Natural Product: NPC56432

Natural Product IDNPC56432
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UWHZIFQPPBDJPM-BQYQJAHWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5281127
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

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 UWHZIFQPPBDJPM-BQYQJAHWSA-N
Standard InCHI InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h7-8H,2-6,9-17H2,1H3,(H,19,20)/p-1/b8-7+
SMILES CCCCCC/C=C/CCCCCCCCCC(=O)[O-]

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   282.26 Volume:   332.192
?
Van der Waals volume.
Dense:   0.85 LogP:   6.671
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.669
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.683
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   2.0
TPSA:   37.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.291 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.033 Fsp3:   0.833
MCE-18:   0.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.159 Fluc inhibitor:   0.193
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.022
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.995 Promiscuous compounds:   0.891

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.08 MDCK Permeability:   -4.736
Pgp-inhibitor:   0.002 Pgp-substrate:   0.002
PAMPA:   0.101
?
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):   0.144
20% Bioavailability (F20%):   0.613 30% Bioavailability (F30%):   0.945
50% Bioavailability (F50%):   0.679

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.792
Plasma Protein Binding (PPB):   99.37% Volume Distribution (VD):   -0.779
Fu: 0.208%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.05
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.089
BSEP inhibitor:   0.996

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.667
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.747
CYP2C9-inhibitor:   0.978 CYP2C9-substrate:   0.882
CYP2D6-inhibitor:   0.981 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.002
?
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):  3.508 Half-life (T1/2):  0.861

ADMET: Toxicity

hERG Blockers:  0.089 hERG Blockers (10um):  0.348
Human Hepatotoxicity (H-HT):  0.693 Drug-induced Liver Injury (DILI):  0.039
AMES Toxicity:  0.013 Rat Oral Acute Toxicity:  0.04
Maximum Recommended Daily Dose:  0.219 Skin Sensitization:  0.993
Carcinogencity:  0.076 Eye Corrosion:  0.834
Eye Irritation:  0.992 Respiratory Toxicity:  0.938
Drug-induced Neurotoxicity:  0.024 Ototoxicity:  0.36
Hematotoxicity:  0.161 Drug-induced Nephrotoxicity:  0.291
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.116 Hek293 Cytotoxicity:  0.064
BCF:   0.737
?
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:   3.906
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.612
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.657
?
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
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-012-0441-5]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1007/s11746-010-1670-2]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.carres.2012.01.012]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.foodcont.2016.09.002]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.jfca.2010.08.006]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.06.003]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2010.12.007]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2016.02.010]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.1016/j.supflu.2018.06.017]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.12691/jfnr-2-5-9]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. branch n.a. PMID[17202693]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[19628108]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota stems n.a. n.a. PMID[20387902]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[22538527]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[24811150]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota seeds n.a. n.a. PMID[25299458]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[26562741]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. PMID[26804051]
NPO42047 Streptomyces longisporoflavus R-19 (DSM10189) Genus Streptomycetaceae Bacteria Seeds Djanga in the Sudanian climatic zone in southwest Burkina Faso 2012-Jun and 2014 PMID[28255501]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[28274428]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[29517238]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30236698]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds Guangzhou, China PMID[30563201]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30583361]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[30599958]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31159190]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. PMID[31625751]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota Seeds n.a. PMID[31861466]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. Along the Valencian coast, Spain 2020-Jun&Jul PMID[35161358]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[36128855]
NPO1300 Dacryodes edulis Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[36235361]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36613240]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[36677629]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. PMID[38358042]
NPO61460 Ficus drupacea Species Moraceae Eukaryota n.a. n.a. n.a. PMID[38409929]
NPO61460 Ficus drupacea Species Moraceae Eukaryota n.a. n.a. n.a. PMID[39272612]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[39375628]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[39519627]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO41124 Oncorhynchus mykiss Species Salmonidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO42047 Streptomyces longisporoflavus R-19 (DSM10189) Genus Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. Database[FooDB]
NPO41124 Oncorhynchus mykiss Species Salmonidae Eukaryota n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Herb n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. Database[FooDB]
NPO41124 Oncorhynchus mykiss Species Salmonidae Eukaryota n.a. n.a. Database[FooDB]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. Database[FooDB]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14821 Sus scrofa domesticus Species Suidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29334 Oplopanax elatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4640 Portulaca oleracea Species Portulacaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12297 Nigella sativa Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13281 Salvia hispanica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1300 Dacryodes edulis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29334 Oplopanax elatus Species Araliaceae 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
NPO12297 Nigella sativa Oil n.a. 0.26 n.a. n.a. % PMID[39375628]
NPO1300 Dacryodes edulis n.a. n.a. 0.98 ± 0.34 n.a. n.a. % PMID[36235361]
NPO13281 Salvia hispanica n.a. n.a. 0.77 ± 0.01 n.a. n.a. % PMID[36613240]
NPO13281 Salvia hispanica n.a. Seeds 6.38 ± 0.12 n.a. n.a. % PMID[30563201]
NPO13281 Salvia hispanica n.a. Seeds 0.80 ± 0.01 n.a. n.a. % PMID[30563201]
NPO14821 Sus scrofa domesticus n.a. n.a. 650 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 1290 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 1130 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 880 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 850 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 840 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 820 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 800 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 680 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 37 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 600 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 78 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 41 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 48 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 52 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 71 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 74 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 450 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 140 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 160 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 190 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 200 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 230 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 380 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 420 n.a. n.a. mg/100g Database [FooDB]
NPO14821 Sus scrofa domesticus n.a. n.a. 440 n.a. n.a. mg/100g Database [FooDB]
NPO41124 Oncorhynchus mykiss n.a. n.a. 128 n.a. n.a. mg/100g Database [FooDB]
NPO42047 Streptomyces longisporoflavus R-19 (DSM10189) n.a. Seeds 0.79 ± 0.02 n.a. n.a. % PMID[28255501]
NPO61460 Ficus drupacea Oil n.a. 0.99 ± 0.06 n.a. n.a. % PMID[39272612]

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 NPC56432 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
1.0 High Similarity NPC262968
0.8929 High Similarity NPC224227
0.8214 Intermediate Similarity NPC184171
0.7667 Intermediate Similarity NPC294548
0.76 Intermediate Similarity NPC67462
0.76 Intermediate Similarity NPC156630
0.5938 Remote Similarity NPC424
0.5938 Remote Similarity NPC36061
0.5938 Remote Similarity NPC69510
0.5938 Remote Similarity NPC77272
0.5938 Remote Similarity NPC290563
0.5938 Remote Similarity NPC139029
0.5938 Remote Similarity NPC281972
0.5938 Remote Similarity NPC261831
0.5938 Remote Similarity NPC87564
0.5625 Remote Similarity NPC281245
0.5588 Remote Similarity NPC255837
0.5588 Remote Similarity NPC168211
0.5455 Remote Similarity NPC92114
0.5429 Remote Similarity NPC154245
0.5429 Remote Similarity NPC85813
0.5429 Remote Similarity NPC223697
0.5429 Remote Similarity NPC6095
0.5294 Remote Similarity NPC95145
0.5294 Remote Similarity NPC325642
0.5294 Remote Similarity NPC65174
0.52 Remote Similarity NPC151719
0.5161 Remote Similarity NPC118654
0.5143 Remote Similarity NPC19305
0.5143 Remote Similarity NPC321062

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC56432 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
1.0 High Similarity NPD28 Approved
1.0 High Similarity NPD29 Phase 4
0.7931 Intermediate Similarity NPD3174 Discontinued
0.76 Intermediate Similarity NPD3206 Approved
0.5938 Remote Similarity NPD3195 Phase 2
0.5938 Remote Similarity NPD3196 Approved
0.5429 Remote Similarity NPD4266 Phase 2
0.5333 Remote Similarity NPD387 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