Around the world, supercomputers have been furiously poring over drug compounds to see if any of them could effectively inhibit COVID-19’s insidious spike proteins, which give the virus both its crown-like appearance and its ability to enter human cells. Now, researchers from the University of Alabama in Huntsville (UAH) are leveraging supercomputing power to tackle a similar question – but this team is looking specifically at naturally occurring compounds.
The researchers, led by Jerome Baudry (a molecular biophysicist at UAH), used molecular docking simulations to examine how 50,000 different natural products interacted with COVID-19’s key proteins. To assess these tens of thousands of candidates, the researchers partnered with HPE, which provided supercomputing resources. Specifically, the researchers used HPE’s Sentinel system – a Texas-based Cray XC50 supercomputer with around 2,000 cores that is cloud-accessible via Microsoft Azure.
With the computing power in-hand (or rather, in-cloud), the researchers were able to complete 20,000 molecular dockings in just eight minutes (down from 24 hours), allowing for 1.2 million more dockings per day. The docking simulations yielded “125 natural products or close derivatives across plants, fungi, the sea and microbes” that possess chemical elements which bind to key proteins on COVID-19. The identified substances span the world, including chemicals found in traditional medicine in regions like Southeast Asia and the Andes in South America. Mesua beccariana, the source of one of the candidate substances, has traditionally been used to treat fever, dyspepsia and other conditions in Malaysia. These candidates will now progress to the next stages of preliminary drug development.
“The combination of the powerful supercomputing technology and expertise from HPE, molecular docking methodology, and a large, diverse data-set of natural products, is what makes this research truly unique,” Baudry said. “We predicted a range of natural products that can now move forward in clinical drug testing, some of which can be found in extracts that come from organisms that grow in our backyards, and some that can only be discovered in remote areas of the world such as in jungles or in the deep sea. We are inspired by these results and it is only the beginning of our journey to unlock more insight that will bring us even closer to conquering COVID-19.”
The results aren’t, of course, a silver bullet.
“None of these natural products are expected to single-handedly be used as a treatment or cure to COVID-19,” Baudry said. “Instead, it is the combination of the chemical structures from this list that are beneficial to drug testing to develop a treatment.”
The researchers are also adamant that overeager readers not turn to self-medication.
“I repeat,” Baudry said, “these organisms or chemicals should not be used as treatments against COVID-19.”
Header image: the molecular docking simulations in action. Image courtesy of UAH.