Structure

Physi-Chem Properties

Molecular Weight:  234.02
Volume:  220.628
LogP:  1.199
LogD:  0.82
LogS:  -2.183
# Rotatable Bonds:  8
TPSA:  23.06
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.279
Synthetic Accessibility Score:  5.586
Fsp3:  0.333
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.877
MDCK Permeability:  2.4210068659158424e-05
Pgp-inhibitor:  0.031
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.992
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.11
Plasma Protein Binding (PPB):  84.82679748535156%
Volume Distribution (VD):  1.069
Pgp-substrate:  3.0501914024353027%

ADMET: Metabolism

CYP1A2-inhibitor:  0.073
CYP1A2-substrate:  0.533
CYP2C19-inhibitor:  0.427
CYP2C19-substrate:  0.783
CYP2C9-inhibitor:  0.191
CYP2C9-substrate:  0.895
CYP2D6-inhibitor:  0.675
CYP2D6-substrate:  0.904
CYP3A4-inhibitor:  0.69
CYP3A4-substrate:  0.253

ADMET: Excretion

Clearance (CL):  9.587
Half-life (T1/2):  0.942

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.087
Drug-inuced Liver Injury (DILI):  0.214
AMES Toxicity:  0.978
Rat Oral Acute Toxicity:  0.199
Maximum Recommended Daily Dose:  0.443
Skin Sensitization:  0.951
Carcinogencity:  0.903
Eye Corrosion:  0.959
Eye Irritation:  0.984
Respiratory Toxicity:  0.971

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Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC168614

Natural Product ID:  NPC168614
Common Name*:   (Z)-Ajoene
IUPAC Name:   (Z)-1-(prop-2-enyldisulfanyl)-3-prop-2-enylsulfinylprop-1-ene
Synonyms:   (Z)-Ajoene
Standard InCHIKey:  IXELFRRANAOWSF-ALCCZGGFSA-N
Standard InCHI:  InChI=1S/C9H14OS3/c1-3-6-11-12-7-5-9-13(10)8-4-2/h3-5,7H,1-2,6,8-9H2/b7-5-
SMILES:  C=CCSS/C=CCS(=O)CC=C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL122289
PubChem CID:   9881148
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000004] Organosulfur compounds
      • [CHEMONTID:0000491] Sulfoxides

*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]
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]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[8350088]
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]
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]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7103 Allium sativum Species Amaryllidaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
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]
NPO7103 Allium sativum 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[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

☑ 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
NPT1557 Individual Protein Glutathione reductase Homo sapiens Inhibition = 50.0 % PMID[537722]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat/Km = 6800.0 M-1 s-1 PMID[537722]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat = 2.6 s-1 PMID[537722]
NPT1557 Individual Protein Glutathione reductase Homo sapiens Km = 380000.0 nM PMID[537722]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat/Km = 6840.0 M-1 s-1 PMID[537722]
NPT1557 Individual Protein Glutathione reductase Homo sapiens k cat = 0.06 s-1 PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi Inhibition = 40.0 % PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi k cat/Km = 340.0 M-1 s-1 PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi Km = 2000000.0 nM PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi k cat = 0.67 s-1 PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi Km >= 2000000.0 nM PMID[537722]
NPT991 Individual Protein Trypanothione reductase Trypanosoma cruzi k cat/Km = 335.0 M-1 s-1 PMID[537722]
NPT2 Others Unspecified IC50 = 15500.0 nM PMID[537723]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 25000.0 nM PMID[537724]
NPT2 Others Unspecified IC50 = 4.0 ug.mL-1 PMID[537725]

☑ 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 NPC168614 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
1.0 High Similarity NPC204251
0.8571 High Similarity NPC2088
0.8276 Intermediate Similarity NPC46648
0.7857 Intermediate Similarity NPC156018
0.7143 Intermediate Similarity NPC220140
0.7143 Intermediate Similarity NPC184203
0.6897 Remote Similarity NPC142438
0.6486 Remote Similarity NPC277288
0.6333 Remote Similarity NPC476550
0.6207 Remote Similarity NPC476548
0.6207 Remote Similarity NPC326758
0.6 Remote Similarity NPC205586
0.5862 Remote Similarity NPC476549

  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 NPC168614 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
NPD

  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