NPASS Compound

Structure

NPC120299 OpenBabel07101718192D 50 52 0 0 1 0 0 0 0 0999 V2000 -1.9216 -9.4500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5717 -9.5736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1673 -4.5057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6466 -6.3010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4923 -3.2659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8994 -0.7377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4444 -2.9484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1424 -0.1605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7646 -2.4788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5290 -0.5772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6501 0.1237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6998 -3.6102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8789 -2.5338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5291 -3.5105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7756 -1.0893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9321 -1.9356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6284 -4.5629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8075 -1.5811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0959 0.2501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8537 -8.0828 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7145 -7.6682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6501 -3.4265 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9996 -1.2369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7646 -0.8240 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9965 -6.1774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0231 0.9124 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7823 -9.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0959 -3.5530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7859 -6.7155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2816 -2.7278 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8603 -1.6514 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9321 -1.3672 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4178 -5.1010 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2102 -1.7751 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1424 -3.1423 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0533 -1.1666 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4444 -0.3544 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5291 0.2077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2785 -4.6865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0533 -0.6663 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9758 0.8410 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3464 -6.0537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3495 -1.3606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3165 1.1391 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3499 -3.7338 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0679 -5.2247 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9317 -2.6041 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4444 -1.4785 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 28 1 0 0 0 0 2 28 1 0 0 0 0 3 29 1 0 0 0 0 4 30 2 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 8 11 2 0 0 0 0 8 12 1 0 0 0 0 9 15 2 0 0 0 0 10 17 2 0 0 0 0 11 16 1 0 0 0 0 12 20 2 0 0 0 0 13 14 2 0 0 0 0 13 18 1 0 0 0 0 14 19 1 0 0 0 0 15 29 1 0 0 0 0 18 34 1 0 0 0 0 19 37 1 0 0 0 0 20 39 1 0 0 0 0 21 22 1 0 0 0 0 21 28 1 0 0 0 0 22 30 1 0 0 0 0 23 29 2 0 0 0 0 24 32 1 0 0 0 0 24 35 1 0 0 0 0 25 33 1 0 0 0 0 25 38 1 0 0 0 0 26 30 1 0 0 0 0 26 47 1 0 0 0 0 27 41 1 0 0 0 0 27 42 1 0 0 0 0 31 5 1 6 0 0 0 31 35 1 0 0 0 0 31 36 1 0 0 0 0 32 16 1 6 0 0 0 32 48 1 0 0 0 0 33 17 1 6 0 0 0 33 49 1 0 0 0 0 34 40 1 0 0 0 0 34 43 1 1 0 0 0 35 44 1 1 0 0 0 36 23 1 6 0 0 0 36 48 1 0 0 0 0 37 41 1 6 0 0 0 37 49 1 0 0 0 0 38 41 1 6 0 0 0 38 50 1 0 0 0 0 39 45 2 0 0 0 0 39 50 1 0 0 0 0 40 46 2 0 0 0 0 40 47 1 0 0 0 0 41 6 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	696.42
Volume:	747.406
LogP:	5.784
LogD:	4.362
LogS:	-5.423
# Rotatable Bonds:	13
TPSA:	128.59
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.098
Synthetic Accessibility Score:	7.162
Fsp3:	0.634
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.758
MDCK Permeability:	1.9512321159709245e-05
Pgp-inhibitor:	0.917
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.149
20% Bioavailability (F20%):	0.34
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.125
Plasma Protein Binding (PPB):	95.81627655029297%
Volume Distribution (VD):	1.344
Pgp-substrate:	1.913177251815796%

ADMET: Metabolism

CYP1A2-inhibitor:	0.026
CYP1A2-substrate:	0.069
CYP2C19-inhibitor:	0.326
CYP2C19-substrate:	0.199
CYP2C9-inhibitor:	0.673
CYP2C9-substrate:	0.06
CYP2D6-inhibitor:	0.021
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.932
CYP3A4-substrate:	0.405

ADMET: Excretion

Clearance (CL):	4.935
Half-life (T1/2):	0.48

ADMET: Toxicity

hERG Blockers:	0.489
Human Hepatotoxicity (H-HT):	0.98
Drug-inuced Liver Injury (DILI):	0.489
AMES Toxicity:	0.96
Rat Oral Acute Toxicity:	0.355
Maximum Recommended Daily Dose:	0.996
Skin Sensitization:	0.957
Carcinogencity:	0.659
Eye Corrosion:	0.003
Eye Irritation:	0.008
Respiratory Toxicity:	0.757

Download Data

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

Natural Product: NPC120299

Natural Product ID:	NPC120299
*Common Name:**	Lasonolide A
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XYYABYHBQHRGAT-ZUFIHRSYSA-N
Standard InCHI:	InChI=1S/C41H60O9/c1-28(2)21-22-30(4)26-47-40(46)34(43)18-13-14-19-37-41(6,27-42)38-25-33(49-37)17-10-7-9-15-29(3)23-36-31(5)35(44)24-32(48-36)16-11-8-12-20-39(45)50-38/h8-15,17,20,23,28,31-38,42-44H,4,7,16,18-19,21-22,24-27H2,1-3,5-6H3/b11-8+,14-13-,15-9+,17-10+,20-12+,29-23-/t31-,32+,33-,34-,35+,36-,37+,38-,41+/m1/s1
SMILES:	OC[C@@]1(C)[C@H](C/C=CC[C@H](C(=O)OCC(=C)CCC(C)C)O)O[C@H]2C[C@H]1OC(=O)/C=C/C=C/C[C@H]1C[C@@H]([C@H]([C@@H](/C=C(C=CC/C=C/2)/C)O1)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL56091
PubChem CID:	11342965
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues

*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
NPO32865	forcepia sp.	Species	Coelosphaeridae	Eukaryota	n.a.	n.a.	n.a.	PMID[15332854]

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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
GI50	6
IC50	3

Activity Type	# Activity
Cell Line	9

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	=	8.6	nM	PMID[451275]
NPT461	Cell Line	PANC-1	Homo sapiens	IC50	=	89.0	nM	PMID[451275]
NPT378	Cell Line	NCI/ADR-RES	Homo sapiens	IC50	=	490.0	nM	PMID[451275]
NPT81	Cell Line	A549	Homo sapiens	GI50	=	20.0	nM	PMID[451274]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	<	3.0	nM	PMID[451274]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	<	3.0	nM	PMID[451274]
NPT81	Cell Line	A549	Homo sapiens	GI50	=	15.0	nM	PMID[451273]
NPT393	Cell Line	HCT-116	Homo sapiens	GI50	=	3.0	nM	PMID[451273]
NPT6565	Cell Line	NCI-H46	Homo sapiens	GI50	<	3.0	nM	PMID[451273]

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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 NPC120299 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	203
0.1-0.2	987
0.2-0.3	3586
0.3-0.4	6456
0.4-0.5	15271
0.5-0.6	8375
0.6-0.7	6657
0.7-0.8	1104
0.8-0.85	50
0.85-0.9	2
0.9-0.95	1
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.989	High Similarity	NPC475653
0.9889	High Similarity	NPC255410
0.9778	High Similarity	NPC300710
0.9574	High Similarity	NPC473596
0.9	High Similarity	NPC199382

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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 NPC120299 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	174
0.1-0.2	1155
0.2-0.3	3395
0.3-0.4	2719
0.4-0.5	1179
0.5-0.6	337
0.6-0.7	178
0.7-0.8	11
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.871	High Similarity	NPD7838	Discovery
0.8469	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.8125	Intermediate Similarity	NPD6698	Approved
0.8125	Intermediate Similarity	NPD46	Approved
0.7677	Intermediate Similarity	NPD7983	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