New Strategies for Designing COVID-19 Antiviral Drugs That Inhibit Important Viral Proteins

Review by Emily Henderson, Bachelor of ScienceNovember 9, 2020

SARS-CoV-2, a respiratory virus that causes COVID-19, attacks the body in multiple steps. Invading cells deep in the lungs, hijacking the mechanisms of human host cells and releasing a copy of itself are the two earliest steps, both of which are essential for viral infection.

New studies provide insight into the design of antiviral drugs for COVID-19 by showing that some existing compounds can inhibit both major proteases (M).^Professional), An important viral protein required for SARS-CoV-2 replication in human cells, and a human protein important for viral invasion into host cells, lysosomal protease catepsin L.

The study, led by researchers at the University of South Florida (USF Health) Morsani Medical College and the University of Arizona School of Pharmacy, today Science Advances..

“If we can develop compounds that shut down or significantly reduce both the invasion and replication processes, such double inhibition may increase the potency of these compounds in the treatment of coronavirus infections,” the researchers said. Principal Investigator Dr. Yu Chen said. USF Health is an associate professor of molecular medicine and has expertise in structure-based drug design. “Metaphorically, it’s like killing two birds with one stone.”

Collaborators at the USF Health-University of Arizona (UA) are based on previous studies that identified and analyzed several promising existing antiviral drugs as candidates for the treatment of COVID-19.All candidates selected to pursue Target M^Professional Blocks the replication of SARS-CoV-2 in human cells grown in the laboratory.

Two of the compounds, calpain inhibitors II and XII, showed less activity against M.^Professional As another drug candidate called GC-376 in biochemical studies. However, calpain inhibitors, especially XII, actually worked better than GC-376 in killing SARS-CoV-2 in cell culture, according to the lead author, a PhD student in Dr. Chen’s lab. Michael Sacco said.

If these calpain inhibitors were less effective at inhibiting the viral’s major proteases, they thought they must be doing something else to explain their antiviral activity. They found that calpain inhibitors are important human host proteases involved in the mediation of SARS-CoV-2 from studies conducted by UA collaborators and principal investigators Jun Wang, PhD. I learned that it can block other proteases, including the calpain L.Invasion of cells.. “

University of South Florida, Dr. Chen’s Lab, PhD Student, Michael Sacco

In this latest study, USF Health researchers used advanced technology, especially X-ray crystallography, to visualize how calpain inhibitors II and XII interact with viral protein M. ..^Professional..

They observed that the calpain II inhibitor matched the target binding site on the surface of the SARS-CoV-2 main protease as expected.

Unexpectedly, they also discovered that calpain XII inhibitors employ a unique composition called the “reverse binding pose” to fit M tightly.^Professional Active binding site. (A snug fit optimizes the interaction of the inhibitor with the target viral protein and reduces the enzymatic activity that aids SARS-CoV-2 growth.)

“Our findings provide useful structural information on how we can design better inhibitors that target this important viral protein in the future,” said Dr. Chen.

In addition to increased efficacy targeting both viral proteases M (desired drug effect at low doses)^Professional Another benefit of dual inhibitors is that they have the potential to reduce drug resistance, Dr. Chen said.

SARS-CoV-2 can mutate or alter the target gene sequence. These viral mutations trick human cells into allowing the virus to attach to the surface membrane of the cell and insert its genetic material, reciprocating the shape of the viral protein with other molecules (including inhibitors) within the cell. It may change the action.

When a virus mutates and continues to reproduce, it can become resistant to certain inhibitors and reduce the effectiveness of the compound.

In other words, if the gene sequence of a virus’s target (lock) changes, the key (inhibitor) will not fit that particular lock. But let’s say you can open two locks with the same key to prevent COVID-19 infection. In this case, the two locks are M.^Professional, Virus-targeted proteins, and cathepsin L, human-targeted proteins.

“It’s difficult for the virus to change both locks (two drug discovery targets) at the same time,” Dr. Chen said. “Therefore, double inhibitors make it more difficult to develop antiviral resistance, as this type of compound remains effective against unchanged human host proteins as the viral protein changes. . “

The USF Health-University of Arizona research team continues to tweak existing antiviral candidates to iM^ProfessionalWe would like to evaluate their stability and performance and use what they have learned to design new COVID-19 drugs. Their next step involves elucidating how calpain inhibitors interact chemically and structurally with cathepsin L.