NPASS Compound

Natural Product: NPC55532

Natural Product ID	NPC55532
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Madagascarensilide B
IUPAC Name	3-[(3S,5R,8R,9S,10S,13R,14S,17R)-3-[(2R,4S,5S,6R)-5-[(2S,3R,4S,5S,6R)-3,5-dihydroxy-4-methoxy-6-methyloxan-2-yl]oxy-4-hydroxy-6-methyloxan-2-yl]oxy-14-hydroxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,15,16,17-tetradecahydrocyclopenta[a]phenanthren-17-yl]-2H-furan-5-one
Synonyms	Madagascarensilide B
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1644523
PubChem CID	53319580
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives [CHEMONTID:0001559] Cardenolide glycosides 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 103109 0 0 0 0 0 0 0 0999 V2000 -10.3737 0.7081 -2.0546 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.0351 0.0875 -1.8206 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.2113 -1.2672 -1.1843 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.2310 -1.1397 0.3201 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.9684 -0.4946 0.7984 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.2372 0.1172 -0.3754 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1480 0.8887 -1.1059 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2687 0.9568 0.1051 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9662 0.6353 -0.2583 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1078 0.2492 0.8890 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5814 -1.1864 0.7760 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0485 1.0627 1.1612 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2214 1.3974 0.1247 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8462 1.3416 -1.2413 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3159 1.6617 -1.1101 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3925 2.9707 -0.5804 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9932 0.7419 0.1708 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0862 1.5974 0.4086 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7258 1.3075 1.7202 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2049 1.2428 1.5848 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5866 0.2360 0.5054 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9770 -1.0921 0.9664 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0995 0.6679 -0.8350 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1868 1.3237 -1.6724 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3472 0.4094 -1.9100 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4672 -0.6169 -0.8124 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0669 0.0139 0.4674 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5124 -0.8944 1.6059 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0145 -0.7742 1.6532 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7110 -0.9402 0.3545 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7173 -2.0601 0.4757 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4321 0.2862 -0.1263 C 0 0 2 0 0 0 0 0 0 0 0 0 7.8058 -0.1917 -1.5443 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6445 -1.0537 -1.9910 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7781 -1.3175 -0.7866 C 0 0 2 0 0 0 0 0 0 0 0 0 5.5737 -2.6910 -0.6965 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6733 0.5916 0.6179 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0608 0.0620 1.7496 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3621 0.6452 2.1494 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0322 0.3664 3.1902 O 0 0 0 0 0 0 0 0 0 0 0 0 10.6895 1.5380 1.1760 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7232 1.5790 0.1893 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0061 1.7078 -0.7607 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1709 -1.5058 1.3815 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3650 -0.4828 0.7700 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2120 -1.2710 1.5113 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.4706 -1.7369 -1.5885 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.5048 1.6667 -1.4862 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6182 0.8543 -3.1337 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.2079 0.0522 -1.6687 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5654 -0.0813 -2.8236 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3916 -1.9187 -1.5369 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3237 -2.1955 0.7134 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1376 0.2434 1.6123 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8374 -0.7191 -0.9898 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0735 -0.2881 -0.9024 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7172 0.2276 1.8547 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3051 -1.8739 1.2947 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4277 -1.4813 -0.2643 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6464 -1.2570 1.3708 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9850 2.4978 0.2835 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7208 0.3198 -1.6394 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3380 2.0495 -1.9432 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7337 1.6768 -2.1591 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0710 2.9679 0.3480 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3696 2.6326 0.5076 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2679 0.3862 2.1330 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5103 2.1046 2.4900 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5725 2.2614 1.3283 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7138 0.9005 2.5106 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8911 -1.1237 0.8551 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4822 -1.9563 0.4453 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1822 -1.2604 2.0445 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7185 -0.2351 -1.3958 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7265 1.5713 -2.6473 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4661 2.2886 -1.1985 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1869 -0.0931 -2.9116 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2639 1.0178 -1.9255 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6795 -1.3873 -1.0971 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5446 0.9959 0.6507 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2880 -1.9604 1.3905 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1084 -0.5757 2.5656 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2326 0.2662 2.0327 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4263 -1.4470 2.4542 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7603 -1.7521 0.2570 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4224 -2.8647 -0.2723 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5745 -2.5545 1.4494 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7691 1.1808 -0.1661 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9771 0.6735 -2.2149 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7452 -0.7754 -1.5221 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0868 -2.0006 -2.4260 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1529 -0.5582 -2.8251 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8522 -3.1641 -1.5348 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6100 -0.6777 2.3912 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3224 2.6081 0.1310 H 0 0 0 0 0 0 0 0 0 0 0 0 10.1879 1.2546 -0.7708 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5054 2.7073 -0.7218 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4340 1.6306 -1.7104 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1350 -1.4429 2.3520 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6698 -1.6429 2.3968 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.0237 -0.6126 1.8895 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.6353 -2.1088 0.9266 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.5424 -2.7050 -1.6162 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 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 13 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 1 21 23 1 0 23 24 1 0 24 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 1 30 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 1 32 37 1 0 37 38 2 0 38 39 1 0 39 40 2 0 39 41 1 0 41 42 1 0 23 43 1 0 5 44 1 0 4 45 1 0 45 46 1 0 3 47 1 0 7 2 1 0 15 9 1 0 43 18 1 0 27 21 1 0 35 30 1 0 42 37 1 0 35 26 1 0 1 48 1 0 1 49 1 0 1 50 1 0 2 51 1 6 3 52 1 1 4 53 1 1 5 54 1 1 6 55 1 6 9 56 1 6 10 57 1 1 11 58 1 0 11 59 1 0 11 60 1 0 13 61 1 1 14 62 1 0 14 63 1 0 15 64 1 6 16 65 1 0 18 66 1 1 19 67 1 0 19 68 1 0 20 69 1 0 20 70 1 0 22 71 1 0 22 72 1 0 22 73 1 0 23 74 1 6 24 75 1 0 24 76 1 0 25 77 1 0 25 78 1 0 26 79 1 6 27 80 1 1 28 81 1 0 28 82 1 0 29 83 1 0 29 84 1 0 31 85 1 0 31 86 1 0 31 87 1 0 32 88 1 6 33 89 1 0 33 90 1 0 34 91 1 0 34 92 1 0 36 93 1 0 38 94 1 0 42 95 1 0 42 96 1 0 43 97 1 0 43 98 1 0 44 99 1 0 46100 1 0 46101 1 0 46102 1 0 47103 1 0 M END

Standard InCHIKey	NURHNSZKAHSMAN-KOIIHKETSA-N
Standard InCHI	InChI=1S/C36H56O11/c1-18-29(39)32(42-5)30(40)33(45-18)47-31-19(2)44-28(16-26(31)37)46-22-8-11-34(3)21(15-22)6-7-25-24(34)9-12-35(4)23(10-13-36(25,35)41)20-14-27(38)43-17-20/h14,18-19,21-26,28-33,37,39-41H,6-13,15-17H2,1-5H3/t18-,19-,21-,22+,23-,24+,25-,26+,28+,29+,30-,31-,32+,33+,34+,35-,36+/m1/s1
SMILES	C[C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](C)O[C@H](C[C@@H]1O)O[C@H]1CC[C@@]2(C)[C@H](CC[C@@H]3[C@@H]2CC[C@]2(C)[C@H](CC[C@]32O)C2=CC(=O)OC2)C1)O)OC)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	664.38	Volume:	662.736 ? Van der Waals volume.
Dense:	1.002	LogP:	2.033 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.67 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.055 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	38.0
TPSA:	153.37 ? Topological Polar Surface Area.	H-Bond Acceptor:	11.0
H-Bond Donor:	4.0	Rings:	7.0
Heavy Atoms:	11.0

MedChem Properties

QED Drug-Likeness Score:	0.245	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	5.577	Fsp³:	0.917
MCE-18:	129.333 ? 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:	0.849	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.017 ? 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:	0.182	Promiscuous compounds:	0.376

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.531	MDCK Permeability:	-5.182
Pgp-inhibitor:	0.662	Pgp-substrate:	0.831
PAMPA:	0.982 ? 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):	0.008
20% Bioavailability (F20%):	0.171	30% Bioavailability (F30%):	0.203
50% Bioavailability (F50%):	0.938

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001	MRP1:	0.715
Plasma Protein Binding (PPB):	71.158%	Volume Distribution (VD):	-0.577
Fu:	25.922% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.997
OATP1B3 inhibitor:	0.786	BCRP inhibitor:	0.139
BSEP inhibitor:	0.99

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.673	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.039
HLM stability:	0.193 ? 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):

3.363

Half-life (T1/2):

4.375

ADMET: Toxicity

hERG Blockers:	0.125	hERG Blockers (10um):	0.783
Human Hepatotoxicity (H-HT):	0.459	Drug-induced Liver Injury (DILI):	0.986
AMES Toxicity:	0.947	Rat Oral Acute Toxicity:	0.983
Maximum Recommended Daily Dose:	1.0	Skin Sensitization:	1.0
Carcinogencity:	0.788	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.975
Drug-induced Neurotoxicity:	0.002	Ototoxicity:	0.938
Hematotoxicity:	0.769	Drug-induced Nephrotoxicity:	0.986
Genotoxicity:	0.999	RPMI-8226 Immunitoxicity:	0.876
A549 Cytotoxicity:	0.751	Hek293 Cytotoxicity:	0.968
BCF:	0.56 ? 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:	3.267 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.789 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.992 ? 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
NPO33348	leptadenia madagascariensis	Species	Apocynaceae	Eukaryota	n.a.	Madagascar dry forest	n.a.	PMID[21159516]
NPO33348	leptadenia madagascariensis	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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	2

Activity Type	# Activity
Cell line	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
NPT179	Cell line	A2780	Homo sapiens	IC50	=	210.0	nM	PMID[12828470]
NPT397	Cell line	NCI-H460	Homo sapiens	IC50	=	680.0	nM	PMID[19805565]

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 NPC55532 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	14431
0.1-0.2	31885
0.2-0.3	3206
0.3-0.4	109
0.4-0.5	103
0.5-0.6	78
0.6-0.7	27
0.7-0.8	4
0.8-0.85	0
0.85-0.9	3
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8519	High Similarity	NPC199428
0.8519	High Similarity	NPC109448
0.8519	High Similarity	NPC310341
0.7907	Intermediate Similarity	NPC72260
0.75	Intermediate Similarity	NPC120390
0.7356	Intermediate Similarity	NPC250556
0.7273	Intermediate Similarity	NPC305574
0.7241	Intermediate Similarity	NPC84949
0.7241	Intermediate Similarity	NPC480562
0.7241	Intermediate Similarity	NPC74945
0.7241	Intermediate Similarity	NPC31354
0.7241	Intermediate Similarity	NPC69576
0.7126	Intermediate Similarity	NPC479356
0.7126	Intermediate Similarity	NPC479355
0.7113	Intermediate Similarity	NPC475590
0.7093	Intermediate Similarity	NPC471633
0.6889	Remote Similarity	NPC93883
0.68	Remote Similarity	NPC74259
0.6705	Remote Similarity	NPC99620
0.6667	Remote Similarity	NPC173555
0.6667	Remote Similarity	NPC5883
0.663	Remote Similarity	NPC193893
0.6522	Remote Similarity	NPC484202
0.6495	Remote Similarity	NPC486143
0.6495	Remote Similarity	NPC125077
0.6495	Remote Similarity	NPC486142
0.6495	Remote Similarity	NPC486149
0.6444	Remote Similarity	NPC486129
0.6374	Remote Similarity	NPC486126
0.6354	Remote Similarity	NPC236973
0.6333	Remote Similarity	NPC479351
0.6333	Remote Similarity	NPC479352
0.6327	Remote Similarity	NPC208193
0.6311	Remote Similarity	NPC475419
0.6226	Remote Similarity	NPC474423
0.6196	Remote Similarity	NPC5311
0.617	Remote Similarity	NPC483822
0.6117	Remote Similarity	NPC486144
0.6117	Remote Similarity	NPC486145
0.6117	Remote Similarity	NPC329636
0.6117	Remote Similarity	NPC486147
0.6117	Remote Similarity	NPC486148
0.6022	Remote Similarity	NPC99080
0.5943	Remote Similarity	NPC474908
0.5922	Remote Similarity	NPC475219
0.5918	Remote Similarity	NPC30483
0.5918	Remote Similarity	NPC470897
0.5882	Remote Similarity	NPC486146
0.5859	Remote Similarity	NPC292467
0.5851	Remote Similarity	NPC469750
0.58	Remote Similarity	NPC475556
0.58	Remote Similarity	NPC311706
0.58	Remote Similarity	NPC486151
0.58	Remote Similarity	NPC608063
0.5794	Remote Similarity	NPC117445
0.5794	Remote Similarity	NPC308262
0.5789	Remote Similarity	NPC76572
0.5789	Remote Similarity	NPC193382
0.5728	Remote Similarity	NPC329986
0.5728	Remote Similarity	NPC140092
0.5686	Remote Similarity	NPC486135
0.5686	Remote Similarity	NPC486137
0.5657	Remote Similarity	NPC103534
0.5657	Remote Similarity	NPC44899
0.5657	Remote Similarity	NPC304260
0.5657	Remote Similarity	NPC29639
0.5648	Remote Similarity	NPC486134
0.5648	Remote Similarity	NPC486141
0.5644	Remote Similarity	NPC480910
0.5644	Remote Similarity	NPC480909
0.5638	Remote Similarity	NPC473852
0.5631	Remote Similarity	NPC232785
0.5631	Remote Similarity	NPC486139
0.5545	Remote Similarity	NPC32177
0.5545	Remote Similarity	NPC469756
0.5545	Remote Similarity	NPC275901
0.5521	Remote Similarity	NPC34390
0.5505	Remote Similarity	NPC329675
0.55	Remote Similarity	NPC488935
0.55	Remote Similarity	NPC488936
0.549	Remote Similarity	NPC188234
0.5437	Remote Similarity	NPC231518
0.5437	Remote Similarity	NPC488944
0.5417	Remote Similarity	NPC196429
0.5408	Remote Similarity	NPC180079
0.537	Remote Similarity	NPC486136
0.5368	Remote Similarity	NPC474418
0.5361	Remote Similarity	NPC6108
0.5361	Remote Similarity	NPC77299
0.5361	Remote Similarity	NPC89514
0.5361	Remote Similarity	NPC480906
0.5361	Remote Similarity	NPC477580
0.534	Remote Similarity	NPC240070
0.5333	Remote Similarity	NPC469749
0.5306	Remote Similarity	NPC152615
0.5306	Remote Similarity	NPC480914
0.5287	Remote Similarity	NPC268829
0.5287	Remote Similarity	NPC295110
0.5204	Remote Similarity	NPC480915
0.5155	Remote Similarity	NPC99728
0.5155	Remote Similarity	NPC87250
0.5155	Remote Similarity	NPC244402
0.5155	Remote Similarity	NPC50305
0.5138	Remote Similarity	NPC479360
0.5138	Remote Similarity	NPC479359
0.5138	Remote Similarity	NPC488943
0.5138	Remote Similarity	NPC488942
0.5098	Remote Similarity	NPC480907
0.5093	Remote Similarity	NPC486138
0.5093	Remote Similarity	NPC276838
0.5051	Remote Similarity	NPC157376
0.5051	Remote Similarity	NPC17896
0.5051	Remote Similarity	NPC469755
0.5051	Remote Similarity	NPC284406
0.5051	Remote Similarity	NPC197707
0.5051	Remote Similarity	NPC251866
0.5051	Remote Similarity	NPC142066
0.5051	Remote Similarity	NPC603972
0.505	Remote Similarity	NPC179412
0.505	Remote Similarity	NPC471356
0.505	Remote Similarity	NPC471353

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC55532 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6054
0.1-0.2	2986
0.2-0.3	94
0.3-0.4	4
0.4-0.5	2
0.5-0.6	2
0.6-0.7	4
0.7-0.8	4
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
0.7907	Intermediate Similarity	NPD8294	Phase 4
0.7778	Intermediate Similarity	NPD8377	Phase 4
0.7356	Intermediate Similarity	NPD7507	Pre-clinical
0.7159	Intermediate Similarity	NPD8335	Phase 4
0.6703	Remote Similarity	NPD8380	Approved
0.6667	Remote Similarity	NPD8296	Phase 4
0.6598	Remote Similarity	NPD8378	Pre-clinical
0.6598	Remote Similarity	NPD8379	Approved
0.5437	Remote Similarity	NPD8033	Approved
0.5051	Remote Similarity	NPD7319	Approved

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