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Scientists design drug to outsmart evolving coronavirus

Although has faded from the headlines, SARS-CoV-2—the coronavirus behind the pandemic—is still rampantly infecting people around the world. Public health officials fear as the virus continues to evolve, it will eventually hit upon a diabolical that renders current treatments ineffective, triggering a new wave of severe infection and social disruption.

In pursuit of new therapies to avoid this dark fate, researchers at Stanford have now unveiled a compound that measures up as a potentially powerful anti-coronavirus drug, detailed in a paper published March 13 in Science Translational Medicine.

Dubbed ML2006a4, the compound works in the same way as Paxlovid—the most effective oral drug available to date—by binding to coronavirus particles and preventing the virus from making copies of itself. Compared to Paxlovid, though, ML2006a4 binds more tightly and durably, courtesy of the Stanford team custom-crafting the compound atom-by-atom.

In preclinical experiments, the compound prevented deadly infections in at a superior rate compared to Paxlovid. In addition, the new compound is potent enough that it could likely be formulated without an additional component present in Paxlovid that poses severe drug interaction concerns.

Importantly, ML2006a4 also performed well against coronavirus variants that have already evolved degrees of resistance to Paxlovid, suggesting the compound's honed affinity makes it less vulnerable to mutant virus .

“At this point entering the fifth year of the pandemic, Paxlovid is our only really good drug against SARS-CoV-2, but it's proven fairly easy for the virus to evolve resistance to it,” said Michael Lin, the senior author of the study, who is an associate professor of neurobiology and of in the schools of Medicine and and a member of Stanford Bio-X.

“As new waves of coronavirus keep crashing down, we need to have alternative that are more tolerant of mutations and not as easy for the virus to defeat.”

For the study, Lin worked closely with lead author Michael Westberg, now an assistant professor at Aarhus University in Denmark. From 2018 until 2022, Westberg worked in Lin's lab as a visiting scholar at Stanford Bio-X through a joint program designed to strengthen international collaborations and the exchange of scientific expertise between Stanford and Denmark.

Atomic-level precision

Before the pandemic outbreak in 2020, Lin's lab had already been investigating the broad class of drugs known as viral protease inhibitors. These drugs target protease enzymes that viruses need for disassembling bulky viral as part of their replication cycle. Like a key fitting into a lock, protease inhibitors occupy the spaces, or , where proteases normally link up with those bulky proteins, thus nipping replication in the bud.

Specifically, the Stanford researchers had gained familiarity with hepatitis C virus protease, which has similarities to coronavirus versions. Although Westberg had come to Stanford to work on other projects, the global emergency prompted a pivot. “When the pandemic hit, we asked if we could put our expertise to good use,” said Lin.

Their early research, posted online in September 2020, demonstrated that a hepatitis C drug, boceprevir, slotted reasonably well into the coronavirus protease site. Other scientists built off those findings, including at the pharmaceutical company Pfizer, which ultimately created Paxlovid and received regulatory approval for its use in December 2021.

“We knew then that we were on the right track,” said Lin, “and we were motivated to keep going and make an even more effective drug.”

The Lin lab pooled its collective chemical knowledge to design improvements to their iterative boceprevir-based compounds. Much of the work involved modifying the compound on the atomic scale in intricately detailed computer models to fit more snugly in the coronavirus protease active site.

“Basically, you put your drug in the active site and you look for gaps where it doesn't tightly fit. Then you fill those gaps,” said Lin.

ML2006a4 reduces lung damage in SARS-CoV-2 infected mice. Credit: Bi-Hung Peng and Chien-Te Tseng (University of Texas Medical Branch)

The Stanford researchers approached this challenge in a rational way by adding different configurations of atoms of carbon, nitrogen, and oxygen to the compounds as permitted by the laws of .

“There's a lot of creativity and intuition involved because everyone is working with the same three atoms, but there are essentially infinite ways to arrange them,” said Lin. “Making these modifications, it's like playing atomic Tetris.”

The resulting compounds were then tested against actual coronavirus particles at the Stanford In Vitro Biosafety Level 3 Service Center. After multiple rounds of honing, Lin's team arrived at the compound designated ML2006a4.

Source: Stanford University