Rapid Drug Screening Platform Developed in Preparation for Next Pandemic
Swift Pandemic Response Expected to Accelerate the Development of Effective Therapeutics
Prof. Yoon Dae-sung’s Team Publishes Paper in Nature Communications 

▲ (From left) Prof. Yoon Dae-sung (corresponding author, Korea University), Jung Hyo-gi (co-first author, MS/PhD Integrated Program at Korea University), Dr. Lee Dong-tak (co-first author, Harvard Medical School), 

Dr. Park Dong-sung (co-first author, formerly Korea University, currently Brookhaven National Laboratory), Prof. Hwang Kyo-seon (corresponding author, Kyung Hee University), Prof. Lee Jeong-hoon (corresponding author, Kwangwoon University)

The research team led by Professor Yoon Dae-sung of the School of Biomedical Engineering has developed a platform for screening potential treatments for novel coronaviruses by rapidly assessing the efficacy of drugs that inhibit the activity of the main protease (Mpro), a crucial protein-degrading enzyme necessary for the survival and replication of the emerging coronavirus. This was achieved by utilizing artificially synthesized engineered amyloid peptides.

The results of this study were published online on March 8 in the prestigious academic journal Nature Communications (IF=16.6).

- Title of paper: Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2
- URL : https://www.nature.com/articles/s41467-024-46296-7

The outcomes of this research are expected to aid the rapid development of effective treatments in anticipation of future pandemics. The emergence of variants of the coronavirus spike protein (Delta, Omicron) during the COVID-19 pandemic has rendered existing vaccines less effective, creating an urgent demand for the development of COVID-19 treatments.

Currently, the drugs being developed for COVID-19 treatment include ▲neutralizing antibodies against the coronavirus spike protein, ▲antiviral drugs targeting virus RNA, and ▲drugs targeting protease enzymes derived from the coronavirus. However, the frequent mutations in the spike protein lead to a continuous decrease in the effectiveness of neutralizing antibodies, and antiviral drugs targeting virus RNA may affect human RNA, leading to genomic damage and genetic disease. As such, it is essential to develop drugs targeting the coronavirus-derived protease enzyme (Mpro), which are free of these drawbacks and side effects. Notably, Paxlovid, a treatment prescribed for confirmed COVID-19 patients and developed by Pfizer, operates by inhibiting the activity of Mpro.

Drugs targeting the virus-derived protease enzyme inhibit the activity of the main protease of SARS-CoV-2 (Mpro), which is involved in the replication of the coronavirus, thereby suppressing the virus's proliferation (Fig. 1). The virus replication mechanism facilitated by Mpro is shared by various types of coronaviruses such as SARS-CoV, MERS-CoV, and HCoV-HKU1.

When comparing the active site sequences of Mpro from SARS-CoV-1 in 2003 and SARS-CoV-2 in 2021, no mutations have occurred over the past 20 years. In the scenario of the next pandemic (COVID-X), the emergence of a novel coronavirus is likely to heavily rely on a similar Mpro for virus proliferation. Therefore, drugs targeting the nearly unchanged active site of Mpro are expected to have low side effects on the human body and maintain high efficacy as a treatment for potential future pandemics similar to COVID-X.

<Figure description_1>

▲ Schematic illustration of coronavirus replication and mechanism of Mpro inhibitors

The research team utilized engineered amyloid peptides to develop a platform for screening potential COVID-19 treatments by monitoring the efficacy of Mpro inhibitors. As shown in Fig. 2, an engineered amyloid peptide (MCAP, Mpro cleavage-site-embedded amyloid peptide) was synthesized by merging the prion protein-derived amyloid sequence (GNNQQNY) and the sequence cleaved by Mpro (LQS). Engineered amyloid peptides tend to aggregate due to the amyloid sequence and are degraded by Mpro due to the Mpro cleavage sequence.

<Figure description_2>

▲ Schematic illustration of engineered amyloid peptide synthesis

The team synthesized engineered amyloid nano-composites by coating engineered amyloid peptides on the surface of gold nanoparticles (Fig. 3a). When the nano-composites react with Mpro, protein aggregates on the surface of the gold nanoparticles are disassembled due to the Mpro cleavage site within the engineered amyloid. As a result, the particles of lower stability undergo aggregation, and the optical properties of the gold nanoparticles cause changes in the color of the solution. The extent of the color change in the solution resulting from the disassembly of the protein aggregates, varies depending on the activity of the Mpro inhibitor reacting with Mpro. This color change can be used to quantitatively measure the activity of the Mpro inhibitor.

<Figure description_3>

▲ (a) Schematic illustration of fabrication of engineered amyloid nano-composites. (b) Schematic illustration of drug screening.

By measuring the color change of the engineered amyloid nano-composite solution using a UV-vis spectrophotometer, the team developed a colorimetric drug screening platform for Mpro inhibitors. Additionally, they validated the functionality of the platform using four known drugs that inhibit Mpro (Fig. 4).

<Figure description_4>

▲ Mpro▲ Validation of the team’s screening platform using Mpro inhibitors

Through these results, the screening platform developed by the research team demonstrated the use of Mpro at a 50 times lower concentration than the conventional fluorescent measurement method. The platform also showed significantly reduced measurement errors. With a measurement time of one to two hours, this method enables high-speed, large-scale screening at levels 1/20 to 1/100 of that of conventional methods. Moreover, the platform does not require complex preprocessing steps, allowing even non-experts to conduct experiments effectively. Therefore, this can be considered a more efficient and economical method of drug screening than traditional fluorescent and cell-based approaches.

The study was supported by a National Research Foundation of Korea grant (NRF-2022R1A2C1091756), Bio & Medical Technology Development Program (No. 2023M3E5E3080743), and the BK21 FOUR Institute of Precision Public Health.