Natural Product: NPC288611

Natural Product IDNPC288611
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SWUJZPBOVFEUQT-GEQWREAYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 45358146
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001253] Quinolines 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 SWUJZPBOVFEUQT-GEQWREAYSA-N
Standard InCHI InChI=1S/C20H24N2O2/c1-3-13-12-22-7-6-14(13)10-19(22)20(23)16-8-15-9-17(24-2)4-5-18(15)21-11-16/h3-5,8-9,11,13-14,19-20,23H,1,6-7,10,12H2,2H3/t13-,14?,19-,20-/m0/s1
SMILES C=C[C@H]1CN2CCC1C[C@H]2[C@H](c1cc2cc(ccc2nc1)OC)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   324.18 Volume:   344.006
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Van der Waals volume.
Dense:   0.942 LogP:   2.559
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.514
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.557
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   21.0
TPSA:   45.59
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Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.878 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.562 Fsp3:   0.45
MCE-18:   73.138
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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:   0.279 Fluc inhibitor:   0.082
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.661
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.207
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.002 Promiscuous compounds:   0.06

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.566 MDCK Permeability:   -4.779
Pgp-inhibitor:   0.995 Pgp-substrate:   0.973
PAMPA:   0.008
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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):   0.0
20% Bioavailability (F20%):   0.018 30% Bioavailability (F30%):   0.072
50% Bioavailability (F50%):   0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.642
Plasma Protein Binding (PPB):   80.105% Volume Distribution (VD):   0.442
Fu: 23.071%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.897 BCRP inhibitor:   0.253
BSEP inhibitor:   0.051

ADMET: Metabolism

CYP1A2-inhibitor:   0.759 CYP1A2-substrate:   0.003
CYP2C19-inhibitor:   0.998 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.971
CYP2D6-inhibitor:   0.722 CYP2D6-substrate:   0.022
CYP3A4-inhibitor:   0.424 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.832
HLM stability:   0.92
?
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):  3.995 Half-life (T1/2):  1.975

ADMET: Toxicity

hERG Blockers:  0.381 hERG Blockers (10um):  0.684
Human Hepatotoxicity (H-HT):  0.562 Drug-induced Liver Injury (DILI):  0.178
AMES Toxicity:  0.266 Rat Oral Acute Toxicity:  0.383
Maximum Recommended Daily Dose:  0.942 Skin Sensitization:  0.027
Carcinogencity:  0.379 Eye Corrosion:  0.0
Eye Irritation:  0.287 Respiratory Toxicity:  0.642
Drug-induced Neurotoxicity:  0.894 Ototoxicity:  0.903
Hematotoxicity:  0.089 Drug-induced Nephrotoxicity:  0.7
Genotoxicity:  0.582 RPMI-8226 Immunitoxicity:  0.079
A549 Cytotoxicity:  0.158 Hek293 Cytotoxicity:  0.522
BCF:   1.058
?
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:   3.622
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.828
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.258
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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
NPO25089 Cinchona calisaya Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[11992775]
NPO25089 Cinchona calisaya Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30377 Cinchona ledgeriana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30377 Cinchona ledgeriana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8614 Cinchona succirubra Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8614 Cinchona succirubra Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25089 Cinchona calisaya Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30377 Cinchona ledgeriana Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8614 Cinchona succirubra Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25089 Cinchona calisaya Species Rubiaceae 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 NPC288611 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
0.6712 Remote Similarity NPC118832
0.6712 Remote Similarity NPC329708
0.5584 Remote Similarity NPC165349
0.5584 Remote Similarity NPC47059
0.5584 Remote Similarity NPC610890
0.5195 Remote Similarity NPC203754
0.5195 Remote Similarity NPC150048

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC288611 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
0.6712 Remote Similarity NPD4038 Phase 4
0.6712 Remote Similarity NPD4039 Phase 4
0.6622 Remote Similarity NPD4033 Approved
0.6622 Remote Similarity NPD4037 Approved
0.6282 Remote Similarity NPD31 Approved
0.6282 Remote Similarity NPD32 Approved
0.6282 Remote Similarity NPD4034 Approved
0.5618 Remote Similarity NPD4036 Approved
0.5584 Remote Similarity NPD4122 Pre-clinical
0.5319 Remote Similarity NPD4035 Approved

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