A Computational Approach to Comparative Analysis of Aflatoxin B1-Specific Aptamers for Detection: Insights into Molecular Interactions and Binding Affinities

Aflatoxins (AFs) are the carcinogenic secondary metabolites produced by fungi such as Aspergillus flavus, A. parasiticus, and A. nomius. These fungi are widespread and have severely contaminated food/feed supplies. The major health consequences of consuming AF-contaminated food/feed are Hepatocellular carcinoma and its associated complications. Therefore, detecting and quantifying AFs in foods and feeds is critical to achieve food safety. Among the available methods, aptamer-based techniques are receiving more attention considering their specificity, sensitivity, low cost, and ease of production and handling. Though AFB₁-specific aptamers have been well studied, ligand–aptamer molecular interactions are not clear. In the present study, the three-dimensional structures of available AFB₁-specific DNA aptamers were predicted using RNA-based web servers with an automated machine translation principle and some manual changes in the script file. Molecular docking was performed between selected DNA aptamers and AFB₁. Molecular docking results revealed that the AFB₁ was located inside the pocket area of the predicted tertiary structures and formed electrostatic interactions with the nucleotides of aptamers. The binding affinities of all aptamers were between -7.3 and -11.7 kcal/mol. This study adds to our understanding of how AFB₁ interacts with all available aptamers. The developed workflow enables the generation and examination of additional appealing ligand–aptamer complexes to detect AF and other mycotoxins.