Natural Product: NPC31849

Natural Product IDNPC31849
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Omphamurin
IUPAC Name 8-[(2S)-2-hydroxy-3-methylbut-3-enyl]-5,7-dimethoxychromen-2-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3426683
PubChem CID 157112
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives

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 NUABNGXDPYIGQM-LBPRGKRZSA-N
Standard InCHI InChI=1S/C16H18O5/c1-9(2)12(17)7-11-14(20-4)8-13(19-3)10-5-6-15(18)21-16(10)11/h5-6,8,12,17H,1,7H2,2-4H3/t12-/m0/s1
SMILES COc1cc(OC)c2c(c1C[C@@H](C(=C)C)O)oc(=O)cc2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   290.12 Volume:   296.312
?
Van der Waals volume.
Dense:   0.979 LogP:   1.96
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.143
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.553
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   13.0
TPSA:   68.9
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.676 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.102 Fsp3:   0.312
MCE-18:   28.0
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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:   0.432 Fluc inhibitor:   0.012
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.974
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.28
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.135 Promiscuous compounds:   0.531

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.74 MDCK Permeability:   -4.454
Pgp-inhibitor:   0.005 Pgp-substrate:   0.001
PAMPA:   0.024
?
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):   0.001
20% Bioavailability (F20%):   0.406 30% Bioavailability (F30%):   0.452
50% Bioavailability (F50%):   0.926

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.851
Plasma Protein Binding (PPB):   92.342% Volume Distribution (VD):   0.254
Fu: 6.602%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.049
BSEP inhibitor:   0.985

ADMET: Metabolism

CYP1A2-inhibitor:   0.015 CYP1A2-substrate:   0.556
CYP2C19-inhibitor:   0.148 CYP2C19-substrate:   0.008
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.068
CYP2D6-inhibitor:   0.867 CYP2D6-substrate:   0.85
CYP3A4-inhibitor:   0.102 CYP3A4-substrate:   0.036
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.047
HLM stability:   0.997
?
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):  11.276 Half-life (T1/2):  1.194

ADMET: Toxicity

hERG Blockers:  0.074 hERG Blockers (10um):  0.237
Human Hepatotoxicity (H-HT):  0.333 Drug-induced Liver Injury (DILI):  0.345
AMES Toxicity:  0.474 Rat Oral Acute Toxicity:  0.265
Maximum Recommended Daily Dose:  0.774 Skin Sensitization:  0.421
Carcinogencity:  0.602 Eye Corrosion:  0.372
Eye Irritation:  0.969 Respiratory Toxicity:  0.375
Drug-induced Neurotoxicity:  0.358 Ototoxicity:  0.349
Hematotoxicity:  0.263 Drug-induced Nephrotoxicity:  0.172
Genotoxicity:  0.89 RPMI-8226 Immunitoxicity:  0.093
A549 Cytotoxicity:  0.013 Hek293 Cytotoxicity:  0.185
BCF:   0.734
?
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:   3.365
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.864
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.126
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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
NPO33003 murraya alata Species Rutaceae Eukaryota leaves n.a. n.a. PMID[25621853]
NPO33003 murraya alata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 12400.0 nM PMID[18077425]

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 NPC31849 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 NPC85085
0.7885 Intermediate Similarity NPC213173
0.7451 Intermediate Similarity NPC472518
0.7368 Intermediate Similarity NPC472525
0.6852 Remote Similarity NPC471828
0.6852 Remote Similarity NPC73413
0.6604 Remote Similarity NPC472517
0.6545 Remote Similarity NPC229128
0.6429 Remote Similarity NPC54503
0.6379 Remote Similarity NPC472519
0.6207 Remote Similarity NPC61499
0.5932 Remote Similarity NPC471826
0.5862 Remote Similarity NPC109675
0.5862 Remote Similarity NPC273772
0.5763 Remote Similarity NPC279851
0.569 Remote Similarity NPC27671
0.569 Remote Similarity NPC253616
0.5593 Remote Similarity NPC62366
0.5469 Remote Similarity NPC472520
0.5424 Remote Similarity NPC50896
0.5424 Remote Similarity NPC326600
0.5333 Remote Similarity NPC472515
0.5333 Remote Similarity NPC144418
0.5167 Remote Similarity NPC472522
0.5161 Remote Similarity NPC173350
0.5082 Remote Similarity NPC188380
0.5082 Remote Similarity NPC224543
0.5077 Remote Similarity NPC26954
0.5077 Remote Similarity NPC38099

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC31849 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