Two recent research accomplishments in which the UAH Department of Biological Sciences closely collaborated with partners from outside the university illustrate the strength in such partnerships.
Dr. Jerome Baudry (pronounced Bō-dre), a molecular biophysicist and the Mrs. Pei-Ling Chan Chair in Biological Sciences, joined with Hewlett Packard Enterprises (HPE) to employ its Cray Sentinel supercomputer to rapidly identify 125 naturally occurring compounds that show promise as treatments for the COVID-19 coronavirus.
In separate research, Dr. Eric Mendenhall, a UAH associate professor of biological science, teamed with the HudsonAlpha Institute for Biotechnology to identify the function of 208 proteins responsible for orchestrating the regulation genes in the human genome. The research was published in Nature in July.
The partnerships were essential to the discoveries, says Dr. Paul Wolf, Biological Sciences chair, and UAH provides an ideal environment to nurture partnerships with industry and other entities.
“Solving complex problems requires integration of a diversity of thought,” Dr. Wolf says.
The Department of Biological sciences at UAH encourages faculty and students to work with each other and with local and national entities on collaborative projects, he says.
“The research successes of Eric Mendenhall and Jerome Baudry illustrate the kind of breakthroughs that can be made with such partnerships,” Dr. Wolf says. “We very much hope to see these collaborations grow in the future.”
Potential COVID treatments
Together Dr. Baudry’s lab and HPE used the Sentinel supercomputer to rapidly assess a batch of 50,000 chemicals to identify 125 naturally occurring compounds with a computational potential for efficacy against COVID-19.
The research was noted in a keynote speech by Antonio Neri, HPE president and CEO, at the HPE Discover Virtual Experience event. Neri told over 100,000 registrants from the computing, scientific and business worlds that the HPE collaboration with Dr. Baudry “allowed his research team to deliver results in weeks versus months or years.”
The idea for an alliance with HPE developed months before the COVID-19 crisis, following a meeting to discuss how to integrate natural products, artificial intelligence and supercomputing.
“One of the presenters, Dr. Rangan Sukumar, is a distinguished technologist in high-performance computing (HPC) and artificial intelligence at HPE,” says Dr. Baudry. “He talked to his colleagues there and they reached out to us to inquire about the possibility of working together.”
As the collaboration was becoming more operational the COVID-19 pandemic developed. Located in UAH’s Shelby Center for Science and Technology, the Baudry Lab was searching for potential precursors to drugs that would help combat the global pandemic.
“At HPE we are committed to being a force for good, and since the start of the COVID-19 outbreak, we have been on a mission to extend our technologies and resources to scientists on the front line of drug discovery,” says Bill Mannel, vice president and general manager of HPC at HPE.
“We found a perfect match with Dr. Baudry and his team at UAH, who have used our cloud-based supercomputer running in Microsoft Azure and a dedicated technical staff to support their research,” Mannel says.
By using the supercomputer through the cloud, the team was able to increase outcomes of drug candidates through biodiversity at an unprecedented speed, he says, saving them years of research and millions of dollars in costs.
“It has also been an honor helping Dr. Baudry realize his vision and be a part of the overall journey to advance treatment efforts to combat COVID-19 and end human suffering.”
The partnership marked the first time a supercomputer was used to assess the treatment efficacy of naturally occurring compounds against the proteins made by COVID-19.
“We used supercomputers to predict natural products most likely to bind to three proteins of the SARS-CoV-2 virus,” says Dr. Baudry. SARS-CoV-2 is the scientific name of the COVID-19 virus.
“Out of the 50,000 natural products that we looked at using supercomputers, we found several hundred to be predicted to be potentially binding on the proteins of interest,” he says. “We further found 125 – but there may be more – that are particularly interesting because they bind right where we want to, they are not too big, not too small and they have the chemical profiles of pharmaceuticals.”
There are many diverse natural sources for the chemicals of interest, Dr. Baudry says.
“Many are from relatively common medicinal plants that can be found in the U.S., and many are from more distant plants from Southeast Asia and South America, as well as from some ground and oceanic bacteria strains and fungi.”
A Biological Safety Level 3 laboratory in Memphis is testing natural products that were identified by the Baudry Lab for their activity against the COVID-19 virus. Chemical molecules found most efficacious will form the basis for future testing for efficacy, tolerance and adverse effects in human trials, a process that might include chemical modifications to make the drug more efficient, better tolerated or both.
“Every drug that ends up surviving this long and winding road of development and testing starts as a hit that binds to a protein. It is this initial event that we are modeling here using supercomputers,” Dr. Baudry says.
The fight against COVID-19 has created a new meeting of modern high-capacity artificial intelligence with humankind’s most ancient healing knowledge, Dr. Baudry says.
“Normally it would take a very long time and a lot of money to achieve that, but with the supercomputers we can perform this initial hit discovery step much faster and cheaper,” he says. “Even five years ago, this would not have been possible.”
Located in a Microsoft Azure data center in Texas, Sentinel made the work more rapid than ever before possible and an HPE team helped facilitate it. Dr. Baudry’s UAH team accessed Sentinel through the cloud with Microsoft Azure.
Sentinel is capable of computing 147 trillion floating point operations per second and can store 830,000 gigabytes of data. That’s as fast as the Earth’s entire population doing 20,000 calculations every second.
At the same time, Dr. Baudry’s lab also collaborated in other COVID-19 research with the Alabama Supercomputing Network and Oak Ridge National Laboratory in Tennessee.
Understanding how cells work
A close collaboration between the UAH lab of Dr. Mendenhall and the lab of Dr. Richard Myers, who is the president, M. A. Loya Chair in Genomics, science director and a faculty investigator at HudsonAlpha, resulted in new understanding of the function of 208 proteins responsible for orchestrating the regulation of genes in the human genome. These proteins and others play major roles in determining the type and function of new cells, a process known as differentiation.
The working partnership was a fundamental building block for the resulting discoveries, says Dr. Myers.
“We have greatly enjoyed and benefited from this close collaboration with Dr. Mendenhall and his team, which involves a combination of complex ‘wet-lab’ experiments and computational analysis and interpretation of large amounts of data,” Dr. Myers says.
“One of the most satisfying things about this work is that we are creating a knowledge base of how human genes are regulated that is being used by thousands of researchers and clinicians around the world,” he says. “The data and findings are made freely available rapidly to everyone, and this has helped to greatly speed up our understanding of the human genome.”
It is critical that genes be turned on and off in different cell and tissue types, but scientists haven’t had a good idea of how that was controlled, says Dr. Mendenhall.
“Ours and many other groups have been working for years to find what regions of the human genome controlled this turning on and off – what we call enhancers and promoters,” he says.
“We wanted to determine what proteins control this turning on and off. These are called transcription factors, and our group looked at where 208 of them function. It was a large number and we helped to add a significant amount of information to how genes are turned on and off.”
Transcription factors can make a cell into a heart cell, a liver cell or even a cancer cell. Their location along the DNA strand, or genome, is critical to what role a cell will play during its lifetime. The genome in each of our cells is identical. It’s the transcription factors that act as the switches to turn on or off genetic functions and differentiate the capabilities of one cell from another.
“We have close to 20,000 genes in our genome, and about 1,800 of these belong to the class called transcription factors, which is a pretty large portion of our genes,” says Dr. Mendenhall.
“These genes code for proteins that work in our nucleus to turn genes on or off by binding to the DNA. Once they bind to the DNA, which is tightly controlled by many chemical and biological mechanisms we don’t yet fully understand, they find a nearby target gene to usually turn on, but occasionally turn off.”
It’s important to have a complete catalog to get a full picture of how genes are controlled, Dr. Mendenhall says. That’s a key part of how humans develop from embryos and it’s important to how our cells do their jobs and keep us healthy.
“An incomplete picture leaves we scientists unsure whether we are missing key transcription factors, or of how to explain why certain transcription factors bind here but not there, or turn this gene on but not that one,” Dr. Mendenhall says. “We have a lot of outstanding questions and a lot of these questions will be easier to answer once we study all 1,800 transcription factors.”
Teams led by Dr. Myers and Dr. Mendenhall employed the latest rapid genetic sequencing techniques, running dozens of parallel experiments at one time to quickly locate and flag transcription factors in a lab-grown line of liver cancer cells called HepG2 that are used for research purposes.
The new discoveries came as part of the $31.5 million National Institutes of Health (NIH) Encyclopedia of DNA Elements (ENCODE) Project to further the construction of a comprehensive list of functional elements in the human genome. A scientific offspring of the Human Genome Project, the ENCODE Project launched in 2003 and is a scientific consortium that is tasked with creating and sharing genomics resources that are used by many scientists to study human health and disease.
Advances in a new technology called CRISPR-Cas9 hastened progress by allowing scientists to test almost any transcription factor. Key to the research was a procedure developed in 2015 by Dr. Myers and Dr. Mendenhall called CETCh-seq.
With CETCh-seq, scientists first use the CRISPR/Cas9 genetic editing technique to design a reagent to modify a genome in cells. Once they are flagged, in the second part of the CETCh-seq method a protocol called ChIP-seq tells them where the transcription proteins are located.
“It took a lot of dead ends,” Dr. Mendenhall says, “but we also found a lot of new questions to pursue that we couldn’t have predicted.”
(Courtesy of UAH)