SEMINARIUM Z FIZYKI BIOLOGICZNEJ I BIOINFORMATYKI
         Instytutu Biochemii i Biofizyki PAN, Instytutu Fizyki PAN,
			 i Zakładu Biofizyki UW

                Wednesday, 12.11.2025, 15:15 (3.15 p.m. CET)                                

    https://zoom.us/j/91976153012?pwd=azNiMWE4UnhPN3lRQlY2UHZHOXVkQT09

                
"From Viral Protein to Antiviral Lead:
An AI-Assisted In Silico Design Journey"

                        
                    Prof. Nevena Ilieva-Litova

        Institute of Information and Communication Technologies,
                   Department of Scientific Computations
                     Bulgarian Academy of Sciences,             
                          Sofia, Bulgaria  

                                       Bogdan Lesyng (UW)
                                       Anna Niedźwiecka (IF PAN)
                                       Piotr Zielenkiewicz (IBB)


ABSTRACT
The COVID-19 pandemic has underscored the role of structural and
computational biophysics in antiviral discovery. In this talk, I will
present an in silico design workflow that connects viral protein
characterization, molecular dynamics simulations, and AI-based modeling.
We focus on two SARS-CoV-2 proteins – the multifunctional helicase NSP13
and the interferon antagonist ORF6 – as potential drug targets. I will
discuss computationally identified and experimentally confirmed inhibitory
motifs and introduce the concepts of protein aptamers and cyclotides as
promising scaffolds for peptide-based antivirals. Using molecular dynamics
simulations and a convolutional neural network (CNN) trained for
interaction assessment, we have explored the feasibility of grafting viral
peptide motifs onto cyclotide scaffolds. Although this approach is still
under experimental validation, the results demonstrate how AI-enhanced in
silico methods can transform structural insights into rational antiviral
design strategies.