Design, Synthesis, and Characterization of a Novel 2'-5'-Linked Amikacin-Binding Aptamer: An Experimental and MD Simulation Study.
Johnsi MathivananZhixue BaiAlan A ChenJia ShengPublished in: ACS chemical biology (2022)
To extend the approach of using RNA aptamers as transient protective groups for the synthesis of novel small-molecule drug derivatives from the existing aminoglycosides, we incorporated 2'-5' phosphodiester backbone modification in a structurally known neomycin RNA aptamer and studied the binding of a series of aminoglycosides using isothermal calorimetry (ITC) and molecular dynamics (MD) simulation. Experimental characterization of amikacin, a commercially available and widely used aminoglycoside for treating bacterial infections, shows that the aptamer A1 with a 2'-5' linkage between G15 and U16 exhibits a sevenfold increase in binding affinity with a lower binding energy compared to the native aptamer. Molecular dynamics (MD) simulation studies rationalize that this noncanonical linkage generates a narrower binding pocket by creating a superspiral RNA helical structure, which improves the ligand's fit in the binding pocket. These results provide new insights into applying 2'-5' linkages to diversify functional RNA aptamers as noncovalent protective groups in the synthesis of aminoglycoside derivatives, which can be further extended to other current drug molecules and complex natural compounds to make new pools of drug candidates more efficiently.
Keyphrases
- molecular dynamics
- density functional theory
- small molecule
- gold nanoparticles
- nucleic acid
- dna binding
- sensitive detection
- binding protein
- pseudomonas aeruginosa
- magnetic nanoparticles
- emergency department
- genome wide
- label free
- adverse drug
- brain injury
- transcription factor
- mass spectrometry
- human immunodeficiency virus