NPASS Compound

Structure

CID99657 OpenBabel06191715442D 40 42 0 0 1 0 0 0 0 0999 V2000 -0.4262 -4.7451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6053 -3.4511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8280 -4.2993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4828 -4.2991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8266 4.2997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8282 4.2995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0796 2.5070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7110 2.2293 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0359 0.4790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5580 1.3063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8272 -1.4333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8889 -2.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0311 -3.2048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6552 -2.8661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0006 2.8665 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8277 -2.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8269 2.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0004 -1.9108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6551 -0.9551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5635 -0.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2840 -3.8004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6553 -3.8215 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0007 3.8219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8151 1.8973 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8276 -1.4331 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8270 1.4335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1250 0.4785 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -1.6548 0.9554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 0.9554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6547 0.9558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8274 -0.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0804 0.4787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0002 -0.9554 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6549 0.0004 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3903 0.3456 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8278 1.4329 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8275 -1.4331 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0806 -0.4767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5632 1.2513 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 2 21 1 0 0 0 0 3 22 1 0 0 0 0 4 22 1 0 0 0 0 5 23 1 0 0 0 0 6 23 1 0 0 0 0 7 24 1 0 0 0 0 8 24 1 0 0 0 0 9 32 1 0 0 0 0 10 32 1 0 0 0 0 11 33 1 0 0 0 0 12 13 1 0 0 0 0 12 18 1 0 0 0 0 13 21 2 0 0 0 0 14 16 1 0 0 0 0 14 22 2 0 0 0 0 15 17 1 0 0 0 0 15 23 2 0 0 0 0 16 25 1 0 0 0 0 17 26 1 0 0 0 0 18 33 1 0 0 0 0 19 25 1 0 0 0 0 20 27 1 0 0 0 0 20 34 1 0 0 0 0 24 28 1 0 0 0 0 25 33 1 6 0 0 0 26 29 1 0 0 0 0 26 30 2 0 0 0 0 27 32 1 0 0 0 0 27 40 1 0 0 0 0 28 36 2 0 0 0 0 29 35 1 0 0 0 0 29 37 2 0 0 0 0 30 34 1 0 0 0 0 30 40 1 0 0 0 0 31 34 1 0 0 0 0 31 35 1 0 0 0 0 31 38 2 0 0 0 0 32 39 1 0 0 0 0 33 35 1 1 0 0 0 34 19 1 1 0 0 0 35 28 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	552.38
Volume:	613.742
LogP:	7.829
LogD:	5.772
LogS:	-5.41
# Rotatable Bonds:	10
TPSA:	80.67
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.223
Synthetic Accessibility Score:	6.377
Fsp3:	0.686
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.193
MDCK Permeability:	1.5474586689379066e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.975
Human Intestinal Absorption (HIA):	0.081
20% Bioavailability (F20%):	0.972
30% Bioavailability (F30%):	0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.821
Plasma Protein Binding (PPB):	82.84616088867188%
Volume Distribution (VD):	2.463
Pgp-substrate:	6.691899299621582%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.166
CYP2C19-inhibitor:	0.21
CYP2C19-substrate:	0.883
CYP2C9-inhibitor:	0.366
CYP2C9-substrate:	0.099
CYP2D6-inhibitor:	0.409
CYP2D6-substrate:	0.013
CYP3A4-inhibitor:	0.846
CYP3A4-substrate:	0.901

ADMET: Excretion

Clearance (CL):	12.731
Half-life (T1/2):	0.036

ADMET: Toxicity

hERG Blockers:	0.001
Human Hepatotoxicity (H-HT):	0.947
Drug-inuced Liver Injury (DILI):	0.825
AMES Toxicity:	0.027
Rat Oral Acute Toxicity:	0.783
Maximum Recommended Daily Dose:	0.084
Skin Sensitization:	0.188
Carcinogencity:	0.607
Eye Corrosion:	0.003
Eye Irritation:	0.021
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC99657

Natural Product ID:	NPC99657
*Common Name:**	Furohyperforin
IUPAC Name:	n.a.
Synonyms:	Furohyperforin
Standard InCHIKey:	SUOQGZCCNGMYHT-VJRKKQGXSA-N
Standard InCHI:	InChI=1S/C35H52O5/c1-21(2)13-12-18-33(11)25(16-14-22(3)4)19-34-20-27(32(9,10)39)40-30(34)26(17-15-23(5)6)29(37)35(33,31(34)38)28(36)24(7)8/h13-15,24-25,27,39H,12,16-20H2,1-11H3/t25-,27?,33+,34-,35-/m0/s1
SMILES:	CC(=CCC[C@]1(C)[C@@H](CC=C(C)C)C[C@]23CC(C(C)(C)O)OC2=C(CC=C(C)C)C(=O)[C@@]1(C(=O)C(C)C)C3=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL397752
PubChem CID:	44427231
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids

*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
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	Roots	n.a.	n.a.	PMID[30024167]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28445039]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18220354]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	callus	n.a.	PMID[15715262]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14735439]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10757735]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1078/0176-1617-00195]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4391	Hypericum perforatum	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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
IC50	2

Activity Type	# Activity
Cell Line	1
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT839	Cell Line	L6	Rattus norvegicus	IC50	=	16100.0	nM	PMID[460941]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	1700.0	nM	PMID[460941]

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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 NPC99657 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	181
0.1-0.2	1153
0.2-0.3	4574
0.3-0.4	8851
0.4-0.5	13046
0.5-0.6	7105
0.6-0.7	6509
0.7-0.8	1214
0.8-0.85	18
0.85-0.9	24
0.9-0.95	11
0.95-1	11

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC472687
1.0	High Similarity	NPC203388
1.0	High Similarity	NPC471331
1.0	High Similarity	NPC471330
0.989	High Similarity	NPC27105

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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 NPC99657 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	154
0.1-0.2	1540
0.2-0.3	3986
0.3-0.4	2300
0.4-0.5	702
0.5-0.6	214
0.6-0.7	199
0.7-0.8	55
0.8-0.85	0
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
0.7624	Intermediate Similarity	NPD5282	Discontinued
0.74	Intermediate Similarity	NPD5328	Approved
0.7339	Intermediate Similarity	NPD6412	Phase 2
0.7328	Intermediate Similarity	NPD6054	Approved
0.7328	Intermediate Similarity	NPD6059	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