title: A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent.
abstract: Antisense oligonucleotides complementary to RNA targets promise generality and ease of drug design. The first systemically administered antisense drug was recently approved for treatment and others are in clinical development. Chemical modifications that increase the hybridization affinity of oligonucleotides are reasoned to confer higher potency, i.e., modified oligonucleotides can be dosed at lower concentrations to achieve the same effect. Surprisingly, shorter and less affine oligonucleotides sometimes display increased potency. To explain this apparent contradiction, increased uptake or decreased propensity to form structures have been suggested as possible mechanisms. Here, we provide an alternative explanation that invokes only the kinetics behind oligonucleotide-mediated cleavage of RNA targets. A model based on the law of mass action predicts, and experiments support, the existence of an optimal binding affinity. Exaggerated affinity, and not length per se, is detrimental to potency. This finding clarifies how to optimally apply high-affinity modifications in the discovery of potent antisense oligonucleotide drugs.
authors.affiliation: 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark [2] Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Lykke
authors.initials: L
authors.lastname: Pedersen
authors.affiliation: 1] Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark [2] Santaris Pharma A/S, Research Division, Hørsholm, Denmark.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Hagedorn
authors.affiliation: Santaris Pharma A/S, Research Division, Hørsholm, Denmark.
authors.forename: Marie Wickström
authors.initials: MW
authors.lastname: Lindholm
authors.affiliation: 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark [2] Center for Computational and Applied Transcriptomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark [3] Santaris Pharma A/S, Research Division, Hørsholm, Denmark.
authors.forename: Morten
authors.initials: M
authors.lastname: Lindow