Exploring the anti-diabetic activity of 2,6-diamino-4-chloropyrimidinium-hydrogen oxalate conjugates: Synthesis, crystal structure, quantum computational, drug-likeness, molecular docking and dynamics simulation

Abstract

Inhibiting carbohydrate-hydrolyzing enzyme has been considered as an effective approach for controlling starch digestion and postprandial blood glucose level. The aim of this study, the salt molecule was prepared to identify potentially effective compound against diabetic activity and discover the inhibitory mechanism of the targeted enzyme, which is determined by In-silico techniques. And also perform the quantum chemical calculation to provide insights about the internal motions of the molecule at the atomic level. The 2,6-diamino-4-chloropyrimidinium-hydrogen oxalate (C4H6ClN4+. C2HO4-) was newly synthesized molecule, which is detailly discussed in this present work. The title compound has been confirmed by single-crystal X-ray diffraction studies, and this structure was refined by the least-square refinement method. The crystal compound exhibited the P-1 space group (centrosymmetric) and the following unit cell parameters: a = 5.5778(6)Å, b = 9.6687(10)Å, c = 9.9144(10)Å, α = 116.342(1) °, β = 92.610(1) °, γ = 106.370(1) °, Z = 2. The molecular structure is stabilized by the networks of N–H···O, O–H···O, C–H···O, and N–H···N hydrogen bond interactions. The Hirshfeld surface (HS) analysis and fingerprint plots revealed strong intermolecular interaction between the molecules. The structural optimization, frontier molecular orbital (FMO), molecular reactivity, molecular electrostatic potential (MEP), and mulliken atomic charges were generated by the density functional theory (DFT) calculated at B3LYP/6-311G++ (d,p) theory level. Drug-likeness and physicochemical properties were predicted. The molecular docking analysis was showed a binding energy of −8.96 kcal/mol within the active site of alpha-amylase, which is responsible for anti-diabetic activity. The protein-ligand complex stability was verified using molecular dynamics studies with 100 ns.