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Alumnus Uses Innovative Software, Supercomputers in Search of COVID-19 Treatment

For the last 10 years, former TLU Chemistry Professor Dr. Jon Bohmann ’91 has been refining the software he developed, Rhodium™, to scan compounds for their viability in treating infectious diseases. As principal scientist in the pharmaceuticals and bioengineering department at Southwest Research Institute (SwRI) in San Antonio, he is now using this innovative technology to search for a compound that can treat COVID-19.

Funded by a $1.9 million, one-year Department Of Defense (DOD) contract from the Henry M. Jackson Foundation for the Advancement of Military Medicine, Dr. Bohmann and his team began exploring treatments in January with 40 million compounds. SwRI is working with the DOD High Performance Computing Modernization Program to rapidly screen potential drug compounds using SwRI’s 3D drug screening software tool, Rhodium™. Using supercomputers speeds up the screening process allowing evaluation of possible therapeutic compounds to increase from 250,000 compounds a day to more than 40 million compounds in just one week. Rhodium first narrowed potential treatments down to 500 therapeutics and again to just a handful with the most potential.

Rhodium takes the 3-D structure of protease, an enzyme of the SARS-CoV-2 virus that causes COVID-19, which breaks down proteins and peptides, and does a virtual screen for drugs that might fit into a void on the surface of the active site to block it. The coronavirus has noticeable protrusions on the surface called spike proteins. One type, S proteins, penetrate host cells and cause infection. Rhodium is looking for compounds that will fit into those proteins like a key within a lock.

“A virus isn’t really alive so much, but it consists of genetic material that gets inserted into a human cell and the cell starts making protein the virus needs,” Bohmann said. “There are spike proteins in SARS-CoV-2 and there are also functional proteins like the protease enzyme. Those proteins have a surface and there are voids where if an active site gets blocked, it can be inhibited or controlled to some extent.”

Rhodium assigns scores in a virtual library where compounds are ranked based on how well they perform when certain filters are applied like how toxicity, reactivity, and if it can be easily manufactured. What makes an organic compound inhibitor different from a drug is that it has to be safe. Bohmann calls the most promising compounds “hits” and says it would be ideal if scientists could find a drug that was already approved to make a new medication without side effects.

“For example, there could be a cholesterol medication that kills the virus,” he said. “And while that might sound good, the dose you would have to take to kill the virus is very high. Pills like Tamiflu and antibiotics are often bigger. Since your body is metabolizing the drug you need enough exposure to kill an infection. Safety is the biggest question when it comes to antivirals. We want compounds that will be the most potent and most selective toward the virus so the amount you need is much smaller and also costs less money to make it. If you can stretch your material out it’s better for manufacturing and dosing. Have we solved that problem? Not yet, but we’re working on it.”

Bohmann admits that back in January he thought COVID-19 would be more like previous outbreaks of SARS or MERS. However, he says the phone calls and emails never stopped and every day became more dire. While there were some peer-reviewed pieces coming out of China at that time, what really caught his eye were the flurry of pre-print servers—websites where people post manuscripts that haven’t been peer reviewed but are sources of emerging information.

“A few months ago, no one had even heard of this disease,” he said. “Although the Rhodium screening happened early on, we’re still working to isolate the virus. It’s like trying to keep a sourdough bread starter kit going. In the wild, the virus propagates in humans and scientists aren’t in the wild. We do have some preliminary results that look very promising, but we’re not done so we don’t know for sure.”

The Rhodium technology was initially developed when Bohmann’s former supervisor at SwRI—and fellow TLU graduate—Stan McHardy encouraged him to write an application with this specific capability. McHardy is now the director for the Center for Innovative Drug Discovery at the University of Texas at San Antonio and the two still work together closely.

“When I first began exploring how I’d do this, I looked into literature and software and found that the tool we needed wasn’t available,” Bohmann said. “We decided to create a tool together and write a grant proposal to hopefully get funding and we did.”

With a Ph.D. in physical chemistry from the University of Wisconsin Madison, Dr. Bohmann has also worked on antiviral research for Texas Biomedical Research Institute, anti-influenza drugs, and a three-year grant program for Ebola treatment funded by the National Institute of Health. He built Rhodium by combining his chemistry background and his experience with computer science research.

“When I was at TLU, I took the Numerical Methods course with Dr. Reza Abbasian and developed a strong interest in computer number crunching,” he said. “There is a pretty clear line between the interests I gained at TLU and my graduate work that I’ve maintained in my professional career. The chemistry research I worked on with Dr Harold Bier in Physical Chemistry and the theoretical chemistry I learned at TLU are lifelong skill sets I’m applying in my career to this day.”

Managing public expectations of his team’s work is also something he hopes people can understand when it comes to the timeline around developing a vaccine.

“As scientists, we feel every moment of the pandemic,” he said. “While the science is going how it should, it’s not a linear path to the cure; it’s these bursts. It’s not like in the first month we had one candidate and then the next month we had several more. I would say we’ll hopefully have four by November.”

Dr. Bohmann says he is grateful to be part of this funded project.

“I recognize it’s a privilege to work on this and the pressure is definitely on,” he said. “It may not be our team that does it, but I think there will be a therapeutic that won’t take excruciatingly long to develop. I’m very glad I can participate in solving this problem.”

About SwRI

Southwest Research Institute, one of the oldest and largest independent, nonprofit, applied research and development organizations in the United States. Founded in 1947, SwRI provides contract research and development services to industrial and government clients in the United States and abroad. SwRI’s headquarters occupy more than 2.3 million-square-feet of office and laboratory space on more than 1,500 acres in San Antonio with technical offices and laboratories across the country and one in Beijing.