When nearly 100 people tuned into a YouTube live stream on April 2, they could be forgiven for thinking they’d showed up to a virtual version of a Medieval Times dinner theater show. Each avatar in the gray dome that is the Nanome software environment wore colored goggles and a colored shirt. The five avatars, each controlled by a scientist, were there to do battle with SARS-CoV-2 in virtual reality (VR).
Rather than lances and swords, however, they wielded molecular weapons.
The live event was hosted by SynBioBeta, and the avatars represented:
- Steve McCloskey, Nanome Founder & CEO (turquoise team)
- Rob Rhinehart, Partner at Mars Bio and Director of The Corona Initiative (red team)
- Robert Scoble, VR guru (yellow team)
- Philip Rosedale, Founder of Second Life (purple team)
- John Cumbers, Founder of SynBioBeta (black team)
John Cumbers welcomed viewers before positioning two molecules containing gray, white, blue, red, and green atoms in front of the group.
McCloskey, nanoengineer and founder of Nanome, explained that the colors of the atoms correspond to the colored elements on the periodic table inside Nanome software: carbons are gray, nitrogens blue, hydrogens white, and chlorine atoms green.
“If you know what these molecules are, type the answer into the chatbox,” Cumbers instructed the audience.
Minutes later, McCloskey awarded viewers with virtual points for correctly identifying the first two molecules as chloroquine and hydroxychloroquine. He explained that these are two small molecule drugs currently used to treat certain diseases of the immune system (formerly used to treat malaria) and certain autoimmune diseases, and that they have been authorized for emergency use to treat COVID-19, the disease caused by the novel coronavirus, SARS-CoV-2. However, efficacy in treating the disease has yet to be shown in studies.
According to McCloskey, there is no consensus in the scientific community about how these drugs work on the molecular level.
“Ohe theory is that the pH is affected, which in turn affects glycosylation of the ACE2 receptor and the binding affinity of the viral spike protein receptor binding domain (RBD),” said Rob Rhinehart, Partner at Mars Bio and Director of The Corona Initiative. The angiotensin-converting enzyme 2 (ACE2) receptor, which is present on many human cell types, is the protein that SARS-CoV-2 attaches to in order to gain entry into human cells.
By examining the structure of this and viral proteins, researchers hope to find areas that drug makers could target to defeat the pandemic roiling the world.
“The ‘-ase’ in protease means to cut,” said Rhinehart. “This protein is responsible for generating the individual proteins that form new viral particles.” Rhinehart took control and loaded a small molecule drug manufactured by Gilead Sciences, remdesivir. He showed how it fits into the pocket inside the protease. “We can see how this could possibly be very effective as a therapeutic by disrupting the function of the protease,” he said. “We don’t know that, though. Remdesivir was actually designed to target the viral RNA polymerase, not the protease.”
McCloskey showed the others a molecule he had designed himself to target the protease and submitted to a crowdsourced drug design competition, and then pointed to 27 amino acids in ACE2 that make contact with the virus’ spike protein; the rest of ACE2 disappeared. “There’s a group at MIT that is producing this peptide chain,” he said. “The idea is to keep the virus from binding to human cells by blocking the RBD.”
Most of the structures the group worked with during the livestream are publicly available and can be visualized in Nanome software for free.
“The pace of problem-solving and collaboration that VR is enabling is unprecedented,” said Cumbers. “VR is becoming a useful tool in science, and because of the way it’s being used in the midst of the COVID-19 crisis, its widespread adoption will likely be accelerated.”
“This is the future,” agreed Robert Scoble, who is a VR guru.
You can watch the full livestream here.
If you are a school or institution working on SARS-CoV-2, Nanome is offering reduced pricing through the month of June.
By Deborah Lynn Bright, Writer at Nanome2