Halmos College Faculty and Students Present Protein Modeling at Virtual Conference

During April, a Halmos College faculty and student team was accepted to the National meeting of the American Society of Biochemistry and Molecular Biology. Originally the symposium was scheduled to be held in San Diego, but due to COVID-19, the event was moved to a virtual platform. The team prepared a video presentation and posted to YouTube to link to the nationwide event.

The team consisted of Halmos faculty members Arthur Sikora, Ph.D., Emily Schmitt Lavin, Ph.D. Halmos College undergraduate students: Feza Abbas, Matthew Hunt, Lyla Abbas, Helana Ghali, Alesa Chabbra, and Mina Ghali. The team modeled two well know inhibitors of HIV-1 protease called Darunavir and Ritonavir. They also used chemical elements of both inhibitors to design a hypothetical new inhibitor that they named “Sharkavir” in honor of the NSU Sharks. The group worked in conjunction with the Center for Biomolecular Modeling as part of their NSF funded project to develop protein modeling research through the CREST (Connecting Researchers, Educators, and STudents) Program.

Human immunodeficiency virus (HIV) affects approximately 37 million people worldwide and results in over 1 million deaths annually. A class of drugs first developed in 1995 inhibits the enzyme HIV-1 protease, thus preventing the maturation of an HIV precursor protein. There are now over 10 protease inhibitors available to treat HIV. Multiple mutations in the protein have made this treatment less effective. Darunavir is currently one of the strongest competitive inhibitors, as it binds effectively to the substrate envelope and has yielded a lower resistance for patients. The most effective treatment is a combination of two of these inhibitors: Darunavir and Ritonavir. In order to explain how these drugs work, the active site of the non-mutated wild-type HIV-1 protease was depicted as a binding box model. The protease inhibitors Darunavir, Ritonavir, and our hypothetical drug, “Sharkavir” were 3D printed to show how they fit into the protease active site. Details of the wild-type HIV-1 protease, as well as the drugs Darunavir, and Ritonavir, were found in the Protein Data Bank files. The new protease inhibitor molecule, “Sharkavir”, was designed as a combination of Darunavir and Ritonavir using Marvin Sketch: a software used to manipulate molecular structures.