Natural Product: NPC2088

Natural Product IDNPC2088
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Allicin
IUPAC Name 3-prop-2-enylsulfinylsulfanylprop-1-ene
Synonyms Allicin; Diallyl Thiosulfinate
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL359965
PubChem CID 65036
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001161] Thiosulfinic acid esters

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 JDLKFOPOAOFWQN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C6H10OS2/c1-3-5-8-9(7)6-4-2/h3-4H,1-2,5-6H2
SMILES C=CCSS(=O)CC=C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   162.02 Volume:   152.868
?
Van der Waals volume.
Dense:   1.06 LogP:   0.781
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.852
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.431
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   2.0
TPSA:   23.06
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.349 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.675 Fsp3:   0.333
MCE-18:   1.0
?
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:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.004 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
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:   0.927 Promiscuous compounds:   0.327

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.495 MDCK Permeability:   -4.579
Pgp-inhibitor:   0.378 Pgp-substrate:   0.068
PAMPA:   0.011
?
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%):   0.05 30% Bioavailability (F30%):   0.648
50% Bioavailability (F50%):   0.622

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.917 MRP1:   0.375
Plasma Protein Binding (PPB):   66.043% Volume Distribution (VD):   0.123
Fu: 32.606%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.001
OATP1B3 inhibitor:   0.0 BCRP inhibitor:   0.06
BSEP inhibitor:   0.518

ADMET: Metabolism

CYP1A2-inhibitor:   0.797 CYP1A2-substrate:   0.964
CYP2C19-inhibitor:   0.894 CYP2C19-substrate:   0.014
CYP2C9-inhibitor:   0.995 CYP2C9-substrate:   0.014
CYP2D6-inhibitor:   0.969 CYP2D6-substrate:   0.642
CYP3A4-inhibitor:   0.004 CYP3A4-substrate:   0.946
CYP2B6-substrate:   0.986 CYP2C8-inhibitor:   0.91
HLM stability:   0.962
?
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):  10.78 Half-life (T1/2):  2.112

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.105
Human Hepatotoxicity (H-HT):  0.185 Drug-induced Liver Injury (DILI):  0.985
AMES Toxicity:  0.885 Rat Oral Acute Toxicity:  0.775
Maximum Recommended Daily Dose:  0.938 Skin Sensitization:  1.0
Carcinogencity:  0.745 Eye Corrosion:  0.981
Eye Irritation:  0.999 Respiratory Toxicity:  0.988
Drug-induced Neurotoxicity:  0.003 Ototoxicity:  0.004
Hematotoxicity:  0.012 Drug-induced Nephrotoxicity:  0.003
Genotoxicity:  0.979 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.003 Hek293 Cytotoxicity:  0.236
BCF:   1.328
?
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:   3.356
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.8
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.408
?
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
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.indcrop.2020.113007]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. DOI[10.3923/pjbs.2013.1138.1144]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. seed n.a. PMID[12381110]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[17262437]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18326559]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota Seeds Zigong, Sichuan Province, China 2004-SEP PMID[20515043]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Essential oil n.a. n.a. PMID[23163425]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[23865201]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. bulb n.a. PMID[24508058]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[25650289]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota garlic skin n.a. n.a. PMID[25726329]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. leaf n.a. PMID[26434122]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[37241721]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[37241721]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[39684509]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO667 Bulbus allii fistulosi n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Bulb n.a. n.a. Database[FooDB]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO667 Bulbus allii fistulosi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18707 Allium ursinum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28923 Allium fistulosum Species Amaryllidaceae 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
NPO18707 Allium ursinum n.a. n.a. 280 + 15 n.a. n.a. μg/g PMID[37241721]
NPO7103 Allium sativum Raw Bulb 1465 150 2780 mg/100g Database [DUKE]
NPO7103 Allium sativum n.a. n.a. 280 + 15 n.a. n.a. μg/g PMID[37241721]

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
NPT346 Individual protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 1910.0 nM PMID[20356305]
NPT214 Individual protein Cathepsin B Homo sapiens Ki = 8600.0 nM PMID[20692829]
NPT346 Individual protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens Activity = 10.0 uM PMID[16408004]
NPT144 Individual protein Telomerase reverse transcriptase Homo sapiens IC50 = 500.0 nM DOI[10.1039/C0MD00241K]
NPT470 Individual protein Rhodesain Trypanosoma brucei rhodesiense Ki = 5310.0 nM PMID[20692829]
NPT472 Individual protein Vanilloid receptor Homo sapiens Activity = 0.099 uM PMID[16408004]
NPT473 Protein complex Amiloride-sensitive sodium channel, ENaC Homo sapiens Inhibition = 77.0 % PMID[22668601]
NPT26255 Single protein Mitochondrial 2-oxodicarboxylate carrier Homo sapiens IC50 = 11.0 nM PMID[32786875]
NPT463 Individual protein HMG-CoA reductase Rattus norvegicus Ratio = 2.07 n.a. PMID[15454225]
NPT463 Individual protein HMG-CoA reductase Rattus norvegicus Decrease = 27.6 % PMID[15454225]
NPT467 Individual protein Transient receptor potential cation channel subfamily A member 1 Mus musculus EC50 = 1320.0 nM PMID[20356305]
NPT468 Individual protein Vanilloid receptor Rattus norvegicus EC50 = 51220.0 nM PMID[20356305]
NPT469 Individual protein Cathepsin L Homo sapiens Ki = 9300.0 nM PMID[20692829]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT464 Cell line Daudi Homo sapiens IC50 = 35300.0 nM PMID[18467007]
NPT165 Cell line HeLa Homo sapiens IC50 = 103500.0 nM PMID[18467007]
NPT465 Cell line NCI-N87 Homo sapiens IC50 = 16800.0 nM PMID[18467007]
NPT116 Cell line HL-60 Homo sapiens IC50 = 5500.0 nM PMID[18467007]
NPT466 Cell line U-937 Homo sapiens IC50 = 19700.0 nM PMID[18467007]
NPT139 Cell line HT-29 Homo sapiens IC50 = 83800.0 nM PMID[18467007]
NPT2028 Cell line SK-N-FI Homo sapiens ED50 = 18.06 uM PMID[32786875]
NPT2380 Cell line SK-N-AS Homo sapiens ED50 = 19.48 uM PMID[32786875]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 5210.0 nM PMID[20692829]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita Activity = 50.0 % PMID[12147760]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MFC = 7.5 ug ml-1 PMID[19949059]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MFC = 15.0 ug ml-1 PMID[19949059]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC = 30.0 ug.mL-1 PMID[19949059]
NPT474 Organism Plasmodium berghei Plasmodium berghei IC50 = 6800.0 nM PMID[22122518]
NPT474 Organism Plasmodium berghei Plasmodium berghei IC50 = 39400.0 nM PMID[22122518]
NPT474 Organism Plasmodium berghei Plasmodium berghei Inhibition = 37.0 % PMID[22122518]
NPT2 Others Unspecified n.a. IC50 = 20.0 nM PMID[18467007]
NPT2 Others Unspecified n.a. Ki = 1040.0 nM PMID[20692829]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 = 13800.0 nM PMID[20692829]
NPT475 Organism Plasmodium yoelii Plasmodium yoelii IC50 = 40000.0 nM PMID[22122518]
NPT26256 Cell line SK-N-BE(2)-M17 Homo sapiens ED50 = 10.27 uM PMID[32786875]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 3.59 mg dl-1 PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 27.6 % PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 50.25 mg dl-1 PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 20.5 % PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 9.44 mg dl-1 PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 39.6 % PMID[15454225]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 2.15 mg/dl PMID[18595719]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 42.69 mg/dl PMID[18595719]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 20.34 mg/dl PMID[18595719]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 36.86 mg/dl PMID[18595719]





 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 NPC2088 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
0.5714 Remote Similarity NPC46648
0.5556 Remote Similarity NPC600941
0.5357 Remote Similarity NPC310746

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC2088 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