Natural Product: NPC3036

Natural Product IDNPC3036
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GVVKSKFIFOYDOK-SECBINFHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3594090
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002507] Homoisoflavonoids
        • [CHEMONTID:0002508] Homoisoflavans
          • [CHEMONTID:0002898] Homoisoflavanones

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 GVVKSKFIFOYDOK-SECBINFHSA-N
Standard InCHI InChI=1S/C16H14O6/c17-10-5-13(20)15-14(6-10)22-7-9(16(15)21)3-8-1-2-11(18)12(19)4-8/h1-2,4-6,9,17-20H,3,7H2/t9-/m1/s1
SMILES Oc1cc(O)c2c(c1)OC[C@H](C2=O)Cc1ccc(c(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   302.08 Volume:   293.909
?
Van der Waals volume.
Dense:   1.028 LogP:   1.873
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.997
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.739
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   107.22
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.632 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.089 Fsp3:   0.188
MCE-18:   57.789
?
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:   1
Colloidal aggregators:   0.553 Fluc inhibitor:   0.541
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.221
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.191
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.408 Promiscuous compounds:   0.411

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.435 MDCK Permeability:   -4.851
Pgp-inhibitor:   0.002 Pgp-substrate:   0.479
PAMPA:   0.323
?
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%):   0.888 30% Bioavailability (F30%):   0.788
50% Bioavailability (F50%):   0.917

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.016 MRP1:   0.888
Plasma Protein Binding (PPB):   92.872% Volume Distribution (VD):   -0.359
Fu: 6.455%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.994
OATP1B3 inhibitor:   0.935 BCRP inhibitor:   0.438
BSEP inhibitor:   0.495

ADMET: Metabolism

CYP1A2-inhibitor:   0.968 CYP1A2-substrate:   0.762
CYP2C19-inhibitor:   0.031 CYP2C19-substrate:   0.815
CYP2C9-inhibitor:   0.986 CYP2C9-substrate:   0.11
CYP2D6-inhibitor:   0.439 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.058 CYP3A4-substrate:   0.75
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.977
?
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):  12.675 Half-life (T1/2):  1.559

ADMET: Toxicity

hERG Blockers:  0.068 hERG Blockers (10um):  0.708
Human Hepatotoxicity (H-HT):  0.724 Drug-induced Liver Injury (DILI):  0.663
AMES Toxicity:  0.84 Rat Oral Acute Toxicity:  0.466
Maximum Recommended Daily Dose:  0.794 Skin Sensitization:  0.985
Carcinogencity:  0.739 Eye Corrosion:  0.05
Eye Irritation:  0.998 Respiratory Toxicity:  0.44
Drug-induced Neurotoxicity:  0.083 Ototoxicity:  0.471
Hematotoxicity:  0.068 Drug-induced Nephrotoxicity:  0.105
Genotoxicity:  0.996 RPMI-8226 Immunitoxicity:  0.042
A549 Cytotoxicity:  0.811 Hek293 Cytotoxicity:  0.721
BCF:   1.345
?
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:   4.024
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.091
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.571
?
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
NPO33045 bellevalia eigii Species Hyacinthaceae Eukaryota Bulbs Irbid, Jordan n.a. PMID[26147490]
NPO40241 Hyacinthaceae Species n.a. n.a. n.a. n.a. n.a. PMID[30951308]
NPO33045 bellevalia eigii Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO40241 Hyacinthaceae Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]

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
NPT400 Cell line MDA-MB-435 Homo sapiens IC50 > 20000.0 nM PMID[24893224]
NPT139 Cell line HT-29 Homo sapiens IC50 > 20000.0 nM PMID[17060532]
NPT737 Cell line HUVEC Homo sapiens GI50 > 100000.0 nM PMID[30951308]
NPT5265 Cell line Y79 Homo sapiens GI50 > 100000.0 nM PMID[30951308]

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 NPC3036 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
0.82 Intermediate Similarity NPC118813
0.7455 Intermediate Similarity NPC472912
0.7222 Intermediate Similarity NPC129853
0.7222 Intermediate Similarity NPC76445
0.7037 Intermediate Similarity NPC105512
0.6909 Remote Similarity NPC235640
0.6842 Remote Similarity NPC482968
0.6833 Remote Similarity NPC482961
0.6667 Remote Similarity NPC472911
0.6034 Remote Similarity NPC284550
0.5714 Remote Similarity NPC261234
0.5667 Remote Similarity NPC96167
0.5517 Remote Similarity NPC170468
0.55 Remote Similarity NPC472909
0.541 Remote Similarity NPC472910
0.541 Remote Similarity NPC269176
0.5323 Remote Similarity NPC222814
0.5161 Remote Similarity NPC245758
0.5079 Remote Similarity NPC472914

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC3036 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