Set a new aim for COVID-19

Durham, NC-To the untrained eye, the single-stranded loops, twists, and creases in the RNA that make up the coronavirus genome look like spaghetti and a jumble of tangled threads.But for researchers like Amanda HargroveThe complex shape that RNA takes when it folds, a professor of chemistry at Duke University, may have untapped therapeutic potential in the fight against COVID-19.

so study Published in the journal Science Advances on November 26, Hargrove et al. Identify compounds that can latch into these 3D structures and block the ability of the virus to replicate.

“These are completely new mechanisms in that sense because they are the first molecules with antiviral activity that specifically target viral RNA,” Hargrove said.

Even more than 18 months after the pandemic, that’s good news. Vaccines that prevent COVID-19 are available, but effective and easy-to-administer drugs that help survive and recover after infection remain limited.

The virus has receded in some parts of the world, but cases are still booming in other parts of the world where vaccines are scarce. Also, even in areas with easy access to the vaccine, the hesitation of the COVID-19 vaccine means that many of the world’s 8 billion people remain vulnerable to infection.

To infect cells, the coronavirus must invade, convey its genetic instructions in the form of RNA, hijack the body’s molecular mechanisms, and make a new copy of itself. The infected cell becomes a virus factory, reading the 30,000-nucleotide “letter” of the virus’s genetic code and stirring the proteins needed for the virus to replicate and spread.

Most antivirals, including remdesivir, molnupiravir, and paxlobid, are the only COVID-19 antivirals that have been or will be approved by the FDA and work by binding to these proteins. However, Hargrove and his colleagues take different approaches. They identified the first molecule to target the viral genome itself. We have identified not only the linear sequences of A, C, G, and U, but also the complex three-dimensional structure in which the RNA strands are folded.

When the first horrifying hint of the pandemic began to make headings, the team, including Hargrove, Brunton Tourbat With Case Western Reserve University Gary Brewer When Mei-Ling Li From Rutgers Already under investigation Drug Candidates That May Fight Another RNA Virus-Enterovirus 71, a Common Cause of Hand-Foot Disease in Children.

They have identified a class of small molecules called amylolide that can bind to hairpin-like folds of the viral genetic material and throw a wrench into the replication of the virus.

To see if the same compound also works against coronavirus, we first put 23 amiloride-based molecules against another non-fatal coronavirus that causes many common colds. I tested it. They identified three compounds that, when added to infected monkey cells, reduce the amount of virus within 24 hours of infection without incidental damage to the host cells. They also showed greater effect at higher doses. Researchers have obtained similar results when testing the molecule in cells infected with SARS-CoV-2, the virus that causes COVID-19.

Further studies have shown that the molecule blocked the accumulation of the virus by binding to the first 800-character site of the viral genome. Most of this series of RNA does not encode the protein itself, but it promotes protein production.

This area is folded to form multiple bulges and hairpin-like structures. Using computer modeling and a technique called nuclear magnetic resonance spectroscopy, researchers were able to analyze these 3D RNA structures and identify where the compounds were bound.

Researchers are trying to figure out exactly how these compounds block the growth of the virus after it binds to the genome.

When it comes to using RNA as a drug discovery target, Hargrove says the field is still in its infancy. Part of the reason is that the RNA structure is unstable.They bounce much more than the corresponding proteins, making it difficult to design molecules that can interact with them in certain ways.

“The binding pocket you’re looking for may not exist in most cases,” Hargrove said.

In addition, 85% of the RNA in infected cells does not belong to the virus, but to the human host ribosome (cell particles made up of RNA and proteins). “There is a sea of ​​competition,” Hargrove said.

But Hargrove has hope. The first small molecule drug that works by binding directly to non-ribosome RNA rather than protein was approved by the FDA last August to treat people with a catastrophic disease called spinal muscular atrophy. rice field. “So there are many challenges, but it’s not impossible,” Hargrove said.

Researchers are applying for patents on their method. They want to modify the compounds to make them more potent and then test them in mice “to see if this is a viable drug candidate”.

Researchers say this isn’t the first time the coronavirus has caused an outbreak, and it’s likely not the last. In the last 20 years, the same virus family has been the cause of SARS. SARS occurred in China, spread to more than 20 countries in 2002, and MERS was first reported in Saudi Arabia in 2012.

The researchers found that the RNA loops and bulges they identified were essentially unchanged by evolution between related coronaviruses in bats, rats, and humans, including those that caused the development of SARS and MERS. I decided. This means that their method may be able to fight more than SARS-CoV-2, the virus that causes COVID-19.

Obviously, it will be a valuable weapon for more antivirals, so we will be better prepared when the next pandemic occurs. Having more medicine at hand has another advantage: fighting resistance. The virus mutates over time. The ability to combine drugs with different mechanisms of action makes the virus resistant to all of them at the same time, making it less likely to be incurable, Hargrove said.

“This is a new way to think about RNA virus antivirals,” says Hargrove.

Researchers have collaborated on seven institutions for this study, including Ratgards University, Case Western Reserve University, Washington University School of Medicine in St. Louis, University of Nebraska-Lincoln, University of Glasgow, and University of Michigan.

This study was supported by the National Institute of Medical Sciences (R35GM124785, GM126833), the Tobacco Settlement Fund (21-5734-0010), the British Medical Research Council (MC_UU_12014 / 12), and Duke University.

Quote: “Amilorides inhibits SARS-CoV-2 replication in vitro by targeting RNA structures” Martina Zafferani, Christina Haddad, Le Luo, Jesse Davila-Calderon, Liang Yuan-Chiu, Christian Shema Mugisha, Adeline Monaghan, Andrew Kennedy, Joseph Yesselman, Robert Gifford, Andrew Tai, Sebla Kutluay, Mei-Ling Li, Gary Brewer, Blanton Tolbert, Amanda Hargrove Science Advances, November 26, 2021. DOI: 10.1126 / sciadv.abl6096