Natural Product: NPC205231

Natural Product IDNPC205231
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 MOJHIZLOKWRPIS-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10374972
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0001146] Indolines

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 MOJHIZLOKWRPIS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C9H7NO3/c1-13-5-2-3-6-7(4-5)10-9(12)8(6)11/h2-4H,1H3,(H,10,11,12)
SMILES COc1ccc2c(c1)NC(=O)C2=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   177.04 Volume:   171.293
?
Van der Waals volume.
Dense:   1.034 LogP:   1.054
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.409
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.107
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   12.0
TPSA:   55.4
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.646 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.022 Fsp3:   0.111
MCE-18:   22.0
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.138 Fluc inhibitor:   0.588
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.597
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.411
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.2 Promiscuous compounds:   0.253

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.594 MDCK Permeability:   -4.363
Pgp-inhibitor:   0.99 Pgp-substrate:   0.007
PAMPA:   0.139
?
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):   0.98
20% Bioavailability (F20%):   0.09 30% Bioavailability (F30%):   0.841
50% Bioavailability (F50%):   0.788

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.028
Plasma Protein Binding (PPB):   94.155% Volume Distribution (VD):   -0.031
Fu: 5.381%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.994
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.184
BSEP inhibitor:   0.924

ADMET: Metabolism

CYP1A2-inhibitor:   0.961 CYP1A2-substrate:   0.004
CYP2C19-inhibitor:   0.015 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.111
CYP3A4-inhibitor:   0.013 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.821
HLM stability:   0.321
?
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):  6.662 Half-life (T1/2):  1.216

ADMET: Toxicity

hERG Blockers:  0.122 hERG Blockers (10um):  0.434
Human Hepatotoxicity (H-HT):  0.821 Drug-induced Liver Injury (DILI):  0.938
AMES Toxicity:  0.835 Rat Oral Acute Toxicity:  0.45
Maximum Recommended Daily Dose:  0.508 Skin Sensitization:  0.458
Carcinogencity:  0.845 Eye Corrosion:  0.075
Eye Irritation:  0.969 Respiratory Toxicity:  0.447
Drug-induced Neurotoxicity:  0.822 Ototoxicity:  0.309
Hematotoxicity:  0.829 Drug-induced Nephrotoxicity:  0.772
Genotoxicity:  0.973 RPMI-8226 Immunitoxicity:  0.105
A549 Cytotoxicity:  0.047 Hek293 Cytotoxicity:  0.412
BCF:   1.4
?
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:   4.079
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.237
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.729
?
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
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. root n.a. PMID[14709883]
NPO20111 Anthemis auriculata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[16643047]
NPO20111 Anthemis auriculata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[521818]
NPO19498 Caesalpinia tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23030 Dalbergia nigra Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22077 Dioscorea tokoro Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22720 Kopsia hainanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20111 Anthemis auriculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21928 Clathrotropis brachypetala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22077 Dioscorea tokoro Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19498 Caesalpinia tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22077 Dioscorea tokoro Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19498 Caesalpinia tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22077 Dioscorea tokoro Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO14915 Uvaria acuminata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19498 Caesalpinia tinctoria Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1020 Petrosimonia monandra Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21928 Clathrotropis brachypetala Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24254 Euphorbia sapinii Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22522 Senecio speciosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23145 Andropogon jwarancusa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22720 Kopsia hainanensis Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19198 Kalmia latifolia Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22077 Dioscorea tokoro Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20111 Anthemis auriculata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23030 Dalbergia nigra Species Fabaceae 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 NPC205231 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
0.5128 Remote Similarity NPC254698

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC205231 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