Natural Product: NPC246587

Natural Product IDNPC246587
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Codamine
IUPAC Name (1S)-1-[(3,4-dimethoxyphenyl)methyl]-6-methoxy-2-methyl-3,4-dihydro-1H-isoquinolin-7-ol
Synonyms Codamine
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL251624
PubChem CID 20056510
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002566] Isoquinolines and derivatives
        • [CHEMONTID:0000054] Benzylisoquinolines

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 OKORHWXYDBSYNO-INIZCTEOSA-N
Standard InCHI InChI=1S/C20H25NO4/c1-21-8-7-14-11-19(24-3)17(22)12-15(14)16(21)9-13-5-6-18(23-2)20(10-13)25-4/h5-6,10-12,16,22H,7-9H2,1-4H3/p+1/t16-/m0/s1
SMILES C[NH+]1CCc2cc(c(cc2[C@@H]1Cc1ccc(c(c1)OC)OC)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   343.18 Volume:   359.146
?
Van der Waals volume.
Dense:   0.956 LogP:   1.889
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.956
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.742
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   17.0
TPSA:   51.16
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   3.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.904 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.685 Fsp3:   0.4
MCE-18:   57.857
?
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:   0.229 Fluc inhibitor:   0.058
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.457
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.453
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.004 Promiscuous compounds:   0.333

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.863 MDCK Permeability:   -4.698
Pgp-inhibitor:   0.758 Pgp-substrate:   0.574
PAMPA:   0.002
?
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):   0.004
20% Bioavailability (F20%):   0.703 30% Bioavailability (F30%):   0.323
50% Bioavailability (F50%):   0.941

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.845 MRP1:   0.941
Plasma Protein Binding (PPB):   51.336% Volume Distribution (VD):   0.028
Fu: 44.852%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.962
OATP1B3 inhibitor:   0.897 BCRP inhibitor:   0.525
BSEP inhibitor:   0.963

ADMET: Metabolism

CYP1A2-inhibitor:   1.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.997 CYP2C9-substrate:   0.148
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.246
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   0.05
CYP2B6-substrate:   0.977 CYP2C8-inhibitor:   0.387
HLM stability:   0.252
?
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):  6.422 Half-life (T1/2):  2.964

ADMET: Toxicity

hERG Blockers:  0.462 hERG Blockers (10um):  0.595
Human Hepatotoxicity (H-HT):  0.722 Drug-induced Liver Injury (DILI):  0.064
AMES Toxicity:  0.549 Rat Oral Acute Toxicity:  0.681
Maximum Recommended Daily Dose:  0.952 Skin Sensitization:  0.361
Carcinogencity:  0.418 Eye Corrosion:  0.002
Eye Irritation:  0.534 Respiratory Toxicity:  0.923
Drug-induced Neurotoxicity:  0.918 Ototoxicity:  0.319
Hematotoxicity:  0.077 Drug-induced Nephrotoxicity:  0.383
Genotoxicity:  0.895 RPMI-8226 Immunitoxicity:  0.076
A549 Cytotoxicity:  0.129 Hek293 Cytotoxicity:  0.273
BCF:   1.273
?
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:   3.674
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.879
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.146
?
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
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1042/BA20020118]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1556/abot.45.2003.3-4.15]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[15019787]
NPO32512 polyalthia cerasoides Species Annonaceae Eukaryota roots n.a. n.a. PMID[17845001]
NPO21782 Nuxia sphaerocephala Species Stilbaceae Eukaryota leaves n.a. n.a. PMID[19299148]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23517479]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[37685099]
NPO260 Cyclacanthia bellae Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21782 Nuxia sphaerocephala Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20090 Dalbergia spruceana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10176 Chrozophora prostrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7312 Aplidium multiplicatum Species Polyclinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2466 Aloe microstigma Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20090 Dalbergia spruceana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13887 Erythrophleum suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21782 Nuxia sphaerocephala Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20090 Dalbergia spruceana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13887 Erythrophleum suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21782 Nuxia sphaerocephala Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13887 Erythrophleum suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20090 Dalbergia spruceana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO23007 Horsfieldia glabra Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20090 Dalbergia spruceana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO260 Cyclacanthia bellae Species Latrunculiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13887 Erythrophleum suaveolens Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19966 Dendrobium amplum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10176 Chrozophora prostrata Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21782 Nuxia sphaerocephala Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17383 Cyperus nipponicus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2466 Aloe microstigma Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7312 Aplidium multiplicatum Species Polyclinidae 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
NPT91 Cell line KB Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17845001]
NPT639 Cell line NCI-H187 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[17845001]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 4.2 ug.mL-1 PMID[17845001]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 5.0 ug.mL-1 PMID[17845001]

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 NPC246587 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
0.7015 Intermediate Similarity NPC42549
0.5882 Remote Similarity NPC250846
0.5429 Remote Similarity NPC9887
0.5231 Remote Similarity NPC97221
0.5091 Remote Similarity NPC470626

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC246587 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