Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling

Area of Science:

• Biochemistry
• Molecular Biology
• Pharmaceutical Sciences

Background:

• RNA aptamers show promise for targeted cancer therapy but face manufacturing cost barriers.
• Current methods for optimizing aptamers, like trial-and-error truncation, are inefficient.
• Prostate-specific membrane antigen (PSMA) is a key target for prostate cancer therapeutics.

Purpose of the Study:

• To develop an efficient and rational method for truncating RNA aptamers for therapeutic applications.
• To create a shorter, cost-effective RNA aptamer targeting PSMA with retained binding and functionality.
• To demonstrate the utility of computational tools for optimizing aptamer design.

Main Methods:

• Employed a rational truncation strategy guided by RNA structural prediction algorithms.
• Utilized protein/RNA docking to identify critical nucleotides for aptamer-target interaction.
• Applied these methods to truncate the A9 aptamer targeting PSMA, resulting in the A9L variant.

Main Results:

• Successfully generated a substantially truncated PSMA aptamer (A9L; 41mer) that maintains high binding affinity and functionality.
• Computational modeling identified key nucleotides essential for PSMA binding and inhibition of enzymatic activity.
• The A9L aptamer is amenable to large-scale chemical synthesis, addressing a key manufacturing hurdle.

Conclusions:

• Rational truncation, aided by computational predictions, is an effective strategy for optimizing therapeutic RNA aptamers.
• The developed A9L aptamer is a promising candidate for targeted prostate cancer therapy due to its retained function and manufacturability.
• This approach offers a generalizable framework for developing other optimized RNA aptamers for clinical use.