Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics.

Autor:	Maksudov F; Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA., Kliuchnikov E; Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA., Pierson D; Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA., Ujwal ML; Inciton, Inc., Andover, MA 01854, USA., Marx KA; Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.; Inciton, Inc., Andover, MA 01854, USA., Chanda A; Technical Operations, Sarepta Therapeutics, Cambridge, MA 02142, USA., Barsegov V; Department of Chemistry, University of Massachusetts, Lowell, MA 01854, USA.; Inciton, Inc., Andover, MA 01854, USA.
Jazyk:	angličtina
Zdroj:	Molecular therapy. Nucleic acids [Mol Ther Nucleic Acids] 2023 Feb 14; Vol. 31, pp. 631-647. Date of Electronic Publication: 2023 Feb 14 (Print Publication: 2023).
DOI:	10.1016/j.omtn.2023.02.007
Abstrakt:	Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm 3 /g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs. Competing Interests: D.P. and A.C. are employees of Sarepta Therapeutics Inc. and may own stock/options in the company. (© 2023 The Author(s).)
Databáze:	MEDLINE
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