Natural Product: NPC509671

Natural Product IDNPC509671
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 6-methoxydiphyllin
IUPAC Name (9~{R},9~{a}~{R})-9-(1,3-benzodioxol-5-yl)-4-hydroxy-5,6,7-trimethoxy-3~{a},4,9,9~{a}-tetrahydro-3~{H}-benzo[f]isobenzofuran-1-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0001392] Lignans, neolignans and related compounds
      • [CHEMONTID:0001510] Lignan lactones

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 YDSHUGJNIUQDAY-OKROVLOASA-N
Standard InCHI InChI=1S/C22H22O8/c1-25-15-7-11-16(10-4-5-13-14(6-10)30-9-29-13)17-12(8-28-22(17)24)19(23)18(11)21(27-3)20(15)26-2/h4-7,12,16-17,19,23H,8-9H2,1-3H3/t12?,16-,17+,19?/m1/s1
SMILES COC1=CC2=C(C(OC)=C1OC)C(O)C1COC(=O)[C@@H]1[C@@H]2C1=CC=C2OCOC2=C1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   414.13 Volume:   398.152
?
Van der Waals volume.
Dense:   1.04 LogP:   1.719
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.07
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.022
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   26.0
TPSA:   92.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.763 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.84 Fsp3:   0.409
MCE-18:   94.839
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.086 Fluc inhibitor:   0.254
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.18
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.143
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.038 Promiscuous compounds:   0.284

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.0 MDCK Permeability:   -4.751
Pgp-inhibitor:   0.017 Pgp-substrate:   0.002
PAMPA:   0.211
?
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%):   0.006 30% Bioavailability (F30%):   0.0
50% Bioavailability (F50%):   0.124

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.996 MRP1:   0.998
Plasma Protein Binding (PPB):   98.551% Volume Distribution (VD):   -0.357
Fu: 2.639%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.172
OATP1B3 inhibitor:   0.498 BCRP inhibitor:   0.0
BSEP inhibitor:   0.994

ADMET: Metabolism

CYP1A2-inhibitor:   0.13 CYP1A2-substrate:   0.129
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.595
CYP2C9-inhibitor:   0.158 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.998
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.056
HLM stability:   0.378
?
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):  3.709 Half-life (T1/2):  2.466

ADMET: Toxicity

hERG Blockers:  0.153 hERG Blockers (10um):  0.599
Human Hepatotoxicity (H-HT):  0.674 Drug-induced Liver Injury (DILI):  0.964
AMES Toxicity:  0.62 Rat Oral Acute Toxicity:  0.474
Maximum Recommended Daily Dose:  0.633 Skin Sensitization:  0.774
Carcinogencity:  0.821 Eye Corrosion:  0.004
Eye Irritation:  0.382 Respiratory Toxicity:  0.765
Drug-induced Neurotoxicity:  0.757 Ototoxicity:  0.783
Hematotoxicity:  0.749 Drug-induced Nephrotoxicity:  0.902
Genotoxicity:  0.845 RPMI-8226 Immunitoxicity:  0.283
A549 Cytotoxicity:  0.497 Hek293 Cytotoxicity:  0.524
BCF:   1.042
?
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:   3.437
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.115
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.038
?
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
NPO53594 Apis species Genus Apidae Eukaryota 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

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 NPC509671 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
0.9322 High Similarity NPC288149
0.8197 Intermediate Similarity NPC207584
0.8197 Intermediate Similarity NPC19947
0.7031 Intermediate Similarity NPC237946
0.7031 Intermediate Similarity NPC32373
0.6618 Remote Similarity NPC119910
0.6 Remote Similarity NPC91634
0.6 Remote Similarity NPC150943
0.6 Remote Similarity NPC268718
0.5833 Remote Similarity NPC470637
0.5588 Remote Similarity NPC218092
0.5588 Remote Similarity NPC239890
0.5588 Remote Similarity NPC209411
0.5588 Remote Similarity NPC246474
0.5588 Remote Similarity NPC162851
0.5479 Remote Similarity NPC96593
0.5429 Remote Similarity NPC178574
0.5286 Remote Similarity NPC80230
0.5286 Remote Similarity NPC104024
0.5286 Remote Similarity NPC101755
0.5286 Remote Similarity NPC304687
0.5286 Remote Similarity NPC65574
0.5211 Remote Similarity NPC262455
0.5211 Remote Similarity NPC177476
0.5139 Remote Similarity NPC149505
0.5139 Remote Similarity NPC480477

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC509671 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
0.7031 Intermediate Similarity NPD4965 Approved
0.7031 Intermediate Similarity NPD4966 Phase 4
0.7031 Intermediate Similarity NPD4967 Phase 2
0.5488 Remote Similarity NPD37 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