Natural Product: NPC222551

Natural Product IDNPC222551
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OZYYOEPXLCPMGL-BQYQJAHWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10468341
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0003467] Linear 1,3-diarylpropanoids
        • [CHEMONTID:0001630] Chalcones and dihydrochalcones
          • [CHEMONTID:0003474] Retrochalcones

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 OZYYOEPXLCPMGL-BQYQJAHWSA-N
Standard InCHI InChI=1S/C16H14O4/c1-20-12-9-15(18)13(16(19)10-12)7-8-14(17)11-5-3-2-4-6-11/h2-10,18-19H,1H3/b8-7+
SMILES COc1cc(c(/C=C/C(=O)c2ccccc2)c(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   270.09 Volume:   282.249
?
Van der Waals volume.
Dense:   0.957 LogP:   3.119
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.209
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.642
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   14.0
TPSA:   66.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.662 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.129 Fsp3:   0.062
MCE-18:   12.0
?
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:   0.814 Fluc inhibitor:   1.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.574
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.864
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.923 Promiscuous compounds:   0.57

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.907 MDCK Permeability:   -4.813
Pgp-inhibitor:   0.083 Pgp-substrate:   0.011
PAMPA:   0.15
?
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):   0.002
20% Bioavailability (F20%):   0.016 30% Bioavailability (F30%):   0.181
50% Bioavailability (F50%):   0.692

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.206 MRP1:   0.377
Plasma Protein Binding (PPB):   98.44% Volume Distribution (VD):   -0.374
Fu: 1.299%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.21
BSEP inhibitor:   0.207

ADMET: Metabolism

CYP1A2-inhibitor:   0.028 CYP1A2-substrate:   0.536
CYP2C19-inhibitor:   0.053 CYP2C19-substrate:   0.969
CYP2C9-inhibitor:   0.987 CYP2C9-substrate:   0.243
CYP2D6-inhibitor:   0.963 CYP2D6-substrate:   0.244
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.058
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.967
HLM stability:   0.866
?
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):  7.415 Half-life (T1/2):  0.988

ADMET: Toxicity

hERG Blockers:  0.141 hERG Blockers (10um):  0.467
Human Hepatotoxicity (H-HT):  0.55 Drug-induced Liver Injury (DILI):  0.794
AMES Toxicity:  0.414 Rat Oral Acute Toxicity:  0.232
Maximum Recommended Daily Dose:  0.661 Skin Sensitization:  0.829
Carcinogencity:  0.261 Eye Corrosion:  0.032
Eye Irritation:  0.98 Respiratory Toxicity:  0.887
Drug-induced Neurotoxicity:  0.463 Ototoxicity:  0.184
Hematotoxicity:  0.167 Drug-induced Nephrotoxicity:  0.382
Genotoxicity:  0.473 RPMI-8226 Immunitoxicity:  0.109
A549 Cytotoxicity:  0.316 Hek293 Cytotoxicity:  0.572
BCF:   1.152
?
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:   3.978
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.974
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.636
?
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
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota stem bark n.a. n.a. PMID[19874044]
NPO5744 Galipea panamensis Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[20423106]
NPO12221 Acacia saligna Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25183120]
NPO7231 Vernonia polyanthes Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26454 Acacia oswaldii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12221 Acacia saligna Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5298 Anastrepha ludens Species Tephritidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13782 Dicranopteris pedata Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28056 Drepanospora viridis Species n.a. Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5744 Galipea panamensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25082 Glycine canescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7038 Helichrysum oreophilum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4288 Lambertella hicoriae Species Rutstroemiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24800 Mentha crispa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1992 Ophiura leptoctenia Species Ophiuridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25109 Paenibacillus polymyxa Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO4930 Philodendron guttiferum Species Araceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1363 Photinia glabra Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8166 Polygala paniculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13782 Dicranopteris pedata Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13782 Dicranopteris pedata Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1992 Ophiura leptoctenia Species Ophiuridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4288 Lambertella hicoriae Species Rutstroemiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26454 Acacia oswaldii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6956 Citrus limonia Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13782 Dicranopteris pedata Species Gleicheniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5744 Galipea panamensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28056 Drepanospora viridis Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8166 Polygala paniculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25109 Paenibacillus polymyxa Species Paenibacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12221 Acacia saligna Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4930 Philodendron guttiferum Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25082 Glycine canescens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7038 Helichrysum oreophilum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO660 Elephas maximus Species Elephantidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1363 Photinia glabra Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24800 Mentha crispa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10501 Mitrephora glabra Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5298 Anastrepha ludens Species Tephritidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7231 Vernonia polyanthes Species Asteraceae 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 NPC222551 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
0.6591 Remote Similarity NPC212631
0.6591 Remote Similarity NPC608685
0.5957 Remote Similarity NPC64359
0.5714 Remote Similarity NPC188646
0.5682 Remote Similarity NPC141523
0.5208 Remote Similarity NPC139813
0.5192 Remote Similarity NPC476333
0.5192 Remote Similarity NPC175098
0.5192 Remote Similarity NPC337373
0.5185 Remote Similarity NPC472368
0.5122 Remote Similarity NPC71664
0.5122 Remote Similarity NPC608893

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC222551 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