NPASS Compound

Natural Product: NPC329727

Natural Product ID	NPC329727
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AYIVMCNWKUCOII-YJKBSPITSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	46881049
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

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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Standard InCHIKey	AYIVMCNWKUCOII-YJKBSPITSA-N
Standard InCHI	InChI=1S/C77H126O43/c1-25-8-13-77(105-20-25)26(2)42-35(120-77)15-32-30-7-6-28-14-29(9-11-75(28,4)31(30)10-12-76(32,42)5)107-61-39(19-81)111-69(57(61)98)104-24-41-48(89)62(116-72-54(95)50(91)46(87)40(112-72)23-103-67-52(93)45(86)36(16-78)109-67)58(99)73(113-41)114-59-34(83)22-102-70(56(59)97)117-63-47(88)37(17-79)110-74(65(63)119-68-51(92)44(85)33(82)21-101-68)115-60-38(18-80)108-66(100)64(55(60)96)118-71-53(94)49(90)43(84)27(3)106-71/h25-74,78-100H,6-24H2,1-5H3/t25-,26-,27-,28-,29-,30+,31-,32-,33-,34+,35-,36-,37+,38+,39-,40+,41+,42-,43-,44-,45-,46+,47+,48+,49+,50-,51+,52+,53+,54+,55-,56+,57+,58+,59-,60-,61-,62-,63-,64+,65+,66+,67+,68-,69+,70-,71-,72-,73-,74-,75-,76-,77+/m0/s1
SMILES	C[C@H]1CC[C@@]2([C@@H](C)[C@H]3[C@H](C[C@H]4[C@@H]5CC[C@H]6C[C@H](CC[C@]6(C)[C@H]5CC[C@]34C)O[C@H]3[C@H](CO)O[C@H]([C@@H]3O)OC[C@@H]3[C@H]([C@@H]([C@H]([C@@H](O3)O[C@H]3[C@@H](CO[C@H]([C@@H]3O)O[C@H]3[C@@H]([C@@H](CO)O[C@H]([C@@H]3O[C@H]3[C@@H]([C@H]([C@H](CO3)O)O)O)O[C@H]3[C@@H](CO)O[C@H]([C@@H]([C@H]3O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)O)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]4[C@@H]([C@H]([C@H](CO)O4)O)O)O3)O)O)O)O)O2)OC1

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1738.77	Volume:	1589.98 ? Van der Waals volume.
Dense:	1.094	LogP:	-1.102 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	-0.088 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.059 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	24.0	Rigid Bonds:	82.0
TPSA:	649.89 ? Topological Polar Surface Area.	H-Bond Acceptor:	43.0
H-Bond Donor:	23.0	Rings:	15.0
Heavy Atoms:	43.0

MedChem Properties

QED Drug-Likeness Score:	0.043	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	8.206	Fsp³:	1.0
MCE-18:	401.143 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.566	Fluc inhibitor:	0.333 ? 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:	0.0 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.466	Promiscuous compounds:	0.159

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-8.396	MDCK Permeability:	-4.212
Pgp-inhibitor:	0.0	Pgp-substrate:	0.999
PAMPA:	1.0 ? 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):	0.992
20% Bioavailability (F20%):	0.477	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.0
Plasma Protein Binding (PPB):	14.485%	Volume Distribution (VD):	-0.432
Fu:	51.301% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.002
BSEP inhibitor:	0.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.999	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
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):

-1.968

Half-life (T1/2):

4.644

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	0.429	Drug-induced Liver Injury (DILI):	0.997
AMES Toxicity:	0.996	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.657	Drug-induced Nephrotoxicity:	0.998
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.79
A549 Cytotoxicity:	0.997	Hek293 Cytotoxicity:	0.849
BCF:	1.062 ? 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:	3.322 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.711 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.533 ? 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
NPO40067	Chlorophytum orchidastrum	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20028106]

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
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	1350.0	nM	PMID[20028106]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	3600.0	nM	PMID[20028106]

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 NPC329727 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	32625
0.1-0.2	15029
0.2-0.3	1701
0.3-0.4	345
0.4-0.5	73
0.5-0.6	58
0.6-0.7	16
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
0.9669	High Similarity	NPC329807
0.9593	High Similarity	NPC481189
0.8605	High Similarity	NPC329820
0.7143	Intermediate Similarity	NPC232037
0.7109	Intermediate Similarity	NPC132080
0.7029	Intermediate Similarity	NPC330026
0.6957	Remote Similarity	NPC481190
0.6693	Remote Similarity	NPC97700
0.6693	Remote Similarity	NPC30856
0.6692	Remote Similarity	NPC470866
0.6562	Remote Similarity	NPC184617
0.648	Remote Similarity	NPC475351
0.6397	Remote Similarity	NPC94086
0.6397	Remote Similarity	NPC473817
0.6391	Remote Similarity	NPC476112
0.6391	Remote Similarity	NPC307534
0.6377	Remote Similarity	NPC220836
0.6316	Remote Similarity	NPC470864
0.6288	Remote Similarity	NPC475625
0.6288	Remote Similarity	NPC116756
0.6269	Remote Similarity	NPC83137
0.6015	Remote Similarity	NPC115165
0.5985	Remote Similarity	NPC233433
0.592	Remote Similarity	NPC206003
0.592	Remote Similarity	NPC473610
0.5909	Remote Similarity	NPC51172
0.5909	Remote Similarity	NPC49032
0.584	Remote Similarity	NPC250393
0.5802	Remote Similarity	NPC473601
0.5778	Remote Similarity	NPC475319
0.5764	Remote Similarity	NPC210569
0.5726	Remote Similarity	NPC177834
0.5683	Remote Similarity	NPC470862
0.5664	Remote Similarity	NPC480556
0.5652	Remote Similarity	NPC232611
0.558	Remote Similarity	NPC473518
0.5556	Remote Similarity	NPC471464
0.5556	Remote Similarity	NPC234352
0.5532	Remote Similarity	NPC84111
0.5532	Remote Similarity	NPC287483
0.5532	Remote Similarity	NPC470865
0.5517	Remote Similarity	NPC473505
0.5515	Remote Similarity	NPC128572
0.5504	Remote Similarity	NPC19400
0.5496	Remote Similarity	NPC6295
0.5442	Remote Similarity	NPC15918
0.5436	Remote Similarity	NPC305771
0.5436	Remote Similarity	NPC263359
0.5436	Remote Similarity	NPC94072
0.5436	Remote Similarity	NPC169816
0.5385	Remote Similarity	NPC107188
0.5385	Remote Similarity	NPC31896
0.5379	Remote Similarity	NPC125324
0.5354	Remote Similarity	NPC325828
0.531	Remote Similarity	NPC470867
0.5306	Remote Similarity	NPC224314
0.5303	Remote Similarity	NPC107962
0.5294	Remote Similarity	NPC602423
0.529	Remote Similarity	NPC151134
0.5282	Remote Similarity	NPC108072
0.5271	Remote Similarity	NPC477451
0.5267	Remote Similarity	NPC211354
0.5232	Remote Similarity	NPC244431
0.5217	Remote Similarity	NPC300557
0.5185	Remote Similarity	NPC160426
0.5177	Remote Similarity	NPC470863
0.5175	Remote Similarity	NPC480554
0.5143	Remote Similarity	NPC98018
0.5143	Remote Similarity	NPC284104
0.5143	Remote Similarity	NPC103616
0.5141	Remote Similarity	NPC475333
0.5141	Remote Similarity	NPC224098
0.5141	Remote Similarity	NPC208383
0.5133	Remote Similarity	NPC79900
0.5113	Remote Similarity	NPC264101
0.5103	Remote Similarity	NPC480553
0.5103	Remote Similarity	NPC477811
0.5075	Remote Similarity	NPC215408
0.5067	Remote Similarity	NPC273002
0.5035	Remote Similarity	NPC309278

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC329727 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8177
0.1-0.2	937
0.2-0.3	29
0.3-0.4	5
0.4-0.5	1
0.5-0.6	1
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
0.5354	Remote Similarity	NPD8171	Phase 2

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