Molecular Docking of Isolated Alkaloids for Possible α-Glucosidase Inhibition

Abstract

Diabetes mellitus, one of the most common endocrine-metabolic disorders, has caused significant morbidity and mortality worldwide. To avoid sugar digestion and postprandial hyperglycemia, it is necessary to inhibit α-glucosidase, a digestive enzyme with an important role in carbohydrate digestion. The criteria for the selection of alkaloids are based on their in vitro and in vivo activities on glucose modulation. The current study assessed the bonding potential of isolated alkaloids with the targeted protein. For this purpose, the 3D structure of the target protein (α-glucosidase) was reproduced using MODELLER 9.20. The modeled 3D structure was then validated and confirmed by using the RAMPAGE, ERRAT, and Verify3D online servers. The molecular docking of 32 alkaloids reported as α-glucosidase inhibitors, along with reference compounds (acarbose and miglitol), was done through MOE-Dock applied in MOE software to predict the binding modes of these drug-like compounds. The results revealed that nummularine-R and vindoline possess striking interactions with active site residues of the target protein, and were analogous to reference ligands. In conclusion, the current study provided a computational background to the α-glucosidase inhibitors tested. This novel information should facilitate the development of new and effective therapeutic compounds for the treatment of diabetes mellitus.

In silico identification and study of potential anti-mosquito juvenile hormone binding protein (MJHBP) compounds as candidates for dengue virus - Vector insecticides

“…The control ligands were imported into the query ligand databases prior to preparation and docking. The database of ligand/control structures was prepared for docking as follows in MOE: protonation at a temperature of 300 K and pH 7.0 and energy minimization, using default parameters - Amber10-EHT force field was used with no periodicity, the constraints were maintained at the rigid water molecule level and partial charges were also applied [ 27 , 28 ].

Fig.

…”

Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach

“…Molecular docking is used to predict the possible binding orientation of the vaccine constructs [ 34 , 35 ]. TLR7/8 complex (TLR8 PDB ID:3w3g) was downloaded from Protein Databank (PDB) ( ).…”

Identification of the active compounds and pharmacological mechanisms of Xiaoqinglong decoction for asthma based on network pharmacology and molecular docking technology

“…In molecular docking, if the ligand can combine with amino acid residue via some chemical bonds(such as H bond, H-π bond or π-π bond)in the active pocket of the receptor and produces a negative binding energy which involving the process of energy complementation and conformational change, then the small molecule ligand and the receptor can form a stable complementation [18]. The more negative docking energy score, the higher binding ability and stability of ligand-receptor [19]. The results of molecular docking in this study show that small molecular ligands selected for docking can bind to the four key target proteins with lower binding energy, except the docking result of beta-sitosterol and PPARG (-3.6 kcal•mol − 1) was not very satisfying (Table 2 and Fig.…”