Chinese researchers have worked on using existing low molecular weight drugs to treat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 disease. This novel coronavirus has a protein breaking enzyme called a protease. These drugs are used to target the main protease of the virus, known as Mpro or 3CLpro. The study titled, “Repurposing low-molecular-weight drugs against the main protease of SARS-CoV-2,” was released before publication on the preprint server biorxiv*.
What was the study about?
The researchers led by first author Jia Gao, belong to the Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China.
They wrote that with the raging pandemic of COVID-19, there is a race to find an effective drug that can kill the virus. The high rate of infection and consequent severe acute respiratory distress syndrome is necessitating ventilator use and also overwhelming healthcare systems, write the researchers. SARS-CoV-2 has managed to infect around 4 million people across the globe and the risk of dying due to the infection is around 7 percent wrote the researchers.
Thus existing drugs are being used to treat SARS-CoV-2. The researchers wrote that this is called the “repurposing” of drugs in order to use them as an emergency treatment against COVID-19.
The team of researchers explained that low-molecular-weight drugs have a higher chance of working against specific targets on the tiny virus. They write that they thus, “propose a strategy to uncover such drugs using the fragment-based approach.”
What was done?
For this study, the team used a “ligand-observed and protein-observed fragment screening approach.” A screening process is often used to see if candidate drug molecules can be used for a specific purpose.
Researchers have extensively studied one of the targets on the novel coronavirus called the main protease (Mpro or 3CLpro). Mpro is important because it plays a role in breaking or cleaving the viral polypeptide or protein chain that has been translated from the viral genetic material or the RNA. On this poly-peoptide are 11 sites where the Mpro can work and cleave. One of these is the “LQ¯SAG (¯denotes the cleavage site),” wrote the researchers. They explain that specific covalent inhibitors have been known to stop these proteases and thus prevent the replication of the virus. This has been seen in the in vitro studies. The team writes that this provides a clue that the Mpro is “druggable,” meaning it could be possible to target this protease enzyme to inhibit the virus.
Why low molecular weight drugs?
The team of researchers explains that there are around 1,060 low molecular weight drugs (weighing 500 Da approximately) compared to 13,550 potential drugs in the Drug banks waiting to be tested in preclinical lab studies against the virus. With so many candidates, it is difficult to find the right candidate. Low molecular weight drugs and those with “intermediate potency and high safety” could be a possible alternative, they explained. Their toxicity or safety profile is also well understood wrote the researchers. They are also less structurally complex, and thus they can be easily matched against the drug targets on the SARS CoV-2 virus, they explained. They wrote that this is the basis of “fragment-based lead discovery.” Fragments of the existing drugs derived from their “pharmacophores” are used to form a fragment library, which is then tested, they wrote.
Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (red) infected with SARS-COV-2 virus particles (yellow), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID
What was found?
From this study, the researchers first found “niacin and hit 1” that was capable of binding to the primary and most important protease enzyme of the SARS-CoV-2 called Mpro. This Mpro activity was thus inhibited when the molecule bound to the “catalytic pocket” of the Mpro.
The team wrote that there is an overlap of the binding sites of niacin and hit 1. This meant that the catalytic pocket of the Mpro might accommodate larger molecules as well, they said. In their search for molecules that could bind to the pocket, they found several including “carmofur, bendamustine, triclabendazole, and emedastine.”
The team noted that these molecules were capable of binding to the catalytic pocket of the Mpro and inhibited it compared to screening, which was practiced before.
Conclusions and implications
The team concluded, “Our work demonstrated that fragment-based approach is a feasible way to uncover low-molecular-weight drugs against SARS-CoV-2, and potentially other targets without specific drug yet.”
They also wrote that a combination of these low molecular weight drugs could show a higher efficacy against the virus compared to a single compound. They wrote that carmofur and bendamustine were found to be more potent, but their safety is a problem as they are essentially anticancer drugs. Alternatively, triclabendazole and emedastine could be better options in terms of safety and efficacy against the virus.
This approach to fragment screening thus could help develop an effective drug not only against SARS CoV-2, which is elusive at the moment but also help develop an effective drug for other diseases for which there have been no therapeutic molecules.
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
- Repurposing low-molecular-weight drugs against the main protease of SARS-CoV-2, Jia Gao, Liang Zhang, Xiaodan Liu, Fudong Li, Rongsheng Ma, Zhongliang Zhu, Jiahai Zhang, Jihui Wu, Yunyu Shi, Yueyin Pan, Yushu Ge, Ke Ruan, bioRxiv 2020.05.05.079848; doi: https://doi.org/10.1101/2020.05.05.079848