Chemical Manipulation of the Endosome Trafficking Machinery: Implications for Oligonucleotide Delivery

Abstract

Antisense oligonucleotides (ASOs), siRNA and splice switching oligonucleotides (SSOs) all have immense potential as therapeutic agents, potential that is now being validated as oligonucleotides enter the clinic. However, progress in oligonucleotide-based therapeutics has been limited by the difficulty in delivering these complex molecules to their sites of action in the cytosol or nucleus of cells within specific tissues. There are two aspects to the delivery problem. The first is that most types of oligonucleotides have poor uptake into non-hepatic tissues. The second is that much of the oligonucleotide that is taken up by cells is entrapped in endosomes where it is pharmacologically inert. It has become increasingly recognized that endosomal trapping is a key constraint on oligonucleotide therapeutics. Thus, many approaches have been devised to address this problem, primarily ones based on various nanoparticle technologies. However, recently an alternative approach has emerged that employs small molecules to manipulate intracellular trafficking processes so as to enhance oligonucleotide actions. This review presents the current status of this chemical biology approach to oligonucleotide delivery and seeks to point out possible paths for future development.

Keywords: delivery; endosome; oligonucleotide; small molecule.

Figure 1

Cell uptake and trafficking of oligonucleotides. Oligonucleotides enter cells via several endocytic pathways that may depend on clathrin, caveolin or dynamin. All uptake pathways initially lead to the early/re-cycling endosome compartment. Most internalized oligonucleotide accumulates in late endosomes/multivesicular bodies (MVB/LEs) and in lysosomes; however, some trafficking to other membrane bound compartments does occur. Within endomembrane compartments, oligonucleotides are pharmacologically inert. However, a very small portion of internalized oligonucleotide can spontaneously escape to the cytosol. The endomembrane system is controlled by a plethora of proteins and protein complexes. The Rab family of GTPases regulates many aspects of trafficking, while individual members can be markers for distinct endomembrane compartments. The formation of intralumenal vesicles (ILVs) within MVBs is regulated by the multi-protein ESCRT complex. The Retromer complex may deliver oligonucleotides to the trans-Golgi instead of to lysosomes.