Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study

Abstract

Due to the difficulties in monoclonal antibody production specific to mycotoxins, aptameric probes have been considered as suitable alternatives. The low efficiency of the SELEX procedure in screening high affinity aptamers for binding mycotoxins as small molecules can be significantly improved through computational techniques.Previously, we designed five new aptamers to aflatoxin B 1 (AFB1) based on a known aptamer sequence (Patent: PCT/CA2010/001 292, Apt1) through a genetic algorithmbased in silico maturation strategy and experimentally measured their affinity to the target toxin. Here, integrated molecular dynamic simulation (MDs) studies with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis to clarify the binding modes, critical interacting nucleic bases and energy component contributions in the six AFB1-binding aptamers. The aptamer F20, which was selected in the first work, showed the best free binding energy and complex stability compared to other aptamers. The trajectory analysis revealed that AFB1 recognized F20 through the groove binding mode along with precise shape complementarity. The MD simulation results revealed that dynamic water intermediate interactions also play a key role in promoting complex stability. According to the MM-PBSA calculations, van der Waals contacts were identified as dominant energy components in all complexes. Interestingly, a high consistency is observed between the experimentally obtained binding affinities of the six aptamers with their free energy solvation. The computational findings, confirmed via previous experiments, highlighted the binding modes, the dynamic hydration of complex components and the total free interacting energy as the crucial criteria in discovering high functional aptameric probes.

Impedimetric Polyaniline-Based Aptasensor for Aflatoxin B1 Determination in Agricultural Products

“…This may be due to the instability of the Apt structure after the formation of Apt/AFB 1 complexes. In the molecular dynamic simulations study of Mousivand and co-workers [ 60 ], the structure of Apt underwent conformational changes, with the formation of a gap between subsequent base pairs of the Apt due to the intercalation of AFB 1 . The Apt sequences applied in their simulation study have the exact same sequences as the Apt used in the present research.…”

Protein DEK and DTA Aptamers: Insight Into the Interaction Mechanisms and the Computational Aptamer Design

“…MM–PBSA is a post-processing end-state method and is widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as protein–DNA binding interaction ( Miller, et al, 2012 ; Hu, et al, 2020 ; Mousivand, et al, 2022 ). From the last 50 ns trajectories at an interval of 20 ps, a total of 2,500 snapshots were applied to calculate the binding free energy.…”

Modification of nitrilase based on computer screening and efficient biosynthesis of 4‐cyanobenzoic acid

“…[17][18][19] PyMOL was used to visually examined the structural integrities of the site-directed mutant models and then generate structural images. [20] CAVER Analyst 2.0 was used to visualize the tunnel, channel, and cavity in static and dynamic structures. [21] Fpocket was used to analyze the activity pockets of nitrilases.…”