Natural Product: NPC103420

Natural Product IDNPC103420
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Morusyunnansins F
IUPAC Name 4-[(2S)-7-hydroxy-8-(3-methylbut-2-enyl)-3,4-dihydro-2H-chromen-2-yl]benzene-1,3-diol
Synonyms Morusyunnansins F
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1951300
PubChem CID 57333040
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003642] 8-prenylated flavans

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 ZKQRTKHIRJLHLJ-IBGZPJMESA-N
Standard InCHI InChI=1S/C20H22O4/c1-12(2)3-7-16-17(22)9-4-13-5-10-19(24-20(13)16)15-8-6-14(21)11-18(15)23/h3-4,6,8-9,11,19,21-23H,5,7,10H2,1-2H3/t19-/m0/s1
SMILES CC(=CCc1c(ccc2CC[C@@H](c3ccc(cc3O)O)Oc12)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   326.15 Volume:   345.512
?
Van der Waals volume.
Dense:   0.944 LogP:   3.728
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.362
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.579
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   69.92
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.732 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.225 Fsp3:   0.3
MCE-18:   58.154
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.889 Fluc inhibitor:   0.937
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.122
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.195
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.503 Promiscuous compounds:   0.092

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.947 MDCK Permeability:   -4.814
Pgp-inhibitor:   0.17 Pgp-substrate:   0.204
PAMPA:   0.029
?
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):   0.004
20% Bioavailability (F20%):   0.972 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.942
Plasma Protein Binding (PPB):   94.351% Volume Distribution (VD):   0.621
Fu: 7.097%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.917
OATP1B3 inhibitor:   0.852 BCRP inhibitor:   0.967
BSEP inhibitor:   0.677

ADMET: Metabolism

CYP1A2-inhibitor:   0.02 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.993 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.873 CYP2C9-substrate:   0.612
CYP2D6-inhibitor:   0.996 CYP2D6-substrate:   0.76
CYP3A4-inhibitor:   0.155 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.001 CYP2C8-inhibitor:   1.0
HLM stability:   1.0
?
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):  3.523 Half-life (T1/2):  1.834

ADMET: Toxicity

hERG Blockers:  0.244 hERG Blockers (10um):  0.633
Human Hepatotoxicity (H-HT):  0.815 Drug-induced Liver Injury (DILI):  0.226
AMES Toxicity:  0.497 Rat Oral Acute Toxicity:  0.83
Maximum Recommended Daily Dose:  0.905 Skin Sensitization:  0.966
Carcinogencity:  0.11 Eye Corrosion:  0.001
Eye Irritation:  0.829 Respiratory Toxicity:  0.988
Drug-induced Neurotoxicity:  0.774 Ototoxicity:  0.541
Hematotoxicity:  0.042 Drug-induced Nephrotoxicity:  0.668
Genotoxicity:  0.924 RPMI-8226 Immunitoxicity:  0.099
A549 Cytotoxicity:  0.814 Hek293 Cytotoxicity:  0.76
BCF:   1.745
?
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:   4.899
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.944
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.528
?
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
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. PMID[22165973]
NPO19617 Crateva religiosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21070 Dendrosicyos socotrana Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19617 Crateva religiosa Species Capparaceae Eukaryota n.a. n.a. Database[FooDB]
NPO5877 Morus yunnanensis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18059 Acacia orites Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21676 Heracleum pastinacifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22808 Hesperocyparis stephensonii Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20337 Ageratina pichinchensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19617 Crateva religiosa Species Capparaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21070 Dendrosicyos socotrana Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19771 Pterocephalus plumosus Species Caprifoliaceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus IC50 = 150.0 nM PMID[22165973]

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 NPC103420 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
0.7885 Intermediate Similarity NPC246648
0.7321 Intermediate Similarity NPC285040
0.6724 Remote Similarity NPC91560
0.6441 Remote Similarity NPC324436
0.6441 Remote Similarity NPC78
0.6333 Remote Similarity NPC102540
0.6094 Remote Similarity NPC276212
0.5625 Remote Similarity NPC285555
0.5484 Remote Similarity NPC164980
0.5484 Remote Similarity NPC274717
0.5397 Remote Similarity NPC107572
0.5397 Remote Similarity NPC32739
0.5385 Remote Similarity NPC470308
0.5385 Remote Similarity NPC470307
0.5323 Remote Similarity NPC197351
0.5179 Remote Similarity NPC106914
0.5179 Remote Similarity NPC86502
0.5156 Remote Similarity NPC306829

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC103420 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