Towards a new generation of therapies based on gene silencing

Proteins are large, complex molecules that perform a number of essential functions in the body and are formed by following the instructions encoded in DNA. By reading the letters of your DNA, cells produce an intermediate RNA molecule that will give rise to the corresponding protein. Most diseases occur with altered protein levels, which are the cause or consequence of the condition itself. RNA plays a key role in diseases with altered protein levels by serving as an intermediary messenger between DNA and protein.

In recent years, research efforts aimed at blocking protein production by intervening RNA molecules have intensified, in order to treat various diseases.

Researchers from the Molecular Modeling and Bioinformatics Laboratory of the Institute for Research in Biomedicine (IRB Barcelona) and the biotechnology company Nostrum Biodiscovery have carried out computational and experimental analyzes to produce predictive models capable of determining the structure, stability, flexibility and biology of targeted drugs to the RNA. The aim is to modulate the expression of certain pathogenic proteins. These RNA-binding molecules are also DNA strands called oligonucleotides that, taking advantage of the Watson-Crick base-pairing model, recruit the target RNA, thus preventing its function.

The study included extensive computational and experimental analyses. The experimental work was carried out at the Experimental Bioinformatics Laboratory, directed by Dr. Isabelle Brun Heath at IRB Barcelona. The team validated their predictions in vitro and obtained outstanding results. It was carried out in collaboration with the leading international biotechnology companies Biogen and Ionis Pharmaceuticals, as well as with the Department of Inorganic and Organic Chemistry of the University of Barcelona and the Rocasolano Institute of Physical Chemistry, in Spain.

The authors of the new study have laid the foundation for the systematic development of RNA binding inhibitors based on antisense oligonucleotide technology. (Image: IRB Barcelona)

“The project aims to establish guidelines for developing optimal oligonucleotides targeting this intermediate step in potentially any protein production process. We now know some of the specific modifications these molecules must undergo to improve their thermostability, specificity, and sensitivity to degradation.” by cellular mechanisms”, explains Dr. Orozco, also a professor in the Department of Biochemistry and Biomedicine at the University of Barcelona.

“The simulation tools that we have developed are an example of precision engineering, since we have systematically studied all the possible modifications in each position of the candidate molecules to amplify their function. This work has only been possible thanks to the technology available at Nostrum Biodiscovery and the key collaboration of top-tier partners, such as Biogen and Ionis Pharmaceuticals,” says Dr. Vito Genna, former postdoctoral researcher at IRB Barcelona and current Director of the Nucleic Acids Department at Nostrum Biodiscovery.

Until now, the investigation of these oligonucleotides has been entirely experimental, and it is a cumbersome process. Now, the biotech company will further develop these predictors to build a machine learning tool (a form of artificial intelligence) that guides researchers working on these types of therapies, saving them time and money.

In the search for effective therapeutic oligonucleotides, researchers have identified three crucial characteristics of any candidate. First, the molecule must form stable hybrids when paired with the corresponding RNA molecule, a process that requires both thermostability and stability over time. Second, it must be resistant to serum nucleases, a property that enhances its availability in the body. Finally, the oligonucleotide must produce hybrids sensitive to RNase H degradation, which is the cellular mechanism responsible for removing RNA molecules and preventing protein formation.

These three key features provide a valuable framework for the development of oligonucleotides that can effectively target and treat diseases by regulating protein production.

A therapeutic approach to address a wide range of diseases

A therapeutic approach with potential to address a wide range of conditions is emerging that interacts with the protein expression pathway and has cross-sectional applicability. This therapy could be used to treat any disease related to the excess of a certain protein or the formation of aberrant variations of some proteins, including infectious diseases that occur with the production of pathogenic proteins in human cells.

This broad spectrum has generated great interest in this type of therapy in recent years, partly due to the relative ease of handling these molecules, their small size, and their cost-effectiveness.

To further advance this therapeutic approach, the researchers will now validate their results in cell culture and try to develop an optimal standard that can serve as the basis for directing a variety of DNA-RNA hybrids, blocking a number of proteins, and treating related diseases.

The study is titled “Controlled Sulfur-Based Engineering Confers Moldability to Phosphorothioate Antisense Oligonucleotides”. And it has been published in the academic journal Nucleic Acids Research. (Source: IRB Barcelona)