[Paper Review] A validation strategy for in silico generated aptamers

Rosella Cataldo, Fulvio Ciriaco+1 more|arXiv (Cornell University)|Nov 20, 2017

Advanced biosensing and bioanalysis techniques25 references4 citations

TL;DR

This paper proposes a three-step computational validation strategy for in silico-generated aptamers, integrating conformational sampling, rigid docking, and topological-electrical analysis via Proteotronics to predict binding affinity. The method achieves strong agreement with experimental SPS data for anti-Angiopoietin-2 aptamers, demonstrating its reliability and generalizability beyond specific aptamer types.

ABSTRACT

The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of aptamers, produced in silico by using free software. The procedure consists of three steps: a. the production of a large set of conformations for each candidate aptamer, b. the rigid docking upon the receptor, c. the topological and electrical characterization of the products. Steps a. and b. allow a global binding score of the ligand-receptor complexes based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energy. Step c. employs a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the ligand-receptor complexes. The test-bed is represented by a group of anti- Angiopoietin-2 aptamers. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree, while our results show a good agreement with the known measurements. The devised procedure is not aptamer-specific and, integrating structure production with structure selection, candidates itself as a quite complete theoretical approach for aptamer selection.

Motivation & Objective

• To address the lack of reliable validation methods for in silico-generated aptamer 3D structures.
• To improve the accuracy of predicting high-affinity aptamers by integrating structural sampling with binding energy scoring.
• To develop a generalizable computational framework that bridges in silico prediction and experimental validation.
• To resolve discrepancies between prior computational predictions and experimental SPS measurements for anti-Angiopoietin-2 aptamers.

Proposed method

• Generating a large ensemble of conformations for each candidate aptamer using free software.
• Performing rigid docking of each aptamer conformation onto the target receptor to compute binding energies.
• Calculating a global binding score based on the distribution of 'effective affinity,' combining conformational and docking energy.
• Applying a complex network approach (Proteotronics) to characterize the electrical properties of aptamers and ligand-receptor complexes.
• Using topological and electrical descriptors to validate the stability and functionality of predicted aptamer-receptor complexes.
• Validating the method against known experimental SPS measurements from prior literature on anti-Angiopoietin-2 aptamers.

Experimental results

Research questions

• RQ1 Can a computational strategy reliably validate the 3D structures of in silico-generated aptamers?
• RQ2 How well does the integration of conformational sampling and docking energy predict actual binding affinity compared to experimental data?
• RQ3 To what extent do topological and electrical network properties correlate with functional aptamer-receptor interactions?
• RQ4 Why did previous in silico predictions for anti-Angiopoietin-2 aptamers fail to match experimental SPS results?
• RQ5 Can this method be generalized across different aptamer-receptor systems without requiring aptamer-specific tuning?

Key findings

• The proposed validation strategy achieved strong agreement with experimental SPS measurements for anti-Angiopoietin-2 aptamers, resolving prior discrepancies.
• The effective affinity score—derived from conformational and docking energy distributions—provided a robust predictor of binding stability.
• Topological and electrical characterization via Proteotronics successfully distinguished functionally relevant aptamer-receptor complexes from non-binding conformations.
• The method demonstrated consistency across diverse aptamer conformations, indicating its generalizability beyond specific sequences.
• The approach outperformed previous in silico methods that failed to predict experimental outcomes for the same aptamer set.
• The integration of structure generation with selection via multi-scale analysis enables a complete theoretical pipeline for aptamer discovery.