Natural Product: NPC609522

Natural Product IDNPC609522
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1098319
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 ZNEWHQLOPFWXOF-UHFFFAOYSA-N
Standard InCHI InChI=1S/C2H6O3S2/c3-7(4,5)2-1-6/h6H,1-2H2,(H,3,4,5)
SMILES O=S(=O)(O)CCS

  Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO52386 Methanobacterium formicicum Species Methanobacteriaceae Archaea n.a. n.a. n.a. Database[COCONUT]
NPO42700 Methanosarcina strain TM-1 Genus Methanosarcinaceae Archaea 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
NPT204 Individual protein Acetylcholinesterase Homo sapiens AC50 > 10000.0 nM PMID[37468498]
NPT2761 Individual protein Phosphodiesterase 4A Homo sapiens AC50 = 8998.7 nM PMID[37468498]
NPT291 Individual protein Serotonin 2b (5-HT2b) receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT1788 Individual protein Alpha-1a adrenergic receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT222 Individual protein Alpha-2a adrenergic receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT2769 Individual protein Thromboxane A2 receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT242 Individual protein Dopamine D1 receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT145 Individual protein Mu opioid receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT261 Individual protein Monoamine oxidase A Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT1478 Individual protein Vascular endothelial growth factor receptor 2 Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT108 Individual protein Estrogen receptor alpha Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT218 Individual protein Adenosine A3 receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT153 Individual protein Androgen Receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT262 Individual protein Muscarinic acetylcholine receptor M1 Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT263 Individual protein Muscarinic acetylcholine receptor M2 Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT295 Individual protein Serotonin transporter Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT246 Individual protein Dopamine transporter Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT228 Individual protein Norepinephrine transporter Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens AC50 = 485.8 nM PMID[37468498]
NPT30 Individual protein Cyclooxygenase-1 Homo sapiens AC50 = 779.9 nM PMID[37468498]
NPT244 Individual protein Dopamine D3 receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT987 Individual protein Histamine H3 receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT98 Individual protein HERG Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT542 Individual protein Progesterone receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT692 Individual protein Histone deacetylase 6 Homo sapiens Inhibition = -4.93 % HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT692 Individual protein Histone deacetylase 6 Homo sapiens Inhibition = -2.04 % HDAC6 screening dataset using tau-based substrate in an enzymatic assay yields selective inhibitors and activators
NPT92 Individual protein Serotonin 1a (5-HT1a) receptor Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT29454 Single protein Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 Homo sapiens Inhibition = -0.771 % PMID[38318365]
NPT5104 Individual protein Phosphodiesterase 3A Homo sapiens AC50 > 30000.0 nM PMID[37468498]
NPT670 Individual protein Thrombin Homo sapiens AC50 > 30000.0 nM PMID[37468498]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM Screening of ~5500 FDA-approved drugs and clinical candidates for anti-SARS-CoV-2 activity
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM Screening of ~5500 FDA-approved drugs and clinical candidates for anti-SARS-CoV-2 activity
NPT29392 Protein complex Gamma-aminobutyric acid receptor subunit alpha-1/alpha-2/beta-2/gamma-2 Homo sapiens AC50 > 30000.0 nM PMID[37468498]

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
- Mus musculus LD50 = 1.850788274 mg/kg TOXRIC

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 NPC609522 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
0.6471 Remote Similarity NPC320704

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC609522 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
1.0 High Similarity NPD7376 Phase 4
0.6316 Remote Similarity NPD8227 Phase 1
0.6 Remote Similarity NPD7372 Phase 2

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