NPASS Compound

Natural Product: NPC474842

Natural Product ID	NPC474842
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Geoditin B
IUPAC Name	[(3Z,3aS,5aR,7S,9aR,9bS)-3a,6,6,9a-tetramethyl-3-[(3E,5E,8E)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-2-oxo-1,4,5,5a,7,8,9,9b-octahydrocyclopenta[a]naphthalen-7-yl] acetate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL484834
PubChem CID	44575709
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

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 78 80 0 0 0 0 0 0 0 0999 V2000 10.8615 3.1120 1.2706 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5113 2.5598 0.9883 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5380 3.3256 0.8010 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3218 1.1203 0.9298 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1198 0.6119 0.6783 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8755 -0.8134 0.6088 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8299 -1.5997 0.7920 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5563 -1.3274 0.3335 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4726 -0.6117 0.1232 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1679 -1.2511 -0.1510 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1062 -0.5162 -0.3565 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7706 -1.0589 -0.6357 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7131 -0.3032 -0.8557 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8043 1.1748 -0.8406 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7634 1.9466 -0.9784 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5915 1.7286 -0.6094 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2623 0.4917 -0.1777 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7145 -0.5676 -1.1338 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0173 -0.3118 -2.5811 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3235 -1.8216 -0.6669 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8322 -1.7937 -0.8866 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4521 -0.4533 -0.7928 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7041 0.5244 0.0687 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9550 0.2403 1.5615 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3193 1.8973 -0.1745 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5567 1.8661 -1.0022 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5568 0.8287 -0.5967 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9207 -0.5544 -0.5580 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4774 -1.3468 -1.7582 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3957 -1.2409 0.6555 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1694 1.1348 0.6547 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5273 1.3894 0.7897 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2237 1.3406 -0.2573 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.1376 1.7073 2.1175 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5174 -2.5179 -0.7151 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3656 -2.8207 0.2739 C 0 0 0 0 0 0 0 0 0 0 0 0 10.7977 4.1936 1.4497 H 0 0 0 0 0 0 0 0 0 0 0 0 11.5333 2.8568 0.4068 H 0 0 0 0 0 0 0 0 0 0 0 0 11.2436 2.5450 2.1595 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1346 0.4277 1.0855 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3262 1.3157 0.5267 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5566 0.4630 0.1553 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1194 -2.2992 -0.1745 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2441 0.5818 -0.3040 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5351 2.5236 0.1640 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8601 2.1736 -1.5634 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7254 0.2087 0.7897 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0376 -0.4572 -3.1330 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3493 0.6869 -2.8422 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6613 -1.1354 -3.0123 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0345 -2.7556 -1.1879 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1841 -1.8797 0.4523 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2390 -2.5544 -0.1678 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0996 -2.2107 -1.8915 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4013 0.0060 -1.8303 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1283 -0.8168 1.7557 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6984 0.9298 1.9979 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9972 0.4921 2.1120 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5841 2.4177 0.7929 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6152 2.6037 -0.6597 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3543 1.7883 -2.0853 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0585 2.8638 -0.8669 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3785 0.8498 -1.3425 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9151 -1.1376 -2.6699 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5699 -1.1697 -1.8519 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3855 -2.4322 -1.4667 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9079 -2.1875 0.9245 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5084 -0.5697 1.5591 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4728 -1.5410 0.4528 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6102 2.5789 2.5980 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1752 2.0558 1.9527 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1695 0.8238 2.7829 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9041 -2.9088 0.1176 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4699 -3.0728 -0.5815 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1949 -2.8282 -1.7321 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3062 -3.3461 0.5054 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6029 -3.0589 1.0289 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0646 -3.1147 -0.7401 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 14 16 1 0 16 17 1 0 17 18 1 0 18 19 1 6 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 1 23 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 28 30 1 0 27 31 1 0 31 32 1 0 32 33 2 0 32 34 1 0 12 35 1 0 8 36 1 0 18 13 1 0 28 22 1 0 23 17 1 0 1 37 1 0 1 38 1 0 1 39 1 0 4 40 1 0 5 41 1 0 9 42 1 0 10 43 1 0 11 44 1 0 16 45 1 0 16 46 1 0 17 47 1 1 19 48 1 0 19 49 1 0 19 50 1 0 20 51 1 0 20 52 1 0 21 53 1 0 21 54 1 0 22 55 1 6 24 56 1 0 24 57 1 0 24 58 1 0 25 59 1 0 25 60 1 0 26 61 1 0 26 62 1 0 27 63 1 6 29 64 1 0 29 65 1 0 29 66 1 0 30 67 1 0 30 68 1 0 30 69 1 0 34 70 1 0 34 71 1 0 34 72 1 0 35 73 1 0 35 74 1 0 35 75 1 0 36 76 1 0 36 77 1 0 36 78 1 0 M END

Standard InCHIKey	CDPPOXOHMOXLAH-SQBDJJPTSA-N
Standard InCHI	InChI=1S/C31H42O5/c1-19(23(34)13-12-21(3)32)10-9-11-20(2)28-24(35)18-26-30(7)17-15-27(36-22(4)33)29(5,6)25(30)14-16-31(26,28)8/h9-13,25-27H,14-18H2,1-8H3/b11-9+,13-12+,19-10+,28-20+/t25-,26-,27-,30-,31-/m0/s1
SMILES	CC(=O)/C=C/C(=O)/C(=C/C=C/C(=C/1C(=O)C[C@@H]2[C@]1(C)CC[C@@H]1[C@]2(C)CC[C@@H](C1(C)C)OC(=O)C)/C)/C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	494.3	Volume:	541.922 ? Van der Waals volume.
Dense:	0.912	LogP:	3.84 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.462 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.454 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	7.0	Rigid Bonds:	23.0
TPSA:	77.51 ? Topological Polar Surface Area.	H-Bond Acceptor:	5.0
H-Bond Donor:	0.0	Rings:	3.0
Heavy Atoms:	5.0

MedChem Properties

QED Drug-Likeness Score:	0.247	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.695	Fsp³:	0.613
MCE-18:	68.32 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.792	Fluc inhibitor:	0.655 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.311 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.034 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.653	Promiscuous compounds:	0.475

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.958	MDCK Permeability:	-4.737
Pgp-inhibitor:	1.0	Pgp-substrate:	0.056
PAMPA:	0.042 ? 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):	0.001
20% Bioavailability (F20%):	0.367	30% Bioavailability (F30%):	0.736
50% Bioavailability (F50%):	0.974

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.928
Plasma Protein Binding (PPB):	98.39%	Volume Distribution (VD):	-0.328
Fu:	1.469% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.984	BCRP inhibitor:	0.007
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.003	CYP1A2-substrate:	0.989
CYP2C19-inhibitor:	0.195	CYP2C19-substrate:	0.969
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.1
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.907	CYP3A4-substrate:	0.974
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.996 ? 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):

7.786

Half-life (T1/2):

0.428

ADMET: Toxicity

hERG Blockers:	0.046	hERG Blockers (10um):	0.206
Human Hepatotoxicity (H-HT):	0.652	Drug-induced Liver Injury (DILI):	0.853
AMES Toxicity:	0.727	Rat Oral Acute Toxicity:	0.278
Maximum Recommended Daily Dose:	0.687	Skin Sensitization:	0.988
Carcinogencity:	0.583	Eye Corrosion:	0.285
Eye Irritation:	0.842	Respiratory Toxicity:	0.592
Drug-induced Neurotoxicity:	0.274	Ototoxicity:	0.268
Hematotoxicity:	0.659	Drug-induced Nephrotoxicity:	0.636
Genotoxicity:	0.886	RPMI-8226 Immunitoxicity:	0.092
A549 Cytotoxicity:	0.249	Hek293 Cytotoxicity:	0.386
BCF:	1.291 ? 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:	4.386 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.927 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.455 ? 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
NPO32624	rhabdastrella aff. distincta	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15620246]
NPO32624	rhabdastrella aff. distincta	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[18826276]

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
IC50	6

Activity Type	# Activity
Cell line	4
Non-molecular	2

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
NPT116	Cell line	HL-60	Homo sapiens	IC50	>	5.0	ug.mL-1	DrugMatrix in vitro pharmacology data
NPT547	Cell line	BGC-823	Homo sapiens	IC50	>	5.0	ug.mL-1	PMID[21616566]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	>	5.0	ug.mL-1	PMID[19902967]
NPT165	Cell line	HeLa	Homo sapiens	IC50	>	5.0	ug.mL-1	DrugMatrix in vivo data: Biochemistry
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	>	5.0	ug.mL-1	PMID[15620246]

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 NPC474842 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	21708
0.1-0.2	24261
0.2-0.3	3621
0.3-0.4	206
0.4-0.5	29
0.5-0.6	20
0.6-0.7	11
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC475965
1.0	High Similarity	NPC604299
0.6923	Remote Similarity	NPC605871
0.6818	Remote Similarity	NPC266955
0.6721	Remote Similarity	NPC329866
0.6721	Remote Similarity	NPC474796
0.6721	Remote Similarity	NPC474797
0.6721	Remote Similarity	NPC602550
0.6308	Remote Similarity	NPC151725
0.6176	Remote Similarity	NPC469874
0.6119	Remote Similarity	NPC473435
0.6119	Remote Similarity	NPC473280
0.6119	Remote Similarity	NPC471078
0.5942	Remote Similarity	NPC106425
0.5942	Remote Similarity	NPC6206
0.5942	Remote Similarity	NPC122324
0.5857	Remote Similarity	NPC10064
0.5857	Remote Similarity	NPC170221
0.5857	Remote Similarity	NPC110937
0.5775	Remote Similarity	NPC155332
0.5775	Remote Similarity	NPC114540
0.5769	Remote Similarity	NPC473617
0.5769	Remote Similarity	NPC473828
0.5694	Remote Similarity	NPC115899
0.5694	Remote Similarity	NPC473482
0.5694	Remote Similarity	NPC473284
0.5616	Remote Similarity	NPC473283
0.5616	Remote Similarity	NPC475526
0.5606	Remote Similarity	NPC2049
0.5513	Remote Similarity	NPC168319
0.5513	Remote Similarity	NPC194028
0.5429	Remote Similarity	NPC473879
0.5077	Remote Similarity	NPC161638

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC474842 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6992
0.1-0.2	2108
0.2-0.3	45
0.3-0.4	5
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