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What do you get when you cross high-performance computing with a neglected virus?

Published paper (Journal Advanced Theory and Simulations): Insights into the Dynamics and Binding Mechanisms of the Alkhumra Virus NS2B/NS3 Protease: A Molecular Dynamics Study
Oct 16th 2025
What do you get when you cross high-performance computing with a neglected virus?

Insights into the Dynamics and Binding Mechanisms of the Alkhumra Virus NS2B/NS3 Protease: A Molecular Dynamics Study

What do you get when you cross high-performance computing with a neglected virus?
A deep dive into molecular dynamics—and maybe, just maybe, the blueprint for future antivirals.

Our latest work, published in Advanced Theory and Simulations, explores the NS2B/NS3 protease of the Alkhumra virus (ALKV)—a rare, tick-borne flavivirus that causes hemorrhagic fever in humans.

"No, it’s not on Big Pharma’s playlist. But with the power of HPC, we gave this overlooked virus the attention it deserves", says Jurica Novak (Centre for Informatics and Computing, Ruđer Bošković Institute, Croatia) and his associates Shivananda Kandagalla and Ramesh Sistla (thinkMolecular Technologies, India).

Using all-atom molecular dynamics and free energy calculations, we revealed:

  • How the NS2B cofactor tames the wild flexibility of the NS3 protease 

  • The key interactions driving protease-cofactor binding (spoiler: it’s not magic, it’s electrostatics)

  • The effects of catalytic triad protonation on active site geometry 

  • And yes, we even screened potential inhibitors from DrugBank—because why not try to outsmart nature with a bit of repurposing?

This study is not just about one virus. It’s a proof-of-concept for how computational science—and especially HPC—can push forward drug discovery for diseases that don’t make headlines (or profits).

Because some problems are too important to ignore, even if they’re not marketable.

Read the paper: https://doi.org/10.1002/adts.202401406
Title: Insights into the Dynamics and Binding Mechanisms of the Alkhumra Virus NS2B/NS3 Protease: A Molecular Dynamics Study

Research supported by the Croatian Science Foundation (IP-2022-4658) and powered by the Supek supercomputer at SRCE, University of Zagreb.

Scientific Paper

Insights into the Dynamics and Binding Mechanisms of the Alkhumra Virus NS2B/NS3 Protease: A Molecular Dynamics Study

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