Natural Product: NPC323948

Natural Product IDNPC323948
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 N,N'-((1Z,3Z)-1,4-Bis(4-Methoxyphenyl)Buta-1,3-Diene-2,3-Diyl)Diformamide
IUPAC Name N-[(1Z,3Z)-3-formamido-1,4-bis(4-methoxyphenyl)buta-1,3-dien-2-yl]formamide
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1813656
PubChem CID 11462296
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related 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 ZRAIRHSUKMHHQT-YZLQMOBTSA-N
Standard InCHI InChI=1S/C20H20N2O4/c1-25-17-7-3-15(4-8-17)11-19(21-13-23)20(22-14-24)12-16-5-9-18(26-2)10-6-16/h3-14H,1-2H3,(H,21,23)(H,22,24)/b19-11-,20-12-
SMILES COC1=CC=C(C=C1)C=C(C(=CC2=CC=C(C=C2)OC)NC=O)NC=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   352.14 Volume:   368.153
?
Van der Waals volume.
Dense:   0.957 LogP:   1.682
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.986
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.49
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The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   16.0
TPSA:   76.66
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Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.537 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.645 Fsp3:   0.1
MCE-18:   12.0
?
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:   0.999 Fluc inhibitor:   0.982
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.622
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.856
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.099 Promiscuous compounds:   0.03

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.73 MDCK Permeability:   -4.608
Pgp-inhibitor:   0.998 Pgp-substrate:   0.002
PAMPA:   0.049
?
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):   0.836
20% Bioavailability (F20%):   0.84 30% Bioavailability (F30%):   0.98
50% Bioavailability (F50%):   0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   79.195% Volume Distribution (VD):   -0.032
Fu: 17.032%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.08
BSEP inhibitor:   0.997

ADMET: Metabolism

CYP1A2-inhibitor:   0.882 CYP1A2-substrate:   0.337
CYP2C19-inhibitor:   0.027 CYP2C19-substrate:   0.65
CYP2C9-inhibitor:   0.286 CYP2C9-substrate:   0.002
CYP2D6-inhibitor:   0.994 CYP2D6-substrate:   0.944
CYP3A4-inhibitor:   0.023 CYP3A4-substrate:   0.001
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.886
?
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):  7.811 Half-life (T1/2):  0.43

ADMET: Toxicity

hERG Blockers:  0.157 hERG Blockers (10um):  0.355
Human Hepatotoxicity (H-HT):  0.491 Drug-induced Liver Injury (DILI):  0.893
AMES Toxicity:  0.692 Rat Oral Acute Toxicity:  0.13
Maximum Recommended Daily Dose:  0.207 Skin Sensitization:  0.127
Carcinogencity:  0.746 Eye Corrosion:  0.0
Eye Irritation:  0.726 Respiratory Toxicity:  0.441
Drug-induced Neurotoxicity:  0.922 Ototoxicity:  0.235
Hematotoxicity:  0.402 Drug-induced Nephrotoxicity:  0.527
Genotoxicity:  0.995 RPMI-8226 Immunitoxicity:  0.107
A549 Cytotoxicity:  0.065 Hek293 Cytotoxicity:  0.36
BCF:   1.388
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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:   3.797
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.342
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.715
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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
NPO21746 Streptomyces peucetius Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[15977277]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17616609]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17929896]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19113967]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19159274]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[19256529]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. isolated from sediment collected using a hand held deep water sampling device at >33 m depth in Vanuatu 2003 PMID[20303767]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21667925]
NPO21746 Streptomyces peucetius Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21667925]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[21954885]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22106303]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota stem bark of Melia azedarach n.a. n.a. PMID[22409377]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23557488]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[23563483]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[7622436]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21746 Streptomyces peucetius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10538 Aspergillus fumigatus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21746 Streptomyces peucetius Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO10538 Aspergillus fumigatus Species Aspergillaceae 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
NPT372 Cell line HOP-92 Homo sapiens IC50 = 890.0 nM PMID[21667925]
NPT397 Cell line NCI-H460 Homo sapiens IC50 = 1120.0 nM PMID[21667925]
NPT399 Cell line SF-295 Homo sapiens IC50 = 700.0 nM PMID[21667925]
NPT380 Cell line U-251 Homo sapiens IC50 = 920.0 nM PMID[21667925]
NPT375 Cell line Malme-3M Homo sapiens IC50 = 650.0 nM PMID[21667925]
NPT170 Cell line SK-MEL-28 Homo sapiens IC50 = 980.0 nM PMID[21667925]
NPT373 Cell line SK-MEL-5 Homo sapiens IC50 = 810.0 nM PMID[21667925]
NPT398 Cell line UACC-62 Homo sapiens IC50 = 750.0 nM PMID[21667925]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 = 840.0 nM PMID[21667925]
NPT376 Cell line A498 Homo sapiens IC50 = 860.0 nM PMID[21667925]
NPT369 Cell line ACHN Homo sapiens IC50 > 2500.0 nM PMID[21667925]
NPT112 Cell line MOLT-4 Homo sapiens IC50 > 2500.0 nM PMID[21667925]

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 NPC323948 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC323948 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