ADME and Inhibitory Target Molecules Predicition of Cyamopsis tetragonoloba
Jerine Peter S, Nagesh Kishan Panchal, Aishwaria V Nair, Kshitija Joshi, Shobhy Sosa Andrews, Evan Prince Sabina*
Department of Biomedical Sciences, School of Bio Science and Technology, VIT, Vellore, Tamil Nadu, 632014.
*Corresponding Author E-mail: eps674@gmail.com
ABSTRACT:
Cyamopsis tetragonoloba is also known as a cluster bean which is an annual legume typically grown in the summer season. Asian and South East Asian countries dominate in the cultivation of this plant and is used as a food source wherein both the seeds as well as the seedpods are consumed. It is also used as feed for cattle and fish. While the immature pods contain a high level of hyaluronic acid, trace amounts of it are seen in the mature pods. It is also the source of the Guar Gum which is made from dried and crushed seeds and chemically, is a neutral polysaccharide containing mannose and galactose units. This is primarily used as a thickening agent and also is known to have certain laxative properties. Previous literature has also suggested its usage in the management of diabetes. The aim of our research is to evaluate the ADME properties and its potential inhibitory target molecule prediction of Cyamopsis tetragonoloba through in-silico analysis. ADME is Absorption, Distribution, Metabolism and Excretion properties that is essential for drug designing. The active compounds of the plant were obtained from literature survey. The canonical SMILES of the compound were retrieved from PubChem database which is submitted to Swiss ADME to obtain its properties. The inhibitory target molecule was obtained from Swiss target prediction online software. The compound were studied to understand its role in molecular pathway which helps in drug designing.
KEYWORDS: ADME, Cyamopsis tetragonoloba, inhibitory target molecule prediction, in-silico.
Legumes are plants belonging to the family Fabaceae, and are unique in their nutritional properties. They produce pods that hold the seeds. Importantly these are known for their nitrogen fixing properties by the root nodules. Cyamopsis tetragonoloba is one such legume that is commonly known as the cluster bean and is distinctively known as a green manure1. It is used as cattle feed and food for fish2. It is also the source of guar gum which is a galactomannanpolysaccharide. Chemically, guar gum is an exo-polysaccharide composed of the sugars galactose and mannose3.
Primarily used as a thickening agent, it is also known to have certain laxative properties. It has also been known for its anti-diabetic properties. Guar gum retards ice crystal growth by slowing mass transfer across the solid/liquid interface. It shows good stability during freeze-thaw cycles. In addition to this, immature pods contain a high level of hyaluronic acid and trace amounts of it are seen in the mature pods4. All these properties make it an ideal candidate for checking any inhibitory properties of the constituent molecules for the purpose of drug designing. One of the efficient ways to achieve this is with the help of bioinformatics tools. In order to do this, the role of the specific compounds must be established as their contribution to metabolism. The ADME properties of certain compounds of this plant were predicted. ADME stands for - absorption, distribution, metabolism, and excretion and describes the disposition of a compound within an organism. This is helpful in determining the drug designing and its role in the metabolism of the organism. Active compounds were found from the literature survey which formed the basis of this study. Further bioinformatics based tools were used to then evaluate these compounds5,6.
Inhibitory target prediction helps to identify the proteins targeted by certain compounds. These compounds bind to certain proteins thereby inhibiting their metabolic and biological functions. Often these compounds bind to primary target proteins as well as off target proteins. Inhibitory target prediction helps to evaluate the efficiency of the binding between the target proteins and the compounds7. Target prediction helps to identify the pharmacokinetics, medical biochemistry and physiochemistry of certain compounds8. Pathway analysis predicts the molecules and energies involved in organisms metabolic pathways. It helps to predict and analyse the role and types of metabolic pathways a compound is involved in. Pathway analysis provides a representation of the relevant pathways in which compounds are involved9.
2. MATERIALS AND METHODS:
2.1 Active Compounds of the Plant Cyamopsis tetragonoloba:
All parts of the plant would have certain compounds that react differently. Some of which may be actively involved in the ADME effects of this plant by activating different pathways and initiating different processes in the body. These were found based on a literature survey and their molecular formula and the PubChem IDs were obtained from the PubChem database. The compounds formed the basis of the study thus conducted. The active compounds of Cyamopsis tetragonoloba are 1,2-Cyclopentanedione, Isopentyl acetate, 3,5-Dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one, 2,3-Dihydro-benzofuran, Acetyl monoglyceride, 1-(p-methoxyphenyl)propene, Ethyl alpha-d-glycopyranoside, Palmitic acid, Ethyl hexadecanoate, Hexopyranosyl hexopyranoside, Phytol, Ethyl (9Z,12Z)-9,12-octadecadienoate, Ethyl (9Z)-9-octadecenoate, Ethyl n-octadecanoate, 2-Hexadecanoyl glycerol, Mono(2-ethylhexyl) phthalate, Ethyl nonadecanoate, Aletamine, Propyleneglycol monoleate, Alpha-Monostearin, Ethyl docosanoate, 3-(2-Hydroxy-3,4-dimethoxyphenyl)-7-chromanol, Nonacosane, beta-Tocopherol, Tetracontane, dl-alpha-Tocopherol, Ergost-5-en-3-ol, Stigmasterol, gamma-Sitosterol, Alpha-amyrin and Lupeol.
2.2 ADME Analysis:
The ADME (Absorption, Distribution, Metabolism and Excretion) analysis of the above compounds was done with the help of the online SwissADME tool that allowed the quantification of the same. SwisADME software helps to predict the pharmacokinetics, medicinal biochemistry, drug likeness and physicochemistry of compounds or molecules. SwissADME helps in drug discovery and medicinal chemistry applications. Here, the analysis was done with the help of the Cannonical Smiles obtained for each compound from the PubChem database. The cannonical smiles obtained are then pasted on the smiles list of SwissADME and then the calculations where run to obtain the ADME properties of each compound.
2.3 Inhibitory Target Prediction of Compounds:
Out of these active compounds, only certain molecules may have any kind of inhibitory properties. An understanding of these, along with the pathways they are involved in, would help in targeted drug designing”. Thus, to analyse this, the targets were predicted with the help of the Swiss Target Prediction, Expasy Medicinal Chemistry. Swiss Target Prediction is an online tool to predict the targets of bioactive small molecules in human and other vertebrates. This is useful to understand the molecular mechanisms underlying a given phenotype or bioactivity, to rationalize possible side-effects or to predict off-targets of known molecules. This tool identifies the target molecules based on their Cannonical Smiles of the compounds obtained from the PubChem database. The cannonical smiles obtained are then pasted on the smiles list of Swiss Target Prediction database and then run to predict the target molecules of each compound
2.4 Pathway Analysis of the Target Molecules:
Many target molecules were obtained from the Target Prediction. Three molecules for each of the compounds were selected. Based on this, the pathways in which these are involved in were found. This was done with the help of a literature survey and previously established work.
3. RESULTS:
3.1 ADME Analysis:
The ADME (Absorption, Distribution, Metabolism and Excretion) analysis of compounds of the plant Cyamopsis tetragonoloba was done with the help of the online SwissADME tool that allowed the quantification of the same. The following results were obtained from the SwissADME software after running the canonical smiles of each compound. The ADME properties of each compound are enlisted in the table below:
Table 1 ADME properties of the compounds derived using the SwissADME software
|
SN |
Molecule |
HA |
HBA |
HBD |
RB |
TPSA |
GA |
LK |
LV |
BS |
|
1 |
1,2-Cyclopentanedione |
7 |
2 |
0 |
0 |
34.1 |
High |
-7.2 |
0 |
0.55 |
|
2 |
Isopentyl acetate |
9 |
2 |
0 |
4 |
26.3 |
High |
-5.5 |
0 |
0.55 |
|
3 |
3,5-Dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one |
10 |
4 |
2 |
0 |
66.8 |
High |
-7.4 |
0 |
0.56 |
|
4 |
2,3-Dihydro-benzofuran |
9 |
1 |
0 |
0 |
9.23 |
High |
-5.5 |
0 |
0.55 |
|
5 |
Acetyl monoglyceride |
9 |
4 |
2 |
4 |
66.8 |
High |
-7.8 |
0 |
0.55 |
|
6 |
1-(p-methoxyphenyl)propene |
11 |
1 |
0 |
2 |
9.23 |
High |
-4.9 |
0 |
0.55 |
|
7 |
Ethyl alpha-d-glycopyranoside |
14 |
6 |
4 |
3 |
99.4 |
High |
-9.2 |
0 |
0.55 |
|
8 |
Palmitic acid |
18 |
2 |
1 |
14 |
37.3 |
High |
-2.8 |
1 |
0.56 |
|
9 |
Ethyl hexadecanoate |
20 |
2 |
0 |
16 |
26.3 |
High |
-2.4 |
1 |
0.55 |
|
10 |
Hexopyranosyl hexopyranoside |
23 |
11 |
8 |
4 |
190 |
Low |
-11 |
2 |
0.17 |
|
11 |
Phytol |
21 |
1 |
1 |
13 |
20.2 |
Low |
-2.3 |
1 |
0.55 |
|
12 |
Ethyl (9Z,12Z)-9,12-octadecadienoate |
22 |
2 |
0 |
16 |
26.3 |
High |
-3 |
1 |
0.55 |
|
13 |
Ethyl (9Z)-9-octadecenoate |
42 |
10 |
3 |
31 |
133 |
Low |
-6.6 |
1 |
0.55 |
|
14 |
Ethyl n-octadecanoate |
22 |
2 |
0 |
18 |
26.3 |
Low |
-1.8 |
1 |
0.55 |
|
15 |
2-Hexadecanoyl glycerol |
39 |
5 |
1 |
33 |
72.8 |
Low |
-0.1 |
2 |
0.17 |
|
16 |
Mono(2-ethylhexyl) phthalate |
24 |
4 |
0 |
11 |
52.6 |
High |
-4.1 |
0 |
0.55 |
|
17 |
Ethyl nonadecanoate |
23 |
2 |
0 |
19 |
26.3 |
Low |
-1.6 |
1 |
0.55 |
|
18 |
Aletamine |
13 |
1 |
1 |
4 |
26 |
High |
-5.2 |
0 |
0.55 |
|
19 |
Propyleneglycol monoleate |
24 |
3 |
1 |
19 |
46.5 |
High |
-3.3 |
1 |
0.55 |
|
20 |
alpha-Monostearin |
25 |
4 |
2 |
20 |
66.8 |
High |
-3.2 |
0 |
0.55 |
|
21 |
Ethyl docosanoate |
26 |
2 |
0 |
22 |
26.3 |
Low |
-0.7 |
1 |
0.55 |
|
22 |
Isomucronulatol |
22 |
5 |
2 |
3 |
68.2 |
High |
-6.1 |
0 |
0.55 |
|
23 |
Nonacosane |
29 |
0 |
0 |
26 |
0 |
Low |
2.1 |
1 |
0.55 |
|
24 |
beta-Tocopherol |
30 |
2 |
1 |
12 |
29.5 |
Low |
-1.5 |
1 |
0.55 |
|
25 |
Tetracontane |
40 |
0 |
0 |
37 |
0 |
Low |
5.4 |
2 |
0.17 |
|
26 |
dl-alpha-Tocopherol |
31 |
2 |
1 |
12 |
29.5 |
Low |
-1.3 |
1 |
0.55 |
|
27 |
Ergost-5-en-3-ol |
29 |
1 |
1 |
5 |
20.2 |
Low |
-2.5 |
1 |
0.55 |
|
28 |
Stigmasterol |
30 |
1 |
1 |
5 |
20.2 |
Low |
-2.7 |
1 |
0.55 |
|
29 |
gamma-Sitosterol |
30 |
1 |
1 |
6 |
20.2 |
Low |
-2.2 |
1 |
0.55 |
|
30 |
Alpha-amyrin |
31 |
1 |
1 |
0 |
20.2 |
Low |
-2.5 |
1 |
0.55 |
|
31 |
Lupeol |
31 |
1 |
1 |
1 |
20.2 |
Low |
-1.9 |
1 |
0.55 |
Heavy atom: HA, H-bond acceptors:– HBA, H-bond donors:- HBD, Rotable bonds :- RB, GI absorption:- GA, log Kp (cm/s) – LK, Lipinski violations:- LV and Bioavailability Score – BS
3.2 Inhibitory Target Prediction of Compounds:
Out of these active compounds, only certain molecules may have any kind of inhibitory properties. Swiss Target Prediction, Expasy Medicinal Chemistry was used to analyse and predict the targets for which the compounds have an inhibitory action.
The important inhibitory target of 1,2-Cyclopentanedione are Nitric oxide synthase, brain; Nitric oxide synthase, inducible and Nitric oxide synthase, endothelial. The important inhibitory target of Isopentyl acetate are Carbonic anhydrase I, Indoleamine 2,3-dioxygenase and Beta-chymotrypsin. The important inhibitory target of 3,5-Dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one are Tyrosinase, D amino-acid oxidase and Thymidine phosphorylase. The important inhibitory target of 2,3-Dihydro-benzofuran are odium channel protein type IV alpha subunit, Serotonin 2a (5-HT2a) receptor and Cannabinoid receptor 1. The important inhibitory target of Acetyl monoglyceride is Protein kinase C alpha, Cytidine deaminase and Beta-glucocerebrosidase. The important inhibitory target of 1-(p-methoxyphenyl) propene are Nuclear factor NF-kappa-B p65 subunit, 2) Quinone reductase 2 and Arachidonate 5-lipoxygenase. The important inhibitory target of Ethyl alpha-d-glycopyranoside are Vascular endothelial growth factor A, Gamma-secretase and Acidic fibroblast growth factor. The important inhibitory target of Palmitic acid are Fatty acid binding protein adipocyte, Peroxisome proliferator-activated receptor alpha and Fatty acid binding protein muscle. The important inhibitory target of Ethyl hexadecanoate are Carbonic anhydrase II, Carbonic anhydrase I and Dual specificity phosphatase Cdc25A.
The important inhibitory target of Hexopyranosyl hexopyranoside is Cyclin-dependent kinase 1, Heat shock protein HSP 90-alpha and Vascular Endothelial growth factor A. The important inhibitory target of Ethyl docosanoate are Vitamin D receptor, Carbonic anhydrase II and Carbonic anhydrase I. The important inhibitory target of Isomucronulatol are Arachidonate 15-lipoxygenase, Arachidonate 1 2-lipoxygenase and Arachidonate 15-lipoxygenase, type II. The important inhibitory target of Nonacosane are Testis-specific androgen -binding protein, Sphingosine kinase 2 and Acetylcholin-esterase. The inhibitory target of Beta-Tocopherol are Serine/threonine- protein kinase AKT, PH domain leucine-rich repeat-containing protein phosphatase 1 and Serine/threonine-protein kinase ILK-1. The inhibitory target of Tetracontane are Testis-specific androgen -binding protein, Acyl coenzyme A: cholesterol acyltransferase and Carboxylesterase 2. The inhibitory target of dl-alpha-Tocopherol are Serine/threonine- protein kinase AKT, Cannabinoid receptor 1 and Cannabinoid receptor 2. The inhibitory target of Ergost-5-en-3-ol are Androgen Receptor, LXR-alpha and HMG-CoA reductase. The inhibitory target of Stigmasterol are Androgen Receptor, Niemann-Pick C1-like protein 1 and HMG-CoA reductase. The inhibitory target of gamma-Sitosterol are Androgen Receptor, HMG-CoA reductase and Cytochrome P450 51. The inhibitory target of Alpha-amyrin are Androgen Receptor, Protein-tyrosine phosphatase 1B and Estrogen receptor alpha. The inhibitory target of Lupeol are 11-beta-hydroxy steroid dehydrogenase 1, UDP-glucuronosyl transferase 2B7 and Androgen Receptor. The inhibitory target of Phytol is Androgen receptor, Dual specificity phosphatase cdc25a and UDP-glucuronosyltransferase 2b7. The inhibitory target of Ethyl (9Z,12Z)-9,12-octadecadienoate are Anandamide amidohydrolase, Cannabinoid receptor 1 and Cannabinoid receptor 2. The inhibitory target of Ethyl (9Z)-9-octadecenoate are Protein kinase C delta, Protein kinase C theta and 11-beta-hydroxysteroid dehydrogenase 1. The inhibitory target of Ethyl n-octadecanoate are Vitamin D receptor and UDP-glucuronosyltransferase 2B7. The inhibitory target of 2-Hexadecanoyl glycerol are Protein kinase C gamma, Protein kinase C epsilon and Protein kinase C eta. The inhibitory target of Mono (2-ethylhexyl) phthalate are Cystic fibrosis transmembrane conductance regulator, Phosphodiesterase 4B and Cathepsin K. The inhibitory target of Ethyl nonadecanoate is Vitamin D receptor Dual specificity phosphatase Cdc25 and UDP-glucuronosyltransferase 2B7. The inhibitory target of Propyleneglycol monoleate are Protein kinase C alpha, Prostaglandin E synthase and Anandamide amidohydrolase. The inhibitory target of Alpha-Monostearin is Protein kinase C alpha, Protein kinase C gamma and Protein kinase C eta.
3.3 Pathway Analysis of the Target Molecules:
Many target molecules were obtained from the Target Prediction. The pathways in which these are molecules are involved in, were listed below.
· Nitric oxide synthase, brain - Positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process.
· Nitric oxide synthase, inducible- cytokine mediated signalling pathway
· Nitric oxide synthase, endothelial - liposaccharide mediated signalling pathway, negative regulation of extrinsic apoptotic signalling pathway via death domain receptors, positive regulation of NOTCH pathway.
· Carbonic anhydrase I - Nitrogen metabolism, metabolic pathways
· Indoleamine 2,3-dioxygenase - Kynurenine pathway
· Beta-chymotrypsin - Protein biosynthesis
· Tyrosinase - Melanine biosynthesis
· D amino-acid oxidase - Glyoxylate metabolism and glycine degradation, Peroxisomal protein import.
· Thymidine phosphorylase - dTMP biosynthesis by salvage pathway
· Sodium channel protein type IV alpha subunit - “Interaction between L1 and ankyrins, Phase 0 rapid depolarization.
· Serotonin 2a (5-HT2a) receptor - G-coupled protein receptor signalling pathway, phospholipase C-activating G protein coupled receptor signalling pathway, phospholipase C-activating serotonin receptor signalling pathway.
· Cannabinoid receptor 1 - G protein coupled receptor signalling pathway, adenylate cyclase modulating G protein coupled receptor signalling pathway, cannabinoid receptor pathway.
· Protein kinase C alpha - MAPK1/3 (ERK1/2)-dependent signaling pathway, activates the integrin heterodimer ITGA2B-ITGB3 through the RAP1GAP pathway for adhesion.
· Cytidine deaminase - cell surface receptor signaling pathway.
· Beta-glucocerebrosidase - cholesterol metabolism, Sphingolipid metabolism, Activated by PKC in the salvage pathway of ceramide formation
· Nuclear factor NF-kappa-B p65 subunit - cytokine-mediated signalling pathway, Fc-epsilon receptor signalling pathway, interleukin-1-mediated signalling pathway, negative regulation of extrinsic apoptotic signalling pathway,, negative regulation of insulin receptor signalling pathway, nucleotide-binding oligomerization domain containing 2 signalling pathway, nucleotide-binding oligomerization domain containing 2 signalling pathway, postsynapse to nucleus signalling pathway, stimulatory C-type lectin receptor signaling pathway, T cell receptor signaling pathway, tumor necrosis factor-mediated signaling pathway.
· Quinone reductase 2 - Detoxification pathway.
· Arachidonate 5-lipoxygenase - leukotriene A4 biosynthesis, cytokine-mediated signaling pathway, interleukin-18-mediated signaling pathway, lipoxygenase pathway.
· Vascular endothelial growth factor A - cytokine-mediated signalling pathway, positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signalling pathway, positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signalling pathway, positive regulation of vascular endothelial growth factor receptor signalling pathway, vascular endothelial growth factor receptor signalling pathway
· Gamma-secretase -vascular endothelial growth factor signalling pathway, VEGF-activated neuropilin signalling pathway, VEGFA-VEGFR2 Pathway.
· Acidic fibroblast growth factor - Fibroblast growth factor receptor signaling pathway.
· Fatty acid binding protein adipocyte - Triglyceride catabolism, Transcriptional regulation of white adipocyte differentiation
· Peroxisome proliferator-activated receptor alpha - peroxisomal beta-oxidation pathway of fatty acids, Nuclear Receptor transcription pathway.
· Fatty acid binding protein muscle - Triglyceride catabolism.
· Carbonic anhydrase II - angiotensin-activated signaling pathway
· Dual specificity phosphatase Cdc25A - Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models
· Heat shock protein HSP 90-alpha - Cytokine-mediated signalling pathway, ERBB2 signalling pathway, Fc-gamma receptor signalling pathway involved in phagocytosis, vascular endothelial growth factor receptor signalling pathway, VEGFA-VEGFR2 Pathway.
· Vascular endothelial growth factor A - Cytokine-mediated signaling pathway, positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signalling pathway, positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signalling pathway, VEGFA-VEGFR2 Pathway, VEGF-activated neuropilin signalling pathway.
· Dual specificity phosphatase cdc25a - Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models.
· UDP-glucuronosyltransferase 2b7 - Artemether Metabolism Pathway, Codeine Action Pathway, Codeine and Morphine Metabolism
· Anandamide amidohydrolase - Arachidonic acid metabolism, Fatty acid metabolism, anandamide degradation.
· Cannabinoid receptor 1 - “adenylate cyclase-modulating G protein-coupled receptor signalling pathway, cannabinoid signalling pathway, G protein-coupled receptor signalling pathway.
· Cannabinoid receptor 2 - G protein-coupled receptor signalling pathway
· Protein kinase C delta - Fc-gamma receptor signalling pathway involved in phagocytosis, interferon-gamma-mediated signalling pathway, intrinsic apoptotic signalling pathway in response to oxidative stress, negative regulation of insulin receptor signalling pathway, positive regulation of apoptotic signalling pathway, stimulatory C-type lectin receptor signalling pathway.
· Protein kinase C theta - Fc-epsilon receptor signalling. Pathway, negative regulation of insulin receptor signalling pathway, T cell receptor signalling pathway.
· 11-beta-hydroxysteroid dehydrogenase 1 - 11-beta-Hydroxylase Deficiency, 17-alpha-Hydroxylase Deficiency, 21-Hydroxylase Deficiency.
· Vitamin D receptor - Bile acid signalling pathway, vitamin D receptor signalling pathway, Nuclear Receptor transcription pathway.
· Dual specificity phosphatase Cdc25A - Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models.
· UDP-glucuronosyltransferase 2B7 - Artemether Metabolism Pathway, Codeine Action Pathway, Codeine and Morphine Metabolism.
· Protein kinase C gamma - Cellular signalling pathways, Beta-catenin independent WNT signalling, G Protein Signalling Pathways, ErbB Signalling Pathway.
· Protein kinase C epsilon - RHOA pathway, Fc-gamma receptor signalling pathway involved in phagocytosis, lipopolysaccharide-mediated signalling pathway, TRAM-dependent toll-like receptor 4 signalling pathway.
· Protein kinase C eta - mTOR pathway, PI3K/AKT pathway, positive regulation of B cell receptor signalling pathway.
· Cystic fibrosis transmembrane conductance regulator - ABC transporter disorders, ABC-family proteins mediated transport, Defective CFTR causes cystic fibrosis, Disorders of trans-membrane transporters.
· Phosphodiesterase 4B - G Protein Signalling Pathways, GPCR downstream signalling, Myometrial Relaxation and Contraction Pathways.
· Cathepsin K - Toll-like receptor signalling pathway, Generic Transcription Pathway, RNA Polymerase II Transcription.
· Vitamin D receptor - Bile acid signalling pathway, vitamin D receptor signalling pathway, Nuclear Receptor transcription pathway.
· Dual specificity phosphatase Cdc25A - Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models.
· UDP-glucuronosyltransferase 2B7 - Artemether Metabolism Pathway, Codeine Action Pathway, Codeine and Morphine Metabolism.
· Protein kinase C alpha - MAPK1/3 (ERK1/2)-dependent signalling pathway,RAP1GAP pathway, apoptotic signalling pathway,ERBB2 signalling pathway, positive regulation of adenylate, cyclase-activating G protein-coupled receptor signalling pathway, positive regulation of lipopolysaccharide-mediated signalling pathway.
· Prostaglandin E synthase - Cyclooxygenase pathway, Acetaminophen Action Pathway, Acetylsalicylic Acid Action Pathway.
· Anandamide amidohydrolase - Arachidonic acid metabolism, Fatty acid metabolism, anandamide degradation.
· Protein kinase C alpha - MAPK1/3 (ERK1/2)-dependent signalling pathway, RAP1GAP pathway, apoptotic signalling pathway,ERBB2 signalling pathway, positive regulation of adenylate, cyclase-activating G protein-coupled receptor signalling pathway, positive regulation of lipopolysaccharide-mediated signalling pathway.
· Protein kinase C gamma - Cellular signalling pathways, Beta-catenin independent WNT signalling, G Protein Signaling Pathways, ErbB Signaling Pathway.
· Androgen Receptor - activation of prostate induction by androgen receptor signalling pathway, androgen receptor signalling pathway, intracellular receptor signalling pathway, negative regulation of extrinsic apoptotic signalling pathway, positive regulation of insulin-like growth factor receptor signalling pathway, Positive regulation of intracellular oestrogen receptor signalling pathway.
· HMG-CoA reductase - Involved in sub-pathway that synthesizes (R)-mevalonate from acetyl-CoA“.
· Cytochrome P450 51 - Involved in the sub-pathway that synthesizes zymosterol from lanosterol.
· Protein-tyrosine phosphatase 1B - growth hormone receptor signalling pathway, insulin receptor signalling pathway, negative regulation of insulin receptor signalling pathway, negative regulation of vascular endothelial growth factor receptor signalling pathway, platelet-derived growth factor receptor-beta signalling pathway, regulation of hepatocyte growth factor receptor signalling pathway, regulation of type I interferon-mediated signalling pathway.
· Estrogen receptor alpha - intracellular oestrogen receptor signalling pathway, intracellular steroid hormone receptor signalling, pathway, phospholipase C-activating G protein-coupled receptor signalling pathway, regulation of intracellular oestrogen receptor signalling pathway, regulation of toll-like receptor signalling pathway, regulation of Wnt signalling pathway.
· 11-beta-hydroxy steroid dehydrogenase 1 - Glucocorticoid biosynthetic process“.
· UDP-glucuronosyl transferase 2B7 - Androgen metabolic process, lipid metabolic process.
4. DISCUSSION:
The ADME properties of all the active compounds of Cyamopsis tetragonoloba were checked using the online tool SwissADME. “This tool gives a comparison between multiple parameters that help one judge the biochemistry and the pharmacokinetics of a molecule thus providing a basis for drug designing. “It uses the canonical SMILES of the compounds to interpret many different aspects such as hydrogen bond donors and acceptors as well as the bioavailability of a particular molecule5. “Another important parameter is the gastro-intestinal absorption which is important to understand the absorption effects of the drug. In addition to this, cell membrane penetration of a drug is determined by the TPSA which stands for the Topological Polar Surface Area, is also estimated by the SwissADME tool10. It is in consideration with the sulphur and the phosphorous atoms11,12. Generally, molecules with a TPSA of over 140Å are not as efficient in entering the cell whereas one with less than 70Å is required for a molecule to cross over the blood-brain barrier12. The Lipinski violations are one of the primary criteria to check the drug likeness of any compound if it were to be administered orally. The five rules suggest that a molecule with ideal characteristics to be used as a drug must have no more than 5 and 10 hydrogen bond donors and acceptors receptively. It must have a molecular weight of less than 500 Da and a lower than 5 octanol-water partition coefficient. Thus, it is imperative that a compound considered for drug development, should have least violations to this rule13,14.
Thus, based on all these factors and our study of the active compounds Cyamopsis tetragonoloba, we understand that the compounds – Isomucronulatol, 3,5-Dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one, 1,2-Cyclopentanedione, Isopentyl acetate as well as 2,3-Dihydro-benzofuran seem ideal candidates for further investigation. With the help of the tabulated information, we were able to compare the probability of binding of our compounds with their target proteins. After analysing carefully it was observed that the highest probability of binding is between the compound palmitic acid and its targets which was 0.935895 compared to the rest of the compounds and target proteins. The probability of binding is important so that we can specifically choose and increase the specificity of our compound to certain target molecules and eliminate the other less specific ones, this will play a major role during drug development. Certain target proteins or receptors were seen more frequently than others15. These include Vitamin D receptor, Androgen receptor and Protein kinase C alpha. This shows us that these targets are of much importance further into effective drug development and its specificity to the host being administered. Two pathways namely G protein signalling pathway and Cytokine mediated signalling pathway were the most common pathways that our targets were involved in. Cytokine mediated signalling pathway is involved in processes such as immunity, cell division, cell death and tumour formation by activating genes through a transcription. Proper functioning of G Protein signalling pathway is necessary to prevent diseases like diabetes, blindness, allergies, depression, and certain cancers16.
5. CONCLUSION:
Cyamopsis tetragonoloba is an important candidate for the study of active and inhibitory targets owing to its many ideal qualities. Based on our study, in Cyamopsis tetragonoloba we suggest the active compounds -Isomucronulatol, 3,5-Dihydroxy-6-methyl-2,3-dihydro-4H-pyran-4-one,1,2-Cyclopentanedione, Isopentyl acetate as well as 2,3-Dihydro-benzofuran for further investigation whereas palmitic acid and its targets could be processed in the future for their inhibitory properties.
6. ACKNOWLEDGMENT:
We would like to thank VIT, Vellore for proving seedgrant money and others required facilities for the research work
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Received on 17.12.2019 Modified on 21.02.2020
Accepted on 11.04.2020 © RJPT All right reserved
Research J. Pharm. and Tech. 2021; 14(1):146-152.
DOI: 10.5958/0974-360X.2021.00026.3