After Sergei and his daughter had been afflicted, researchers identified a Novichok nerve agent (A-234) as the poison. It had been found on clothing and at a pizzeria where Sergei and Yulia ate before falling ill. The first police officer who responded to the scene was also hospitalized after being poisoned by the substance.

Scientists immediately began studying the deadly poison, which had been created by Soviet chemists in the 1970s. U.K. officials promptly accused Russia of the poisoning.

View from Nanome: A-232 (ball and stick) travels from acetylcholinesterase’s gorge opening (left) to the enzyme’s deep active center.

The Russian Whistleblower

The West is aware of this class of nerve agents thanks to the work of one whistleblower. In 1992, former Soviet military chemist Vil Mirzayanov lay bare the program’s existence.

In his 2008 memoir, State Secrets: An Insider’s Chronicle of the Russian Chemical Weapons Program, Mirzayanov writes that the compounds, which include five phosphoramidites in total, are similar to nerve agents like sarin, soman, and tabun. But, due to unique characteristics, the Novichoks are considered more deadly. Sergei and Yulia likely survived only because they were exposed to a small amount through the skin.

“[I]t would be extremely dangerous to try to make these compounds,” says Mohamed Abou-Donia, a neurobiologist at Duke University in Durham, North Carolina. “You could easily get yourself killed.”

Nanome advisor Zoran Radić, a chemist at the University of California, San Diego (UCSD), used Nanome’s molecular visualization software to better understand how the Novichok worked.

Radić used paper-drawn 2D sketches to create a coordinate file of A-234 in the Protein Data Bank’s PDB format.

He then imported it into Nanome, our VR-based molecular visualization software. “It is relatively simple,” Radić told RCSB’s Education Corner. “I created models in a classical model building software, saved it in PDB format, then opened it in Nanome.”

Using Nanome, Radić was able to stand right up to the molecule and perceive its geometries, as well as the electronic features [of the enzyme and the nerve agent].

Radić likes using Nanome’s VR software more than 2D glasses, 3D-glasses, and other classical approaches to molecular visualization.

“…[T]he ability to computationally optimize ligand geometry and its interaction with macromolecule in VR in real time comes as an immense bonus,” he said.

Radić presents his findings at conferences using Nanome’s VR tool. By doing so, audiences can observe interactions projected onto a 2D screen. Radić can take hold of a molecule in his hands to manipulate it in Nanome.

“A Chinese proverb says that an image is worth a thousand words,” Radić told RCSB. “VR representation adds another dimension and an order of magnitude to it. Essentially, inherently compressed information is instantaneously unfolded in VR.”