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Molecular docking analysis of compounds from Lycopersicon esculentum with the insulin receptor to combat type 2 diabetes

It is known that tomato (Lycopersicon esculentum) contains bioactive compounds to combat type-2 diabetes. Therefore, it is of interest to document data from the molecular docking analysis of compounds from Lycopersicon esculentum with the insulin receptors to combat type-2 diabetes. We report the binding features of cinnamic acid, chlorogenic acid, gallic acid & glucoside with insulin receptors for further consideration.


Background:
Type-2 diabetes is one of the greatest global health emergencies of the twenty-first century. Insulin resistance is believed to be the key event contributing to the progression of the disease in type-2 diabetes. Insulin resistance results in reduced glucose absorption by peripheral tissues, as well as improvements in lipid homeostasis. Several tissues have a crucial role to play in the development of insulin resistance and type-2 diabetes. Insulin Receptor (IR) is a ©Biomedical Informatics (2020) tetrameric protein composed of two extracellular alpha subunits and two transmembrane beta subunits [1]. The binding of insulin to the alpha subunit of IR induces conformational changes in the receptor leading to the activation of the tyrosine kinase beta subunit. Activated IR also has capacity to auto phosphorylate and phosphorylate intracellular substrates which are necessary for the initiation of additional cellular responses to insulin [2][3][4]. Such activities result in activation of downstream signaling molecules that participate in the insulin-signaling pathway [5]. Insulin signaling, including activation of IR tyrosine kinase, was disrupted in most patients with diabetes mellitus. This insulin resistance contributes to hyperglycemia as well as other metabolic disorders of the disease [6]. Therefore, compounds that increase the function of the insulin receptor tyrosine kinase may be useful in the treatment of diabetes mellitus.
It is known that tomato (Lycopersicon esculentum) contains bioactive compounds to combat type-2 diabetes [7,8]. Therefore, it is of interest to document data from the molecular docking analysis of compounds from Lycopersicon esculentum with the insulin receptors to combat type-2 diabetes. We report the binding features of Cinnamicacid, Chlorogenicacid, Gallicacid & Glucoside with insulin receptors for further consideration. Therefore, it is of interest to document data from the molecular docking analysis of compounds from Lycopersicon esculentum with the insulin receptors to combat type-2 diabetes.

Materials and Methods: Protein target:
The high-resolution structure of Insulin receptor was downloaded from PDB (PDB Id: 1IRK) [9] (Figure 1).

Ligand preparation:
12 compounds identified from the tomato plant were selected from the literature. The structures of these compounds have been retrieved from the PubChem Compound Database in the Spatial Data File (.SDF) file format and converted to the PDB file format using the Online Smile Translator. Energy minimization of ligands was performed using ChemBio 3D Ultra 12.0, based on the method stated.

Molecular docking:
The Patchdock server was used to determine the interaction between the insulin receptor and the selected compounds.

Results and Discussion:
Docking was performed using the PatchDock software between the lead compounds present in Tomato Plants targeting 1IRK to determine the binding efficiency in the form of Atomic Contact Energy (ACE) as shown in Table-1. ACE is a good parameter/indicator to know the docking efficiency of target molecules with lead compounds under the Patch Dock system. All of the selected compounds showed a good interaction with the target insulin protein receptorBased on the score parameters and the H-bond information; we selected the best four compounds.
©Biomedical Informatics (2020) Among them, chlorogenicacid has an ACE value of-141.17 kcal / mol. In order to analysis the docking the H -bond details, docked structure was visualized using PYMOL software. This study showed that the selected four compounds had more than two Hbond interactions with the target insulin receptor protein. Vijayalakshmi et al., 2015[12] stated that if the H-bond interaction was more, the binding affinity of the ligand was higher.

Conclusion:
We report the binding features of cinnamicacid, chlorogenicacid, gallicacid & glucoside with insulin receptors for further consideration.