Natural Product: NPC593485

Natural Product IDNPC593485
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 7-Acetyllycopsamine
IUPAC Name [(7~{R},8~{R})-7-acetoxy-5,6,7,8-tetrahydro-3~{H}-pyrrolizin-1-yl]methyl (2~{S})-2-hydroxy-2-[(1~{S})-1-hydroxyethyl]-3-methyl-butanoate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 RKDOFSJTBIDAHX-OFSOMGBPSA-N
Standard InCHI InChI=1S/C17H27NO6/c1-10(2)17(22,11(3)19)16(21)23-9-13-5-7-18-8-6-14(15(13)18)24-12(4)20/h5,10-11,14-15,19,22H,6-9H2,1-4H3/t11-,14+,15+,17-/m0/s1
SMILES CC(=O)O[C@@H]1CCN2CC=C(COC(=O)[C@](O)(C(C)C)[C@H](C)O)[C@H]12

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   341.18 Volume:   341.304
?
Van der Waals volume.
Dense:   1.0 LogP:   1.333
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.461
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.749
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   11.0
TPSA:   96.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.528 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.294 Fsp3:   0.765
MCE-18:   39.667
?
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:   0.294 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.029
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.006 Promiscuous compounds:   0.393

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.254 MDCK Permeability:   -5.021
Pgp-inhibitor:   0.036 Pgp-substrate:   0.718
PAMPA:   0.709
?
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):   0.191
20% Bioavailability (F20%):   0.985 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.01 MRP1:   0.991
Plasma Protein Binding (PPB):   39.616% Volume Distribution (VD):   -0.137
Fu: 59.818%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.997
OATP1B3 inhibitor:   0.995 BCRP inhibitor:   0.02
BSEP inhibitor:   0.568

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.014
CYP2C19-inhibitor:   0.032 CYP2C19-substrate:   0.455
CYP2C9-inhibitor:   0.005 CYP2C9-substrate:   0.03
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.003 CYP3A4-substrate:   0.974
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.989
HLM stability:   0.823
?
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):  7.99 Half-life (T1/2):  2.091

ADMET: Toxicity

hERG Blockers:  0.079 hERG Blockers (10um):  0.357
Human Hepatotoxicity (H-HT):  0.899 Drug-induced Liver Injury (DILI):  0.07
AMES Toxicity:  0.572 Rat Oral Acute Toxicity:  0.575
Maximum Recommended Daily Dose:  0.698 Skin Sensitization:  0.99
Carcinogencity:  0.966 Eye Corrosion:  0.005
Eye Irritation:  0.203 Respiratory Toxicity:  0.54
Drug-induced Neurotoxicity:  0.586 Ototoxicity:  0.327
Hematotoxicity:  0.29 Drug-induced Nephrotoxicity:  0.477
Genotoxicity:  0.987 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.083 Hek293 Cytotoxicity:  0.342
BCF:   0.502
?
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:   3.282
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.822
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.071
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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
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26680 Amsinckia intermedia Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO57965 Anchusa arvensis (L.) Bieb. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO43587 Anchusa officinalis L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO50460 Borago officinalis L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO53088 Symphytum asperum Lepech. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44484 Symphytum bulbosum K. F. Schimp. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52568 Symphytum officinale L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO47550 Symphytum tuberosum L. Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48061 Symphytum x.uplandicum Genus Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO46276 Echium horridum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO51974 Echium rauwolfii Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15142 Echium plantagineum Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26680 Amsinckia intermedia Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15142 Echium plantagineum Species Boraginaceae 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 NPC593485 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
0.7288 Intermediate Similarity NPC608959
0.7241 Intermediate Similarity NPC608751
0.6897 Remote Similarity NPC30911
0.6897 Remote Similarity NPC608092
0.678 Remote Similarity NPC130124
0.678 Remote Similarity NPC193471
0.678 Remote Similarity NPC608663
0.6721 Remote Similarity NPC316984
0.6721 Remote Similarity NPC23963
0.6557 Remote Similarity NPC47857
0.6557 Remote Similarity NPC181510
0.6557 Remote Similarity NPC168758
0.6557 Remote Similarity NPC602310
0.6557 Remote Similarity NPC609037
0.6452 Remote Similarity NPC201889
0.6452 Remote Similarity NPC106791
0.6452 Remote Similarity NPC607716
0.625 Remote Similarity NPC279833
0.625 Remote Similarity NPC173690
0.625 Remote Similarity NPC80439
0.5469 Remote Similarity NPC610562
0.5441 Remote Similarity NPC600980
0.5079 Remote Similarity NPC64168

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC593485 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
0.6897 Remote Similarity NPD2204 Approved

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