28)6/h7,17-18,20-24,31-33H,8-16H2,1-6H3,(H,34,35)/t17-,18+,20-,21-,22-,23+,24+,26+,27+,28-,29-,30+/m1/s1
SMILES:	OC[C@]1(C)[C@@H](O)[C@H](O)C[C@]2([C@H]1CC[C@@]1([C@@H]2CC=C2[C@@]1(C)CC[C@@]1([C@H]2[C@@H](C)[C@@H](CC1)C)C(=O)O)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL404313
PubChem CID:	119034
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO30384	Combretum quadrangulare	Species	Combretaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9934464]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[97292]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8917504]
NPO1425	Salvia palaestina	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6677714]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5583807]
NPO20150	Erythrina sacleuxii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33170684]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27807341]
NPO4734	Syzygium nervosum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27797185]
NPO20081	Mycobacterium tuberculosis	Species	Mycobacteriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[27242221]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26996316]

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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
EC50	9
GI50	2
IC50	55
MIC	5
Others	31

Activity Type	# Activity
Cell Line	53
CELL-LINE	3
Individual Protein	23
NON-MOLECULAR	4
Organism	14
Others	4
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	Inhibition	=	70.0	%	PMID[514374]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.05	%	PMID[514373]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	16.11	%	PMID[514372]
NPT1274	Individual Protein	DNA repair protein RAD52 homolog	Homo sapiens	IC50	>	800000.0	nM	PMID[514371]
NPT1274	Individual Protein	DNA repair protein RAD52 homolog	Homo sapiens	IC50	>	100000.0	nM	PMID[514371]
NPT81	Cell Line	A549	Homo sapiens	IC50	=	41020.0	nM	PMID[514370]
NPT65	Cell Line	HepG2	Homo sapiens	IC50	=	35370.0	nM	PMID[514370]
NPT550	Cell Line	T-24	Homo sapiens	IC50	=	43970.0	nM	PMID[514370]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	44820.0	nM	PMID[514370]
NPT81	Cell Line	A549	Homo sapiens	Activity	<	5.0	%	PMID[514370]

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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 NPC263548 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	216
0.1-0.2	1337
0.2-0.3	4696
0.3-0.4	12926
0.4-0.5	10194
0.5-0.6	5561
0.6-0.7	4780
0.7-0.8	2211
0.8-0.85	437
0.85-0.9	131
0.9-0.95	147
0.95-1	61

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC282395
1.0	High Similarity	NPC88116
1.0	High Similarity	NPC299996
1.0	High Similarity	NPC32407
1.0	High Similarity	NPC231063

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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 NPC263548 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	193
0.1-0.2	1724
0.2-0.3	3772
0.3-0.4	2320
0.4-0.5	673
0.5-0.6	230
0.6-0.7	179
0.7-0.8	52
0.8-0.85	4
0.85-0.9	2
0.9-0.95	1
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9111	High Similarity	NPD7515	Phase 2
0.871	High Similarity	NPD7748	Approved
0.8632	High Similarity	NPD7902	Approved
0.8316	Intermediate Similarity	NPD7901	Clinical (unspecified phase)
0.8316	Intermediate Similarity	NPD7900	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