Natural Product: NPC129948

Natural Product IDNPC129948
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IUWMJMIMXOEDKV-VNTMZGSJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 71625127
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0003686] Furanoid lignans

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 IUWMJMIMXOEDKV-VNTMZGSJSA-N
Standard InCHI InChI=1S/C20H22O8/c1-25-15-7-11(3-5-13(15)21)17-19(23)9-28-18(20(19,24)10-27-17)12-4-6-14(22)16(8-12)26-2/h3-8,17-18,21-24H,9-10H2,1-2H3/t17-,18-,19+,20+/m0/s1
SMILES COc1cc(ccc1O)[C@H]1[C@@]2(CO[C@@H](c3ccc(c(c3)OC)O)[C@@]2(CO1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   390.13 Volume:   374.753
?
Van der Waals volume.
Dense:   1.041 LogP:   1.096
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.407
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.865
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   21.0
TPSA:   117.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   4.0 Rings:   4.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.619 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.049 Fsp3:   0.4
MCE-18:   89.143
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.039 Fluc inhibitor:   0.341
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.014
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.076
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.317 Promiscuous compounds:   0.228

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.199 MDCK Permeability:   -4.744
Pgp-inhibitor:   0.0 Pgp-substrate:   0.411
PAMPA:   0.814
?
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):   0.088
20% Bioavailability (F20%):   0.608 30% Bioavailability (F30%):   0.477
50% Bioavailability (F50%):   0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.038 MRP1:   0.846
Plasma Protein Binding (PPB):   80.808% Volume Distribution (VD):   -0.209
Fu: 21.627%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.257
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.01 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.663 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.08 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.0
?
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):  5.451 Half-life (T1/2):  4.521

ADMET: Toxicity

hERG Blockers:  0.087 hERG Blockers (10um):  0.399
Human Hepatotoxicity (H-HT):  0.745 Drug-induced Liver Injury (DILI):  0.512
AMES Toxicity:  0.85 Rat Oral Acute Toxicity:  0.464
Maximum Recommended Daily Dose:  0.356 Skin Sensitization:  0.91
Carcinogencity:  0.311 Eye Corrosion:  0.001
Eye Irritation:  0.844 Respiratory Toxicity:  0.257
Drug-induced Neurotoxicity:  0.332 Ototoxicity:  0.406
Hematotoxicity:  0.209 Drug-induced Nephrotoxicity:  0.509
Genotoxicity:  0.879 RPMI-8226 Immunitoxicity:  0.223
A549 Cytotoxicity:  0.132 Hek293 Cytotoxicity:  0.371
BCF:   0.868
?
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:   3.268
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.046
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.594
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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
NPO7437 Lonchocarpus costaricensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1305 Eriophyllum confertiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7437 Lonchocarpus costaricensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1305 Eriophyllum confertiflorum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26873 Echinochloa crus-galli Species Poaceae 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 NPC129948 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 NPC4940
0.6275 Remote Similarity NPC181049
0.5968 Remote Similarity NPC18979
0.587 Remote Similarity NPC115207
0.587 Remote Similarity NPC158079
0.587 Remote Similarity NPC228346
0.587 Remote Similarity NPC40432
0.587 Remote Similarity NPC161557
0.5833 Remote Similarity NPC147379
0.5833 Remote Similarity NPC470804
0.5652 Remote Similarity NPC209567
0.5636 Remote Similarity NPC23646
0.5636 Remote Similarity NPC485397
0.5532 Remote Similarity NPC242807
0.5532 Remote Similarity NPC153739
0.551 Remote Similarity NPC469480
0.5435 Remote Similarity NPC282703
0.5435 Remote Similarity NPC184733
0.5435 Remote Similarity NPC128208
0.5435 Remote Similarity NPC129570
0.5435 Remote Similarity NPC63238
0.5435 Remote Similarity NPC602603
0.54 Remote Similarity NPC126409
0.54 Remote Similarity NPC99572
0.5385 Remote Similarity NPC478955
0.5385 Remote Similarity NPC478700
0.5357 Remote Similarity NPC277804
0.5208 Remote Similarity NPC142985
0.5147 Remote Similarity NPC469586
0.5106 Remote Similarity NPC606519
0.5102 Remote Similarity NPC137487
0.5094 Remote Similarity NPC27843
0.5094 Remote Similarity NPC7171
0.5091 Remote Similarity NPC480701

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC129948 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