Docking information and results

Published: 16 May 2022| Version 1 | DOI: 10.17632/3zb47wv49k.1
Contributor:
Hiwa Ahmad

Description

Streptozotocin (STZ) induces hyperglycaemia associated with inflammatory disorders and is currently found in the methanolic extract from leaves of Onopordum acanthium (OAE). OAE has been discovered to treat diabetic complications. The objective of this study is to evaluate the ameliorative role of OAE on pancreatic islets injury and myocardial inflammation in diabetic rats. The steam extract of OAE contains six compounds (catechin, kaempferol, syringic acid, p-coumaric acid and epicatechin). The binding site affinity was done between extract compounds with antidiabetic receptors: insulin-like growth factor 1 kinase (PDB ID: 1K3A), glycogen phosphorylase (PDB ID: 1NOI), α-amylase, α-glucosidase (PDB ID: 1OSE), sulphonyl urease (PDB ID: 2E5Z) and glucagon-like peptide-1 (PDB ID: 3IOL). The energy required by syringic acid to bind with insulin-like growth factor 1 kinase (PDB ID: 1K3A) was the lowest at −5.2 kcal/mol, followed by the free energy required by p-coumaric acid (−5.3 kcal/mol), gallic acid (−5.8 kcal/mol), epicatechin (−7.0 kcal/mol), kaempferol (−7.1 kcal/mol) and glibenclamide (−8.0 kcal/mol). All compounds showed binding values of energy from −8.8 to −4.6 kcal/mol. The highest energy was found for catechin (Table 6) (Figure 8) and epicatechin binding with α-glucosidase (PDB ID: 1UOK) and α- amylase (PDB ID: 1OSE) of −8.4 kcal/mol and −7.7 kcal/mol, respectively. Amino acids involved in the formation of a catechin complex with α-glucosidase were GLU387 (H-bond), pHE163, ALA143, LYS293, ASP 285 (H-bond), GLN 330 (H-bond) and ARG415. Kaempferol showed the highest binding site energy interaction with glycogen phosphorylase (−8.1 kcal/mol) (Table 6) (Figure 8) compared to the rest of the naturally extracted compounds after glibenclamide (−8.8 kcal/mol). Amino acids involved were GLU124, 654, ARG93, LYS655, 544 and PRO658. Similar binding site energy (−6.0 kcal/mol) has been observed for the interaction of catechin, kaempferol, epicatechin and glibenclamide with sulphonyl urease (PDB ID: 2E5Z). The amino acids involved in the interaction of glibenclamide with sulphonyl urease are ALA 48, SER 3, ARG 47 and GLY 7. Glucagon-like peptide-1 (PDB ID: 3IOL) interaction with glibenclamide showed the highest binding site energy of (−7.6 kcal/mol) followed by kaempferol (−6.5 kcal/mol), catechin and epicatechin (−6.3 kcal/mol), respectively (Table 6). selective NSAID for COX-1, COX-2) 1CVU, 1IQM, 3FCU, 3LN1 and 3N8Y. Kaempferol has shown the highest binding site of −8.5 and −9.3 kcal/mol with the receptors of integrin αIIbβ3 (PDB ID: 3FCU) and COX-1(PDB ID: 3N8Y) respectively, with amino acids of PHE171, 419, 21, ALA359, ILE360, LEU421, ARG422 and SER420 in 3FCU and CYS36, 47, ILE46, GLY45, PRO153, GLN461, LEU152, GLU465, GLY45 in COX-1 (PDB ID: 3N8Y) (). The interaction of epicatechin with amino acid residue in COX-2 (PDB ID:3LN1) ar

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This is the docking study of several compounds

Institutions

Hawler Medical University

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Molecular Docking

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