Natural Product: NPC1408

Natural Product IDNPC1408
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Orbiculin D
IUPAC Name n.a.
Synonyms Orbiculin D
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL493857
PubChem CID 10649050
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002051] Agarofurans

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 YYBGZSCZDKPXGD-CLWMZTKQSA-N
Standard InCHI InChI=1S/C27H32O9/c1-15-10-11-20(33-16(2)28)26(5)21(34-23(29)18-8-6-12-31-18)14-17-22(27(15,26)36-25(17,3)4)35-24(30)19-9-7-13-32-19/h6-9,12-13,15,17,20-22H,10-11,14H2,1-5H3/t15-,17-,20+,21+,22-,26+,27-/m1/s1
SMILES C[C@@H]1CC[C@@H]([C@@]2(C)[C@H](C[C@@H]3[C@H]([C@]12OC3(C)C)OC(=O)c1ccco1)OC(=O)c1ccco1)OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   500.2 Volume:   493.423
?
Van der Waals volume.
Dense:   1.014 LogP:   3.228
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.131
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.097
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   27.0
TPSA:   114.41
?
Topological Polar Surface Area.
H-Bond Acceptor:   9.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.43 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.764 Fsp3:   0.593
MCE-18:   153.395
?
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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.292 Fluc inhibitor:   0.321
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.004
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.251 Promiscuous compounds:   0.132

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.967 MDCK Permeability:   -4.65
Pgp-inhibitor:   0.773 Pgp-substrate:   0.276
PAMPA:   0.171
?
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):   0.001
20% Bioavailability (F20%):   0.686 30% Bioavailability (F30%):   0.507
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.752 MRP1:   0.971
Plasma Protein Binding (PPB):   88.842% Volume Distribution (VD):   -0.419
Fu: 9.913%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.988
OATP1B3 inhibitor:   0.933 BCRP inhibitor:   0.479
BSEP inhibitor:   0.957

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.999
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.988
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.017
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.037
CYP3A4-inhibitor:   0.935 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.999
?
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):  5.504 Half-life (T1/2):  0.59

ADMET: Toxicity

hERG Blockers:  0.097 hERG Blockers (10um):  0.374
Human Hepatotoxicity (H-HT):  0.212 Drug-induced Liver Injury (DILI):  0.977
AMES Toxicity:  0.798 Rat Oral Acute Toxicity:  0.601
Maximum Recommended Daily Dose:  0.438 Skin Sensitization:  0.869
Carcinogencity:  0.934 Eye Corrosion:  0.004
Eye Irritation:  0.668 Respiratory Toxicity:  0.201
Drug-induced Neurotoxicity:  0.167 Ototoxicity:  0.232
Hematotoxicity:  0.097 Drug-induced Nephrotoxicity:  0.465
Genotoxicity:  0.971 RPMI-8226 Immunitoxicity:  0.076
A549 Cytotoxicity:  0.289 Hek293 Cytotoxicity:  0.427
BCF:   0.78
?
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:   3.582
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.097
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.645
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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
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[10346948]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. root n.a. PMID[10346948]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[11170672]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. root n.a. PMID[11809076]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota Seeds n.a. n.a. PMID[18507472]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[23421714]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[27791375]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. root n.a. PMID[9461657]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[9461657]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6349 Celastrus orbiculatus Species Celastraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6349 Celastrus orbiculatus Species Celastraceae 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
NPT113 Cell line RAW264.7 Mus musculus IC50 = 36700.0 nM PMID[11809076]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 43600.0 nM PMID[11809076]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 16800.0 nM PMID[10346948]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 17800.0 nM PMID[10346948]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 1200.0 nM PMID[10346948]
NPT2 Others Unspecified n.a. Ratio IC50 = 14.8 n.a. PMID[10346948]

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 NPC1408 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
0.8209 Intermediate Similarity NPC475039
0.8209 Intermediate Similarity NPC476035
0.7385 Intermediate Similarity NPC159520
0.7015 Intermediate Similarity NPC246841
0.6184 Remote Similarity NPC88593
0.6184 Remote Similarity NPC14499
0.5882 Remote Similarity NPC283375
0.5652 Remote Similarity NPC474608
0.5429 Remote Similarity NPC183122
0.5119 Remote Similarity NPC483870

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC1408 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