NPASS Compound

Natural Product: NPC130427

Natural Product ID	NPC130427
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Bryonioside F
IUPAC Name	(3S,8S,9R,10R,13R,14S,17R)-17-[(2R)-6-hydroxy-6-methyl-5-oxoheptan-2-yl]-4,4,9,13,14-pentamethyl-3-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,2,3,7,8,10,12,15,16,17-decahydrocyclopenta[a]phenanthren-11-one
Synonyms	bryonioside F
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL451089
PubChem CID	10985073
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal glycosides [CHEMONTID:0002364] Steroidal saponins [CHEMONTID:0001687] Cucurbitacin glycosides

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 103107 0 0 0 0 0 0 0 0999 V2000 -4.7820 2.6242 -1.3106 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8996 1.1784 -1.7526 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.3677 0.8266 -1.6437 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8782 0.9822 -0.2276 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3255 0.6258 -0.1588 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8901 0.2729 -1.1814 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1102 0.6788 1.0882 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3157 1.5806 0.9342 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5691 -0.7443 1.3839 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2428 1.1220 2.0973 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0280 0.2350 -0.9480 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1419 -1.1838 -1.3675 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7350 -1.7982 -1.4386 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9551 -0.8105 -0.6211 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5132 -1.0710 0.7767 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4560 -0.9052 -0.7082 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1298 -1.7164 0.5447 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2642 -1.7843 0.9752 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1014 -0.8848 0.6645 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6856 0.2604 -0.1490 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6891 0.1464 -1.2958 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9746 0.7702 -0.7589 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2724 0.3129 0.6354 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5284 -0.9200 1.0788 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5580 -0.9438 2.5896 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2547 -2.1342 0.5812 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6354 0.0315 0.6995 O 0 0 0 0 0 0 0 0 0 0 0 0 6.3066 0.8236 1.5959 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0932 -0.0346 2.5411 C 0 0 1 0 0 0 0 0 0 0 0 0 7.9015 -1.0331 1.7518 C 0 0 2 0 0 0 0 0 0 0 0 0 8.1502 -0.5016 0.3794 C 0 0 1 0 0 0 0 0 0 0 0 0 8.2716 1.0057 0.3542 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5206 1.4230 -1.0798 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4569 1.1436 -1.9156 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1852 1.6434 0.8837 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4235 -0.9796 -0.0146 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2812 -2.2790 1.7011 O 0 0 0 0 0 0 0 0 0 0 0 0 7.9123 0.7262 3.3823 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2938 0.3973 -0.5953 C 0 0 1 0 0 0 0 0 0 0 0 0 0.4373 1.2308 -1.8565 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6338 1.2191 0.2278 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 1.5875 1.3143 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9425 1.5483 -0.4142 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5441 0.4540 -1.2132 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4079 0.4111 -2.6803 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9943 3.1583 -1.8840 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7705 3.1331 -1.5008 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5885 2.7641 -0.2499 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6821 1.2131 -2.8272 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6298 -0.1452 -2.0676 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8984 1.5939 -2.2481 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3632 0.2396 0.4481 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6776 1.9659 0.1935 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.5742 1.6369 -0.1420 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.1839 1.1274 1.4615 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0910 2.5844 1.3438 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.0738 -0.8259 2.3596 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.2501 -1.0504 0.5710 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6779 -1.4061 1.3095 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0576 2.0755 1.9014 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3176 0.4817 0.0907 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8307 -1.8154 -0.7438 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5588 -1.3330 -2.4072 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8057 -2.7881 -0.8966 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3904 -2.0197 -2.4281 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6361 -1.2212 0.7026 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2691 -2.1292 1.0874 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3461 -0.2991 1.4993 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1630 -1.5182 -1.5687 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6163 -1.2150 1.4477 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5041 -2.7450 0.3818 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5498 -2.6407 1.5743 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9331 1.1794 0.4710 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4118 0.4708 -2.2631 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9959 -0.9408 -1.4673 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8068 0.5799 -1.4642 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8209 1.8696 -0.7319 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0971 1.1367 1.3889 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2815 -1.7190 2.9074 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5566 -1.2399 2.9642 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8838 0.0351 3.0019 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1588 -1.8403 0.0108 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5979 -2.7831 1.4135 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6545 -2.7792 -0.0820 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6294 1.5345 2.1323 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3737 -0.6042 3.1765 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8563 -1.1867 2.3101 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4650 -0.8785 -0.4033 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2209 1.2400 0.9036 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4115 0.9222 -1.5071 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7268 2.5163 -1.1581 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3859 1.8075 -2.6563 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9045 -1.3880 0.7242 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6774 -2.8170 0.9708 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8148 0.3596 3.3127 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3244 2.0769 -1.9189 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3363 1.9276 -1.7737 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5253 0.6819 -2.7781 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6402 1.6406 0.4836 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9613 2.5527 -0.8458 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2861 -0.0549 -3.2242 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2866 1.4367 -3.0840 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5988 -0.2860 -3.0712 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 2 0 5 7 1 0 7 8 1 0 7 9 1 0 7 10 1 0 2 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 1 14 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 24 26 1 0 23 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 32 35 1 0 31 36 1 0 30 37 1 0 29 38 1 0 20 39 1 0 39 40 1 6 39 41 1 0 41 42 2 0 41 43 1 0 43 44 1 0 44 45 1 6 44 11 1 0 44 14 1 0 39 16 1 0 24 19 1 0 35 28 1 0 1 46 1 0 1 47 1 0 1 48 1 0 2 49 1 6 3 50 1 0 3 51 1 0 4 52 1 0 4 53 1 0 8 54 1 0 8 55 1 0 8 56 1 0 9 57 1 0 9 58 1 0 9 59 1 0 10 60 1 0 11 61 1 1 12 62 1 0 12 63 1 0 13 64 1 0 13 65 1 0 15 66 1 0 15 67 1 0 15 68 1 0 16 69 1 6 17 70 1 0 17 71 1 0 18 72 1 0 20 73 1 1 21 74 1 0 21 75 1 0 22 76 1 0 22 77 1 0 23 78 1 1 25 79 1 0 25 80 1 0 25 81 1 0 26 82 1 0 26 83 1 0 26 84 1 0 28 85 1 1 29 86 1 1 30 87 1 1 31 88 1 6 32 89 1 1 33 90 1 0 33 91 1 0 34 92 1 0 36 93 1 0 37 94 1 0 38 95 1 0 40 96 1 0 40 97 1 0 40 98 1 0 43 99 1 0 43100 1 0 45101 1 0 45102 1 0 45103 1 0 M END

Standard InCHIKey	IMFAPKVFQZYYJK-CKPIZJOLSA-N
Standard InCHI	InChI=1S/C36H58O9/c1-19(9-13-25(38)33(4,5)43)20-15-16-34(6)24-12-10-21-22(36(24,8)26(39)17-35(20,34)7)11-14-27(32(21,2)3)45-31-30(42)29(41)28(40)23(18-37)44-31/h10,19-20,22-24,27-31,37,40-43H,9,11-18H2,1-8H3/t19-,20-,22-,23-,24+,27+,28-,29+,30-,31+,34+,35-,36+/m1/s1
SMILES	C[C@H](CCC(=O)C(C)(C)O)[C@H]1CC[C@@]2(C)[C@@H]3CC=C4[C@@H](CC[C@@H](C4(C)C)O[C@H]4[C@@H]([C@H]([C@@H]([C@@H](CO)O4)O)O)O)[C@]3(C)C(=O)C[C@]12C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	634.41	Volume:	659.632 ? Van der Waals volume.
Dense:	0.962	LogP:	3.105 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.522 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.556 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	8.0	Rigid Bonds:	28.0
TPSA:	153.75 ? Topological Polar Surface Area.	H-Bond Acceptor:	9.0
H-Bond Donor:	5.0	Rings:	5.0
Heavy Atoms:	9.0

MedChem Properties

QED Drug-Likeness Score:	0.252	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.419	Fsp³:	0.889
MCE-18:	110.029 ? 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:	0.957	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.205	Promiscuous compounds:	0.33

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.455	MDCK Permeability:	-5.107
Pgp-inhibitor:	0.62	Pgp-substrate:	0.015
PAMPA:	0.893 ? 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%):	0.037	30% Bioavailability (F30%):	0.638
50% Bioavailability (F50%):	0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002	MRP1:	0.647
Plasma Protein Binding (PPB):	80.443%	Volume Distribution (VD):	-0.433
Fu:	15.545% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.429
BSEP inhibitor:	0.986

ADMET: Metabolism

CYP1A2-inhibitor:	0.013	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.121	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.769
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.0 ? 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):

2.412

Half-life (T1/2):

1.552

ADMET: Toxicity

hERG Blockers:	0.029	hERG Blockers (10um):	0.036
Human Hepatotoxicity (H-HT):	0.742	Drug-induced Liver Injury (DILI):	0.656
AMES Toxicity:	0.808	Rat Oral Acute Toxicity:	0.062
Maximum Recommended Daily Dose:	0.086	Skin Sensitization:	0.997
Carcinogencity:	0.595	Eye Corrosion:	0.0
Eye Irritation:	0.003	Respiratory Toxicity:	0.058
Drug-induced Neurotoxicity:	0.007	Ototoxicity:	0.97
Hematotoxicity:	0.842	Drug-induced Nephrotoxicity:	0.919
Genotoxicity:	0.955	RPMI-8226 Immunitoxicity:	0.123
A549 Cytotoxicity:	0.312	Hek293 Cytotoxicity:	0.679
BCF:	1.299 ? 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:	3.629 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.235 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.454 ? 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
NPO33132	bryonia dioica	Species	Cucurbitaceae	Eukaryota	Roots	n.a.	n.a.	PMID[11858752]
NPO33132	bryonia dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17503850]

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
Inhibition	4
Activity	1

Activity Type	# Activity
Cell line	1
Others	4

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	60.0	%	PMID[23398362]
NPT2	Others	Unspecified	n.a.	Inhibition	=	0.0	%	PMID[16202590]
NPT2	Others	Unspecified	n.a.	Inhibition	=	29.2	%	PMID[23586849]
NPT2	Others	Unspecified	n.a.	Inhibition	=	71.4	%	PMID[24597894]
NPT2	Others	Unspecified	n.a.	Inhibition	=	97.6	%	DrugMatrix in vivo data: Pathology

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 NPC130427 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	18607
0.1-0.2	24849
0.2-0.3	5394
0.3-0.4	941
0.4-0.5	44
0.5-0.6	8
0.6-0.7	8
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8553	High Similarity	NPC154856
0.8214	Intermediate Similarity	NPC474557
0.8205	Intermediate Similarity	NPC74727
0.7738	Intermediate Similarity	NPC485578
0.7558	Intermediate Similarity	NPC279638
0.7079	Intermediate Similarity	NPC474265
0.7065	Intermediate Similarity	NPC485579
0.6566	Remote Similarity	NPC485580
0.6353	Remote Similarity	NPC221562
0.6316	Remote Similarity	NPC473882
0.6279	Remote Similarity	NPC52241
0.6235	Remote Similarity	NPC75608
0.6129	Remote Similarity	NPC210420
0.6092	Remote Similarity	NPC187400
0.6026	Remote Similarity	NPC474245
0.5978	Remote Similarity	NPC309448
0.5851	Remote Similarity	NPC190395
0.5667	Remote Similarity	NPC475317
0.5556	Remote Similarity	NPC34562
0.55	Remote Similarity	NPC302057
0.5474	Remote Similarity	NPC606839
0.5248	Remote Similarity	NPC168899
0.5248	Remote Similarity	NPC69273

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC130427 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6914
0.1-0.2	2127
0.2-0.3	105
0.3-0.4	3
0.4-0.5	1
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