NPASS Compound

Natural Product: NPC596066

Natural Product ID	NPC596066
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2~{R},3~{S},4~{S},5~{R},6~{S})-6-[2-[3-[(2~{S},3~{R},4~{S},5~{S},6~{S})-6-carboxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]oxy-4-hydroxy-5-methoxy-phenyl]-5-hydroxy-4-oxo-chromen-7-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-carboxylic acid
IUPAC Name	(2~{R},3~{S},4~{S},5~{R},6~{S})-6-[2-[3-[(2~{S},3~{R},4~{S},5~{S},6~{S})-6-carboxy-3,4,5-trihydroxy-tetrahydropyran-2-yl]oxy-4-hydroxy-5-methoxy-phenyl]-5-hydroxy-4-oxo-chromen-7-yl]oxy-3,4,5-trihydroxy-tetrahydropyran-2-carboxylic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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

RDKit 3D 75 79 0 0 0 0 0 0 0 0999 V2000 -1.2914 -4.0370 -2.0397 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5733 -3.4871 -1.8280 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6764 -2.2621 -1.1961 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5391 -1.6029 -0.7865 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5980 -0.3793 -0.1527 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3428 0.2641 0.2573 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3140 1.4860 0.8940 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8989 2.0736 1.2726 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9704 3.1724 1.8480 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0725 1.4052 0.9963 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3094 1.9083 1.3327 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3653 3.1474 1.9801 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4839 1.2198 1.0461 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4222 0.0017 0.4093 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5394 -0.7160 0.1042 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8312 -0.3065 0.3968 C 0 0 2 0 0 0 0 0 0 0 0 0 7.5533 -0.2011 -0.8002 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7690 0.4397 -0.5727 C 0 0 1 0 0 0 0 0 0 0 0 0 8.6604 1.9002 -0.6186 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5651 2.5036 -0.8379 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7682 2.6963 -0.4214 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4205 -0.0272 0.7032 C 0 0 1 0 0 0 0 0 0 0 0 0 9.1109 0.7522 1.8000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9558 -1.4546 0.9251 C 0 0 2 0 0 0 0 0 0 0 0 0 9.1240 -2.1462 -0.2830 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4716 -1.4365 1.2119 C 0 0 1 0 0 0 0 0 0 0 0 0 7.2786 -1.0888 2.5491 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1464 -0.4812 0.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9814 0.1880 0.3582 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8039 -0.3213 0.0223 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8234 0.1588 0.0559 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0369 -0.4559 -0.3351 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2098 0.2025 -0.0608 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5141 -0.0774 -0.2815 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.0396 0.8858 -1.1659 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3839 0.6577 -1.4288 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.8077 1.5066 -2.5536 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9904 2.2730 -3.1013 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.1457 1.4328 -2.9917 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.2521 0.9928 -0.2322 C 0 0 1 0 0 0 0 0 0 0 0 0 -10.2255 0.0548 0.0139 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.3287 1.1546 0.9573 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.6912 2.3713 0.9913 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3804 -0.0168 0.9732 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1546 -1.1723 0.9978 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9155 -1.6700 -0.9602 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0354 -2.3687 -1.3895 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6937 -4.0669 -1.0849 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7000 -3.4848 -2.7856 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4349 -5.0981 -2.3347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5637 -2.0349 -0.9547 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2262 2.0209 1.1168 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4299 3.1585 2.9899 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3919 1.7073 1.3545 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9570 0.6536 0.9041 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4304 0.1346 -1.4356 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6291 3.6492 -0.1047 H 0 0 0 0 0 0 0 0 0 0 0 0 10.5242 -0.0497 0.5990 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0173 1.6996 1.5485 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5564 -1.8784 1.7340 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4361 -2.8642 -0.2974 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9789 -2.3933 1.0206 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3138 -1.8864 3.1154 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0781 -1.4341 -0.4183 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9197 1.1158 0.5486 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6728 -1.0383 -0.7903 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5915 -0.4068 -1.6741 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4224 2.1226 -3.6744 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7427 1.9737 -0.3860 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.3172 -0.1773 0.9640 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.9578 1.0665 1.8628 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2871 3.0156 1.4706 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7785 -0.0092 1.8946 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6095 -1.9964 0.9361 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0576 -2.6397 -2.3606 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 2 0 11 12 1 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 18 22 1 0 22 23 1 0 22 24 1 0 24 25 1 0 24 26 1 0 26 27 1 0 14 28 1 0 28 29 2 0 29 30 1 0 5 31 2 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 2 0 37 39 1 0 36 40 1 0 40 41 1 0 40 42 1 0 42 43 1 0 42 44 1 0 44 45 1 0 32 46 2 0 46 47 1 0 46 3 1 0 30 6 1 0 44 34 1 0 29 10 1 0 26 16 1 0 1 48 1 0 1 49 1 0 1 50 1 0 4 51 1 0 7 52 1 0 12 53 1 0 13 54 1 0 16 55 1 1 18 56 1 6 21 57 1 0 22 58 1 6 23 59 1 0 24 60 1 1 25 61 1 0 26 62 1 1 27 63 1 0 28 64 1 0 31 65 1 0 34 66 1 6 36 67 1 6 39 68 1 0 40 69 1 6 41 70 1 0 42 71 1 1 43 72 1 0 44 73 1 1 45 74 1 0 47 75 1 0 M END

Standard InCHIKey	CVQDTIXQCRHCMN-LGOSEKGLSA-N
Standard InCHI	InChI=1S/C28H28O19/c1-42-13-2-7(3-14(16(13)31)45-28-22(37)18(33)20(35)24(47-28)26(40)41)11-6-10(30)15-9(29)4-8(5-12(15)44-11)43-27-21(36)17(32)19(34)23(46-27)25(38)39/h2-6,17-24,27-29,31-37H,1H3,(H,38,39)(H,40,41)/t17-,18-,19-,20-,21+,22+,23+,24-,27+,28+/m0/s1
SMILES	COC1=CC(C2=CC(=O)C3=C(O)C=C(O[C@@H]4O[C@@H](C(=O)O)[C@@H](O)[C@H](O)[C@H]4O)C=C3O2)=CC(O[C@@H]2O[C@H](C(=O)O)[C@@H](O)[C@H](O)[C@H]2O)=C1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	668.12	Volume:	590.711 ? Van der Waals volume.
Dense:	1.131	LogP:	-0.016 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	0.76 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.706 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	32.0
TPSA:	312.8 ? Topological Polar Surface Area.	H-Bond Acceptor:	19.0
H-Bond Donor:	10.0	Rings:	5.0
Heavy Atoms:	19.0

MedChem Properties

QED Drug-Likeness Score:	0.118	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.894	Fsp³:	0.393
MCE-18:	129.974 ? 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:	1	PAINS Alert:	0
Colloidal aggregators:	0.435	Fluc inhibitor:	0.245 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.956 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.869 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.159	Promiscuous compounds:	0.514

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.395	MDCK Permeability:	-5.16
Pgp-inhibitor:	0.0	Pgp-substrate:	0.775
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):	0.231
20% Bioavailability (F20%):	0.004	30% Bioavailability (F30%):	0.05
50% Bioavailability (F50%):	0.737

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.995
Plasma Protein Binding (PPB):	74.209%	Volume Distribution (VD):	-0.303
Fu:	21.898% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.003
OATP1B3 inhibitor:	0.224	BCRP inhibitor:	0.086
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.004
HLM stability:	0.002 ? 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):

0.677

Half-life (T1/2):

7.047

ADMET: Toxicity

hERG Blockers:	0.002	hERG Blockers (10um):	0.007
Human Hepatotoxicity (H-HT):	0.454	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.756	Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.005	Skin Sensitization:	0.992
Carcinogencity:	0.013	Eye Corrosion:	0.0
Eye Irritation:	0.075	Respiratory Toxicity:	0.002
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	0.956
Hematotoxicity:	0.13	Drug-induced Nephrotoxicity:	0.909
Genotoxicity:	0.981	RPMI-8226 Immunitoxicity:	0.061
A549 Cytotoxicity:	0.005	Hek293 Cytotoxicity:	0.02
BCF:	0.145 ? 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:	2.682 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.312 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.368 ? 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
NPO9209	Rhizomnium magnifolium	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28098	Rhizomnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28098	Rhizomnium pseudopunctatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9209	Rhizomnium magnifolium	Species	Mniaceae	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

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

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 NPC596066 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	26403
0.1-0.2	21045
0.2-0.3	1825
0.3-0.4	432
0.4-0.5	113
0.5-0.6	31
0.6-0.7	5
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8182	Intermediate Similarity	NPC608742
0.7821	Intermediate Similarity	NPC282169
0.7821	Intermediate Similarity	NPC20505
0.6548	Remote Similarity	NPC237435
0.6471	Remote Similarity	NPC43211
0.625	Remote Similarity	NPC48479
0.625	Remote Similarity	NPC600989
0.6092	Remote Similarity	NPC115760
0.5851	Remote Similarity	NPC46202
0.5816	Remote Similarity	NPC253685
0.573	Remote Similarity	NPC601144
0.5682	Remote Similarity	NPC101191
0.5667	Remote Similarity	NPC311830
0.5618	Remote Similarity	NPC135277
0.5618	Remote Similarity	NPC210094
0.5567	Remote Similarity	NPC229409
0.5556	Remote Similarity	NPC610187
0.5521	Remote Similarity	NPC64051
0.5455	Remote Similarity	NPC95090
0.5455	Remote Similarity	NPC27408
0.5402	Remote Similarity	NPC473043
0.5393	Remote Similarity	NPC181712
0.5385	Remote Similarity	NPC22832
0.5385	Remote Similarity	NPC243930
0.5341	Remote Similarity	NPC19709
0.5281	Remote Similarity	NPC189142
0.5281	Remote Similarity	NPC77660
0.5227	Remote Similarity	NPC331652
0.5195	Remote Similarity	NPC33265
0.5169	Remote Similarity	NPC261866
0.5169	Remote Similarity	NPC39360
0.5169	Remote Similarity	NPC29763
0.5169	Remote Similarity	NPC210003
0.5165	Remote Similarity	NPC27942
0.5161	Remote Similarity	NPC607707
0.5149	Remote Similarity	NPC479765
0.5125	Remote Similarity	NPC137062
0.5054	Remote Similarity	NPC264735
0.505	Remote Similarity	NPC479766

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC596066 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4690
0.1-0.2	4399
0.2-0.3	53
0.3-0.4	6
0.4-0.5	1
0.5-0.6	0
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.6548	Remote Similarity	NPD4338	Clinical (unspecified phase)

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