NPASS Compound

Natural Product: NPC472394

Natural Product ID	NPC472394
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	KCVBKOGPGLTLNX-KQDCEKGYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL339923
PubChem CID	15378568
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

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 82 85 0 0 0 0 0 0 0 0999 V2000 -4.2592 0.2256 0.6108 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9132 0.1440 1.1636 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9415 0.8581 0.6180 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2599 0.9224 -0.8101 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9604 -0.4137 -1.4326 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5274 -0.7919 -1.5382 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2502 -0.0539 -2.5919 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5100 0.6138 -2.1797 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5050 -0.2454 -1.4544 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6199 -1.2966 -0.7487 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1313 -2.4713 -0.6812 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3187 -0.7479 -0.2955 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1960 -1.1040 0.9958 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2809 -0.0118 2.0494 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8616 1.2877 1.5909 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0679 2.3109 1.0523 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4977 1.9431 2.8018 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2875 -0.5402 3.0696 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5714 -0.7185 2.3375 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3788 -1.5850 2.6927 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5769 -2.0934 1.6294 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0971 -3.3165 2.0372 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0912 -3.6199 1.8488 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0051 -4.2808 2.7085 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2215 0.3646 -0.4532 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5931 0.3473 -0.4182 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1839 -0.2439 -1.3471 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3981 0.9666 0.6242 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7949 1.6136 1.6825 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5237 2.2044 2.6900 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9048 2.1580 2.6548 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5072 1.5161 1.6040 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7735 0.9231 0.5941 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5520 -2.2622 -1.9936 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5921 -0.6621 -2.6364 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5382 -1.5776 -2.9578 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8969 -2.3117 -2.0349 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0858 -1.6683 -4.3305 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4036 1.5759 -1.1951 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4153 2.7704 -1.9305 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2771 3.2532 -2.2474 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6663 3.4639 -2.3350 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4987 -0.2621 -0.3145 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7069 1.2641 0.6970 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9219 -0.3177 1.3638 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4093 1.5666 -1.2292 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3906 -1.1633 -0.7255 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3714 0.7716 -3.0602 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4706 -0.7151 -3.4818 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0051 0.9227 -3.1510 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2971 1.5879 -1.6679 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1690 -0.7323 -2.1762 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1087 -2.7411 -1.0771 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6138 -3.2931 -0.2356 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5600 0.3847 -0.2230 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2322 -1.5706 0.9026 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6360 0.1790 2.5859 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1513 2.1241 1.2405 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0558 3.3358 1.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1367 2.6045 -0.0227 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6462 3.0459 2.5559 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4800 1.5918 3.0780 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7589 2.0051 3.6527 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8928 -1.4875 3.4738 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4020 0.1221 3.9510 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4684 -4.6070 3.6435 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1702 -5.1921 2.1043 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9622 -3.8146 3.0341 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6967 1.6787 1.7571 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9862 2.6981 3.5019 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4608 2.6259 3.4541 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5878 1.4547 1.5319 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3127 0.4215 -0.2283 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4393 -2.5300 -2.4511 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8551 -2.9457 -1.1981 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2672 -2.4170 -2.8347 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4207 -1.2672 -5.1011 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0686 -1.1388 -4.4273 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2950 -2.7382 -4.6248 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4121 4.0929 -3.2331 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5082 2.7846 -2.5133 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8939 4.2252 -1.5386 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 15 17 1 0 14 18 1 0 18 19 1 0 19 20 2 0 13 21 1 0 21 22 1 0 22 23 2 0 22 24 1 0 9 25 1 0 25 26 1 0 26 27 2 0 26 28 1 0 28 29 2 0 29 30 1 0 30 31 2 0 31 32 1 0 32 33 2 0 6 34 1 0 5 35 1 0 35 36 1 0 36 37 2 0 36 38 1 0 4 39 1 0 39 40 1 0 40 41 2 0 40 42 1 0 19 2 1 0 15 3 1 0 12 6 1 0 33 28 1 0 1 43 1 0 1 44 1 0 1 45 1 0 4 46 1 0 5 47 1 0 7 48 1 0 7 49 1 0 8 50 1 0 8 51 1 0 9 52 1 0 11 53 1 0 11 54 1 0 12 55 1 0 13 56 1 0 14 57 1 0 16 58 1 0 16 59 1 0 16 60 1 0 17 61 1 0 17 62 1 0 17 63 1 0 18 64 1 0 18 65 1 0 24 66 1 0 24 67 1 0 24 68 1 0 29 69 1 0 30 70 1 0 31 71 1 0 32 72 1 0 33 73 1 0 34 74 1 0 34 75 1 0 34 76 1 0 38 77 1 0 38 78 1 0 38 79 1 0 42 80 1 0 42 81 1 0 42 82 1 0 M END

Standard InCHIKey	KCVBKOGPGLTLNX-KQDCEKGYSA-N
Standard InCHI	InChI=1S/C33H40O9/c1-17-24(37)16-23-28(39-19(3)34)27-18(2)25(42-31(38)22-12-10-9-11-13-22)14-15-33(27,8)30(41-21(5)36)29(40-20(4)35)26(17)32(23,6)7/h9-13,23,25,27-30H,2,14-16H2,1,3-8H3/t23-,25-,27-,28+,29+,30-,33+/m0/s1
SMILES	CC1=C2C(C(C3(CCC(C(=C)C3C(C(C2(C)C)CC1=O)OC(=O)C)OC(=O)C4=CC=CC=C4)C)OC(=O)C)OC(=O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	580.27	Volume:	597.846 ? Van der Waals volume.
Dense:	0.971	LogP:	3.559 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.411 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.052 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	9.0	Rigid Bonds:	29.0
TPSA:	122.27 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	0.0	Rings:	4.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.271	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.339	Fsp³:	0.545
MCE-18:	113.235 ? 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:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.39	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.032 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.376 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.196	Promiscuous compounds:	0.001

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.869	MDCK Permeability:	-4.561
Pgp-inhibitor:	0.999	Pgp-substrate:	0.273
PAMPA:	0.354 ? 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):	0.002
20% Bioavailability (F20%):	0.013	30% Bioavailability (F30%):	0.277
50% Bioavailability (F50%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004	MRP1:	1.0
Plasma Protein Binding (PPB):	95.475%	Volume Distribution (VD):	0.034
Fu:	4.598% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.07
OATP1B3 inhibitor:	0.989	BCRP inhibitor:	0.006
BSEP inhibitor:	0.997

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.326
CYP2C19-inhibitor:	0.01	CYP2C19-substrate:	0.001
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.005
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.035
CYP3A4-inhibitor:	0.14	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.998 ? 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):

2.721

Half-life (T1/2):

0.675

ADMET: Toxicity

hERG Blockers:	0.022	hERG Blockers (10um):	0.347
Human Hepatotoxicity (H-HT):	0.347	Drug-induced Liver Injury (DILI):	0.95
AMES Toxicity:	0.157	Rat Oral Acute Toxicity:	0.113
Maximum Recommended Daily Dose:	0.756	Skin Sensitization:	0.254
Carcinogencity:	0.499	Eye Corrosion:	0.0
Eye Irritation:	0.021	Respiratory Toxicity:	0.006
Drug-induced Neurotoxicity:	0.742	Ototoxicity:	0.773
Hematotoxicity:	0.055	Drug-induced Nephrotoxicity:	0.295
Genotoxicity:	0.795	RPMI-8226 Immunitoxicity:	0.056
A549 Cytotoxicity:	0.077	Hek293 Cytotoxicity:	0.459
BCF:	0.756 ? 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:	3.901 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.963 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.344 ? 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
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[14987066]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844936]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974623]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[15974623]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24820	Taxus cuspidata	Species	Taxaceae	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

Activity Type	# Activity
Activity	1

Activity Type	# Activity
Others	1

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
NPT2	Others	Unspecified	n.a.	Activity	=	87.0	%	PMID[19093848]

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 NPC472394 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	15144
0.1-0.2	32638
0.2-0.3	1716
0.3-0.4	319
0.4-0.5	18
0.5-0.6	7
0.6-0.7	5
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8806	High Similarity	NPC472395
0.75	Intermediate Similarity	NPC472374
0.7467	Intermediate Similarity	NPC471880
0.7397	Intermediate Similarity	NPC469742
0.7308	Intermediate Similarity	NPC472371
0.7297	Intermediate Similarity	NPC607515
0.7231	Intermediate Similarity	NPC608702
0.7013	Intermediate Similarity	NPC473541
0.6957	Remote Similarity	NPC472389
0.6842	Remote Similarity	NPC472361
0.6585	Remote Similarity	NPC475400
0.6494	Remote Similarity	NPC472437
0.6154	Remote Similarity	NPC472372
0.5949	Remote Similarity	NPC473749
0.5926	Remote Similarity	NPC475493
0.5875	Remote Similarity	NPC195224
0.5714	Remote Similarity	NPC605842
0.5412	Remote Similarity	NPC472388
0.5405	Remote Similarity	NPC8196
0.5294	Remote Similarity	NPC472418

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472394 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3945
0.1-0.2	5061
0.2-0.3	143
0.3-0.4	1
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
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
		NPD

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