A team at UC San Francisco and Gladstone Institutes has developed new drug candidates that show great promise against the virus that causes COVID-19 and potentially other coronaviruses that could cause future pandemics.

In preclinical testing, the compounds performed better than Paxlovid against SARS-CoV-2 and the Middle East Respiratory Syndrome (MERS) virus, which periodically causes deadly outbreaks around the world.

“In three years, we’ve moved as fast as a pharmaceutical company would have, from start to finish, developing drug candidates against a totally new pathogen,” said Charles Craik, PhD, UCSF professor of pharmaceutical chemistry and co-corresponding author of the paper, which appears April 23 in Science Advances.

These compounds could inhibit coronaviruses in general, giving us a head start against the next pandemic. We need to get them across the finish line and into clinical trials.” 

Charles Craik, PhD, UCSF professor of pharmaceutical chemistry 

The work was funded by a grant from the National Institute of Allergy and Infectious Diseases (NIAID) to prepare for the next coronavirus epidemic – work that pharmaceutical companies have largely abandoned. But the grant to UCSF has since been terminated, and the group’s antiviral drug candidates face an uncertain future.

The discovery came out of UCSF’s Antiviral Drug Discovery (AViDD) Center for Pathogens of Pandemic Concern, which funded the work of several hundred scientists at UCSF and beyond. It is one of nine centers that NIAD created in 2022 to bolster the nation’s pandemic preparedness. 

From virtual to real-world drug candidates

Three years ago, the UCSF AViDD grant supercharged the efforts of the UCSF Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG). QCRG, which was founded in 2020 by QBI’s director, Nevan Krogan, PhD, brought together 800 scientists from more than 40 institutions across the world. 

From this group, he assembled hundreds of scientists from 43 labs across UCSF, Gladstone Institutes, and a wide range of domestic and international institutions – including Mount Sinai, Northwestern, MIT, the University of Toronto, the University of Alberta, University College London, Institut Pasteur, and others – and obtained one of the nine AViDD center grants in the country.

“COVID was our wake-up call to apply all our resources and know-how toward new therapies and future pandemic preparedness,” said Krogan, UCSF professor of cellular and molecular pharmacology, co-author of the paper, and a leading expert on the biology of infectious disease. “The AViDD funding, which is now in peril, was poised to help us produce potent and necessary antivirals in record time.”

For the project that led to the new SARS-CoV-2 drug candidates, Craik, who had experience designing drugs against HIV, partnered with the UCSF labs of Brian Shoichet, PhD; Adam Renslo, PhD; Kliment Verba, PhD; and Krogan, as well as Melanie Ott, PhD (Gladstone Institutes). 

The group focused on the major protease (MPro), a type of enzyme, or protease, that breaks proteins into smaller pieces like a pair of molecular scissors. SARS-CoV-2 uses MPro to trim viral proteins into usable parts, which the virus then uses to replicate in human cells. Viral proteases have often been the target of attempts to make antiviral drugs, most notably for HIV. 

Shoichet’s molecular docking program, a virtual system to test how different molecules interact with proteins, helped the team identify a few dozen molecular structures, out of millions, that mildly blocked MPro – a starting point for developing real-world drug candidates.

The Renslo lab then synthesized hundreds of new molecules based on the virtual molecules, which the Craik lab tested against MPro in the laboratory. 

“We spent 18 months going back and forth with different molecules that fit reasonably well inside of MPro, but were still mediocre at blocking it,” Craik said. “Our progress stalled. Something had to give.”

Jamming the viral scissors

Two of Renslo’s post-doctoral researchers, Gilles DeGotte, PhD, and Luca Lizzadro, PhD, were responsible for designing and then making the new molecules in the lab. They were given a task “that in the pharmaceutical industry would have been assigned to a much larger team of medicinal chemists,” according to Renslo, who is a co-corresponding author of the paper. 

Lizzadro improved the synthesis (like a recipe) for making the molecules and found a way to make them fit more snugly into the “active site” of MPro, blocking its ability to cut proteins, like jamming open a pair of scissors.

DeGotte, meanwhile, used “click chemistry” to improve the molecules’ fit in MPro even further. This involved introducing a molecular adapter that would make it easier to swap different chemical shapes onto each new drug candidate. 

Tyler Detomasi, PhD, a post-doctoral researcher in the Craik Lab, showed that in two such molecules, named AVI-4516 and AVI-4773, the molecular adapter had, itself, bonded to the MPro active site. These molecules weren’t just a perfect fit for MPro – they were glued within the jaws of the scissors.

Fortunately, AVI-4516 and AVI-4773 didn’t block any human proteases, which are important for human health. Verba’s lab generated atomic-scale images of the compounds bound to MPro, helping the team to optimize the fit and prove that they were permanently stuck inside the viral enzyme.

“This was our lucky break and gave us some very special molecules,” Craik said. “They only react when they’re already inside this viral protease, but not to any of our own human proteases, giving us hope that they could have minimal side effects in people.”

A new generation of effective antivirals 

With rising confidence that AVI-4516 and AVI-4773 effectively blocked MPro, Ott, a virologist, tested them against live SARS-CoV-2, first in petri dishes and then in mice. 

Ott had tested hundreds of drug candidates against SARS-CoV-2 by this point.

“It’s very challenging to fight viruses in general, let alone SARS-CoV-2, but these new compounds were some of the best, if not the best, we had ever seen, in terms of eliminating infection,” said Ott, who is a co-corresponding author of the paper.

The two drug candidates looked promising as disease therapies. They potently blocked their target; they traveled efficiently through the body, ensuring they reached their target; and at least in mice, they appeared safe. 

In a tantalizing follow-up experiment, a further-optimized version of the molecules effectively blocked variants of SARS-CoV-2 like Delta, as well as MERS, a less prevalent but much more deadly coronavirus. 

The team believes their drug candidates, once shepherded through clinical trials to demonstrate safety in humans, could be kept “on the shelf” ready to fight the next pandemic caused by a coronavirus.

“These compounds are easy to modify and should be easy to manufacture,” Renslo said. “AViDD enabled us to discover important new counter measures for an important class of viral pathogens. It’s critical that we see this project through to clinical studies to ensure we’re better prepared for the next pandemic.”