By Jerry Duggan | Bond LSC
As countries hang their hopes on the drug remdesivir for battling COVID-19, recent modeling and computer-aided drug evaluation at the University of Missouri caution to keep an open mind to other drug treatments.
Kamlendra Singh at MU’s Bond Life Sciences Center assessed remdesivir and several other drugs for long-term success in treating coronavirus causing the pandemic across the world. His results were published April 26 in the journal Pathogens.
“Remdesivir is working against COVID-19, but these other drugs are in no way inferior to it,” said Singh, the assistant director of the MU Molecular Interactions Core, Bond LSC investigator and MU associate research professor of Molecular Microbiology and Immunology in the School of Medicine. “They are all FDA approved and we believe, based on our research, that they are worth looking into as a form of treatment.
Working with colleagues at the Karolinska Institutet in Stockholm, Sweden, where he has an appointment, Singh and his team started their COVID-19 specific research in earnest on February 20. Through a combination of bioinformatics, molecular modeling and computer-aided drug design, they evaluated antiviral medicines remdesivir, favipiravir, 5-Fluorouracil and ribavirin for their effectiveness against COVID-19, and possible resistance under pressure of these compounds.
While Singh agrees that remdesivir works against COVID-19, he sees potential weaknesses of the drug and believes alternatives could supplement its use.
The team first assessed at the Gilead pharmaceutical remdesivir to inhibit SARS-CoV-2 viral polymerase, an antiviral drug originally used to treat Ebola. Remdesivir is one of the most highly touted drugs at this point in the fight against COVID-19. But Singh’s findings indicate SARS-CoV-2, — the causative agent of COVID-19 — is capable of mutating — that is, developing alterations in its genome — that could help it develop resistance to the drug.
Armed with this conclusion, Singh’s team looked at three additional compounds to treat the virus. With T-705, also known as favipiravir, they concluded COVID-19 could also develop resistance, but its past effectiveness as a broad-spectrum inhibitor of RNA viruses made it worth a look as a potential option to treat COVID-19. Favipiravir, which has been approved in Japan as an anti-influenza drug, was recently approved in Italy and China for treatment of COVID-19. Favipiravir is currently undergoing testing regarding its viability against COVID-19 and results are pending.
Additionally, Singh’s lab conducted research on two other broad-spectrum RNA polymerase inhibitors: 5-Fluorouracil and ribavirin. Singh examined 5-Fluorouracil because RNA polymerase (the enzyme that copies the virus genome) from SARS-CoV-2 is structurally similar to the RNA polymerases from human Rhinovirus and Foot-and-Mouth disease viruses and 5-FU shows effectiveness against these viruses. Due to this structural similarity, it stood to reason that 5-Fluorouracil may also have some effectiveness in treating COVID-19.
Ribavirin — one of the most widely used, broad spectrum inhibitors of RNA-viruses — shows unique properties that make it a prime candidate to bind to the active site of COVID-19. By binding to the active site, ribavirin theoretically could stop the replication of the viral genome and slow the spread of COVID-19 within an individual’s body. Still, doubt remains regarding its effectiveness since the virus can likely develop resistance to ribavirin through mutations or other mechanisms.
Singh has been working on coronaviruses — a broader category of viruses of which COVID-19 is just one specific manifestation — since his arrival at MU in 2009, so he is no stranger to this area of research. His broad goal is to ultimately have his research discoveries “make a difference in the lives of patients.”
He started his work on COVID-19 with the same goal in mind.
“I did not start my research on COVID-19 in order to write this paper and have it published,” he said. “I just wanted to do my part and spend some time researching compounds that could potentially be effective against COVID-19.”
As detailed as Singh’s findings are, he is quick to acknowledge that he is part of a global scientific community and had a team of professionals within his lab, especially Dr. Kyle Hill (a postdoctoral associate) that helped him to complete this work.
“This progress is not made by individuals, but by teams,” he said. “I have a talented group of individuals working with me and collaborating with me. I am well aware of their expertise and I know how to best utilize their skills.”
Ujjwal Neogi, who works at Karolinska Institutet, spearheaded the bioinformatics portion of the research. Ujjwal also helped in conceptualizing the idea of exploring already existing drugs to treat COVID-19. This work involved analyzing genetic code of the viruses, binding of the drugs with the target, and analyzing sequences of DNA, RNA, or protein to identify regions of similarity to find the most unchanging, widespread target for using a drug. This is important work since the smallest of differences in nucleotide sequence can result in mutations that would render these proposed COVID-19 treatments ineffective. Neogi was assisted with these tasks by Kyle Hill at the Bond LSC.
Anoop Ambikan (at Karolinska Institute) used R, a statistical computing and graphics program, to help put together the models and graphics behind this research. Xiao Heng, a member of the faculty at MU, used her expertise in biochemistry to help Singh conceptualize the research trajectory. Thomas Quinn, director of MU’s Molecular Interactions Core in the Bond LSC, helped with editing and advising throughout the process. Siddappa Byrareddy (University of Nebraska Medical Center, Omaha, Nebraska) brought previous experience with the topic of treating SARS, a form of coronavirus. Anders Sönnerborg, Singh’s longtime collaborator at Karolinska, provided funding for this work and is the one who takes the drugs to the clinic if they demonstrate potential. His involvement was important from the start of the process. Stefan Sarafianos, a former Bond LSC investigator and current collaborator had engaged with Singh in similar viral research in the past, and he imparted a lot of knowledge to Singh that enabled this research.
Taking a deeper look at potential drugs in an analytical way like this contributes to the University of Missouri System’s NextGen Precision Health Initiative. The NextGen Initiative aims to improve large-scale interdisciplinary collaboration in pursuit of life-changing precision health advancements and research.
While Singh concedes that none of his team’s work constitutes a guaranteed effective form of treatment against the virus, he feels that researchers have an obligation to continue working on a cure, and should not accept the status quo of hundreds of thousands of deaths globally. He also makes clear that for now this is all dry lab work. But plans are already in place to test these drugs in the wet lab for the validation once the appropriate protocols are established. Funding from the Karolinska Institute and the submission of two recent COVID related VA grant applications with Drs. Deutscher and Whaley-Connell will support compound validation and additional novel compound discovery and characterization.
“These treatments, if they turn out to be effective, all have limitations,” he admitted. “But, in the midst of a global pandemic, they are worth taking a deeper look at, because we have reason to believe, based on our research, that all of these drugs could potentially be effective in treating COVID-19.”
Kamlendra Singh is Assistant Director of the MU Molecular Interactions Core and an MU Associate Research Professor of Veterinary Pathology in the Collage of Veterinary Medicine (as of May 1, 2020).
Read more details about this research in “Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs,” published April 26 in the journal Pathogens.