Molecular Docking Studies of Phenolic Compounds from Syzygium cumini with Multiple Targets of Type 2 Diabetes

Diabetes mellitus (or simply diabetes) is a long-lasting disorder of food metabolism characterized by hyperglycemia, originating due to defect in insulin secretion, insulin function or both leading to tissue and vascular damage and resulting in a variety of complications (Bastaki, 2005; Cade, 2008; Grewal et al., 2014; Grewal et al., 2016). It is currently one of the largest global health emergencies; according to the International Diabetes Federation, in 2017 there were 425 million adults estimated to have diabetes, and the number is likely to reach 629 million by 2045 (IDF). Type 2 diabetes (T2D) affecting more than 90% of all the diabetic patients, is a long-term disordered food metabolism caused by declined insulin action (Kohei, 2010; Olokoba et al., 2012). Although a variety of medicines are available for T2D therapeutics, no single drug is useful for achieving long-term control of normal blood glucose levels in majority of patients. Due to this reason, general practitioners prescribe combination of antidiabetic agents for T2D therapy and overdose of antidiabetic medicines could lead to severe hypoglycemia resulting in brutal toxic and side effects. This caused the scientific community to search for new antidiabetic drugs (Olokoba et al., 2012; Osadebe et al., 2014). Large numbers of plants and parts of plants were reported with their antidiabetic properties. Various types of plant-derived active principles representing several bioactive compounds have established their beneficial role for possible use in T2D therapeutics (Patil et al., 2011; Ibrahim et al., 2013; Kumar et al., 2012). Syzygium cumini (Linn.) is an economically important tropical fruit tree belonging to the family Myrtaceae largely grown in Indian subcontinent along with some other parts of South Asia including Bangladesh, Sri Lanka, Nepal, Pakistan, Burma and Indonesia. It is also cultivated in some parts of Africa and South America (Swami et al., 2012; Srivastava and Chandra, 2013). It is commonly known as jamun in India, black plum in Europe, jambolan in Spanish spoken countries, and Jambolac in Brazil. It is also known as java plum, Indian blackberry, Portuguese plum, Malabar plum, purple plum, Jamaica and damson plum (Ayyanar and Subash-Babu, 2012; Chagas et al., 2015). Various types of secondary metabolites like flavonoids (quercetin, rutin, catechin, kaempferol, myricetin, isoquercetin, Molecular Docking Studies of Phenolic Compounds from Syzygium cumini with Multiple Targets of Type 2 Diabetes


In Silico Prediction of Pharmacokinetic Parameters
All the selected molecules were analyzed for prediction of pharmacokinetic parameters related to absorption, distribution, metabolism, and excretion (ADME) by employing FAF-Drugs4 server; and evaluated using Lipinski's rule of five for drug-likeness (

Molecular Docking Studies
In silico molecular docking studies were carried out for the selected molecules in the binding site of target proteins using AutoDock Vina (

Pharmacokinetic Parameters
ADME properties including molecular weight (MW), partition coefficient (log P), topological polar surface area (tPSA), water solubility (log S w ), hydrogen bond acceptors (HBA), hydrogen bond donors (HBD), solubility (mg/ mL) and number of rotatable bonds were predicted for all the molecules selected for docking studies. Almost all the compounds showed good pharmacokinetic parameters and drug-like properties as contrived by Lipinski's rule of five (Table 1).

Molecular Docking Study
The docking simulations were carried out by energy minimization and optimization of selected ligands in the binding site of target protein (PDB entries: 3L4T, 4A5S, 1Q5K, 3IMX and 5EE7 for AG, DPP4, GSK3, GK and GCR, respectively). The reference ligands was docked into the active site of target proteins; and the docked reference ligands produced a similar binding pattern and superposition on the binding mode of co-crystallized ligand validating accuracy of docking methodology. The docking score (binding free energy, ΔG, kcal/mol) of the selected compounds with various target proteins are presented in Table 2. Amongst the compounds tested in silico, myricetin, catechin and rutin showed appreciable binding interactions with AG; quercetin, catechin and rutin with DPP4; rutin with GCR, kaempferol with GK; and ferulic acid and rutin with GSK3 as determined by analysing the binding interactions of the selected best docked poses and ΔG of the best docked poses. The docking studies of these molecules suggested a complimentary fit in the binding site of the target proteins. For the rest of the molecules, the molecules had a different orientation and binding pattern (flipping) in the binding site of the target protein possibly due to steric clashes of the substituents. Best docked compounds were further analyzed in details using PyMOL. Overlay of the docked poses of myricetin, catechin and rutin with that of PDB Ligand 3L4T in the binding site of AG showed that these molecules had the similar binding and orientation pattern in the binding site of enzyme as that of co-crystallized ligand (BJ2661 i.e.,    Overlay of the docked pose of kaempferol with that of PDB Ligand 3IMX in the allosteric site of GK showed that it had the similar binding and orientation pattern in the allosteric binding site of GK enzyme as that of co-crystallized activator ((2R)-3-cyclopentyl-N-(5-methoxy [1,3]thiazolo [5,4-b] pyridin-2-yl)-2-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl} propanamide) (Figure 5a). Kaempferol was found to bind to an allosteric pocket of GK protein, which is about 20Å remote from the glucose binding site. The docked pose of kaempferol showed the H-bond interaction between hydroxyl and carbonyl group of chromene-4-one with backbone carbonyl and amide NH of Arg63 on GK protein with H-bond distance of 4.9 Å and 4.7 Å respectively (Figure 5b).  Overlay of the docked pose of rutin with that of PDB Ligand 1Q5K in the binding site of GSK3 showed that it had the similar binding and orientation pattern in the binding site of GSK3 enzyme as that of co-crystallized ligand (N-(4-methoxybenzyl)-N'-(5-nitro-1,3-thiazol-2-yl) urea) (Figure 6a). The docked pose of rutin in binding site of GSK3 showed the H-bond interactions between 'OH' of glucose and carbonyl of Pro136; 'OH' of oxychromen-4one and carbonyl of Val135; and carbonyl of oxychromen-4-one and amide 'NH' of Val135 with H-bond distance of 2.7 Å, 3.5 Å, and 3.8 Å respectively (Figure 6b).

Conclusion
Molecular docking studies using AutoDock vina and AutoDock Tools was performed to explore the binding mechanism of the selected natural phenolic compounds from S. cumini with multiple targets associated with T2D. In current in silico docking study, results clearly demonstrated that amongst the compounds tested in silico, rutin showed appreciable binding with multiple targets of T2D including α-glucosidase, dipeptidyl peptidase 4, glycogen synthase kinase 3, and glucagon receptor. Catechin was found to inhibit both α-glucosidase, and dipeptidyl peptidase 4. Myricetin was found to inhibit AG and quercetin was found to inhibit DPP4. Kaempferol was found to activate allosterically GK protein. In silico study is actually an added advantage to screen the type 2 antidiabetic agents and natural phenolic compounds may serve as useful leads for the synthesis of clinically useful and safe type 2 antidiabetic agents. However, structural modifications and further studies on these natural phenolic compounds are required to develop safe and potent natural type 2 antidiabetic agents.