A new tool for the design of oligonucleotide therapeutics

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Antisense therapy

Antisense therapy is a form of treatment that uses antisense oligonucleotides (ASOs) to target messenger RNA (mRNA). ASOs are capable of altering mRNA expression through a variety of mechanisms. Several ASOs have been approved in the United States, European Union, and elsewhere.

Approved therapies

Approved therapies include Batten disease (Milasen), Cytomegalovirus retinitis (Fomivirsen), Duchenne muscular dystrophy (eteplirsen, golodirsen, viltolarsen), Familial chylomicronaemia syndrome (Volanesorsen), Familial hypercholesterolemia (mipomersen), Hereditary transthyretin-mediated amyloidosis, (Inotersen), Spinal muscular atrophy (nusinersen).

Amyotrophic lateral sclerosis

Tofersen (also known as IONIS-SOD1Rx and BIIB067) is currently being tested in a phase 3 trial for amyotrophic lateral sclerosis (ALS) due to mutations in the SOD1 gene. Results from a phase 1/2 trial have been promising. It is being developed by Biogen under a licensing agreement with Ionis Pharmaceuticals.

Design of oligonucleotide therapeutics

The development of oligonucleotide therapeutics remains challenging as they often have unintended off-target effects and cause non-specific hepatic and renal toxicity. Additionally, it is exceptionally difficult to deliver oligonucleotides to most tissue types and organs.

This can result in the need for tissue specific delivery systems and several siRNA compounds have advanced into development using this paradigm. Designing antisense oligonucleotides (ASOs) and siRNA can be logistically challenging given the many competing design criteria that can be incorporated into the selection of tool or therapeutic sequences.

Design considerations may include splice variants, cross-species targeting for validation, single nucleotide polymorphisms (SNPs), secondary structure, undesirable motifs (e.g. toxic, poly-A, or poly-G repeats), complementarity with off-target sequences, intron/exon boundaries, chemical modification pattern of nucleotides, and predicted activity.

These factors need to be weighed according to the intended use of the oligonucleotide. For example, compounds designed as in vitro tools only need to be active in a single species, whereas it is advantageous for therapeutic oligonucleotides to be active in model organisms as well as patients. A number of computational tools have been developed to address different aspects of the design process.

PFizer RNAi Enumeration and Design tool

In the present paper, the scientists describe PFRED ( PFizer RNAi Enumeration and Design tool), a client-server software system designed to assist with the entire oligonucleotide design process, starting with the specification of a target gene (Ensembl ID) and culminating in the design of siRNAs or RNase H-dependent antisense oligonucleotides. Sequences are chosen using bioinformatics algorithms built upon careful mining of the sequence-activity relationships found in public datasets as well as internal collections.

The tool provides researchers with a user-friendly interface where the only required input is an accession number for the target gene and it returns a list of properties that are believed to contribute to the efficacy of an siRNA or ASO. These properties include human transcripts and cross-species homology, GC content, SNPs, intron-exon boundary, duplex thermodynamics, efficacy prediction score and off-target matches.

An automated oligonucleotide selection procedure is available to quickly select one potential set of sequences with an appropriate property profile. The selection protocol can be customized by the user through changes of the selection cutoffs or the addition of alternate design parameters and algorithms.

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