TY - JOUR
T1 - Sequence- and structure-dependent cytotoxicity of phosphorothioate and 2¢-O-methyl modified single-stranded oligonucleotides
AU - Croft, Laura V.
AU - Fisher, Mark
AU - Barbhuiya, Tabassum Khair
AU - El-Kamand, Serene
AU - Beard, Samuel
AU - Rajapakse, Aleksandra
AU - Gamsjaeger, Roland
AU - Cubeddu, Liza
AU - Bolderson, Emma
AU - O'Byrne, Ken
AU - Richard, Derek
AU - Gandhi, Neha S.
N1 - Publisher Copyright:
Copyright 2024, Mary Ann Liebert, Inc., publishers.
PY - 2024/6/1
Y1 - 2024/6/1
N2 - Single-stranded oligonucleotides (SSOs) are a rapidly expanding class of therapeutics that comprises antisense oligonucleotides, microRNAs, and aptamers, with ten clinically approved molecules. Chemical modifications such as the phosphorothioate backbone and the 2′-O-methyl ribose can improve the stability and pharmacokinetic properties of therapeutic SSOs, but they can also lead to toxicity in vitro and in vivo through nonspecific interactions with cellular proteins, gene expression changes, disturbed RNA processing, and changes in nuclear structures and protein distribution. In this study, we screened a mini library of 277 phosphorothioate and 2′-O-methyl-modified SSOs, with or without mRNA complementarity, for cytotoxic properties in two cancer cell lines. Using circular dichroism, nucleic magnetic resonance, and molecular dynamics simulations, we show that phosphorothioate- and 2′-O-methyl-modified SSOs that form stable hairpin structures through Watson-Crick base pairing are more likely to be cytotoxic than those that exist in an extended conformation. In addition, moderate and highly cytotoxic SSOs in our dataset have a higher mean purine composition than pyrimidine. Overall, our study demonstrates a structure-cytotoxicity relationship and indicates that the formation of stable hairpins should be a consideration when designing SSOs toward optimal therapeutic profiles.
AB - Single-stranded oligonucleotides (SSOs) are a rapidly expanding class of therapeutics that comprises antisense oligonucleotides, microRNAs, and aptamers, with ten clinically approved molecules. Chemical modifications such as the phosphorothioate backbone and the 2′-O-methyl ribose can improve the stability and pharmacokinetic properties of therapeutic SSOs, but they can also lead to toxicity in vitro and in vivo through nonspecific interactions with cellular proteins, gene expression changes, disturbed RNA processing, and changes in nuclear structures and protein distribution. In this study, we screened a mini library of 277 phosphorothioate and 2′-O-methyl-modified SSOs, with or without mRNA complementarity, for cytotoxic properties in two cancer cell lines. Using circular dichroism, nucleic magnetic resonance, and molecular dynamics simulations, we show that phosphorothioate- and 2′-O-methyl-modified SSOs that form stable hairpin structures through Watson-Crick base pairing are more likely to be cytotoxic than those that exist in an extended conformation. In addition, moderate and highly cytotoxic SSOs in our dataset have a higher mean purine composition than pyrimidine. Overall, our study demonstrates a structure-cytotoxicity relationship and indicates that the formation of stable hairpins should be a consideration when designing SSOs toward optimal therapeutic profiles.
UR - https://hdl.handle.net/1959.7/uws:77077
U2 - 10.1089/nat.2023.0056
DO - 10.1089/nat.2023.0056
M3 - Article
C2 - 38648015
SN - 2159-3337
VL - 34
SP - 143
EP - 155
JO - Nucleic Acid Therapeutics
JF - Nucleic Acid Therapeutics
IS - 3
ER -