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New Coronavirus Database Could Help Vaccine Efforts

By LIDA TUNESI

The coronavirus pandemic has led the scientific community to work at levels of collaboration and speed rarely seen before. Now, a team of researchers from Lehman College and The Graduate Center have created a repository of information that could benefit drug and vaccine researchers, and they’re sharing the information online.

The repository contains molecular maps and spreadsheets detailing how water interacts with the novel coronavirus. The data is available to all via GitHub. The researchers, including Ph.D. students Brian Olson, Anthony Cruz, Lieyang Chen, Mossa Ghattas, Yeonji Ji, Kunhui Huang, and Professor Tom Kurtzman (Lehman College, The Graduate Center) discuss their work and how they hope the maps will be of use in a paper published in Journal of Computer-Aided Molecular Design.

“By knowing how the water interacts with the coronavirus proteins, we can design small molecules that will displace the water molecules more effectively and make interactions complementary to the protein surface,” Cruz said.

These kinds of maps have become more and more common in drug development, but the software involved is often only available for commercial use, and using it requires expertise that not all researchers have. The CUNY team wants to knock down these barriers to research.

Our bodies are largely made of water. When the virus enters the body, water molecules bind to the virus’ proteins. For a drug molecule trying to latch onto the virus, some of these water molecules create favorable conditions that help it bind, but some of them need to be pushed out of the way. Solvation thermodynamic maps show researchers which water molecules need to stay and which need to go, Cruz explained.

The repository includes water-binding information for three different drug targets on the SARS-CoV-2 virus.

A pharmaceutical scientist might use these maps to see how to modify an existing drug so that it can displace the right water molecules, helping it bind more strongly to the virus. Researchers could also use the solvation maps to rank a slew of drug choices according to which interact with the water molecules the best.