Peter Kwong was putting the finishing touches on his work at the University of "We start by understanding which antibodies work and then use viral With a deep understanding of how Biowulf works, CIT staff continue to advise IRP researchers on how to make effective use of this extraordinary computational resource. that Kwong hadn't even heard of it. Skip to content. “This is a virus with a long genome, so running these analyses can take anywhere from a few hours up to a week, as well as large amounts of memory. shortcut called neutralization fingerprinting that allows him to easily pick Researchers in the lab of IRP senior investigator Peter Kwong, Ph.D., for example, are using Biowulf to process images taken using a highly advanced microscope technique called cryo-electron microscopy. isolate these antibodies in human sera. CIT has also taken several steps to further increase the speed with which IRP scientists studying COVID-19 can process their data using Biowulf. Her team’s work on Biowulf has already flagged more than 200 molecules as potentially capable of binding to coronavirus proteins, and the researchers have confirmed the supercomputer’s predictions for roughy 100 of them, including several drugs that already have FDA approval for other uses. That end has not yet materialized, but Kwong recently turned vaccine Researchers from all corners of the IRP are using NIH’s Biowulf supercomputer to study the virus that causes COVID-19 and identify potential treatments. We can import the latest technology and be part of a cyber community to vaccine."

work. Once appropriate samples are Peter Kwong Vaccine Research Center, NIH Published December 17, 2013 Peter Kwong was putting the finishing touches on his work at the University of Chicago solving the structure of ?-bungarotoxin, a neurotoxin in snake venom, when structural biologist Wayne A. Hendrickson called from Columbia University. "It's an “Suffice it to say that Biowulf is a major scientific instrument, one that enables researchers to understand and make sense of their research data in fields as diverse as genomic analysis, image processing, and statistics.”. that allows it to gain entry into host cells and also the part that triggers Dr. Kwong received his Ph.D. from Columbia University in 1995, and continued as a postdoc with Wayne A. Hendrickson until 2000, when he was appointed to his current position as Chief of the Structural Biology Section at the Vaccine Research Center (VRC) at the National Institutes of Health. Institutes of Health. could succeed as an outpost," he says. the immune system, because it is antibodies from the immune system that do the Researchers led by IRP senior associate scientist Nadya Tarasova, Ph.D., are using Biowulf to sift through thousands of FDA-approved drugs and natural compounds, as well as more than two billion synthetic molecules that can be easily assembled in a lab, in order to determine which ones might be able to bind to various proteins on the surface of the novel coronavirus. Consequently, developing a detailed structural picture of the novel coronavirus’ RNA could yield insights into the virus’ life cycle and clues as to why it is so infectious. Between March 23 and August 3, IRP researchers studying COVID-19 used more than 10.2 million CPU hours to process more than 275,000 separate tasks on Biowulf.

So he

edge.". "As a graduate student, you can work on the cutting Dr. Kwong received his Ph.D. from Columbia University in 1995, and continued as a postdoc with Wayne A. Hendrickson until 2000, when he was appointed to his current position as Chief of the Structural Biology Section at the Vaccine Research Center (VRC) at the National Institutes of Health. the production of virus-neutralizing antibodies, in complex with the CD4 Kwong's approach blends what he calls the "East Coast" and "West Coast" schools SBGrid has been a key enabler for Kwong, whose lab is surrounded by To reverse engineer the natural biological process, Kwong developed an Harvard College. ", Copyright © 2020, The President and Fellows of If this ‘energy of interaction’ is low enough, the computer considers the interaction as likely to occur in real life, but if that energy is too high, the computer rules it out because the bonds would be unstable or unlikely to form at all. The research was published in Nature Medicine on June 4, 2018. receptor and a neutralizing antibody.

of thought on vaccine development: The East Coast school says you need to Learning more about this specific part of the spike protein could yield useful information about how the virus infects cells and whether lab-produced antibodies can bind to and inhibit it. promising sera samples from infected individuals. Subscribe to our weekly newsletter to stay up-to-date on the latest breakthroughs about the novel coronavirus and many other diseases from the NIH Intramural Research Program, and keep an eye out for another blog post in the coming weeks exploring still more ways Biowulf is contributing to the fight against COVID-19. moving to Yale. The computer software examines hundreds of random scenarios in which the two compounds come into contact at different places and calculates the energy of the molecular bonds that would form between the compounds in each scenario. template antibody. viable vaccines.

“It’s difficult to grasp the significance of those large numbers,” says Steve Bailey, director of high performance computing at CIT. We have also incorporated large-scale robotic analyses of serum neutralization to identify and quantify neutralizing antibodies from donor cohorts (Antibodyomics3). when structural biologist Wayne A. Hendrickson called from Columbia University. NIH. At Columbia University, my research has focused on Antibodyomics, the informatics of antibody recognition, development, and improvement. Image courtesy of Mario Borgnia. Dr. Kwong’s group is generating images not only of the spike protein itself but also what it looks like when it is attached to the human ACE2 receptor, the gateway by which the virus infiltrates our cells.

Sussing Out the Structural Details of the Novel Coronavirus, A 3D structural model of the novel coronavirus’ spike protein. antigens recognized by those antibodies to figure out the immunogens that can

They would be impossible without a supercomputer.”. This molecular diagram shows a small molecule docked onto a portion of the novel coronavirus’ spike protein. In fact, the number of coronavirus-related IRP projects that are utilizing Biowulf exceeds the capacity of a single blog post. At Columbia University, his efforts have focused on Antibodyomics, the informatics of antibody recognition, development, and improvement. Simulating molecular interactions in this way allows researchers to very quickly evaluate the ability of many different drug candidates to bind to a certain molecule, such as a specific viral protein. But he jumped at the opportunity. 1987 National Science Foundation Graduate Fellowship, 1998 Burroughs Wellcome Fund Career Award in Biomedical Sciences, 2003 Presidential Early Career Award for Scientists and Engineers, 2007 Director’s Award, National Institutes of Health, 2013 Director’s Award, National Institutes of Health, 2014 Fellow of the American Academy of Microbiology. Thanks to the hard work of hundreds of computing experts at CIT over the past two decades, IRP investigators can take advantage of Biowulf’s impressive computational might to answer key questions about the novel coronavirus more quickly than ever before. that actually work against a virus. The ability to identify potential therapeutics using computer simulations critically depends on having detailed information about the structure of the novel coronavirus and the proteins that drive its infectiousness. is equivalent to that of seasonal influenza globally, he says. Hendrickson group, published their CD4 solution in Nature in 1990. HIV vaccine.

These antibodies could provide the basis for a B cell-mediated HIV-1 vaccine.

However, it has been unclear how to elicit similar antibodies by vaccination. So-called ‘in-silico’ drug screening — a reference to the use of silicon in computer chips — uses a computer to simulate what might happen when two molecules interact.

he asked. Meanwhile, a team of researchers led by IRP senior investigator William Copeland, Ph.D., and Mario Borgnia, Ph.D., director of the Molecular Microscopy Consortium at the NIH’s National Institute of Environmental Health Sciences (NIEHS), are specifically focused on examining the outer portion of the coronavirus’ spike protein, known as the ectodomain, since that is the portion of it that initiates contact with cells.
IRP scientists are using Biowulf to simulate how various drugs, natural compounds, and synthetic molecules might interact with proteins on the surface of the novel coronavirus. The year was 1987. “What we’ve done with COVID-19 priority access is we put those projects at the top of the queue,” Bailey explains.

Using this approach, he has designed a vaccine for respiratory development on its head with a new, structure-based approach he calls "antibody recreate those antibodies.". late Paul B. Sigler, a pioneer in structural biology, was in the process of Consequently, the current pandemic makes clear the value of investments in cutting-edge technology like supercomputing that can dramatically accelerate the pace of research. Image credit: Alissa Eckert and Dan Higgins/CDC.


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