Summer at Brookhaven National Laboratory

Leena Alzafarani and Amber Connell

This past summer, students Leena Alzafarani and Amber Connell hoped to make the best use of their time off from school by participating in a safe yet rewarding academic experience.  They decided to join the six-week High School Research Program (HSRP) at Brookhaven National Labs.

Throughout the program Alzafarani and Connell were usually required to attend the lab physically for mentorshipsthough accommodations were made to ensure all students were safe during the COVID-19 pandemicThey took their studies online, with every group of students assigned a different project to work on. 

Alzafarani and Connell were assigned a project entitled “The Effects of SARS- Coronavirus-2 Mutations on the Empirical Affinity of Antiviral Candidates.” Although this hailstorm of new vaccines and anti-virals is both necessary and welcome for the ongoing pandemic, it raises an important question regarding the likely effective lifespan of new treatments for SARS-CoV-2.  

Obtained from Main Protease Mutation. Portrays the unique mutations from MPro sequences utilizing colored labels. (Amber Connell)


In the HSRP, they combined information from two publicly available databases to estimate the probable functional lifetime of new SARS-CoV-2 therapies.

Utilizing an emerging database of mutations to determine the speed at which SARS-CoV2 is mutating, they estimated the effect of these mutations on the surface of the viral proteins.

The students also used a growing database of molecules that bind to the surface of SARS-CoV2 to model the effect of these mutations on the binding of small chemicals to the surface of the main protease (MPro).  

In the end, Alzafarani and Connell’s conclusions were based on 12635 binding energy points of 133 potential antivirals to 47 MPro mutants. For each mutant that binds to MPro, less than 5% of the mutations affected the binding.

Run each antiviral PDBQT with grid box coordinates against each Mutated Protein structure using an AutoDockVina Script to record the binding energy and affinity. (Amber Connell)

Given the rate at which novel mutations are observed, they empirically speculated that the antiviral drugs that target the SARS-CoV2 main protease will have aexpected lifetime measured in years rather than months. 

In simpler terms, once a vaccine is released to the public, it will be a decent amount of time for the COVID-19 protein to mutate. 

Results were recorded on Programs such as AutoDockVina and COOT. (Amber Connell)