Natural Product: NPC37622

Natural Product IDNPC37622
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (E)-Butylidenephthalide
IUPAC Name (3E)-3-butylidene-2-benzofuran-1-one
Synonyms (Z)-3-Butylidenephthalide
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1765390
PubChem CID 5352899
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0004191] Isocoumarans
        • [CHEMONTID:0003409] Isobenzofuranones

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 WMBOCUXXNSOQHM-DHZHZOJOSA-N
Standard InCHI InChI=1S/C12H12O2/c1-2-3-8-11-9-6-4-5-7-10(9)12(13)14-11/h4-8H,2-3H2,1H3/b11-8+
SMILES CCC/C=C1/OC(=O)c2c1cccc2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   188.08 Volume:   203.394
?
Van der Waals volume.
Dense:   0.925 LogP:   2.814
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.615
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.123
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   12.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   2.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.667 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.45 Fsp3:   0.25
MCE-18:   20.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.182 Fluc inhibitor:   0.096
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.353
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.302
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.902 Promiscuous compounds:   0.474

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.435 MDCK Permeability:   -4.586
Pgp-inhibitor:   0.756 Pgp-substrate:   0.008
PAMPA:   0.062
?
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):   0.019
20% Bioavailability (F20%):   0.034 30% Bioavailability (F30%):   0.147
50% Bioavailability (F50%):   0.232

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.434 MRP1:   0.682
Plasma Protein Binding (PPB):   98.777% Volume Distribution (VD):   -0.267
Fu: 1.213%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.701
OATP1B3 inhibitor:   0.726 BCRP inhibitor:   0.07
BSEP inhibitor:   0.928

ADMET: Metabolism

CYP1A2-inhibitor:   0.168 CYP1A2-substrate:   0.995
CYP2C19-inhibitor:   0.008 CYP2C19-substrate:   0.892
CYP2C9-inhibitor:   0.775 CYP2C9-substrate:   0.026
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.039
CYP2B6-substrate:   0.002 CYP2C8-inhibitor:   1.0
HLM stability:   0.976
?
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):  4.933 Half-life (T1/2):  1.231

ADMET: Toxicity

hERG Blockers:  0.129 hERG Blockers (10um):  0.55
Human Hepatotoxicity (H-HT):  0.636 Drug-induced Liver Injury (DILI):  0.616
AMES Toxicity:  0.563 Rat Oral Acute Toxicity:  0.162
Maximum Recommended Daily Dose:  0.367 Skin Sensitization:  0.993
Carcinogencity:  0.558 Eye Corrosion:  0.483
Eye Irritation:  0.997 Respiratory Toxicity:  0.591
Drug-induced Neurotoxicity:  0.278 Ototoxicity:  0.195
Hematotoxicity:  0.448 Drug-induced Nephrotoxicity:  0.681
Genotoxicity:  0.185 RPMI-8226 Immunitoxicity:  0.055
A549 Cytotoxicity:  0.061 Hek293 Cytotoxicity:  0.042
BCF:   1.293
?
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:   4.152
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.192
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.974
?
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
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[11374978]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15679317]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. root n.a. PMID[17997069]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. sclerotium n.a. PMID[21250700]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[26521454]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[36838931]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37480748]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[37656744]
NPO22834 Rhizoma chuanxiong n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29438 Radix chuanxiong Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2154 Ligusticum tenuissimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO29438 Radix chuanxiong Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22834 Rhizoma chuanxiong n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2154 Ligusticum tenuissimum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11474 Ligusticum jeholense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2921 Angelica acutiloba Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11438 Angelica gigas Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25369 Levisticum officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18951 Ligusticum sinense Species Apiaceae 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
NPO15462 Angelica sinensis Oil n.a. 1.56 ± 0.56 n.a. n.a. % PMID[37480748]
NPO25369 Levisticum officinale Other Root 84.4 15.3 153.5 mg/100g Database [DUKE]

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
NPT1648 Individual protein Oligo-1,6-glucosidase Saccharomyces cerevisiae S288c Ki = 4860.0 nM PMID[23398496]
NPT1648 Individual protein Oligo-1,6-glucosidase Saccharomyces cerevisiae S288c IC50 = 2350000.0 nM PMID[23398496]
NPT24816 Single protein Alpha-mannosidase Canavalia ensiformis IC50 = 41000.0 nM PMID[31927314]
NPT526 Individual protein Alpha-glucosidase MAL62 Saccharomyces cerevisiae IC50 = 2350000.0 nM PMID[20879744]
NPT526 Individual protein Alpha-glucosidase MAL62 Saccharomyces cerevisiae Ki = 4860000.0 nM PMID[20879744]
NPT496 Individual protein Alpha-L-fucosidase 1 Bos taurus IC50 = 82000.0 nM PMID[31927314]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT2524 Organism Tyrophagus putrescentiae Tyrophagus putrescentiae RatioLC50 = 0.64 n.a. PMID[16508176]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae RatioLC50 = 2.78 n.a. PMID[16508176]
NPT1077 Organism Drosophila melanogaster Drosophila melanogaster RatioLC50 = 0.01 n.a. PMID[16508176]
NPT1077 Organism Drosophila melanogaster Drosophila melanogaster Ratio = 3.91 n.a. PMID[16508176]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = -9.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -24.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -41.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -42.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 20.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -6.9 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -18.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -23.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 35.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 27.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 12.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 3.5 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 3.3 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -5.2 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 1.5 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -0.3 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -12.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -7.4 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -9.1 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = -21.7 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 41.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 23.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 19.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 7.6 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 16.0 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 2.5 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 6.7 % PMID[20879744]
NPT32 Organism Mus musculus Mus musculus Activity = 6.4 % PMID[20879744]
NPT2524 Organism Tyrophagus putrescentiae Tyrophagus putrescentiae mortality = 12.3 % PMID[16508176]
NPT2524 Organism Tyrophagus putrescentiae Tyrophagus putrescentiae mortality = 33.0 % PMID[16508176]
NPT2524 Organism Tyrophagus putrescentiae Tyrophagus putrescentiae mortality = 52.9 % PMID[16508176]
NPT2524 Organism Tyrophagus putrescentiae Tyrophagus putrescentiae mortality = 57.2 % PMID[16508176]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 12.2 % PMID[16508176]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 51.6 % PMID[16508176]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 94.7 % PMID[16508176]
NPT2525 Organism Dermatophagoides farinae Dermatophagoides farinae mortality = 100.0 % PMID[16508176]





 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
- Drosophila melanogaster LC50 = 2070000.0 nM PMID[16508176]
- Drosophila melanogaster LD50 = 0.94 ug PMID[16508176]
- Tyrophagus putrescentiae LC50 = 25.56 microg/cm2 PMID[16508176]
- Dermatophagoides farinae LC50 = 4.67 microg/cm2 PMID[16508176]

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 NPC37622 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 NPC30594

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC37622 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
NPD

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