CBE Distinguished Professor Alex Neimark (PI) and Research Assistant Professor Kolattukudy Santo (Co-PI) have received an award from the Pittsburgh Supercomputing Center (PSC) to study adsorption of pulmonary surfactants on Spike proteins of Covid-19 coronavirus variants by microseconds long molecular dynamics (MD) simulations on Anton 2 special-purpose supercomputer. Anton 2 is the next- generation specialized supercomputer generously made available by D.E. Shaw Research and hosted by PSC through Grant R01GM116961 from the National Institutes of Health. Highly competitive Anton 2 grants are awarded by a committee of the National Research Council (NRC) at the National Academies of Science. Anton 2 dramatically increases the speed of molecular dynamics (MD) simulations compared to available state-of-the-art systems and allows to investigate biological phenomena that due to their intrinsically long time and space scales have been outside the reach of even the most powerful general- purpose scientific computers. The proposed research aims to identify the molecular mechanisms of adsorption of the lung surfactant lipids, cholesterol, and proteins on the specific regions of S-protein receptor-binding domain (RBD) of the original CoV-2 and its Delta and Omicron variants. The results of this project will inform the clinical search for therapeutic surfactants capable of preventing and curing Covid-19 infections by obstructing the coronavirus binding with cell proteins.
This grant provides an allocation of 230,000 molecular dynamics units of computer time