Engineered Branaplam Aptamers Exploit Structural Elements from Natural Riboswitches.

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Drug candidates failing clinical trials for efficacy may possess valuable safety and bioavailability profiles.
• Drug repurposing requires specific molecular recognition agents, such as aptamers, to bind target compounds.
• Branaplam, a small molecule, was previously explored for spinal muscular atrophy and Huntington's disease.

Purpose of the Study:

• To develop a high-affinity RNA aptamer capable of specifically binding the drug candidate branaplam.
• To explore the potential for repurposing branaplam by creating a novel molecular binder.

Main Methods:

• In vitro selection (SELEX) was performed on a combinatorial RNA pool based on a Guanine-I riboswitch aptamer scaffold.
• Rational design and reselection were utilized to optimize the binding affinity of selected aptamer candidates.
• Structural analysis of the resulting aptamer variant was conducted, comparing it to the native riboswitch scaffold.

Main Results:

• A 48-nucleotide RNA aptamer with a dissociation constant (Kd) of approximately 150 nM for branaplam was successfully developed.
• The optimized aptamer retained key structural elements (pseudoknot, P2, P3) but lacked the P1 element crucial for natural riboswitch function.
• An alternative aptamer candidate was identified using a TPP riboswitch scaffold, indicating further development potential.

Conclusions:

• A specific and high-affinity RNA aptamer for branaplam has been engineered.
• This aptamer provides a tool for potential drug repurposing of branaplam, capitalizing on its existing safety data.
• The study demonstrates the versatility of riboswitch scaffolds in aptamer development for small molecules.