General-purpose virus-neutralizing engulfing shells with modular target-specificity

Project Information

VIROFIGHT

Grant agreement ID: 899619

DOI

10.3030/899619

Project closed

EC signature date 26 May 2020

Start date 1 June 2020

End date 30 November 2024

Funded under

• EXCELLENT SCIENCE - Future and Emerging Technologies (FET)

Total cost

€ 3 880 942,50

EU contribution

€ 3 880 942,50

Coordinated by

TECHNISCHE UNIVERSITAET MUENCHEN
Germany

Periodic Reporting for period 3 - VIROFIGHT (General-purpose virus-neutralizing engulfing shells with modular target-specificity)

Reporting period: 2022-12-01 to 2024-11-30

Summary of the context and overall objectives of the project

Viruses pose a major threat to human health and society, causing widespread infections that lead to suffering and significant financial burdens. Many of the viruses listed by the World Health Organization (WHO) still lack effective treatments, and available antiviral drugs often require early-stage administration to be effective. In response, the VIROFIGHT project pioneered a revolutionary antiviral strategy by developing synthetic nano-shells designed to capture and neutralize entire viruses. Unlike conventional antivirals that target specific viral proteins or enzymes, this approach provided a broad-spectrum solution against multiple viral pathogens.
To achieve this goal, the VIROFIGHT consortium integrated expertise from supramolecular chemistry, molecular nanoengineering, and virology. The project’s primary objectives included:
• Developing pre-assembled nano-shells capable of recognizing and engulfing viral particles.
• Engineering self-assembling molecular shells that polymerize on viral surfaces, preventing host cell interactions.
• Exploring RNA aptamers and protein-based molecular binders for virus-specific targeting.
• Validating these technologies through neutralization assays and preparing for potential in vivo testing.
This novel antiviral strategy aimed to provide broadly applicable antiviral treatments, reduce the scale and impact of viral infections, and contribute to global pandemic preparedness.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The VIROFIGHT project pursued two complementary approaches to virus neutralization:
Pre-Assembled DNA Origami Nano-Shells
Using DNA origami technology, the consortium successfully fabricated size-adaptable nano-shells capable of encapsulating viruses. These structures ranged from 40 nm to 280 nm, making them suitable for trapping most spherical human viruses. Functionalization with heparan sulfates (HS) further enhanced their virus-binding capabilities, enabling the trapping of up to ten different viruses and virus-like particles (VLPs) from various families. These results were confirmed through negative stain TEM and cryo-electron microscopy (cryo-EM).
Additionally, antibody-functionalized nano-shells were tested for their ability to capture and neutralize specific viral targets. Notably, DNA shells decorated with anti-hepatitis B virus (HBV) antibodies demonstrated enhanced virus-blocking efficiency, surpassing the neutralization potential of free antibodies.
Self-Assembling Molecular Shells
The second approach focused on virus-triggered polymerization, where molecular building blocks assembled into virus-neutralizing structures on the viral surface. The team developed:
• Protein scaffolds inspired by natural immune defense mechanisms.
• De novo protein-based viral binders, designed to target viral glycosylation patterns.
• Oligomerized neutralizers, which demonstrated potent inhibition of Influenza, HIV, and SARS-CoV-2 in nanomolar concentration ranges.
These self-assembling shells effectively prevented viral interaction with host cells, reducing viral infectivity.
Aptamer-Based Molecular Binders
To enhance virus targeting, the consortium developed RNA aptamers, which serve as high-affinity virus binders. The team successfully:
Established an aptamer selection pipeline to generate strain-specific and strain-insensitive aptamers.
Developed high-affinity RNA aptamers against the SARS-CoV-2 spike protein.
Integrated aptamers into nano-shells, demonstrating their potential as “molecular glue” for trapping viruses.
However, challenges remained in identifying universal aptamers that bind across multiple virus strains.
Neutralization Assays and In Vitro Validation
The project validated its nano-shells and protein-based neutralizers through live-virus neutralization assays in in vitro assays with human cell lines using:
• Hepatitis B virus (HBV)
• Adenoviruses
• SARS-CoV-2
• Influenza virus
Results confirmed that DNA origami nano-shells functionalized with antibodies enhanced neutralization efficiency beyond that of free antibodies. Protein-based Griffithsin derivatives also showed strong inhibition against Influenza and HIV-1 pseudotypes, further supporting the potential of this approach. A spin-off company was established that obtained additional funding, allowing to further advance the technology and testing compounds in animals.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The VIROFIGHT project represents a breakthrough in antiviral technology, offering a paradigm shift in how viral infections are treated. Unlike traditional antivirals that target specific proteins or viral replication mechanisms, VIROFIGHT’s nano-shells provide a broadly applicable, modular approach to neutralizing diverse viral pathogens.
Progress Beyond the State of the Art
Key scientific advancements include:
• First-of-its-kind virus-engulfing nano-shells, engineered using DNA origami and protein design, with demonstrated effectiveness in trapping and neutralizing multiple virus families.
• Protein-based viral inhibitors, leveraging engineered oligomeric binders, such as Griffithsin derivatives, which exhibited broad-spectrum neutralization against Influenza, HIV, and SARS-CoV-2.
• High-affinity aptamer selection pipeline, successfully applied to SARS-CoV-2 spike proteins, opening the possibility of rapid aptamer discovery for new viruses.
• Enhanced neutralization efficiency of antibody-functionalized nano-shells, demonstrating improved performance over free antibodies in HBV and adenovirus models.
Potential Impacts and Socio-Economic Benefits
The impact of VIROFIGHT extends far beyond the laboratory, with significant societal, economic, and technological implications:
• Public Health and Pandemic Preparedness: The technology could be deployed as a universal antiviral platform, capable of neutralizing newly emerging viruses, potentially mitigating future pandemics.
• Cost Reduction in Healthcare: By providing a broad-spectrum solution, VIROFIGHT could reduce reliance on expensive virus-specific treatments, lowering healthcare costs.
• Biotechnology and Industrial Innovation: The project contributed to the European technology industry, leading to multiple patent filings and the foundation of a spin-off company focused on further development.
• Environmental and Food Safety Applications: Beyond medical applications, nano-shell technology could be adapted to purify water and food from viral contaminants, providing additional public health benefits.
Conclusion
The VIROFIGHT project successfully developed and validated nano-shell-based antiviral strategies that could redefine how viral infections are treated. The project has demonstrated remarkable scientific progress, with broad potential applications in medicine, pandemic preparedness, and biotechnology. VIROFIGHT represents a pioneering step toward universal antiviral treatments, with the promise of long-term societal impact and commercial viability.

Key Findings and Developments of the VIROFIGHT project