Natural Product: NPC151191

Natural Product IDNPC151191
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
KWUXNWWMRBXQRC-BBBXVDCKSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14707301
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 KWUXNWWMRBXQRC-BBBXVDCKSA-N
Standard InCHI InChI=1S/C30H48O4/c1-18(2)19-9-14-29(25(33)34)15-16-30(17-31)20(24(19)29)7-8-22-27(5)12-11-23(32)26(3,4)21(27)10-13-28(22,30)6/h19-24,31-32H,1,7-17H2,2-6H3,(H,33,34)/t19-,20+,21-,22+,23-,24+,27-,28+,29-,30-/m0/s1
SMILES C=C(C)[C@@H]1CC[C@@]2(CC[C@]3(CO)[C@H](CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O)[C@@H]12)C(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   472.36 Volume:   514.542
?
Van der Waals volume.
Dense:   0.918 LogP:   3.384
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.026
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.532
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The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   27.0
TPSA:   77.76
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Topological Polar Surface Area.
H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.436 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.921 Fsp3:   0.9
MCE-18:   104.0
?
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:   0 PAINS Alert:   0
Colloidal aggregators:   0.781 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.345 Promiscuous compounds:   0.24

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.494 MDCK Permeability:   -5.098
Pgp-inhibitor:   0.0 Pgp-substrate:   0.104
PAMPA:   0.972
?
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%):   0.213 30% Bioavailability (F30%):   0.259
50% Bioavailability (F50%):   0.971

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.872 MRP1:   0.983
Plasma Protein Binding (PPB):   92.005% Volume Distribution (VD):   -0.293
Fu: 8.311%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.992
OATP1B3 inhibitor:   0.886 BCRP inhibitor:   0.253
BSEP inhibitor:   0.06

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.012 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.049 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.0
?
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):  5.333 Half-life (T1/2):  1.096

ADMET: Toxicity

hERG Blockers:  0.061 hERG Blockers (10um):  0.079
Human Hepatotoxicity (H-HT):  0.733 Drug-induced Liver Injury (DILI):  0.506
AMES Toxicity:  0.31 Rat Oral Acute Toxicity:  0.224
Maximum Recommended Daily Dose:  0.558 Skin Sensitization:  0.973
Carcinogencity:  0.931 Eye Corrosion:  0.051
Eye Irritation:  0.833 Respiratory Toxicity:  0.94
Drug-induced Neurotoxicity:  0.049 Ototoxicity:  0.601
Hematotoxicity:  0.423 Drug-induced Nephrotoxicity:  0.659
Genotoxicity:  0.641 RPMI-8226 Immunitoxicity:  0.018
A549 Cytotoxicity:  0.126 Hek293 Cytotoxicity:  0.174
BCF:   0.796
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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:   3.501
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.105
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.418
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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
NPO1072 Aspergillus oryzae Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[20797856]
NPO1072 Aspergillus oryzae Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22026385]
NPO1072 Aspergillus oryzae Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24116376]
NPO40939 Syzygium corticosum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[30057155]
NPO1072 Aspergillus oryzae Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1072 Aspergillus oryzae Species Aspergillaceae 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
NPT721 Individual protein Nuclear factor NF-kappa-B p65 subunit Homo sapiens IC50 > 10000.0 nM PMID[30057155]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT139 Cell line HT-29 Homo sapiens IC50 > 10000.0 nM PMID[30057155]
NPT82 Cell line MDA-MB-231 Homo sapiens IC50 > 10000.0 nM PMID[30057155]
NPT400 Cell line MDA-MB-435 Homo sapiens IC50 > 10000.0 nM PMID[30057155]
NPT377 Cell line OVCAR-3 Homo sapiens IC50 > 10000.0 nM PMID[30057155]

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 NPC151191 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
0.8448 Intermediate Similarity NPC264317
0.8448 Intermediate Similarity NPC294438
0.7742 Intermediate Similarity NPC16377
0.7619 Intermediate Similarity NPC488213
0.7419 Intermediate Similarity NPC488164
0.7419 Intermediate Similarity NPC264005
0.6923 Remote Similarity NPC2783
0.6471 Remote Similarity NPC488165
0.6462 Remote Similarity NPC30583
0.6364 Remote Similarity NPC488506
0.6364 Remote Similarity NPC220498
0.6364 Remote Similarity NPC30322
0.6269 Remote Similarity NPC201655
0.6119 Remote Similarity NPC476071
0.6119 Remote Similarity NPC213832
0.6087 Remote Similarity NPC269360
0.597 Remote Similarity NPC80590
0.5942 Remote Similarity NPC18064
0.5909 Remote Similarity NPC472608
0.5882 Remote Similarity NPC291373
0.5846 Remote Similarity NPC68828
0.5821 Remote Similarity NPC192744
0.5694 Remote Similarity NPC169933
0.5694 Remote Similarity NPC600004
0.5652 Remote Similarity NPC24772
0.5652 Remote Similarity NPC211162
0.5652 Remote Similarity NPC183374
0.5652 Remote Similarity NPC33768
0.5634 Remote Similarity NPC475061
0.5634 Remote Similarity NPC601275
0.5581 Remote Similarity NPC488208
0.5571 Remote Similarity NPC271974
0.5571 Remote Similarity NPC277399
0.5571 Remote Similarity NPC195395
0.5571 Remote Similarity NPC247312
0.5556 Remote Similarity NPC486704
0.5556 Remote Similarity NPC611139
0.5541 Remote Similarity NPC481311
0.5506 Remote Similarity NPC487490
0.5493 Remote Similarity NPC4309
0.5455 Remote Similarity NPC93662
0.5417 Remote Similarity NPC474719
0.5385 Remote Similarity NPC606354
0.5375 Remote Similarity NPC486709
0.5373 Remote Similarity NPC246445
0.5342 Remote Similarity NPC160506
0.5278 Remote Similarity NPC274330
0.5275 Remote Similarity NPC488207
0.527 Remote Similarity NPC478841
0.527 Remote Similarity NPC488166
0.527 Remote Similarity NPC601176
0.527 Remote Similarity NPC607677
0.5211 Remote Similarity NPC474686
0.5181 Remote Similarity NPC486699
0.5132 Remote Similarity NPC603461
0.5125 Remote Similarity NPC605397
0.5077 Remote Similarity NPC192638
0.5077 Remote Similarity NPC25511
0.5077 Remote Similarity NPC600137
0.5075 Remote Similarity NPC231256
0.5075 Remote Similarity NPC178383
0.5068 Remote Similarity NPC57954
0.5068 Remote Similarity NPC198664
0.5067 Remote Similarity NPC293564
0.5067 Remote Similarity NPC606728
0.5067 Remote Similarity NPC608379
0.5063 Remote Similarity NPC602512
0.5059 Remote Similarity NPC290349

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC151191 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
0.8448 Intermediate Similarity NPD7520 Phase 1
0.5342 Remote Similarity NPD8035 Phase 2

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