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A Multi-Engine Consensus Docking Pipeline for RNA Aptamer Screening Against ACC Oxidase (ACO): Statistical
Héctor Ramón Martínez-de la Hoya1, Cristian Patricia Cabrales-Arellano2, Josué Ortiz-Medina1,3
1Division of Research and Postgraduate Studies, Tecnológico Nacional de México/I.T. Durango, Blvd. Felipe Pescador 1830, Durango 34080, Mexico.
International Journal of Molecular Sciences
|July 15, 2026
Summary
Researchers developed AptaDock to find RNA aptamers that inhibit ethylene production in fruits. This computational tool screens aptamer libraries against key enzymes, aiming to reduce postharvest losses without toxic chemicals.
Area of Science:
- Biotechnology
- Computational Biology
- Agricultural Science
Background:
- Postharvest losses in climacteric fruits are significantly influenced by ethylene.
- Inhibiting ethylene biosynthesis is a key strategy to mitigate these losses.
- RNA aptamers offer a non-toxic alternative to chemical inhibitors for enzyme modulation.
Purpose of the Study:
- To develop and validate a computational pipeline for screening RNA aptamers against ethylene biosynthesis enzymes.
- To identify potential RNA aptamers targeting ACC oxidase (ACO) and ACC synthase (ACS).
- To automate the screening workflow into a user-friendly application.
Main Methods:
- A computational pipeline integrating ITD DOCK, HDOCK Lite, and HADDOCK3 docking engines was employed.
- Large libraries of RNA aptamers were screened against ACC oxidase (ACO).
- A Random Forest model was used to assess sequence-based prediction capabilities, with a positive control using HADDOCK3 energy components.
Main Results:
- Docking engine scores for 9813 aptamers against ACO showed complementary performance.
- Sequence-only features failed to predict docking scores, indicating the necessity of structural docking.
- A pilot screening against ACC synthase (ACS) suggested pipeline generalizability and identified potential dual-target aptamers.
Conclusions:
- The developed computational pipeline, AptaDock, effectively screens RNA aptamers against ethylene biosynthesis enzymes.
- The study highlights the potential of RNA aptamers for sustainable postharvest loss reduction in fruits.
- AptaDock provides an automated solution for identifying novel aptamer candidates for agricultural applications.