Natural Product: NPC28425

Natural Product IDNPC28425
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Aristolactam Aiiia
IUPAC Name n.a.
Synonyms SCH-546909
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL388956
PubChem CID 10356352
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002663] Aristolactams

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 PFXGXKFPTAJYHV-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H11NO4/c1-21-15-12(19)6-10-13-11(17-16(10)20)4-7-2-3-8(18)5-9(7)14(13)15/h2-6,18-19H,1H3,(H,17,20)
SMILES COc1c(O)cc2c3c1c1cc(O)ccc1cc3N=C2O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   281.07 Volume:   276.132
?
Van der Waals volume.
Dense:   1.018 LogP:   2.513
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.251
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.377
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   19.0
TPSA:   82.28
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   3.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.597 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.094 Fsp3:   0.062
MCE-18:   44.0
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.884 Fluc inhibitor:   0.584
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.917
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.767
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.059 Promiscuous compounds:   0.308

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.002 MDCK Permeability:   -4.81
Pgp-inhibitor:   0.007 Pgp-substrate:   0.919
PAMPA:   0.951
?
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):   0.115
20% Bioavailability (F20%):   0.648 30% Bioavailability (F30%):   0.623
50% Bioavailability (F50%):   0.961

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.006 MRP1:   0.879
Plasma Protein Binding (PPB):   93.696% Volume Distribution (VD):   -0.654
Fu: 6.216%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.817
OATP1B3 inhibitor:   0.972 BCRP inhibitor:   0.376
BSEP inhibitor:   0.379

ADMET: Metabolism

CYP1A2-inhibitor:   0.105 CYP1A2-substrate:   0.03
CYP2C19-inhibitor:   0.33 CYP2C19-substrate:   0.178
CYP2C9-inhibitor:   0.888 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.989 CYP2D6-substrate:   0.129
CYP3A4-inhibitor:   0.147 CYP3A4-substrate:   0.014
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.956
HLM stability:   0.346
?
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):  3.907 Half-life (T1/2):  1.688

ADMET: Toxicity

hERG Blockers:  0.097 hERG Blockers (10um):  0.32
Human Hepatotoxicity (H-HT):  0.833 Drug-induced Liver Injury (DILI):  0.926
AMES Toxicity:  0.771 Rat Oral Acute Toxicity:  0.543
Maximum Recommended Daily Dose:  0.7 Skin Sensitization:  0.825
Carcinogencity:  0.672 Eye Corrosion:  0.0
Eye Irritation:  0.939 Respiratory Toxicity:  0.911
Drug-induced Neurotoxicity:  0.452 Ototoxicity:  0.625
Hematotoxicity:  0.546 Drug-induced Nephrotoxicity:  0.671
Genotoxicity:  0.771 RPMI-8226 Immunitoxicity:  0.11
A549 Cytotoxicity:  0.392 Hek293 Cytotoxicity:  0.612
BCF:   1.212
?
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:   3.758
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.717
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.12
?
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
NPO18509 Fissistigma oldhamii Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10978218]
NPO23507 Fissistigma balansae Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10978218]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[11040054]
NPO2884 Annona squamosa Species Annonaceae Eukaryota seeds n.a. n.a. PMID[11141125]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[12398544]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota Stems n.a. n.a. PMID[12880323]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[16724856]
NPO18509 Fissistigma oldhamii Species Annonaceae Eukaryota stem n.a. n.a. PMID[17081761]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[18419154]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[19296389]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[19900811]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[20097074]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. PMID[21353775]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[21910504]
NPO2884 Annona squamosa Species Annonaceae Eukaryota seeds n.a. n.a. PMID[22011319]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. seed n.a. PMID[22011319]
NPO2884 Annona squamosa Species Annonaceae Eukaryota Barks n.a. n.a. PMID[2348205]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. aerial part n.a. PMID[8237383]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[8368081]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. fruit n.a. PMID[8786370]
NPO2884 Annona squamosa Species Annonaceae Eukaryota bark n.a. n.a. PMID[9214729]
NPO18509 Fissistigma oldhamii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23507 Fissistigma balansae Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. Database[FooDB]
NPO2884 Annona squamosa Species Annonaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18443 Aristolochia manshuriensis Species Aristolochiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4865 Piper kadsura Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10517 Aconitum vilmorini Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23507 Fissistigma balansae Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18509 Fissistigma oldhamii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2884 Annona squamosa Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11236 Mycale mytilorum Species Mycalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9769 Mortonia palmeri 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
NPT1371 Individual protein Cyclin-dependent kinase 2 Homo sapiens IC50 = 140.0 nM PMID[20097074]
NPT1423 Individual protein Cyclin-dependent kinase 1 Homo sapiens IC50 = 200.0 nM PMID[20097066]
NPT2213 Individual protein Cyclin-dependent kinase 4 Homo sapiens IC50 = 2000.0 nM PMID[20097066]
NPT1432 Individual protein Serine/threonine-protein kinase Aurora-A Homo sapiens IC50 = 5000.0 nM PMID[20097066]
NPT1423 Individual protein Cyclin-dependent kinase 1 Homo sapiens IC50 = 214.0 nM PMID[20097074]
NPT2213 Individual protein Cyclin-dependent kinase 4 Homo sapiens IC50 = 1420.0 nM PMID[20097074]
NPT1433 Individual protein Serine/threonine-protein kinase Aurora-B Homo sapiens IC50 = 2140.0 nM PMID[20097074]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1076 Cell line B-cells n.a. IC50 = 19200.0 nM PMID[17081761]
NPT83 Cell line MCF7 Homo sapiens IC50 > 10.0 nM PMID[20097066]
NPT83 Cell line MCF7 Homo sapiens IC50 = 3000.0 nM PMID[20097066]
NPT20967 Cell line Platelet n.a. Inhibition = 90.6 % PMID[10978218]
NPT20967 Cell line Platelet n.a. Inhibition = 56.9 % PMID[10978218]
NPT20967 Cell line Platelet n.a. Inhibition = 39.6 % PMID[10978218]
NPT20967 Cell line Platelet n.a. Inhibition = 80.7 % PMID[10978218]
NPT2 Others Unspecified n.a. IC50 = 18500.0 nM PMID[17081761]
NPT2 Others Unspecified n.a. Ratio CC50/IC50 > 5.0 n.a. PMID[17081761]
NPT2 Others Unspecified n.a. IC50 > 50000.0 nM PMID[20097066]
NPT2 Others Unspecified n.a. IC50 = 35335.0 nM PMID[20097074]

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 NPC28425 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
0.8077 Intermediate Similarity NPC119579
0.7193 Intermediate Similarity NPC215747
0.6897 Remote Similarity NPC55512
0.6724 Remote Similarity NPC180253
0.619 Remote Similarity NPC112676
0.5667 Remote Similarity NPC22928
0.5397 Remote Similarity NPC294244
0.5167 Remote Similarity NPC265383
0.5161 Remote Similarity NPC311936

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC28425 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