NPASS Compound

Structure

CID296482 OpenBabel06191716102D 26 29 0 0 0 0 0 0 0 0999 V2000 1.3660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9670 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -5.0000 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 1.3660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3793 -6.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3793 -4.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8978 3.1709 0.0000 Cl 0 5 0 0 0 0 0 0 0 0 0 0 1 22 1 0 0 0 0 2 23 1 0 0 0 0 3 4 2 0 0 0 0 3 12 1 0 0 0 0 4 17 1 0 0 0 0 5 6 1 0 0 0 0 5 13 1 0 0 0 0 6 21 1 0 0 0 0 7 12 2 0 0 0 0 7 16 1 0 0 0 0 8 13 2 0 0 0 0 8 18 1 0 0 0 0 9 14 2 0 0 0 0 9 19 1 0 0 0 0 10 15 2 0 0 0 0 10 21 1 0 0 0 0 11 24 1 0 0 0 0 11 25 1 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 14 16 1 0 0 0 0 15 20 1 0 0 0 0 16 21 2 0 0 0 0 17 20 2 0 0 0 0 17 22 1 0 0 0 0 18 19 2 0 0 0 0 18 24 1 0 0 0 0 19 25 1 0 0 0 0 20 23 1 0 0 0 0 M CHG 2 21 1 26 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	336.12
Volume:	338.078
LogP:	4.309
LogD:	3.482
LogS:	-6.311
# Rotatable Bonds:	2
TPSA:	40.8
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.674
Synthetic Accessibility Score:	2.787
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.202
MDCK Permeability:	3.455935438978486e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.014
30% Bioavailability (F30%):	0.192

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.914
Plasma Protein Binding (PPB):	93.10327911376953%
Volume Distribution (VD):	1.217
Pgp-substrate:	2.335495948791504%

ADMET: Metabolism

CYP1A2-inhibitor:	0.854
CYP1A2-substrate:	0.9
CYP2C19-inhibitor:	0.062
CYP2C19-substrate:	0.851
CYP2C9-inhibitor:	0.014
CYP2C9-substrate:	0.833
CYP2D6-inhibitor:	0.956
CYP2D6-substrate:	0.934
CYP3A4-inhibitor:	0.465
CYP3A4-substrate:	0.496

ADMET: Excretion

Clearance (CL):	12.703
Half-life (T1/2):	0.219

ADMET: Toxicity

hERG Blockers:	0.275
Human Hepatotoxicity (H-HT):	0.097
Drug-inuced Liver Injury (DILI):	0.696
AMES Toxicity:	0.406
Rat Oral Acute Toxicity:	0.063
Maximum Recommended Daily Dose:	0.885
Skin Sensitization:	0.869
Carcinogencity:	0.906
Eye Corrosion:	0.003
Eye Irritation:	0.026
Respiratory Toxicity:	0.84

Download Data

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

Natural Product: NPC296482

Natural Product ID:	NPC296482
*Common Name:**	Berberine Chloride
IUPAC Name:	n.a.
Synonyms:	Berberine Chloride; GNF-Pf-4545
Standard InCHIKey:	VKJGBAJNNALVAV-UHFFFAOYSA-M
Standard InCHI:	InChI=1S/C20H18NO4.ClH/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2;/h3-4,7-10H,5-6,11H2,1-2H3;1H/q+1;/p-1
SMILES:	COc1c(OC)ccc2c1c[n+]1CCc3c(c1c2)cc1c(c3)OCO1.[Cl-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL12089
PubChem CID:	6426334 12456
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001909] Protoberberine alkaloids and derivatives

*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
NPO1074	Hydrastis canadensis	Species	Ranunculaceae	Eukaryota	roots	n.a.	n.a.	PMID[9784149]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9748373]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	Indo-Pacific	n.a.	PMID[7494145]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[32243140]
NPO40655	Synoicum sp. Ascidian	Strain	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[31967465]
NPO40718	Indian beech tree	Strain	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[30108931]
NPO1074	Hydrastis canadensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29091439]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[27336796]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26863083]
NPO32617	dysidea sp.	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26551342]

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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
AC50	6
EC50	5
GI50	77
IC50	109
Kd	3
Ki	14
LD50	3
MIC	87
Others	241
Potency	173

Activity Type	# Activity
Cell Line	177
CELL-LINE	4
Individual Protein	147
NON-MOLECULAR	13
Organism	162
Others	184
SINGLE PROTEIN	7
Tissue	5
Uncleic Acid	19

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	16930.1	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	10590.9	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	3920	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	2750.1	nM	PubChem BioAssay data set
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	2451	nM	PubChem BioAssay data set
NPT152	Individual Protein	Nuclear factor erythroid 2-related factor 2	Homo sapiens	Potency	n.a.	5955.3	nM	PubChem BioAssay data set
NPT106	Individual Protein	Peroxisome proliferator-activated receptor delta	Homo sapiens	Potency	n.a.	23708.3	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	1104.8	nM	PubChem BioAssay data set
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	1344.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	26832.5	nM	PubChem BioAssay data set

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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 NPC296482 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	637
0.1-0.2	3744
0.2-0.3	13204
0.3-0.4	4938
0.4-0.5	13531
0.5-0.6	4363
0.6-0.7	1911
0.7-0.8	296
0.8-0.85	30
0.85-0.9	22
0.9-0.95	13
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC202768
1.0	High Similarity	NPC53069
0.9789	High Similarity	NPC96405
0.9789	High Similarity	NPC171409
0.9734	High Similarity	NPC313189

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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 NPC296482 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	361
0.1-0.2	659
0.2-0.3	877
0.3-0.4	1467
0.4-0.5	2708
0.5-0.6	2174
0.6-0.7	792
0.7-0.8	106
0.8-0.85	1
0.85-0.9	1
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD3815	Phase 1
1.0	High Similarity	NPD3816	Phase 1
0.91	High Similarity	NPD3763	Approved
0.9043	High Similarity	NPD3922	Approved
0.9043	High Similarity	NPD3923	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