NPASS Compound

Natural Product: NPC50228

Natural Product ID	NPC50228
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Mezzettiaside 9
IUPAC Name	[(2S,3S,4S,5R,6R)-4-[(2S,3R,4R,5S,6S)-3,4-diacetyloxy-5-hydroxy-6-methyloxan-2-yl]oxy-5-hydroxy-2-methyl-6-octoxyoxan-3-yl] hexanoate
Synonyms	Mezzettiaside 9
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL443164
PubChem CID	10054386
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

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 94 95 0 0 0 0 0 0 0 0999 V2000 9.1378 3.4091 0.7273 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6905 2.1564 1.4934 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2574 1.1500 0.4666 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7975 -0.1504 1.0780 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6179 0.0578 2.0039 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1598 -1.2307 2.6257 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7203 -2.2432 1.6230 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5463 -1.7378 0.7841 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4696 -1.4241 1.4728 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3072 -0.9670 1.0173 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0606 -1.6458 1.3982 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1686 -0.9840 0.8554 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0471 0.4644 0.6075 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2711 1.0816 0.8312 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9050 1.4272 -0.5227 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1901 0.3551 1.5146 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0742 1.2143 1.2906 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0212 1.9692 0.6615 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9986 2.0199 -0.6128 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0723 2.7300 1.3550 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9916 3.4456 0.3922 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0444 4.1672 1.1991 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9988 4.9189 0.3003 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6620 3.9376 -0.6499 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5959 -1.5980 -0.3300 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7899 -2.3351 -0.1590 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9283 -1.6622 -0.9024 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.8715 -1.9253 -2.3771 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6113 -3.3701 -2.7100 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2698 -4.2063 -1.5005 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4860 -4.8646 -0.8814 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5173 -3.5959 -0.5516 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5777 -3.5135 -3.6343 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0682 -1.4862 -2.9910 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0946 -0.5071 -3.9782 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9531 -0.0323 -4.2922 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3343 -0.0230 -4.6407 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1787 -1.9614 -0.3280 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0281 -1.1059 0.3125 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6644 0.0691 0.4092 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3398 -1.5026 0.8876 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9866 -2.9747 0.9585 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8392 4.3273 1.2783 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2408 3.4003 0.6282 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6088 3.4261 -0.2503 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5400 1.8199 2.0977 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7910 2.4050 2.1148 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0865 0.9128 -0.2214 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3775 1.5482 -0.1144 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5988 -0.6635 1.6457 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4558 -0.7764 0.2083 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8360 0.5707 1.4223 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8768 0.7539 2.8357 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9842 -1.6090 3.2663 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2763 -1.0036 3.2642 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5501 -2.4239 0.9140 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4962 -3.2331 2.0669 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9409 -0.8321 0.2764 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4121 -2.4762 -0.0623 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3488 -0.8655 -0.0823 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9326 -1.6446 2.5264 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0087 -1.2066 1.5976 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3156 0.6887 -0.4939 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1615 2.0925 1.3360 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2601 1.0119 -1.3335 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9294 1.0171 -0.5709 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9547 2.5414 -0.6706 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5872 3.5186 1.9861 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6923 2.0805 1.9957 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5323 2.7375 -0.2728 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4708 4.2086 -0.2173 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6585 3.4349 1.7912 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5790 4.8697 1.9138 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5407 5.7293 -0.2777 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7888 5.3792 0.9589 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.7217 4.2598 -0.8029 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1265 3.9731 -1.6313 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6372 2.9443 -0.1718 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0621 -2.2864 0.9166 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8116 -0.5794 -0.7399 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0500 -1.3428 -2.8367 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4949 -3.8597 -3.2025 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6311 -5.0809 -1.8588 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3847 -4.4614 -1.4077 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4346 -5.9518 -0.9946 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5354 -4.5757 0.1888 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2896 -4.4797 -3.5668 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0110 0.3602 -5.6541 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0003 -0.8801 -4.8383 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8073 0.8066 -4.0735 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7002 -0.7184 1.6031 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0951 -1.7386 0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1490 -2.4058 1.5088 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8880 -3.2489 0.6697 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 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 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 14 16 1 0 13 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 12 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 1 0 29 33 1 0 28 34 1 0 34 35 1 0 35 36 2 0 35 37 1 0 27 38 1 0 38 39 1 0 39 40 2 0 39 41 1 0 11 42 1 0 16 10 1 0 32 26 1 0 1 43 1 0 1 44 1 0 1 45 1 0 2 46 1 0 2 47 1 0 3 48 1 0 3 49 1 0 4 50 1 0 4 51 1 0 5 52 1 0 5 53 1 0 6 54 1 0 6 55 1 0 7 56 1 0 7 57 1 0 8 58 1 0 8 59 1 0 10 60 1 6 11 61 1 1 12 62 1 1 13 63 1 6 14 64 1 1 15 65 1 0 15 66 1 0 15 67 1 0 20 68 1 0 20 69 1 0 21 70 1 0 21 71 1 0 22 72 1 0 22 73 1 0 23 74 1 0 23 75 1 0 24 76 1 0 24 77 1 0 24 78 1 0 26 79 1 1 27 80 1 6 28 81 1 6 29 82 1 6 30 83 1 6 31 84 1 0 31 85 1 0 31 86 1 0 33 87 1 0 37 88 1 0 37 89 1 0 37 90 1 0 41 91 1 0 41 92 1 0 41 93 1 0 42 94 1 0 M END

Standard InCHIKey	RDCMFBVGEZABQK-UWVAMOTESA-N
Standard InCHI	InChI=1S/C30H52O12/c1-7-9-11-12-13-15-17-36-29-24(35)27(25(19(4)38-29)41-22(33)16-14-10-8-2)42-30-28(40-21(6)32)26(39-20(5)31)23(34)18(3)37-30/h18-19,23-30,34-35H,7-17H2,1-6H3/t18-,19-,23-,24+,25-,26+,27-,28+,29+,30-/m0/s1
SMILES	CCCCCCCCO[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)OC(=O)CCCCC)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)OC(=O)C)OC(=O)C)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	604.35	Volume:	607.896 ? Van der Waals volume.
Dense:	0.994	LogP:	3.815 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.747 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.596 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	20.0	Rigid Bonds:	15.0
TPSA:	156.28 ? Topological Polar Surface Area.	H-Bond Acceptor:	12.0
H-Bond Donor:	2.0	Rings:	2.0
Heavy Atoms:	12.0

MedChem Properties

QED Drug-Likeness Score:	0.142	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	4.57	Fsp³:	0.9
MCE-18:	44.667 ? 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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.803	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.311	Promiscuous compounds:	0.302

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.355	MDCK Permeability:	-4.962
Pgp-inhibitor:	0.602	Pgp-substrate:	0.992
PAMPA:	0.604 ? 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):	0.792
20% Bioavailability (F20%):	0.836	30% Bioavailability (F30%):	0.949
50% Bioavailability (F50%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.995
Plasma Protein Binding (PPB):	90.153%	Volume Distribution (VD):	0.23
Fu:	9.498% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.652
OATP1B3 inhibitor:	0.974	BCRP inhibitor:	0.094
BSEP inhibitor:	0.979

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.997
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.324
CYP2C9-inhibitor:	0.001	CYP2C9-substrate:	0.428
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.151
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.994 ? 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):

3.82

Half-life (T1/2):

1.006

ADMET: Toxicity

hERG Blockers:	0.057	hERG Blockers (10um):	0.354
Human Hepatotoxicity (H-HT):	0.328	Drug-induced Liver Injury (DILI):	0.808
AMES Toxicity:	0.427	Rat Oral Acute Toxicity:	0.091
Maximum Recommended Daily Dose:	0.006	Skin Sensitization:	0.998
Carcinogencity:	0.035	Eye Corrosion:	0.202
Eye Irritation:	0.605	Respiratory Toxicity:	0.063
Drug-induced Neurotoxicity:	0.002	Ototoxicity:	0.78
Hematotoxicity:	0.414	Drug-induced Nephrotoxicity:	0.331
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.092
A549 Cytotoxicity:	0.6	Hek293 Cytotoxicity:	0.092
BCF:	0.682 ? 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:	4.093 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.628 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.734 ? 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
NPO25657	Mezzettia leptopoda	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9868159]
NPO25657	Mezzettia leptopoda	Species	Annonaceae	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
ED50	10
MIC	6
IC50	1

Activity Type	# Activity
Cell line	9
Organism	6
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
NPT1034	Cell line	Lu1	Homo sapiens	ED50	=	5.4	ug ml-1	PMID[16933888]
NPT1851	Cell line	Col2	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[25815139]
NPT91	Cell line	KB	Homo sapiens	ED50	=	11.3	ug ml-1	PMID[9599261]
NPT91	Cell line	KB	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[18177011]
NPT858	Cell line	LNCaP	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[22409377]
NPT91	Cell line	KB	Homo sapiens	ED50	=	19.0	uM	PMID[21080703]
NPT1034	Cell line	Lu1	Homo sapiens	ED50	=	9.0	uM	PMID[19738007]
NPT397	Cell line	NCI-H460	Homo sapiens	IC50	=	151000.0	nM	PMID[12617583]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	>	20.0	ug ml-1	PMID[25729554]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	ED50	>	20.0	uM	PMID[25729554]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	16000.0	nM	PMID[15050621]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	32000.0	nM	PMID[10785413]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	32000.0	nM	PMID[8254344]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	32000.0	nM	DrugMatrix in vitro pharmacology data
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	32000.0	nM	DrugMatrix in vitro pharmacology data

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 NPC50228 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	20255
0.1-0.2	26899
0.2-0.3	2484
0.3-0.4	186
0.4-0.5	24
0.5-0.6	2
0.6-0.7	2
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8103	Intermediate Similarity	NPC39266
0.807	Intermediate Similarity	NPC211428
0.75	Intermediate Similarity	NPC225748
0.746	Intermediate Similarity	NPC9763
0.7385	Intermediate Similarity	NPC169085
0.7377	Intermediate Similarity	NPC97736
0.6269	Remote Similarity	NPC52268
0.6197	Remote Similarity	NPC53760
0.5797	Remote Similarity	NPC67099
0.5606	Remote Similarity	NPC471761

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC50228 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6689
0.1-0.2	2349
0.2-0.3	107
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