November 19, 2024
Barry Bunin, PhD
Founder & CEO
Collaborative Drug Discovery
“Deep Learning AI Model Scans 'Dark Matter' of Genomic Data to Find 70,000 Never-Before-Seen RNA Viruses.” That’s the headline for FIERCE Biotech’s coverage of findings of a team led by Eddie Holmes, Ph.D., an evolutionary biologist and virologist at the University of Sydney, working with Mang Shi, Ph.D., a virologist at Sun Yat-sen University in China, Holmes
told FIERCE Biotech that dirt from any backyard will yield novel viruses. But sequencing all the genetic material in a pile of dirt will also produce a lot of so-called “dark matter,” DNA and RNA that don’t closely match any known organism. To find the RNA viruses hiding in this “dark matter,” the researchers took advantage of one thing all RNA viruses have in common: the RNA polymerase enzyme. This is the protein RNA viruses use to copy their genomes when they replicate. Because of its vital function, its structure is highly conserved, even though the sequence of the gene that codes for it can vary widely. “We trained this AI method to recognize the structure of every RNA polymerase known,” Holmes said, explaining that the program, called LucaProt, can then sort through new data and seek out RNA sequences that produce proteins that look like RNA polymerase. “Lo and behold, it finds them. It finds lots and lots and lots of them.”
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Tissue Regeneration: Can MicroRNA “Turn a 70-Year-Old Heart into a 40-Year-Old Heart”? The Wall Street Journal explores this question in an article about tissue-engineering techniques in the works to regrow heart muscle after a heart attack and repair lungs and other organs. The idea “is really to restore function to the organ such that the quality of life of that person is normalized,” says Peter Schultz, President and Chief Executive of Scripps Research in La Jolla, Calif., which is testing medicines to regenerate hearts, lungs and other organs. Peter Schultz was my Biochemistry lecturer in graduate school and signed my thesis, so I pay extra attention to his work. I recall Pete joking about needing these types of treatments before he gets too old himself during ACS talks (everyone in the Schultz group could do funny impressions about backpacks not doing work, researchers do, etc.). These treatments eventually might also be used to reverse the effects of aging, Schultz says. If they prove effective in people with disease, he says, they could be tested in healthy people to see if they can, say, “turn a 70-year-old heart into a 40-year-old heart.” The article notes that Dr. Mauro Giacca, Head of the School of Cardiovascular and Metabolic Medicine & Sciences at King’s College London, is developing a therapeutic that uses microRNA, molecules that help regulate how genes are expressed, to induce surviving cardiac cells after a heart attack to multiply. Tests in pigs showed the therapeutic improved the heart’s pumping function, increasing muscle and reducing scar tissue. He is testing delivering the therapeutic by injection to the heart in pigs, he says, using two types of lipid nanoparticles similar to those in messenger RNA vaccines for Covid-19.
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Removing Pancreatic Cancer’s Invisibility Cloak. One reason pancreatic cancer is so deadly is that it has evolved a protective mechanism to make it invisible to the immune system. Researchers may have found a way to strip away this invisibility cloak according to an article in Drug Discovery News about a new study published in BMJ Journals. Bruno Sainz Jr., a molecular oncologist at the Sols-Morreale Biomedical Research Institute (IIBM), and co-author of the study says the team showed that pancreatic cancer stem cells evade the immune system by producing peptidoglycan recognition protein 1 (PGLYRP1), a protein usually produced by neutrophils to attack bacteria. He says: “It's a really awesome defense mechanism that the cancers themselves have to make themselves not visible. It's very, very surprising. We did not expect any of this.” This ability to hide from the immune system makes them resistant to chemotherapy, enabling them to metastasize. Researchers found that when they eliminated PGLYRP1 from cancer stem cells, immune cells successfully recognized and destroyed them. Sainz says: “If you are able to attack and eliminate these cells, then you could potentially cure the cancer.” Anything to help for Pancreatic Cancer would be desperately welcomed.
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“It’s Not Just Obesity. Drugs like Ozempic Will Change the World.” That’s the headline from a normally reserved The Economist. While the growing promise for GLP-1 receptor agonists is widely known in our world of drug discovery, it is interesting to see mainstream publications take notice. The Economist writes: “Every day seems to bring more exciting news. First the drugs tackled diabetes. Then, with just an injection a week, they took on obesity. Now they are being found to treat cardiovascular and kidney disease, and are being tested for Alzheimer’s and addiction. It is early days yet, but GLP-1 receptor agonists have all the makings of one of the most successful classes of drugs in history. As they become cheaper and easier to use, they promise to dramatically improve the lives of more than a billion people—with profound consequences for industry, the economy and society.” As if to drive home the point, the New York Times carries an article headlined “The Breakthrough Drug to Conquer Addiction: Ozempic?”
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Barry A. Bunin, PhD, is the Founder & CEO of Collaborative Drug Discovery, which provides a modern approach to drug discovery research informatics trusted globally by thousands of leading researchers. The CDD Vault is a hosted biological and chemical database that securely manages your private and external data.