The Sars-CoV-2 coronavirus uses a special mechanism to multiply: so-called reading frame shifts mean that the protein machines of the cell read the letter code of the viral genome offset by one letter in some cases and thus, depending on which reading frame they use, different proteins produce. Sars-CoV-2 is dependent on the proteins from both reading frames. Researchers have now shed light on how the mechanism works exactly and how it can be disrupted with chemical substances. Your results thus provide new starting points for the development of drugs against Covid-19.
When viruses multiply in the body, they use the resources of the cells they attack. The cell’s own protein machines, the ribosomes, read the genome of the virus and use this plan to build the viral proteins. In each case, three letters in the genome code for one amino acid of the protein. It is usually very important that the ribosomes do not slip in the sequence of letters. Otherwise they incorporate the wrong amino acids and the resulting protein would not be functional. However, some viruses, including Sars-CoV-2, are specifically dependent on such reading frame shifts, so-called frame shifting. Your genome encodes two different blueprints, depending on whether the RNA is read normally or offset by one letter. In order to ensure that some of the ribosomes “slip”, the viral RNA is folded in a complex manner.
Disrupt the viral reproduction
A team led by Pramod Bhatt from ETH Zurich has now examined this mechanism, which is important for coronaviruses, in more detail. Under the cryo-electron microscope, they made the interactions between the virus RNA and the ribosomes visible. Their result: Due to the special folding of the RNA, the genetic strand remains attached to the ribosome at a certain point and forces the protein machine into a strained conformation. This causes the ribosome to slip by one letter in some cases. Instead of U_UUA_AAC, it reads UUU_AAA_C. “As a result, two different viral proteins are synthesized; one thing, if no frameshifting takes place, the other as a result of frameshifting, ”said the researchers.
In the test tube and on living cells, Bhatt and his colleagues also tested how they can use chemical substances to specifically disrupt the shift. To do this, they used two compounds for which previous studies had suggested that they could influence frameshifting. In fact, both substances reduced viral replication by a thousand to ten thousand fold. Only one of the two substances, the fluoroquinolone merafloxacin, actually hindered the reading frame shift, while the other substance possibly worked via a different mechanism. Merafloxacin was researched in the 1980s as an antibiotic against, among other things, tuberculosis, but development was discontinued.
Frameshifting as a goal for therapeutic measures
Both active ingredients were not toxic to the cells treated with them. However, they are out of the question as drugs against Covid-19. Even if they reduced the production of Sars-CoV-2, they weren’t effective enough to actually fight the disease. However, the researchers are optimistic that their results can spark new drug development. “Although the potency range for the compounds we tested is not what one would expect from potential drug candidates, it still offers a starting point for high-throughput screening and proves that frameshifting is a useful target for therapeutic measures against Sars-CoV-2 “, So the authors.
The findings could also be helpful in relation to other viruses. Since frame shifting does not occur in human cells, but is essential for many viruses, this mechanism is a promising target. “Our future work will focus on understanding the cellular defense mechanisms that suppress viral frameshifting, as this could be useful for developing drugs with similar activity,” says Bhatt’s colleague Nenad Ban.
Source: Pramod Bhatt (ETH Zurich, Switzerland) et al., Science, doi: 10.1126 / science.abf3546