Natural Product: NPC178025

Natural Product IDNPC178025
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Sinocalycanchinensin H
IUPAC Name n.a.
Synonyms Sinocalycanchinensin H
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1774192
PubChem CID 52952953
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002321] Cycloartanols and derivatives

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 SIWDILYVABWYRB-FMSZTUEUSA-N
Standard InCHI InChI=1S/C29H44O3/c1-18(7-6-8-19(2)25(31)32)21-11-13-27(5)24-10-9-22-20(3)23(30)12-14-28(22)17-29(24,28)16-15-26(21,27)4/h8,18,20-22,24H,6-7,9-17H2,1-5H3,(H,31,32)/b19-8+/t18-,20+,21-,22+,24+,26-,27+,28-,29+/m1/s1
SMILES C[C@@H]([C@H]1CC[C@@]2([C@]1(C)CC[C@@]13[C@H]2CC[C@@H]2[C@]3(C1)CCC(=O)[C@H]2C)C)CC/C=C(/C(=O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   440.33 Volume:   485.819
?
Van der Waals volume.
Dense:   0.906 LogP:   4.384
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.34
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.895
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The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   25.0
TPSA:   54.37
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Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.466 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.525 Fsp3:   0.862
MCE-18:   127.037
?
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.777 Fluc inhibitor:   0.001
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.509 Promiscuous compounds:   0.196

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.483 MDCK Permeability:   -5.043
Pgp-inhibitor:   0.091 Pgp-substrate:   0.0
PAMPA:   0.835
?
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):   0.005
20% Bioavailability (F20%):   0.097 30% Bioavailability (F30%):   0.448
50% Bioavailability (F50%):   0.911

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.407
Plasma Protein Binding (PPB):   93.811% Volume Distribution (VD):   -0.546
Fu: 7.538%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.426
BSEP inhibitor:   0.985

ADMET: Metabolism

CYP1A2-inhibitor:   0.008 CYP1A2-substrate:   0.006
CYP2C19-inhibitor:   0.925 CYP2C19-substrate:   0.478
CYP2C9-inhibitor:   0.016 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.991
HLM stability:   0.632
?
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):  6.186 Half-life (T1/2):  0.642

ADMET: Toxicity

hERG Blockers:  0.048 hERG Blockers (10um):  0.076
Human Hepatotoxicity (H-HT):  0.768 Drug-induced Liver Injury (DILI):  0.413
AMES Toxicity:  0.184 Rat Oral Acute Toxicity:  0.258
Maximum Recommended Daily Dose:  0.356 Skin Sensitization:  0.824
Carcinogencity:  0.535 Eye Corrosion:  0.006
Eye Irritation:  0.435 Respiratory Toxicity:  0.898
Drug-induced Neurotoxicity:  0.045 Ototoxicity:  0.663
Hematotoxicity:  0.65 Drug-induced Nephrotoxicity:  0.686
Genotoxicity:  0.872 RPMI-8226 Immunitoxicity:  0.035
A549 Cytotoxicity:  0.075 Hek293 Cytotoxicity:  0.127
BCF:   1.74
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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:   4.651
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.797
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.333
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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
NPO33379 sinocalycanthus chinensis Species n.a. n.a. leaves n.a. n.a. PMID[21493075]
NPO33379 sinocalycanthus chinensis 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
NPT91 Cell line KB Homo sapiens IC50 = 18.6 ug.mL-1 PMID[25871261]
NPT83 Cell line MCF7 Homo sapiens IC50 = 18.6 ug.mL-1 PMID[21074425]
NPT111 Cell line K562 Homo sapiens IC50 = 19.4 ug.mL-1 PMID[20815366]
NPT111 Cell line K562 Homo sapiens IC50 = 14.8 ug.mL-1 PMID[8496706]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 18.8 ug.mL-1 PMID[21493075]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 17.2 ug.mL-1 PMID[21493075]

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 NPC178025 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 NPC181743
0.7627 Intermediate Similarity NPC16287
0.7143 Intermediate Similarity NPC29152
0.6774 Remote Similarity NPC236618
0.6615 Remote Similarity NPC66344
0.6613 Remote Similarity NPC110923
0.6613 Remote Similarity NPC74296
0.6364 Remote Similarity NPC23217
0.6333 Remote Similarity NPC168824
0.6308 Remote Similarity NPC186975
0.6269 Remote Similarity NPC156546
0.623 Remote Similarity NPC189917
0.623 Remote Similarity NPC96812
0.6212 Remote Similarity NPC117122
0.6056 Remote Similarity NPC470113
0.5672 Remote Similarity NPC195366
0.5672 Remote Similarity NPC60350
0.5672 Remote Similarity NPC114743
0.5493 Remote Similarity NPC479655
0.5429 Remote Similarity NPC476174
0.5224 Remote Similarity NPC474962
0.5217 Remote Similarity NPC476293
0.5181 Remote Similarity NPC293052
0.5156 Remote Similarity NPC214770
0.5156 Remote Similarity NPC477856
0.5147 Remote Similarity NPC476186
0.5068 Remote Similarity NPC479651

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC178025 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