Research led by IQAC-CSIC and the University of Barcelona (UB) has developed a new therapeutic tool that inhibits the proliferation of the SARS-CoV-2 virus, which causes COVID-19. This genomic tool can be used to attack other viral diseases that still have no treatment and is an example of the therapeutic potential of oligonucleotides.
Ramon Eritja (third from the left) and Anna Aviñó (fifth from the left), with their team in the IQAC-CSIC laboratory
The research is based on the use of molecules known as polypurine hairpins (PPRH). These are oligonucleotide sequences (small strands of DNA) designed to have a very high affinity for a particular area of the viral genome.
The graphic designation ‘hairpins’ comes from the fact that they are designed to form hairpin structures. The two ‘arms’ of the hairpin have the same sequence, only in reverse, like the image reflected in a mirror, explains CSIC researcher Ramon Eritja. This increases their ability to bind specifically to RNA or DNA sequences.
In this way, they trap and immobilise specific sequences, thus preventing the expression of the corresponding protein. The ability to adapt this molecular tool to a specific disease depends, therefore, on finding the sequence that the hairpin should carry for each case.
In this research, the team led by Carlos J. Ciudad and Verònica Noé, from the University of Barcelona (UB), and the team led by Ramon Eritja and Anna Aviñó, from the Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) and CIBER-BBN, have designed polypurine hairpins to stop the replication of the SARS-CoV-2 virus.
Ramon Eritja's team is an expert in nucleic acids, especially in modified or conjugated nucleotides and their use in therapies, and Carlos J. Ciudad's team is one of the few working on PPRH in Spain.
Pictured, the two PPRHs designed in the work: CC1, left, which binds to the region of the RNA that codes for the replicase enzyme that the virus needs to replicate; and CC3 (right), which binds to the coding region of the Spike protein, essential in infection in human cells. The PPRH have a structure reminiscent of a clip or hairpin; hence its name
Researchers Miguel Chillón, from the Autonomous University of Barcelona (INc, UAB), and Noemí Sevilla and José Manuel Rojas, from the Centre for Animal Health Research (CISA, INIA of the CSIC) have also played an important role. The research has received support from La Marató de TV3 2020, dedicated to promoting research against COVID-19.
As Carlos J. Ciudad explains, ‘specifically, one of the arms of each chain of the CC1-PPRH and CC3-PPRH polypurines binds specifically to a fragment of the RNA genome of the virus -a sequence of polypyrimidines-, through Watson-Crick bonds’.
‘Specifically, CC1-PPRH binds to the RNA region encoding the replicase enzyme, which is essential for virus replication, while CC3-PPRH binds to the coding region of the Spike protein, which plays a key role in infection in human cells,’ the researcher continues.
The new therapeutic technique has been successfully validated in vivo in laboratory animal models expressing the human ACE2 receptor, with the collaboration of the Centre for Animal Health Research (CISA-INIA-CSIC). Also, at the Centre for Animal Biotechnology and Gene Therapy (CBATEG) of the UAB, in vitro studies have been carried out in primate Vero E6 cells that have the ACE-2 receptor as an entry route for the SARS-CoV-2 virus.
This work demonstrates for the first time the use of PPRH oligonucleotides against coronavirus, but its use in the treatment of other diseases such as cancer is also being investigated.
This is the first scientific work that describes how PPRHs can act as therapeutic agents and that they can stop the replication of the SARS-CoV-2 virus, which for practical purposes would be equivalent to a prevention and cure therapy, says Ramon Eritja.
Previously, the same team, together with researchers from the Institute of Microelectronics of Barcelona IMB-CNM-CSIC and the Aragon Nanoscience and Materials Institute (INMA, CSIC-UNIZAR) had described the use of polypurine hairpins as a new diagnostic method to detect RNA viruses such as SARS-CoV-2 (International Journal of Molecular Sciences, 2023).
El potencial de los oligonucleótidos como terapia genómica
‘It has been shown that genomic tools can be a strategy for many diseases,’ says Ramon Eritja. This work demonstrates for the first time their use against coronavirus, but their use in cancer treatment is also being investigated. It is a strategy in which, instead of applying a drug for attacking the toxic element, a genomic tool is applied intervene earlier, preventing either the synthesis of a toxic protein or the replication of a virus or cell, for example.
This approach is particularly promising for the case of genetic diseases. In this regard, Ramon Eritja explains, 2016 and 2017 marked a milestone when it was shown for the first time that antisense oligonucleotide therapy could be effective in the treatment of spinal muscular atrophy (SMA), a devastating neuromuscular disorder characterised by the loss of motor neurons in the spinal cord, muscle atrophy and premature death or severe disability.
Reference articles:
Ciudad, Carlos J.; Valiuska, Simona; Rojas, José Manuel; Nogales-Altozano, Pablo; Aviñó, Anna; Eritja, Ramón; Chillón, Miguel; Sevilla, Noemí; Noé, Verónique. «Polypurine reverse hoogsteen hairpins as a therapeutic tool for SARS-CoV-2 infection». The Journal of Biological Chemistry, octubre de 2024. DOI: 10.1016/j.jbc.2024.107884
Aviñó, A.; Cuestas-Ayllón, C.; Gutiérrez-Capitán, M.; Vilaplana, L.; Grazu, V.; Noé, V.; Balada, E.; Baldi, A.; Félix, A. J.; Aubets, E.; Valiuska, S.; Domínguez, A.; Gargallo, R.; Eritja, R.; Marco, M. P.; Fernández-Sánchez, C.; Martínez de la Fuente, J.; Ciudad, C. J. «Detection of SARS-CoV-2 Virus by Triplex Enhanced Nucleic Acid Detection Assay (TENADA)». International Journal of Molecular Sciences, desembre de 2022. Doi: 10.3390/ijms232315258