Amazon com : AWS High Performance Computing helps find potential COVID cures

Researchers in France used Amazon Web Services (AWS) High Performance Computing (HPC) to isolate two chemical compounds that could slow or stop the spread of COVID-19 and potentially reduce its severity. The discoveries were made by analyzing the molecular structures of a key “protease,” a large molecule responsible for regulating chemical reactions in the virus. With a deeper understanding of the molecule’s unique structural properties, the researchers discovered vulnerable areas of the protease and mapped the weaknesses to two new synthesizable compounds – in other words, new potential drugs. If you think of the Protease as an impossibly large skyscraper with millions of locked doors, AWS’s suite of HPC systems allowed researchers to sort through and find the right keys to unlock new compounds and treatments much faster than in the past.

“Previously, such efforts would have taken months, if not years,” said Robert Marino, CEO of qubit pharma, which worked with researchers from Italy, France, Switzerland and Enamine, a chemical company, to carry out the analysis and synthesis of the compounds. “Now we’re able to make those discoveries in months.” The compounds continue to be tested in a pre-clinical setting, and their effectiveness as a treatment or cure is being evaluated by regulatory agencies.

Although the power of cloud computing is already impressive, Marino said the impact and ability to apply massive computing power to isolate new connections and find new cures will only increase over the next five to 10 years. Much of the medical and biological research community envisions the development of quantum computing, a form of computing that uses the variable states of quantum mechanics – the forces within atoms – to store information, rather than using the traditional ones and zeros for storage bits.

While quantum computing is still in its infancy, that’s the ambition of the researchers working at qubit and places like that AWS Center for Quantum Computing at Cal Techis to unleash the power of quantum computing to exponentially accelerate computational tasks. The speed increases that researchers anticipate for certain computing tasks are mind-boggling. For example, a problem that a conventional supercomputer would solve in 10,000 years could theoretically be solved in just a few minutes by a quantum machine. In other words, solving problems that are essentially impossible with classical computing becomes possible when we move into the realm of quantum computing.

According to Marino, the real value of quantum computing for medical research lies not so much in the processing speed, but in the complexity that a quantum computer can handle in solving problems. Biological molecules exist in amazingly complicated systems. Proteins, sugars, fats, DNA, RNA, and a multitude of chemical markers in between interact, bend, change shape, divide, and grow around one another. In addition, researchers need to understand the effects of temperature, pressure, salinity and environmental variables that cause a molecule to change shape and property. Being able to map all of these factors at once and perform analysis right away is the future of medical research, Marino said. So far, only quantum computing hints at the power to handle so much data and computational costs.

Still, the discovery of these two potential COVID-19 treatments relied on an impressive array of high-performance computing systems. The Sorbonne University’s Theoretical Chemistry Laboratory created the original map of COVID-19 in May 2020 as infections were skyrocketing. They relied on France’s national supercomputing center and AWS services to run the simulations and model the proteins that make coronaviruses.

More simulationswere conducted on the AWS Cloud with funds from special COVID-19 grants made by AWS to accelerate treatments and cures for the disease. Additionally, the research teams relied on Amazon Elastic Compute Cloud (Amazon EC2) with NVIDIA GPUs and EC2 On-Demand to search the vast chemical libraries indexing the potential cures; Amazon Elastic File System (Amazon EFS) provided researchers with scalable and encrypted file storage; and Tinker-HP, hosted on AWS, provided high-performance molecular dynamics software. With these tools, the team was able to search through vast libraries of data and examine potential cures that previously might have been left out due to time and cost constraints.

COVID-19 is just one disease targeted by this HPC computing approach, Marino said. Qubit also uses its proprietary software with AWS’s computing and analytics services to find potential cures for cancer and other serious diseases.