Recent developments in molecular docking technology applied in food science: a review

Abstract

Molecular docking is a theoretical simulation method based on bioinformatics, which studies the interaction between molecules (such as ligands and receptors), and predicts their binding modes and affinity via a computer platform. This technology acts as a promising mean in medicinal chemistry such as structurebased rational drug design, which is accepted by researchers in the scientific community. During recent years, various fundamental studies involving biomolecular interaction in the food matrix have gradually emerged. The remarkable advantages of molecular docking such as predicting experiments are attracting increasing attention for its application potential in various fields. This review presents the theory and software development of molecular docking, and emphasises its application in the field of food science, including nutritional components and food safety. Moreover, the operational mechanisms of molecular docking are further summarised in this review.

Anthocyanins from Aronia melanocarpa Induce Apoptosis in Caco‐2 Cells through Wnt/β‐Catenin Signaling Pathway

“…The results obtained are similar to the inhibition of β‐catenin by the flavonoids studied by Hira Iftikhar [13] . In general, tumor formation occurs due to the abnormal Wnt signaling by nuclear accumulation of β‐catenin as a result of glycogen synthetase kinase‐3 (GSK‐3)β inactivation [14] . According to molecular docking results, we proposed that four anthocyanins could be more potent inhibitors of β‐catenin.…”

“…[13] In general, tumor formation occurs due to the abnormal Wnt signaling by nuclear accumulation of β-catenin as a result of glycogen synthetase kinase-3 (GSK-3)β inactivation. [14] According to molecular docking results, we proposed that four anthocyanins could be more potent inhibitors of β-catenin. Therefore, we speculated that AMA had a certain inhibition on Wnt/βcatenin signaling pathway and then carried out cell assay to study and verify it.…”

Glycogen Phosphorylase: A Drug Target of Amino Alcohols in Echinococcus granulosus, Predicted by a Computer-Aided Method

“…However, this is the predicted docking pocket, more experiments, such as the mutation of crucial residues will reveal the accurate residues responsible for the activity of EgGps and for protein-ligand interaction. Based on these data, together with molecular dynamics simulations which can evaluate the molecular flexibility of ligands and receptors, more accurate docking and virtual screening methods (Tao et al, 2019;Wang et al, 2020), the promising hits targets EgGps will be found and benefit the development of anti-echinococcal compounds. The interactions of these compounds with Gps were proven in vitro by determining the activity of Gps in PSC homogenates.…”

Molecular Functionality of Plant Proteins from Low- to High-Solid Systems with Ligand and Co-Solute

“…More recently, molecular docking simulations (MDS) show promise in direct elucidation of the specific binding sides being involved in such interactions and the affinity between the two active constituents [101]. In general, molecular docking will examine a range of hypothetical protein structures to decide on the most stable configuration on energetic grounds taking into consideration the non-covalent interactions that stabilise the complex [102].…”

“…The types of software include, AutoDock, DOCK, GOLD, ICM, Glide, Surflex, Affinity, LigandFit, Discovery Studio and many others are well-reviewed in the literature [102,104,105]. The most recent docking programs in the last 5 years are CABS-dock, FlexAID, GalaxyPepDock, LightDock and MOLS 2.0 [106][107][108][109][110].…”