Natural Product: NPC115556

Natural Product IDNPC115556
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 YGPRSGKVLATIHT-UQCMEYCASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5281172
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001775] Amaryllidaceae alkaloids
        • [CHEMONTID:0004123] Crinine- and Haemanthamine-type amaryllidaceae alkaloids

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 YGPRSGKVLATIHT-UQCMEYCASA-N
Standard InCHI InChI=1S/C17H19NO4/c1-20-11-2-3-17-12-6-14-13(21-9-22-14)4-10(12)7-18(8-16(17)19)15(17)5-11/h2-4,6,11,15-16,19H,5,7-9H2,1H3/t11-,15-,16+,17-/m0/s1
SMILES CO[C@H]1C=C[C@]23c4cc5c(cc4CN(C[C@H]3O)[C@H]2C1)OCO5

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   301.13 Volume:   295.418
?
Van der Waals volume.
Dense:   1.019 LogP:   0.858
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.02
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.343
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   23.0
TPSA:   51.16
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.79 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.217 Fsp3:   0.529
MCE-18:   94.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.223 Fluc inhibitor:   0.004
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.189
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.014
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.003 Promiscuous compounds:   0.332

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.895 MDCK Permeability:   -4.726
Pgp-inhibitor:   0.1 Pgp-substrate:   0.822
PAMPA:   0.286
?
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%):   0.122 30% Bioavailability (F30%):   0.008
50% Bioavailability (F50%):   0.492

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.54 MRP1:   0.86
Plasma Protein Binding (PPB):   62.968% Volume Distribution (VD):   0.3
Fu: 34.28%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.981
OATP1B3 inhibitor:   0.876 BCRP inhibitor:   0.013
BSEP inhibitor:   0.992

ADMET: Metabolism

CYP1A2-inhibitor:   0.413 CYP1A2-substrate:   0.023
CYP2C19-inhibitor:   0.901 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.552 CYP2C9-substrate:   0.969
CYP2D6-inhibitor:   0.987 CYP2D6-substrate:   0.842
CYP3A4-inhibitor:   0.03 CYP3A4-substrate:   0.776
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.152
?
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):  8.319 Half-life (T1/2):  2.572

ADMET: Toxicity

hERG Blockers:  0.164 hERG Blockers (10um):  0.371
Human Hepatotoxicity (H-HT):  0.652 Drug-induced Liver Injury (DILI):  0.297
AMES Toxicity:  0.657 Rat Oral Acute Toxicity:  0.659
Maximum Recommended Daily Dose:  0.924 Skin Sensitization:  0.43
Carcinogencity:  0.851 Eye Corrosion:  0.003
Eye Irritation:  0.588 Respiratory Toxicity:  0.888
Drug-induced Neurotoxicity:  0.215 Ototoxicity:  0.653
Hematotoxicity:  0.325 Drug-induced Nephrotoxicity:  0.734
Genotoxicity:  0.71 RPMI-8226 Immunitoxicity:  0.098
A549 Cytotoxicity:  0.069 Hek293 Cytotoxicity:  0.245
BCF:   0.435
?
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:   3.03
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.717
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.711
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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
NPO9457 Machaerium opacum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11473 Viburnum lantana Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19776 Hesperocyparis arizonica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9485 Haplopappus deserticola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11000 Eupatorium laevigatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9144 Atriplex parvifolia Species Chenopodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1412 Artemisia juncea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9485 Haplopappus deserticola Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9457 Machaerium opacum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11473 Viburnum lantana Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11000 Eupatorium laevigatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19776 Hesperocyparis arizonica Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1412 Artemisia juncea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9927 Crinum asiaticum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3630 Crotalaria crispata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9144 Atriplex parvifolia Species Chenopodiaceae 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

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 NPC115556 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 NPC266176
1.0 High Similarity NPC158148
1.0 High Similarity NPC290759
1.0 High Similarity NPC82533
0.8413 Intermediate Similarity NPC474470
0.7576 Intermediate Similarity NPC244554
0.6875 Remote Similarity NPC58766
0.6875 Remote Similarity NPC475686
0.6716 Remote Similarity NPC225597
0.6515 Remote Similarity NPC78733
0.6056 Remote Similarity NPC609368
0.5882 Remote Similarity NPC247972
0.5616 Remote Similarity NPC218614
0.5616 Remote Similarity NPC607661
0.5417 Remote Similarity NPC252960
0.5139 Remote Similarity NPC65403
0.507 Remote Similarity NPC215829
0.5067 Remote Similarity NPC75958

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC115556 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