Natural Product: NPC124478

Natural Product IDNPC124478
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Puerarin
IUPAC Name 7-hydroxy-3-(4-hydroxyphenyl)-8-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]chromen-4-one
Synonyms Puerarin
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL486386
PubChem CID 5281807
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002896] Isoflavonoid C-glycosides

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 HKEAFJYKMMKDOR-VPRICQMDSA-N
Standard InCHI InChI=1S/C21H20O9/c22-7-14-17(26)18(27)19(28)21(30-14)15-13(24)6-5-11-16(25)12(8-29-20(11)15)9-1-3-10(23)4-2-9/h1-6,8,14,17-19,21-24,26-28H,7H2/t14-,17-,18+,19-,21+/m1/s1
SMILES c1cc(ccc1c1coc2c(ccc(c2[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O)c1=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   416.11 Volume:   395.567
?
Van der Waals volume.
Dense:   1.052 LogP:   0.339
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.968
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.215
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   24.0
TPSA:   160.82
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   6.0 Rings:   4.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.355 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.859 Fsp3:   0.286
MCE-18:   84.259
?
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:   0.588 Fluc inhibitor:   0.198
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.957
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.589
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.283 Promiscuous compounds:   0.253

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.355 MDCK Permeability:   -5.104
Pgp-inhibitor:   0.0 Pgp-substrate:   0.257
PAMPA:   1.0
?
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):   0.758
20% Bioavailability (F20%):   0.582 30% Bioavailability (F30%):   0.987
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.039 MRP1:   0.165
Plasma Protein Binding (PPB):   78.729% Volume Distribution (VD):   -0.008
Fu: 23.582%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.22
OATP1B3 inhibitor:   0.967 BCRP inhibitor:   0.014
BSEP inhibitor:   0.014

ADMET: Metabolism

CYP1A2-inhibitor:   0.024 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.079
CYP2C9-inhibitor:   0.274 CYP2C9-substrate:   0.007
CYP2D6-inhibitor:   0.069 CYP2D6-substrate:   0.004
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.028
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.953
HLM stability:   0.004
?
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):  3.85 Half-life (T1/2):  4.179

ADMET: Toxicity

hERG Blockers:  0.033 hERG Blockers (10um):  0.172
Human Hepatotoxicity (H-HT):  0.669 Drug-induced Liver Injury (DILI):  0.807
AMES Toxicity:  0.786 Rat Oral Acute Toxicity:  0.108
Maximum Recommended Daily Dose:  0.117 Skin Sensitization:  0.963
Carcinogencity:  0.292 Eye Corrosion:  0.0
Eye Irritation:  0.587 Respiratory Toxicity:  0.068
Drug-induced Neurotoxicity:  0.049 Ototoxicity:  0.884
Hematotoxicity:  0.152 Drug-induced Nephrotoxicity:  0.461
Genotoxicity:  0.869 RPMI-8226 Immunitoxicity:  0.102
A549 Cytotoxicity:  0.419 Hek293 Cytotoxicity:  0.435
BCF:   0.639
?
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:   3.224
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.504
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.898
?
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
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2008.08.002]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.lwt.2014.11.023]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/jf00025a020]
NPO9446 Asterias rathbuni Species Asteriidae Eukaryota n.a. n.a. n.a. PMID[11473430]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19829679]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. root n.a. PMID[21087019]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22314230]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23521110]
NPO30303 Pueraria lobata Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25679337]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota roots n.a. n.a. PMID[26259802]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26690274]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. PMID[27617953]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota Roots n.a. n.a. PMID[28257196]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37569279]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9834167]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30303 Pueraria lobata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9446 Asterias rathbuni Species Asteriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5081 Amorphinopsis foetida Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6243 Fomes fastuosus Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13715 Bertya dimerostigma Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31315 Pueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30892 Pueraria thomsonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30303 Pueraria lobata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31315 Pueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30303 Pueraria lobata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30892 Pueraria thomsonii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5986 Ziziphus jujuba Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25653 Spatholobus suberectus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5479 Astragalus wiedemannianus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9446 Asterias rathbuni Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17774 Hemerocallis fulva Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25932 Delphinium barbeyi Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6243 Fomes fastuosus Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8707.1 Pueraria montana var. lobata Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29401 Bupleurum chinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5081 Amorphinopsis foetida Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8707.2 Pueraria montana var. thomsonii Varieties Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13715 Bertya dimerostigma Species Euphorbiaceae 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
NPT3000 Individual protein Monoglyceride lipase Homo sapiens Inhibition = 52.0 % DOI[10.1039/C4MD00186A]
NPT233 Individual protein Carbonic anhydrase II Homo sapiens Ki > 10000.0 nM PMID[26498393]
NPT1062 Individual protein Carbonic anhydrase IV Homo sapiens Ki > 10000.0 nM PMID[26498393]
NPT142 Individual protein Fatty acid binding protein adipocyte Homo sapiens Inhibition = 1.71 % PMID[28738306]
NPT955 Individual protein Carbonic anhydrase VII Homo sapiens Ki = 452.6 nM PMID[26498393]
NPT7 Individual protein Thioredoxin reductase 1, cytoplasmic Rattus norvegicus Potency n.a. 31622.8 nM PubChem BioAssay data set
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 15.04 % DOI[10.6019/CHEMBL4495564]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = -39.42 % DOI[10.6019/CHEMBL4495564]
NPT949 Individual protein Carbonic anhydrase XII Homo sapiens Ki = 515.0 nM PMID[26498393]
NPT622 Individual protein Solute carrier organic anion transporter family member 2B1 Homo sapiens Inhibition < 20.0 % PMID[37252098]
NPT947 Individual protein Carbonic anhydrase I Homo sapiens Ki > 10000.0 nM PMID[26498393]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT520 Cell line 3T3-L1 Mus musculus FC = 1.5 n.a. PMID[20605096]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 2332.3 nM PubChem BioAssay data set
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 13115.4 nM PubChem BioAssay data set
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 5.17 % DOI[10.21203/rs.3.rs-23951/v1]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.08 % DOI[10.6019/CHEMBL4495565]
NPT20555 Organism SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -0.17 % DOI[10.6019/CHEMBL4495565]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 108.0 % PMID[12828463]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 145.0 % PMID[12828463]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT65 Cell line HepG2 Homo sapiens Survival = 41.29 % PMID[27717545]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 33.5 mg kg-1 PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 13.4 mmol/L PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 1.01 a.u. PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 0.88 a.u. PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 80.0 % PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 16.5 mmol/L PMID[12828463]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 3.9 mmol/L PMID[12828463]





 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 NPC124478 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
0.7606 Intermediate Similarity NPC177308
0.7089 Intermediate Similarity NPC607879
0.557 Remote Similarity NPC209846
0.5119 Remote Similarity NPC161749
0.506 Remote Similarity NPC112701

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC124478 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 NPD4380 Phase 2
0.5119 Remote Similarity NPD4381 Clinical (unspecified phase)

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