Natural Product: NPC157898

Natural Product IDNPC157898
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VOQFGNABAAEXTC-PZPWNCOQSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3402768
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 VOQFGNABAAEXTC-PZPWNCOQSA-N
Standard InCHI InChI=1S/C23H24O10/c1-12(24)14-4-6-15(7-5-14)32-23-22(30)21(29)20(28)18(33-23)11-31-19(27)9-3-13-2-8-16(25)17(26)10-13/h2-10,18,20-23,25-26,28-30H,11H2,1H3/b9-3+/t18-,20-,21+,22-,23-/m1/s1
SMILES CC(=O)c1ccc(cc1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)/C=C/c2ccc(c(c2)O)O)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   460.14 Volume:   444.869
?
Van der Waals volume.
Dense:   1.034 LogP:   1.439
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.772
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.009
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   21.0
TPSA:   162.98
?
Topological Polar Surface Area.
H-Bond Acceptor:   10.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.172 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.701 Fsp3:   0.304
MCE-18:   70.0
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.749 Fluc inhibitor:   0.995
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.166
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.806
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.194 Promiscuous compounds:   0.38

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.003 MDCK Permeability:   -5.23
Pgp-inhibitor:   0.002 Pgp-substrate:   0.007
PAMPA:   0.905
?
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):   0.615
20% Bioavailability (F20%):   0.951 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.026 MRP1:   0.003
Plasma Protein Binding (PPB):   82.362% Volume Distribution (VD):   -0.388
Fu: 15.187%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
BSEP inhibitor:   0.158

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.001
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.002
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.011
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.479
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.998
HLM stability:   0.968
?
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):  4.556 Half-life (T1/2):  3.073

ADMET: Toxicity

hERG Blockers:  0.083 hERG Blockers (10um):  0.445
Human Hepatotoxicity (H-HT):  0.561 Drug-induced Liver Injury (DILI):  0.911
AMES Toxicity:  0.942 Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.09 Skin Sensitization:  0.999
Carcinogencity:  0.236 Eye Corrosion:  0.0
Eye Irritation:  0.423 Respiratory Toxicity:  0.014
Drug-induced Neurotoxicity:  0.009 Ototoxicity:  0.942
Hematotoxicity:  0.151 Drug-induced Nephrotoxicity:  0.449
Genotoxicity:  0.772 RPMI-8226 Immunitoxicity:  0.062
A549 Cytotoxicity:  0.615 Hek293 Cytotoxicity:  0.317
BCF:   0.584
?
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:   3.287
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.844
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.27
?
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
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. whole plant n.a. PMID[21428416]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22870812]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23435948]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[25737008]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11100 Artemisia capillaris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11100 Artemisia capillaris Species Asteraceae 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
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 290800.0 nM PMID[1517742]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 1277100.0 nM PMID[18973387]
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 8000.0 nM PMID[23701598]

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 NPC157898 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
0.8615 High Similarity NPC291153
0.7534 Intermediate Similarity NPC476867
0.7162 Intermediate Similarity NPC291296
0.7143 Intermediate Similarity NPC476870
0.6933 Remote Similarity NPC10205
0.6842 Remote Similarity NPC471405
0.6753 Remote Similarity NPC157816
0.6753 Remote Similarity NPC476864
0.6627 Remote Similarity NPC476871
0.6582 Remote Similarity NPC476868
0.6463 Remote Similarity NPC488081
0.6316 Remote Similarity NPC137813
0.625 Remote Similarity NPC470572
0.6125 Remote Similarity NPC204937
0.6118 Remote Similarity NPC133984
0.6081 Remote Similarity NPC229784
0.6049 Remote Similarity NPC476866
0.6 Remote Similarity NPC186406
0.6 Remote Similarity NPC287597
0.5976 Remote Similarity NPC488082
0.5942 Remote Similarity NPC476873
0.5882 Remote Similarity NPC479769
0.587 Remote Similarity NPC214621
0.587 Remote Similarity NPC34267
0.587 Remote Similarity NPC81042
0.5833 Remote Similarity NPC476865
0.573 Remote Similarity NPC67134
0.5699 Remote Similarity NPC603856
0.5696 Remote Similarity NPC219677
0.5663 Remote Similarity NPC476869
0.5638 Remote Similarity NPC599948
0.5634 Remote Similarity NPC79908
0.5581 Remote Similarity NPC472876
0.5543 Remote Similarity NPC477629
0.5542 Remote Similarity NPC220942
0.5522 Remote Similarity NPC192229
0.551 Remote Similarity NPC139571
0.5455 Remote Similarity NPC11411
0.5443 Remote Similarity NPC34293
0.5435 Remote Similarity NPC270675
0.5435 Remote Similarity NPC195685
0.5402 Remote Similarity NPC479767
0.5376 Remote Similarity NPC80068
0.5326 Remote Similarity NPC476620
0.5316 Remote Similarity NPC199977
0.5263 Remote Similarity NPC223426
0.5213 Remote Similarity NPC85751
0.5213 Remote Similarity NPC19240
0.52 Remote Similarity NPC479768
0.519 Remote Similarity NPC473924
0.519 Remote Similarity NPC78363
0.5128 Remote Similarity NPC479473
0.5128 Remote Similarity NPC275721
0.5128 Remote Similarity NPC288416
0.5128 Remote Similarity NPC479468
0.5128 Remote Similarity NPC479474
0.5104 Remote Similarity NPC472994
0.507 Remote Similarity NPC232880
0.5063 Remote Similarity NPC477293
0.5063 Remote Similarity NPC606353
0.506 Remote Similarity NPC292443
0.5057 Remote Similarity NPC64141
0.5056 Remote Similarity NPC83743
0.5055 Remote Similarity NPC175230
0.5051 Remote Similarity NPC480796
0.5051 Remote Similarity NPC472993

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC157898 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