Natural Product: NPC188871

Natural Product IDNPC188871
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 3,7-O-Dimethylquercetin
IUPAC Name 2-(3,4-dihydroxyphenyl)-5-hydroxy-3,7-dimethoxychromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL164861
PubChem CID 5280417
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002592] 7-O-methylated flavonoids

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 LUJAXSNNYBCFEE-UHFFFAOYSA-N
Standard InCHI InChI=1S/C17H14O7/c1-22-9-6-12(20)14-13(7-9)24-16(17(23-2)15(14)21)8-3-4-10(18)11(19)5-8/h3-7,18-20H,1-2H3
SMILES COc1cc(O)c2c(c1)oc(c(c2=O)OC)c1ccc(c(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   330.07 Volume:   317.359
?
Van der Waals volume.
Dense:   1.04 LogP:   2.425
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.313
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.988
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   18.0
TPSA:   109.36
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   3.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.633 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.414 Fsp3:   0.118
MCE-18:   19.0
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.504 Fluc inhibitor:   0.458
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.958
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.684
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.391 Promiscuous compounds:   0.846

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.067 MDCK Permeability:   -4.778
Pgp-inhibitor:   0.364 Pgp-substrate:   0.029
PAMPA:   0.158
?
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):   0.171
20% Bioavailability (F20%):   0.332 30% Bioavailability (F30%):   0.836
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.743
Plasma Protein Binding (PPB):   96.113% Volume Distribution (VD):   -0.431
Fu: 3.388%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.744
OATP1B3 inhibitor:   0.996 BCRP inhibitor:   0.959
BSEP inhibitor:   0.922

ADMET: Metabolism

CYP1A2-inhibitor:   0.99 CYP1A2-substrate:   0.104
CYP2C19-inhibitor:   0.148 CYP2C19-substrate:   0.047
CYP2C9-inhibitor:   0.495 CYP2C9-substrate:   0.002
CYP2D6-inhibitor:   0.93 CYP2D6-substrate:   0.991
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.026
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.99
HLM stability:   0.983
?
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):  10.071 Half-life (T1/2):  1.277

ADMET: Toxicity

hERG Blockers:  0.072 hERG Blockers (10um):  0.563
Human Hepatotoxicity (H-HT):  0.36 Drug-induced Liver Injury (DILI):  0.878
AMES Toxicity:  0.588 Rat Oral Acute Toxicity:  0.44
Maximum Recommended Daily Dose:  0.654 Skin Sensitization:  0.859
Carcinogencity:  0.695 Eye Corrosion:  0.464
Eye Irritation:  0.991 Respiratory Toxicity:  0.651
Drug-induced Neurotoxicity:  0.023 Ototoxicity:  0.224
Hematotoxicity:  0.097 Drug-induced Nephrotoxicity:  0.031
Genotoxicity:  0.862 RPMI-8226 Immunitoxicity:  0.03
A549 Cytotoxicity:  0.512 Hek293 Cytotoxicity:  0.362
BCF:   1.184
?
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:   3.809
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.665
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.224
?
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
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[15787457]
NPO12604 Phakellia dendyi Species Bubaridae Eukaryota n.a. Byron Strait, Papua New Guinea 2003 PMID[18327911]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[19420770]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. leaf n.a. PMID[21319848]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[21800859]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[21800859]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[23127886]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[23234407]
NPO17376 Bacillus amyloliquefaciens Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23265519]
NPO17376 Bacillus amyloliquefaciens Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[24698790]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota seeds Nanning, Guangxi Province, China 2013-APR PMID[26398312]
NPO17376 Bacillus amyloliquefaciens Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[27934031]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[32544201]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[3655803]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[39419301]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17376 Bacillus amyloliquefaciens Species Bacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29935 Caesalpinia sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Title]
NPO28927 Gutierrezia microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17376 Bacillus amyloliquefaciens Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18048 Phlomis crinita Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19778 Streptomyces flaveus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO7081 Sidastrum tehuacanum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3220 Aberia caffra n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12604 Phakellia dendyi Species Bubaridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16803 Libanothamnus occultus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3034 Lonchocarpus yucatanensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1540 Scopolia tangutica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21559 Blumea balsamifera Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6819 Cardopatium corymbosum Species Asteraceae 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
NPO18048 Phlomis crinita Methanolic extract Flowers 0.42 ± 0.02 n.a. n.a. % PMID[39419301]

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
NPT1720 Individual protein Plasminogen Homo sapiens IC50 = 1500.0 nM PMID[15787457]
NPT1606 Individual protein NADPH oxidase 4 Homo sapiens IC50 = 1020.0 nM PMID[20731357]
NPT1606 Individual protein NADPH oxidase 4 Homo sapiens Inhibition = 88.0 % PMID[20731357]
NPT1628 Individual protein Thrombin Oryctolagus cuniculus TT = 22.5 s PMID[22647223]
NPT1628 Individual protein Thrombin Oryctolagus cuniculus PT = 7.3 s PMID[22647223]
NPT1628 Individual protein Thrombin Oryctolagus cuniculus APTT = 54.7 s PMID[22647223]
NPT1628 Individual protein Thrombin Oryctolagus cuniculus Activity = 7.3 g/L PMID[22647223]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT189 Cell line Vero Chlorocebus aethiops CyD50 = 10.0 ug ml-1 PMID[1847431]
NPT168 Cell line P388 Mus musculus ED50 = 3.2 ug ml-1 PMID[3655803]
NPT71 Cell line HEK293 Homo sapiens Inhibition = 43.41 % PMID[20731357]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 5800.0 nM PMID[23234407]
NPT113 Cell line RAW264.7 Mus musculus IC50 = 3500.0 nM PMID[23234407]
NPT1668 Cell line NCI-H157 Homo sapiens IC50 = 12970.0 nM PMID[25139569]
NPT81 Cell line A549 Homo sapiens IC50 = 5400.0 nM PMID[25139569]
NPT1669 Cell line NCI-H1792 Homo sapiens IC50 = 19670.0 nM PMID[25139569]
NPT455 Cell line NCI-H522 Homo sapiens IC50 > 50000.0 nM PMID[25139569]
NPT379 Cell line HOP-62 Homo sapiens IC50 = 13180.0 nM PMID[25139569]
NPT387 Cell line M14 Homo sapiens IC50 = 21660.0 nM PMID[25139569]
NPT165 Cell line HeLa Homo sapiens IC50 = 11120.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 7020.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 460.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 15570.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 23960.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 39570.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 21320.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 24100.0 nM PMID[25139569]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 5280.0 nM PMID[25139569]
NPT22995 Cell line B16-F0 Mus musculus Activity = 187.6 % PMID[24853321]
NPT22995 Cell line B16-F0 Mus musculus Activity = 304.3 % PMID[24853321]
NPT22995 Cell line B16-F0 Mus musculus Activity = 134.0 % PMID[24853321]
NPT22995 Cell line B16-F0 Mus musculus Activity = 265.5 % PMID[24853321]
NPT22995 Cell line B16-F0 Mus musculus Activity = 222.8 % PMID[24853321]
NPT22995 Cell line B16-F0 Mus musculus Activity = 171.2 % PMID[24853321]
NPT1048 Organism Poliovirus Human enterovirus C ED99 = 0.3 ug ml-1 PMID[1847431]
NPT35 Others n.a. n.a. IC50 = 102950.0 nM PMID[23234407]

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 NPC188871 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
0.84 Intermediate Similarity NPC146679
0.7843 Intermediate Similarity NPC103904
0.7843 Intermediate Similarity NPC262094
0.7778 Intermediate Similarity NPC78326
0.7736 Intermediate Similarity NPC270620
0.7593 Intermediate Similarity NPC58382
0.7358 Intermediate Similarity NPC87125
0.7358 Intermediate Similarity NPC76376
0.7273 Intermediate Similarity NPC236769
0.7222 Intermediate Similarity NPC108406
0.7222 Intermediate Similarity NPC305663
0.7222 Intermediate Similarity NPC18772
0.7037 Intermediate Similarity NPC286342
0.6964 Remote Similarity NPC206604
0.6909 Remote Similarity NPC607913
0.6786 Remote Similarity NPC246204
0.6727 Remote Similarity NPC214138
0.6727 Remote Similarity NPC163524
0.6716 Remote Similarity NPC84362
0.6716 Remote Similarity NPC271692
0.6667 Remote Similarity NPC99671
0.6607 Remote Similarity NPC100916
0.6545 Remote Similarity NPC287979
0.6491 Remote Similarity NPC200388
0.6429 Remote Similarity NPC149127
0.6429 Remote Similarity NPC176665
0.6429 Remote Similarity NPC610660
0.6379 Remote Similarity NPC55619
0.6207 Remote Similarity NPC153758
0.614 Remote Similarity NPC260895
0.614 Remote Similarity NPC143799
0.614 Remote Similarity NPC234133
0.614 Remote Similarity NPC130894
0.614 Remote Similarity NPC605755
0.6087 Remote Similarity NPC136042
0.6034 Remote Similarity NPC22472
0.5965 Remote Similarity NPC90582
0.5965 Remote Similarity NPC103342
0.5862 Remote Similarity NPC101830
0.5789 Remote Similarity NPC606920
0.5775 Remote Similarity NPC46420
0.5738 Remote Similarity NPC252933
0.5738 Remote Similarity NPC137062
0.569 Remote Similarity NPC127447
0.569 Remote Similarity NPC152042
0.569 Remote Similarity NPC29353
0.5676 Remote Similarity NPC605784
0.5667 Remote Similarity NPC300943
0.5667 Remote Similarity NPC200740
0.5667 Remote Similarity NPC605582
0.5634 Remote Similarity NPC158674
0.5593 Remote Similarity NPC59951
0.5593 Remote Similarity NPC110070
0.5593 Remote Similarity NPC605144
0.5574 Remote Similarity NPC25495
0.5574 Remote Similarity NPC179126
0.5574 Remote Similarity NPC18607
0.5574 Remote Similarity NPC223579
0.55 Remote Similarity NPC32420
0.5488 Remote Similarity NPC486577
0.5484 Remote Similarity NPC261004
0.5484 Remote Similarity NPC279989
0.5424 Remote Similarity NPC43243
0.5424 Remote Similarity NPC266960
0.5424 Remote Similarity NPC184536
0.541 Remote Similarity NPC82325
0.541 Remote Similarity NPC166753
0.5333 Remote Similarity NPC33265
0.5333 Remote Similarity NPC48479
0.5333 Remote Similarity NPC32557
0.5333 Remote Similarity NPC486841
0.5323 Remote Similarity NPC124784
0.5323 Remote Similarity NPC177298
0.5323 Remote Similarity NPC195202
0.5323 Remote Similarity NPC603112
0.5278 Remote Similarity NPC249281
0.527 Remote Similarity NPC478468
0.5254 Remote Similarity NPC607530
0.5246 Remote Similarity NPC9609
0.5246 Remote Similarity NPC25270
0.5246 Remote Similarity NPC162313
0.5238 Remote Similarity NPC152166
0.5205 Remote Similarity NPC297987
0.52 Remote Similarity NPC611303
0.5167 Remote Similarity NPC203891
0.5167 Remote Similarity NPC189960
0.5167 Remote Similarity NPC123886
0.5167 Remote Similarity NPC98661
0.5161 Remote Similarity NPC176300
0.5147 Remote Similarity NPC76833
0.5135 Remote Similarity NPC27640
0.5085 Remote Similarity NPC62042
0.5082 Remote Similarity NPC270465
0.5082 Remote Similarity NPC606763
0.5082 Remote Similarity NPC610359
0.5079 Remote Similarity NPC603596
0.5068 Remote Similarity NPC238376

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC188871 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
0.5059 Remote Similarity NPD7251 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