Natural Product: NPC470861

Natural Product IDNPC470861
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Capsicoside A
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2271370
PubChem CID 76323353
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

Standard InCHIKey MFHFOWCCIUBMFM-JIQRIUMBSA-N
Standard InCHI InChI=1S/C63H106O35/c1-21(20-86-55-46(80)42(76)37(71)30(14-64)88-55)7-10-63(85)22(2)36-29(98-63)12-26-24-6-5-23-11-28(27(70)13-62(23,4)25(24)8-9-61(26,36)3)87-56-49(83)45(79)51(35(19-69)93-56)94-60-54(53(41(75)34(18-68)92-60)96-58-48(82)44(78)39(73)32(16-66)90-58)97-59-50(84)52(40(74)33(17-67)91-59)95-57-47(81)43(77)38(72)31(15-65)89-57/h21-60,64-85H,5-20H2,1-4H3/t21-,22+,23+,24-,25+,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?/m1/s1
SMILES OC[C@H]1O[C@@H](O[C@@H]2C[C@@H]3CC[C@@H]4[C@@H]([C@]3(C[C@H]2O)C)CC[C@]2([C@H]4C[C@H]3[C@@H]2[C@@H](C(O3)(O)CC[C@H](CO[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)C)C)C)[C@@H]([C@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1422.65 Volume:   1311.74
?
Van der Waals volume.
Dense:   1.085 LogP:   -1.263
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.281
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.956
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   22.0 Rigid Bonds:   60.0
TPSA:   565.05
?
Topological Polar Surface Area.
H-Bond Acceptor:   35.0
H-Bond Donor:   22.0 Rings:   11.0
Heavy Atoms:   35.0

MedChem Properties

QED Drug-Likeness Score:   0.045 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.798 Fsp3:   1.0
MCE-18:   227.778
?
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:   0.47 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
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:   0.484 Promiscuous compounds:   0.228

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.969 MDCK Permeability:   -4.967
Pgp-inhibitor:   0.0 Pgp-substrate:   0.993
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):   1.0
20% Bioavailability (F20%):   0.203 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.0
Plasma Protein Binding (PPB):   19.614% Volume Distribution (VD):   -0.416
Fu: 44.02%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
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:   0.996 CYP3A4-substrate:   0.993
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.901
HLM stability:   0.09
?
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):  -1.846 Half-life (T1/2):  4.919

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.827 Drug-induced Liver Injury (DILI):  0.988
AMES Toxicity:  1.0 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.008 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.954 Drug-induced Nephrotoxicity:  0.997
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.34
A549 Cytotoxicity:  0.999 Hek293 Cytotoxicity:  0.887
BCF:   0.871
?
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:   3.196
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.491
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.43
?
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
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1007/BF00232372]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Granola: the 1999 growing season DOI[10.1016/S0956-7135(03)00077-X]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. seeds n.a. n.a. PMID[12105963]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. PMID[2831703]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[FooDB]
NPO16501.2 Capsicum annuum Under-species n.a. n.a. n.a. n.a. Database[Phenol-Explorer]

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

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
NPT4127 Organism Pseudomonas stutzeri Pseudomonas stutzeri MIC > 1000.0 ug.mL-1 PMID[22123322]
NPT729 Organism Micrococcus luteus Micrococcus luteus MIC > 1000.0 ug.mL-1 PMID[3934384]
NPT1825 Organism Lactobacillus plantarum Lactobacillus plantarum MIC = 1000.0 ug.mL-1 PMID[2509708]
NPT4130 Organism Lactobacillus rhamnosus Lactobacillus rhamnosus MIC = 1000.0 ug.mL-1 PMID[10762047]
NPT4131 Organism Bacillus licheniformis DSM 13=ATCC 14580 Bacillus licheniformis DSM 13=ATCC 14580 MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT19 Organism Escherichia coli Escherichia coli MIC > 1000.0 ug.mL-1 PMID[22123322]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 1000.0 ug.mL-1 PMID[22123322]
NPT4128 Organism Lactobacillus fermentum Lactobacillus fermentum MIC = 1000.0 ug.mL-1 PMID[22123322]
NPT4129 Organism Lactobacillus casei Lactobacillus casei MIC = 1000.0 ug.mL-1 PMID[22123322]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT2922 Organism Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT2567 Organism Trichoderma viride Hypocrea rufa MIC > 1000.0 ug.mL-1 PMID[2509708]
NPT923 Organism Rhizopus oryzae Rhizopus oryzae MIC = 1000.0 ug.mL-1 PMID[17958396]
NPT4132 Organism Setophoma terrestris Setophoma terrestris MIC = 1000.0 ug.mL-1 PMID[17958396]
NPT3086 Organism Penicillium expansum Penicillium expansum MIC = 1000.0 ug.mL-1 PMID[17958396]
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 1000.0 ug.mL-1 PMID[10762047]

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
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 NPC470861 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8788 High Similarity NPC51520
0.8788 High Similarity NPC303069
0.8515 High Similarity NPC470863
0.8113 Intermediate Similarity NPC84111
0.8113 Intermediate Similarity NPC287483
0.8113 Intermediate Similarity NPC470865
0.7685 Intermediate Similarity NPC470862
0.7593 Intermediate Similarity NPC92710
0.7453 Intermediate Similarity NPC98018
0.7453 Intermediate Similarity NPC284104
0.7453 Intermediate Similarity NPC103616
0.7009 Intermediate Similarity NPC273002
0.6957 Remote Similarity NPC470867
0.6726 Remote Similarity NPC232611
0.6607 Remote Similarity NPC115165
0.6522 Remote Similarity NPC470864
0.6466 Remote Similarity NPC83137
0.641 Remote Similarity NPC92297
0.625 Remote Similarity NPC470866
0.6228 Remote Similarity NPC184617
0.6134 Remote Similarity NPC132080
0.6095 Remote Similarity NPC291203
0.6095 Remote Similarity NPC217205
0.6087 Remote Similarity NPC102016
0.6087 Remote Similarity NPC95051
0.6047 Remote Similarity NPC481190
0.6016 Remote Similarity NPC248202
0.5929 Remote Similarity NPC473601
0.5882 Remote Similarity NPC232037
0.5878 Remote Similarity NPC330026
0.5859 Remote Similarity NPC263359
0.5833 Remote Similarity NPC218571
0.5833 Remote Similarity NPC487615
0.5827 Remote Similarity NPC208832
0.5798 Remote Similarity NPC473518
0.5748 Remote Similarity NPC210569
0.5738 Remote Similarity NPC256983
0.5667 Remote Similarity NPC116756
0.5546 Remote Similarity NPC97700
0.5546 Remote Similarity NPC30856
0.5487 Remote Similarity NPC485601
0.5476 Remote Similarity NPC262050
0.5472 Remote Similarity NPC485600
0.5462 Remote Similarity NPC151134
0.5433 Remote Similarity NPC190939
0.5426 Remote Similarity NPC220836
0.5403 Remote Similarity NPC476112
0.5403 Remote Similarity NPC307534
0.5379 Remote Similarity NPC244431
0.5345 Remote Similarity NPC485599
0.5328 Remote Similarity NPC247037
0.5289 Remote Similarity NPC73243
0.5289 Remote Similarity NPC244086
0.5289 Remote Similarity NPC84956
0.5285 Remote Similarity NPC475625
0.528 Remote Similarity NPC23808
0.528 Remote Similarity NPC87998
0.5273 Remote Similarity NPC485602
0.5267 Remote Similarity NPC79900
0.5197 Remote Similarity NPC31896
0.5194 Remote Similarity NPC94086
0.5194 Remote Similarity NPC473817
0.5164 Remote Similarity NPC308459
0.5128 Remote Similarity NPC195297
0.5126 Remote Similarity NPC98696
0.5106 Remote Similarity NPC329820
0.5089 Remote Similarity NPC294686
0.5088 Remote Similarity NPC206003
0.5088 Remote Similarity NPC473610
0.5079 Remote Similarity NPC249265
0.5043 Remote Similarity NPC476538
0.5043 Remote Similarity NPC476539
0.5042 Remote Similarity NPC475351

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC470861 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  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