Natural Product: NPC522309

Natural Product IDNPC522309
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 9-(1,3-benzodioxol-5-yl)-1-pyrrolidin-1-yl-nona-2,8-dien-1-one
IUPAC Name 9-(1,3-benzodioxol-5-yl)-1-pyrrolidin-1-yl-nona-2,8-dien-1-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey BYKNKNBUHGFXQF-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H25NO3/c22-20(21-13-7-8-14-21)10-6-4-2-1-3-5-9-17-11-12-18-19(15-17)24-16-23-18/h5-6,9-12,15H,1-4,7-8,13-14,16H2
SMILES O=C(C=CCCCCC=CC1=CC=C2OCOC2=C1)N1CCCC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   327.18 Volume:   350.355
?
Van der Waals volume.
Dense:   0.934 LogP:   4.204
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.271
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.651
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   18.0
TPSA:   38.77
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.557 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.439 Fsp3:   0.45
MCE-18:   32.828
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.578 Fluc inhibitor:   0.997
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.398
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.805
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.015 Promiscuous compounds:   0.057

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.589 MDCK Permeability:   -4.658
Pgp-inhibitor:   0.733 Pgp-substrate:   0.006
PAMPA:   0.018
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.003
20% Bioavailability (F20%):   0.082 30% Bioavailability (F30%):   0.006
50% Bioavailability (F50%):   0.397

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.96 MRP1:   0.497
Plasma Protein Binding (PPB):   96.955% Volume Distribution (VD):   0.122
Fu: 2.704%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.726
OATP1B3 inhibitor:   0.873 BCRP inhibitor:   0.089
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.254 CYP1A2-substrate:   0.679
CYP2C19-inhibitor:   0.778 CYP2C19-substrate:   0.979
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.87
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.995
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.501 CYP2C8-inhibitor:   1.0
HLM stability:   0.679
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  4.614 Half-life (T1/2):  0.399

ADMET: Toxicity

hERG Blockers:  0.548 hERG Blockers (10um):  0.678
Human Hepatotoxicity (H-HT):  0.534 Drug-induced Liver Injury (DILI):  0.025
AMES Toxicity:  0.602 Rat Oral Acute Toxicity:  0.207
Maximum Recommended Daily Dose:  0.453 Skin Sensitization:  0.999
Carcinogencity:  0.214 Eye Corrosion:  0.376
Eye Irritation:  0.869 Respiratory Toxicity:  0.515
Drug-induced Neurotoxicity:  0.293 Ototoxicity:  0.315
Hematotoxicity:  0.148 Drug-induced Nephrotoxicity:  0.633
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.121
A549 Cytotoxicity:  0.57 Hek293 Cytotoxicity:  0.633
BCF:   1.518
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.188
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.679
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.063
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16872768]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota whole plants Sendai, Miyagi Prefecture, Japan 2000-Sep PMID[17243725]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. whole plant n.a. PMID[17397219]
NPO26237 Piper longum Species Piperaceae Eukaryota fruits n.a. n.a. PMID[20839888]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota whole plant Luxi County, Yunnan Province, China 2008-OCT PMID[21158422]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. whole plant n.a. PMID[21158422]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. Kego Nature Reserve, Hatinh Province, Vietnam 2008-DEC PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota aerial parts Kego Nature Reserve, Hatinh Province, Vietnam 2008-DEC PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. twig n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. inflorescence n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. leaf n.a. PMID[21973101]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. stem n.a. PMID[21973101]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[22940450]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota leaves, twigs, and fruits Nui Chua National Park (11 43' N; 109 08' E; 730 m alt.), Ninh Thuan Province, Vietnam 2010-Jan PMID[23301897]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[23434420]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[31621322]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1912 Acanthosyris paulo-alvinii Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO992 Betula alnoides Species Betulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5657 Oocystis polymorpha Species Oocystaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO61 Phoebe grandis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6614 Rubus pileatus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30128 Piper boehmeriaefolium Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2846 Piper sarmentosum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6614 Rubus pileatus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO992 Betula alnoides Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5657 Oocystis polymorpha Species Oocystaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO61 Phoebe grandis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4720 Aglaia perviridis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26237 Piper longum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3803 Ardisia japonica Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1912 Acanthosyris paulo-alvinii Species Cervantesiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

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 Organism Name 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

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC522309 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC193673
0.9796 High Similarity NPC230698
0.9796 High Similarity NPC99078
0.9796 High Similarity NPC96406
0.9 High Similarity NPC159150
0.8679 High Similarity NPC328419
0.8519 High Similarity NPC220923
0.8519 High Similarity NPC196609
0.7818 Intermediate Similarity NPC103947
0.7818 Intermediate Similarity NPC45783
0.7679 Intermediate Similarity NPC73883
0.7679 Intermediate Similarity NPC251454
0.7636 Intermediate Similarity NPC318862
0.7273 Intermediate Similarity NPC194359
0.7273 Intermediate Similarity NPC28641
0.7273 Intermediate Similarity NPC180647
0.7273 Intermediate Similarity NPC225745
0.7037 Intermediate Similarity NPC94280
0.6923 Remote Similarity NPC217574
0.6909 Remote Similarity NPC255817
0.6909 Remote Similarity NPC136330
0.6792 Remote Similarity NPC167096
0.6792 Remote Similarity NPC605721
0.6667 Remote Similarity NPC205178
0.6667 Remote Similarity NPC227218
0.6379 Remote Similarity NPC248505
0.6071 Remote Similarity NPC470707
0.5938 Remote Similarity NPC270811
0.5938 Remote Similarity NPC471073
0.5873 Remote Similarity NPC152186
0.5781 Remote Similarity NPC156944
0.5763 Remote Similarity NPC252107
0.5625 Remote Similarity NPC95366
0.5606 Remote Similarity NPC71105
0.5522 Remote Similarity NPC41331
0.5522 Remote Similarity NPC291449
0.5385 Remote Similarity NPC191302
0.5323 Remote Similarity NPC145446
0.5323 Remote Similarity NPC137172
0.5167 Remote Similarity NPC469808
0.5161 Remote Similarity NPC69670
0.5098 Remote Similarity NPC127326

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC522309 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.6909 Remote Similarity NPD2492 Phase 2

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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