Natural Product: NPC473262

Natural Product IDNPC473262
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(5S,6R)-7,9-Dibromo-N-[4-[[(5S,6R,7R)-7,9-Dibromo-6-Hydroxy-8-Oxo-1-Oxa-2-Azaspiro[4.5]Deca-2,9-Diene-3-Carbonyl]Amino]Butyl]-6-Hydroxy-8-Methoxy-1-Oxa-2-Azaspiro[4.5]Deca-2,7,9-Triene-3-Carboxamide
IUPAC Name (5S,6R)-7,9-dibromo-N-[4-[[(5S,6R,7R)-7,9-dibromo-6-hydroxy-8-oxo-1-oxa-2-azaspiro[4.5]deca-2,9-diene-3-carbonyl]amino]butyl]-6-hydroxy-8-methoxy-1-oxa-2-azaspiro[4.5]deca-2,7,9-triene-3-carboxamide
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL388349
PubChem CID 44424480
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0004325] Cyclohexenones

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 ONDRQQMSEBCZNC-ONIYMPRESA-N
Standard InCHI InChI=1S/C23H24Br4N4O8/c1-37-17-11(25)7-23(19(34)15(17)27)9-13(31-39-23)21(36)29-5-3-2-4-28-20(35)12-8-22(38-30-12)6-10(24)16(32)14(26)18(22)33/h6-7,14,18-19,33-34H,2-5,8-9H2,1H3,(H,28,35)(H,29,36)/t14-,18-,19-,22+,23+/m0/s1
SMILES COC1=C(C(C2(CC(=NO2)C(=O)NCCCCNC(=O)C3=NOC4(C3)C=C(C(=O)C(C4O)Br)Br)C=C1Br)O)Br

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   799.83 Volume:   542.49
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Van der Waals volume.
Dense:   1.474 LogP:   2.493
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.347
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.812
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The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   25.0
TPSA:   168.14
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Topological Polar Surface Area.
H-Bond Acceptor:   12.0
H-Bond Donor:   4.0 Rings:   4.0
Heavy Atoms:   16.0

MedChem Properties

QED Drug-Likeness Score:   0.214 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.813 Fsp3:   0.522
MCE-18:   102.0
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   1
Colloidal aggregators:   0.538 Fluc inhibitor:   0.003
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.086
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.582
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.371 Promiscuous compounds:   0.0

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.824 MDCK Permeability:   -4.687
Pgp-inhibitor:   0.013 Pgp-substrate:   0.004
PAMPA:   0.999
?
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):   0.855
20% Bioavailability (F20%):   0.122 30% Bioavailability (F30%):   0.927
50% Bioavailability (F50%):   0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.965
Plasma Protein Binding (PPB):   95.988% Volume Distribution (VD):   -0.21
Fu: 3.178%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.855

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.147
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.984
CYP3A4-inhibitor:   0.073 CYP3A4-substrate:   0.004
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.143
?
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):  0.763 Half-life (T1/2):  4.282

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.325
Human Hepatotoxicity (H-HT):  0.12 Drug-induced Liver Injury (DILI):  0.999
AMES Toxicity:  0.996 Rat Oral Acute Toxicity:  0.991
Maximum Recommended Daily Dose:  0.999 Skin Sensitization:  1.0
Carcinogencity:  0.981 Eye Corrosion:  0.0
Eye Irritation:  0.12 Respiratory Toxicity:  0.996
Drug-induced Neurotoxicity:  0.747 Ototoxicity:  0.779
Hematotoxicity:  0.004 Drug-induced Nephrotoxicity:  0.115
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.034
A549 Cytotoxicity:  0.018 Hek293 Cytotoxicity:  0.95
BCF:   1.071
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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:   4.034
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.611
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.097
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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
NPO8996 Aplysina gerardogreeni Species Aplysinidae Eukaryota n.a. n.a. n.a. PMID[17512741]
NPO8996 Aplysina gerardogreeni Species Aplysinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8996 Aplysina gerardogreeni Species Aplysinidae 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
NPT139 Cell line HT-29 Homo sapiens GI50 = 3400.0 nM PMID[26035018]
NPT82 Cell line MDA-MB-231 Homo sapiens GI50 = 2900.0 nM PMID[23398362]
NPT82 Cell line MDA-MB-231 Homo sapiens TGI = 4700.0 nM PMID[20430633]
NPT81 Cell line A549 Homo sapiens GI50 = 5600.0 nM PMID[23398362]
NPT81 Cell line A549 Homo sapiens TGI > 10.0 ug.mL-1 PMID[23398362]
NPT139 Cell line HT-29 Homo sapiens TGI = 4900.0 nM PMID[24617951]

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 NPC473262 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 NPC202166
0.9355 High Similarity NPC473261
0.9355 High Similarity NPC300912
0.8305 Intermediate Similarity NPC1702
0.7742 Intermediate Similarity NPC158672
0.7419 Intermediate Similarity NPC470892
0.7419 Intermediate Similarity NPC172626
0.7083 Intermediate Similarity NPC470886
0.6866 Remote Similarity NPC487917
0.6667 Remote Similarity NPC145149
0.6486 Remote Similarity NPC260270
0.6447 Remote Similarity NPC130714
0.6316 Remote Similarity NPC66855
0.6133 Remote Similarity NPC313173
0.6104 Remote Similarity NPC181086
0.6066 Remote Similarity NPC30521
0.5844 Remote Similarity NPC81079
0.5844 Remote Similarity NPC304257
0.5694 Remote Similarity NPC473683
0.5679 Remote Similarity NPC477220
0.5679 Remote Similarity NPC608121
0.5595 Remote Similarity NPC483876
0.5595 Remote Similarity NPC600925
0.5595 Remote Similarity NPC607066
0.557 Remote Similarity NPC487872
0.557 Remote Similarity NPC600759
0.557 Remote Similarity NPC608122
0.5529 Remote Similarity NPC202866
0.5465 Remote Similarity NPC601097
0.5455 Remote Similarity NPC289324
0.5432 Remote Similarity NPC201900
0.5402 Remote Similarity NPC77435
0.5402 Remote Similarity NPC259071
0.5366 Remote Similarity NPC487873
0.5281 Remote Similarity NPC603425
0.5222 Remote Similarity NPC480151
0.5165 Remote Similarity NPC606574
0.5116 Remote Similarity NPC487915
0.5109 Remote Similarity NPC611077
0.5057 Remote Similarity NPC487914
0.5057 Remote Similarity NPC489611
0.5057 Remote Similarity NPC604329
0.5054 Remote Similarity NPC607100

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC473262 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