Researchers seek antiviral molecules for the treatment of COVID-19

Synthetic compounds and molecules derived from natural products belonging to Brazil’s biodiversity are being screened by teams at the Center for Innovation in Biodiversity and Drug Discovery, which is supported by FAPESP.

By Maria Fernanda Ziegler  |  Agência FAPESP – Researchers affiliated with the Center for Innovation in Biodiversity and Drug Discovery (CIBFar) at the University of São Paulo (Brazil) are looking for potential antivirals for the treatment of COVID-19 among synthetic compounds and natural products that are part of Brazil’s biodiversity while also conducting drug repurposing studies.

The goal is to screen repositories and databases for chemical compounds capable of blocking the action of nonstructural proteins secreted by the novel coronavirus SARS-CoV-2. Nonstructural proteins are produced in the infected organism but are not part of the virus. Some are essential to viral replication or assembly within infected cells.

“When the virus invades the cell, it makes copies of its own genetic material [RNA in the case of SARS-CoV-2] in order to multiply and advance through the infected organism. Part of the viral genome produces viral surface proteins as well as 16 nonstructural proteins, which appear only after cells are invaded. These molecules are responsible for replicating the viral genome. Our goal is to find a compound that ‘sticks’ to some of these nonstructural proteins so as to block replication of the virus,” said Glaucius Oliva, principal investigator for CIBFar, a Research, Innovation and Dissemination Center (RIDC) funded by FAPESP and hosted by the University of São Paulo’s São Carlos Institute of Physics (IFSC-USP).

The multidisciplinary project is supported by FAPESP and involves researchers at the university’s Institute of Biomedical Sciences (ICB-USP), São Carlos Institute of Chemistry (IQSC-USP) and Ribeirão Preto School of Pharmaceutical Sciences (FCFRP-USP), as well as colleagues at São Paulo State University (UNESP) and the University of Campinas (UNICAMP).

Two screening processes

Compounds are selected by two different methods. One is virtual screening using computational techniques such as artificial intelligence and 3D crystallography to identify compounds with a chemical structure capable of binding to the nonstructural proteins of the target virus to inhibit its replication.

The second method consists of experimental assays to determine whether the molecules inhibit the enzymes involved in the replication process. This is only possible thanks to CIBFar’s production of key recombinant enzymes in the viral life cycle, including the SARS-CoV-2 main protease (Mpro), which breaks down proteins into the amino acids that are used as building blocks for viral replication.

“We produce Mpro at CIBFar, and we’re performing inhibition assays with natural and synthetic compounds,” Oliva said. “The virus needs this enzyme to cut the long chain of proteins encoded by its genome. The various parts of the chain are then assembled to form the replication complex.”

The selection of enzyme-inhibiting molecules will be validated in assays performed at ICB-USP to test whether they do indeed prevent viruses isolated from Brazilian patients from invading and infecting human cells. “The results of these virtual or experimental procedures will have to be confirmed in laboratory tests using cultured cells, and after that in animal testing, followed by clinical trials with actual patients. Drug development invariably takes a long time because we have to be quite sure the molecule is safe and effective,” Oliva said.

Wealth of biodiversity

For Oliva, one of the features of the project that makes it special is the screening of natural products belonging to Brazilian biodiversity, which is possible largely due to the existence of a database with information on the structures of more than 54,000 natural molecules maintained by UNESP’s Center for Natural Product Bioassays, Biosynthesis and Ecophysiology (NuBBE). The repository was developed with support from CIBFar (read more at: agencia.fapesp.br/32314).  

“It can take five to ten years to prove the efficacy and safety of a molecule that’s never been used as a drug before. However, we have something different in Brazil: access to natural products and the use of extracts known to traditional cultures,” Oliva said. 

Plants and microorganisms, he added, are important sources of medicinal compounds. They have neither an immune system nor the ability to travel, so they use chemical compounds as their main weapon against predators and invaders. 

“Natural selection has ensured the development of synthesizing pathways for the production of protective molecules over millions of years or even billions [in the case of bacteria and fungi],” he said. “Given the great wealth of biodiversity in Brazil and the important work already done to identify, characterize and catalog these molecules, it’s possible to find compounds derived from natural products that can combat the pandemic.”

Drug repurposing

The project also has a drug repurposing dimension. The researchers are evaluating 1,500 compounds approved by the United States’ Food and Drug Administration for human use. Depending on the capacity of ICB-USP to perform cellular assays, they may also screen thousands of compounds from the libraries of Medicines for Malaria Ventures (MMV) as well as several other collections created by projects in progress in the state of São Paulo.

According to Oliva, drug repurposing can be a vital shortcut to new drug development because existing drugs have already passed the relevant safety tests. “These will be the first molecules we evaluate, even though the number of successful drug repurposing cases is quite small,” he said.