Natural Product: NPC476169

Natural Product IDNPC476169
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Sophoronol
IUPAC Name 3,5,7-trihydroxy-3-(5-methoxy-2,2-dimethylchromen-6-yl)-2H-chromen-4-one
Synonyms Sophoronol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL550446
PubChem CID 15138471
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0001612] Isoflavans
          • [CHEMONTID:0001827] Isoflavanones
            • [CHEMONTID:0003525] 3'-prenylated isoflavanones

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 SYJLLCMGTNPNAB-UHFFFAOYSA-N
Standard InCHI InChI=1S/C21H20O7/c1-20(2)7-6-12-15(28-20)5-4-13(18(12)26-3)21(25)10-27-16-9-11(22)8-14(23)17(16)19(21)24/h4-9,22-23,25H,10H2,1-3H3
SMILES CC1(C=CC2=C(O1)C=CC(=C2OC)C3(COC4=CC(=CC(=C4C3=O)O)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   384.12 Volume:   377.986
?
Van der Waals volume.
Dense:   1.016 LogP:   2.505
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.454
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.334
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   23.0
TPSA:   105.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   4.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.731 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.729 Fsp3:   0.286
MCE-18:   87.0
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.13 Fluc inhibitor:   0.314
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.563
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.499
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.186 Promiscuous compounds:   0.331

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.052 MDCK Permeability:   -4.784
Pgp-inhibitor:   0.033 Pgp-substrate:   0.316
PAMPA:   0.808
?
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):   0.008
20% Bioavailability (F20%):   0.162 30% Bioavailability (F30%):   0.641
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.113 MRP1:   0.931
Plasma Protein Binding (PPB):   96.324% Volume Distribution (VD):   0.205
Fu: 2.662%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.92
OATP1B3 inhibitor:   0.991 BCRP inhibitor:   0.873
BSEP inhibitor:   0.501

ADMET: Metabolism

CYP1A2-inhibitor:   0.898 CYP1A2-substrate:   0.471
CYP2C19-inhibitor:   0.359 CYP2C19-substrate:   0.072
CYP2C9-inhibitor:   0.998 CYP2C9-substrate:   0.026
CYP2D6-inhibitor:   0.4 CYP2D6-substrate:   0.988
CYP3A4-inhibitor:   0.11 CYP3A4-substrate:   0.076
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.971
HLM stability:   0.65
?
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):  7.129 Half-life (T1/2):  1.287

ADMET: Toxicity

hERG Blockers:  0.098 hERG Blockers (10um):  0.51
Human Hepatotoxicity (H-HT):  0.544 Drug-induced Liver Injury (DILI):  0.275
AMES Toxicity:  0.718 Rat Oral Acute Toxicity:  0.541
Maximum Recommended Daily Dose:  0.673 Skin Sensitization:  0.557
Carcinogencity:  0.778 Eye Corrosion:  0.005
Eye Irritation:  0.872 Respiratory Toxicity:  0.872
Drug-induced Neurotoxicity:  0.227 Ototoxicity:  0.349
Hematotoxicity:  0.178 Drug-induced Nephrotoxicity:  0.293
Genotoxicity:  0.666 RPMI-8226 Immunitoxicity:  0.134
A549 Cytotoxicity:  0.19 Hek293 Cytotoxicity:  0.583
BCF:   1.674
?
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:   4.136
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.725
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.946
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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
NPO3544 Sophora mollis Species Fabaceae Eukaryota roots n.a. n.a. PMID[19572738]
NPO3544 Sophora mollis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3544 Sophora mollis Species Fabaceae 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
NPT1161 Cell line CHO Cricetulus griseus IC50 = 222700.0 nM PMID[26425784]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 114500.0 nM PMID[16417306]
NPT2 Others Unspecified n.a. Ratio IC50 = 2.0 n.a. PMID[26425784]

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 NPC476169 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
0.6418 Remote Similarity NPC210597
0.5972 Remote Similarity NPC471115
0.5692 Remote Similarity NPC277032
0.5541 Remote Similarity NPC41301
0.52 Remote Similarity NPC92805
0.5132 Remote Similarity NPC262585
0.5125 Remote Similarity NPC482757
0.5067 Remote Similarity NPC138205

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC476169 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