Structural insight into antisense gapmer-RNA oligomer duplexes through molecular dynamics simulations

Abstract

There is an extensive research carrying out on antisense technology and the molecules entering into clinical trials are increasing rapidly. Phosphorothioate (PS) is a chemical modification in which nonbridged oxygen is replaced with a sulfur, consequently providing resistance against nuclease activity. The 2'-4' conformationally restricted nucleoside has the structural features of both 2'-O-methoxy ethyl RNA (MOE), which shows good toxicity profile, and locked nucleic acid (LNA), which shows good binding affinity towards the target RNA. These modifications have been studied and suggested that they can be a potential therapeutic agents in antisense therapy. Mipomersen (ISIS 301012), which contains the novel nucleoside modification has been used to target to apolipoprotein (Apo B), which reduces LDL cholesterol by 6–41%. In this study, classical molecular dynamics (MD) simulations were performed on six different antisense gapmer/target-RNA oligomer duplexes (LNA-PS-LNA/RNA, RcMOE-PS-RcMOE/RNA, ScMOE-PS-ScMOE/RNA, MOE-PS-MOE/RNA, PS-DNA/RNA and DNA/RNA) to investigate the structural dynamics, stability and solvation properties. The LNA, MOE nucleotides present in respective duplexes are showing the structure of A-form and the PS-DNA nucleotides resemble the structure of B-form helix with respect to some of the helical parameters. Free energy calculations suggest that the oligomer, which contains LNA binds to the RNA strongly than other modifications as shown in experimental results. The MOE modified nucleotide, which although had a lower binding affinity but higher solvent accessible surface area (SASA) compared to the other modifications, may be influencing the toxicity and hence may be used it in Mipomersen, the second antisense molecule which is approved by FDA.

Communicated by Ramaswamy H. Sarma

Keywords:

• MD simulations
• antisense oligonucleotides
• gapmer
• chemically modified nucleic acids
• 2′-O-methoxyehtyl RNA
• free-energy

Acknowledgements

Authors Mallikarjunachari Uppuladinne acknowledges National PARAM Supercomputing Facility (NPSF) and Bioinformatics Resources and Applications Facility (BRAF) of C-DAC, for providing supercomputing facility to carryout long molecular dynamics simulations and team members for supporting in detailed discussions.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

Uddhavesh Sonavane and Ramesh Deka acknowledges the Department of Biotechnology, Government of India, for financial support of this work (DBT project No. BT/PR16182/NER/95/92/2015).