Structure

Physi-Chem Properties

Molecular Weight:  162.02
Volume:  152.868
LogP:  1.325
LogD:  0.503
LogS:  -1.556
# Rotatable Bonds:  5
TPSA:  23.06
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.349
Synthetic Accessibility Score:  5.675
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.746
MDCK Permeability:  3.437045234022662e-05
Pgp-inhibitor:  0.074
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.275
30% Bioavailability (F30%):  0.904

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.512
Plasma Protein Binding (PPB):  78.12403869628906%
Volume Distribution (VD):  0.853
Pgp-substrate:  3.606455087661743%

ADMET: Metabolism

CYP1A2-inhibitor:  0.069
CYP1A2-substrate:  0.447
CYP2C19-inhibitor:  0.061
CYP2C19-substrate:  0.797
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.872
CYP2D6-inhibitor:  0.098
CYP2D6-substrate:  0.883
CYP3A4-inhibitor:  0.079
CYP3A4-substrate:  0.247

ADMET: Excretion

Clearance (CL):  10.372
Half-life (T1/2):  0.774

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.042
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.955
Rat Oral Acute Toxicity:  0.381
Maximum Recommended Daily Dose:  0.103
Skin Sensitization:  0.945
Carcinogencity:  0.851
Eye Corrosion:  0.989
Eye Irritation:  0.994
Respiratory Toxicity:  0.938

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  Natural Product: NPC2088

Natural Product ID:  NPC2088
Common Name*:   Allicin
IUPAC Name:   3-prop-2-enylsulfinylsulfanylprop-1-ene
Synonyms:   Allicin; Diallyl Thiosulfinate
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
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

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  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[10.3923/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[8350088]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota 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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota Flower 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 Plant 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]
NPO667 Bulbus allii fistulosi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO8321 Allium chinense Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7103 Allium sativum 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]
NPO28923 Allium fistulosum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4520 Allium macrostemon Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
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[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 NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO7103 NPC2088 Raw Bulb 1465 150 2780 mg/100g Database [DUKE]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT463 Individual Protein HMG-CoA reductase Rattus norvegicus Ratio = 2.07 n.a. PMID[495513]
NPT463 Individual Protein HMG-CoA reductase Rattus norvegicus Decrease = 27.6 % PMID[495513]
NPT464 Cell Line Daudi Homo sapiens IC50 = 35300.0 nM PMID[495514]
NPT165 Cell Line HeLa Homo sapiens IC50 = 103500.0 nM PMID[495514]
NPT465 Cell Line NCI-N87 Homo sapiens IC50 = 16800.0 nM PMID[495514]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 5500.0 nM PMID[495514]
NPT466 Cell Line U-937 Homo sapiens IC50 = 19700.0 nM PMID[495514]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 83800.0 nM PMID[495514]
NPT467 Individual Protein Transient receptor potential cation channel subfamily A member 1 Mus musculus EC50 = 1320.0 nM PMID[495516]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 1910.0 nM PMID[495516]
NPT468 Individual Protein Vanilloid receptor Rattus norvegicus EC50 = 51220.0 nM PMID[495516]
NPT214 Individual Protein Cathepsin B Homo sapiens Ki = 8600.0 nM PMID[495517]
NPT469 Individual Protein Cathepsin L Homo sapiens Ki = 9300.0 nM PMID[495517]
NPT470 Individual Protein Rhodesain Trypanosoma brucei rhodesiense Ki = 5310.0 nM PMID[495517]
NPT472 Individual Protein Vanilloid receptor Homo sapiens Activity = 0.099 uM PMID[495518]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens Activity = 10.0 uM PMID[495518]
NPT144 Individual Protein Telomerase reverse transcriptase Homo sapiens IC50 = 500.0 nM PMID[495523]
NPT2028 Cell Line SK-N-FI Homo sapiens ED50 = 18.06 uM PMID[495525]
NPT2380 Cell Line SK-N-AS Homo sapiens ED50 = 19.48 uM PMID[495525]
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 3.59 mg dl-1 PMID[495513]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 27.6 % PMID[495513]
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 50.25 mg dl-1 PMID[495513]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 20.5 % PMID[495513]
NPT29 Organism Rattus norvegicus Rattus norvegicus Weight = 9.44 mg dl-1 PMID[495513]
NPT29 Organism Rattus norvegicus Rattus norvegicus Decrease = 39.6 % PMID[495513]
NPT2 Others Unspecified IC50 = 20.0 nM PMID[495514]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 2.15 mg/dl PMID[495515]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 42.69 mg/dl PMID[495515]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 20.34 mg/dl PMID[495515]
NPT29 Organism Rattus norvegicus Rattus norvegicus Activity = 36.86 mg/dl PMID[495515]
NPT2 Others Unspecified Ki = 1040.0 nM PMID[495517]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 5210.0 nM PMID[495517]
NPT471 Organism Trypanosoma brucei brucei Trypanosoma brucei brucei IC50 = 13800.0 nM PMID[495517]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MFC = 7.5 ug ml-1 PMID[495519]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MFC = 15.0 ug ml-1 PMID[495519]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC = 30.0 ug.mL-1 PMID[495519]
NPT473 Protein Complex Amiloride-sensitive sodium channel, ENaC Homo sapiens Inhibition = 77.0 % PMID[495520]
NPT474 Organism Plasmodium berghei Plasmodium berghei IC50 = 6800.0 nM PMID[495521]
NPT474 Organism Plasmodium berghei Plasmodium berghei IC50 = 39400.0 nM PMID[495521]
NPT474 Organism Plasmodium berghei Plasmodium berghei Inhibition = 37.0 % PMID[495521]
NPT475 Organism Plasmodium yoelii Plasmodium yoelii IC50 = 40000.0 nM PMID[495521]
NPT450 Organism Meloidogyne incognita Meloidogyne incognita Activity = 50.0 % PMID[495522]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 18.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 28.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 13.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 24.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 0.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 15.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 10.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 25.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 22.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 20.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 31.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 17.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 29.0 mm PMID[495524]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IZ = 27.0 mm PMID[495524]
NPT26255 SINGLE PROTEIN Mitochondrial 2-oxodicarboxylate carrier Homo sapiens IC50 = 11.0 nM PMID[495525]
NPT26256 CELL-LINE SK-N-BE(2)-M17 Homo sapiens ED50 = 10.27 uM PMID[495525]
NPT2 Others Unspecified ED50 = 9.21 uM PMID[495525]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  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>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.96 High Similarity NPC46648
0.8571 High Similarity NPC168614
0.8571 High Similarity NPC204251
0.8333 Intermediate Similarity NPC220140
0.8333 Intermediate Similarity NPC184203
0.8 Intermediate Similarity NPC142438
0.72 Intermediate Similarity NPC476548
0.72 Intermediate Similarity NPC326758
0.7037 Intermediate Similarity NPC156018
0.68 Remote Similarity NPC476549
0.6765 Remote Similarity NPC277288
0.6667 Remote Similarity NPC476550
0.6216 Remote Similarity NPC205586

  Chemically structural similarity: II. 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>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.5862 Remote Similarity NPD8550 Phase 3
0.5862 Remote Similarity NPD8552 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8229 Phase 3
0.5667 Remote Similarity NPD8227 Approved
0.5667 Remote Similarity NPD8230 Phase 3

  Bioactivity similarity: Similar Natural Products in NPASS

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