Natural Product: NPC242115

Natural Product IDNPC242115
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DQZRHRLTSJNVBC-DLBZAZTESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 132607006
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

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 DQZRHRLTSJNVBC-DLBZAZTESA-N
Standard InCHI InChI=1S/C17H16O7/c1-22-9-6-11(19)14-13(7-9)24-17(16(21)15(14)20)8-3-4-10(18)12(5-8)23-2/h3-7,16-19,21H,1-2H3/t16-,17+/m0/s1
SMILES COc1cc(c2c(c1)O[C@H](c1ccc(c(c1)OC)O)[C@H](C2=O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   332.09 Volume:   319.995
?
Van der Waals volume.
Dense:   1.038 LogP:   1.476
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.866
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.734
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   105.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.787 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.177 Fsp3:   0.235
MCE-18:   60.619
?
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:   1
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.524 Fluc inhibitor:   0.557
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.209
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.299
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.305 Promiscuous compounds:   0.276

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.43 MDCK Permeability:   -4.837
Pgp-inhibitor:   0.903 Pgp-substrate:   0.148
PAMPA:   0.037
?
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):   0.042
20% Bioavailability (F20%):   0.022 30% Bioavailability (F30%):   0.359
50% Bioavailability (F50%):   0.957

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.596
Plasma Protein Binding (PPB):   93.207% Volume Distribution (VD):   -0.113
Fu: 6.859%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.96
BSEP inhibitor:   0.762

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.002
CYP2C19-inhibitor:   0.019 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.705 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.012 CYP2D6-substrate:   0.508
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   0.271
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.052
HLM stability:   0.007
?
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):  8.703 Half-life (T1/2):  1.954

ADMET: Toxicity

hERG Blockers:  0.081 hERG Blockers (10um):  0.404
Human Hepatotoxicity (H-HT):  0.523 Drug-induced Liver Injury (DILI):  0.631
AMES Toxicity:  0.67 Rat Oral Acute Toxicity:  0.265
Maximum Recommended Daily Dose:  0.404 Skin Sensitization:  0.781
Carcinogencity:  0.376 Eye Corrosion:  0.007
Eye Irritation:  0.902 Respiratory Toxicity:  0.798
Drug-induced Neurotoxicity:  0.211 Ototoxicity:  0.539
Hematotoxicity:  0.377 Drug-induced Nephrotoxicity:  0.644
Genotoxicity:  0.781 RPMI-8226 Immunitoxicity:  0.213
A549 Cytotoxicity:  0.37 Hek293 Cytotoxicity:  0.46
BCF:   0.941
?
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:   3.552
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.468
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.777
?
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
NPO27122 Plumbago scandens Species Plumbaginaceae Eukaryota n.a. root n.a. PMID[14762525]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. PMID[22305790]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. PMID[36235241]
NPO25864 Kunzea ericoides Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38370080]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. PMID[38986200]
NPO27457 Eupatorium capillifolium Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[6790676]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO25767 Aplysia juliana Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27445 Artemisia filifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27457 Eupatorium capillifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. Database[FooDB]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27261 Carica papaya Species Caricaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25767 Aplysia juliana Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27445 Artemisia filifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23377 Stephanitis pyrioides Species Tingidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23438 Berchemia formosana Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26067 Acacia sutherlandii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27261 Carica papaya Species Caricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25864 Kunzea ericoides Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27457 Eupatorium capillifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27122 Plumbago scandens Species Plumbaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27281 Grindelia spathulata 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 NPC242115 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
0.7692 Intermediate Similarity NPC176869
0.7692 Intermediate Similarity NPC3779
0.7636 Intermediate Similarity NPC326037
0.7636 Intermediate Similarity NPC13858
0.717 Intermediate Similarity NPC122828
0.6964 Remote Similarity NPC52530
0.6 Remote Similarity NPC36916
0.6 Remote Similarity NPC36
0.6 Remote Similarity NPC7154
0.6 Remote Similarity NPC125039
0.6 Remote Similarity NPC7688
0.5915 Remote Similarity NPC138688
0.5915 Remote Similarity NPC72787
0.5915 Remote Similarity NPC217795
0.5915 Remote Similarity NPC58223
0.5862 Remote Similarity NPC306441
0.5714 Remote Similarity NPC606364
0.5616 Remote Similarity NPC279209
0.5616 Remote Similarity NPC102277
0.5616 Remote Similarity NPC479117
0.5593 Remote Similarity NPC308992
0.5593 Remote Similarity NPC44721
0.5593 Remote Similarity NPC211466
0.5593 Remote Similarity NPC605332
0.5574 Remote Similarity NPC320825
0.5541 Remote Similarity NPC472625
0.5541 Remote Similarity NPC287328
0.5541 Remote Similarity NPC471213
0.5517 Remote Similarity NPC62290
0.5517 Remote Similarity NPC142731
0.5517 Remote Similarity NPC326506
0.5467 Remote Similarity NPC471499
0.5429 Remote Similarity NPC163191
0.5405 Remote Similarity NPC236934
0.5323 Remote Similarity NPC16435
0.5246 Remote Similarity NPC36835
0.5246 Remote Similarity NPC246162
0.5246 Remote Similarity NPC9743
0.5246 Remote Similarity NPC260491
0.5246 Remote Similarity NPC61506
0.5246 Remote Similarity NPC240476
0.5246 Remote Similarity NPC250922
0.5167 Remote Similarity NPC201837
0.5082 Remote Similarity NPC471500
0.5082 Remote Similarity NPC263449

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC242115 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
0.6 Remote Similarity NPD6166 Phase 2
0.6 Remote Similarity NPD6167 Clinical (unspecified phase)
0.6 Remote Similarity NPD6168 Clinical (unspecified phase)

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