In Silico Aptamer Docking Studies: From a Retrospective Validation to a Prospective Case Study-TIM3 Aptamers Binding

Area of Science:

• Computational biology
• Structural biology
• Biochemistry

Background:

• Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a powerful technology for aptamer discovery.
• Integrating in silico methods with SELEX can enhance aptamer design and selection.
• Understanding aptamer-target interactions is crucial for therapeutic applications.

Purpose of the Study:

• To develop and validate a computational workflow for predicting aptamer-protein binding modes and prioritizing aptamers.
• To investigate the binding of murine TIM3 aptamers using 3D RNA modeling and protein docking.
• To identify potential binding sites and explain cross-reactivity differences between murine and human TIM-3.

Main Methods:

• A workflow combining 2D structure prediction, 3D RNA modeling (Rosetta), and protein-ligand docking (3dRPC).
• Cluster analysis of docked poses to identify binding sites and interactions.
• Validation across five study cases and prospective assessment of novel aptamers.

Main Results:

• The computational workflow successfully predicted binding modes and prioritized aptamers in validation cases.
• A plausible binding site and mode for murine TIM3 aptamers were identified, potentially explaining species-specific binding.
• Cluster analysis proved useful in identifying binding sites and reproducing experimental interactions.

Conclusions:

• The proposed in silico workflow, including cluster analysis, is effective for predicting aptamer-protein binding and prioritizing aptamers.
• This method can aid in understanding aptamer-target interactions and designing aptamers with desired specificities, such as for TIM3.
• The findings contribute to the rational design of aptamer-based therapeutics.