Polypurine hairpins found to effectively halt SARS-CoV-2 replication

University of BarcelonaDec 3 2024

A study led by the University of Barcelona and the Spanish National Research Council's Institute for Advanced Chemistry of Catalonia (IQAC - CSIC) presents a new therapeutic tool capable of inhibiting the proliferation of the SARS-CoV-2 virus that causes COVID-19. The results open up new perspectives in the fight against this coronavirus and other viral diseases that still have no medical treatment, such as the Crimean-Congo haemorrhagic fever (CCHFV).

The paper, published on The Journal of Biological Chemistry, is led by experts Carlos J. Ciudad and Verónica Noé, from the UB's Faculty of Pharmacy and Food Sciences and the Institute of Nanoscience and Nanotechnology (IN²UB), in collaboration with Ramon Eritja and Anna Aviñó, from the CSIC's IQAC and the Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN). Researchers Miguel Chillón, from the Institute of Neuroscience of the Universitat Autònoma de Barcelona (INc - UAB) and Noemí Sevilla and José Manuel Rojas, from the Animal Health Research Centre (CISA - CSIC) have also played an important role. The study has also received the support of La Marató de TV3 2020, dedicated to promoting research against COVID-19.

Polypurine hairpins to inhibit the virus that causes COVID-19

​​​In May 2023, the World Health Organization declared that the COVID-19 pandemic was no longer a global emergency. However, many people worldwide are still infected by the SARS-CoV-2 virus.

The new methodology is based on the ability of molecules known as Polypurine Reverse Hoogsteen Hairpins (PPRH) to slow the replication of the SARS-CoV-2 virus. This is the first scientific paper to describe how PPRH can act as a therapeutic agent and inhibit the growth of a pathogenic virus.

PPRHs are short, simple DNA molecules — single-stranded oligonucleotides — that have a high affinity for specific RNA sequences. The study reveals for the first time how polypurine hairpins — CC1-PPRH and CC3-PPRH — can block the activity of this virus that has RNA as its genetic material.

Professor Carlos J. Ciudad, from the UB's Department of Biochemistry and Physiology, says that "one of the arms of each chain of the CC1-PPRH and CC3-PPRH polypurines binds specifically to a fragment of the virus RNA genome — a sequence of polypyrimidines — via Watson-Crick bonds". "Specifically, CC1-PPRH binds to the region of the RNA that encodes the replicase enzyme — 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 notes.

The new therapeutic technique has been validated in vivo in laboratory animal models expressing the human ACE2 receptor, with the collaboration of CISA-INIA (CSIC). In vitro studies have been carried out in the facilities of the Centre for Animal Biotechnology and Gene Therapy (CBATEG) on Vero E6 cells that have the ACE2 receptor as an entry route for the SARS-CoV-2 virus. "The results indicate that both CC1-PPRH and CC3-PPRH are very effective in Vero-E6 cells. In transgenic mice, CC1-PPRH binds specifically to the area of the genome that codes for the replicase protein, thereby inhibiting virus replication", adds the expert.

From virus detection to cancer therapy

These results open a new perspective in the antiviral fight, and they broaden the biomedical applications of PPRHs from diagnostics to therapeutic actions. Previously, the team 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). The methodology, which is more effective and faster than PCR testing, relies on the high affinity of PPRHs to capture viral RNA and set up a detection signal of the viral agent upon contact with samples from the affected patient. This detection technique is known as TENADA (triplex enhanced nucleic acid detection assay).

Apart from the detection of SARS-CoV-2 virus, the TENADA technique can also be used to detect influenza A (H1N1) and respiratory syncytial virus (RSV), which causes respiratory pathologies. "They are also applied in diagnostic techniques in other areas of biomedicine: they are biosensors to determine the degree of methylation of the PAX-5 gene in cancer, and also to detect the gene encoding the mtLSU rRNA ribosomal subunit in the Pneumocystis jirovecii fungus, responsible for severe pneumonia", adds the researcher.

In cancer therapy, polypurine hairpins have been successfully applied to silence gene expressions of different cancer-related genes — telomerase synthesis, survivin, topoisomerase, etc. — and non-medication targets (KRAS and c-MYC). They have also been used as tools for repairing point mutations at the endogenous locus of a gene and for gene editing techniques related to exon skipping.