Journal Article

FZJ-2026-04477

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Single-stranded nucleic acid binding enhances the in vitro catalytic activity of Chikungunya virus nsP2 protease

Mastalipour, M. ; Olivier, D. S. ; Coronado, M. A. ; Dingley, A. J.FZJ* ; Siahaan, R. A. ; Drees, A. ; Ahlers, C. ; Fischer, M. ; Willbold, D. ; Eberle, R. J. (Corresponding author)

2026
Elsevier [Amsterdam]

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Please use a persistent id in citations: doi:10.1016/j.bbadva.2026.100198

Abstract: Chikungunya virus (CHIKV) is an emerging arbovirus whose replication relies on the multifunctional nonstructural protein 2 (nsP2), particularly its viral protease (nsP2pro), which is essential for polyprotein processing. In this study, we investigated how interactions with nucleic acids influence nsP2pro activity. Using High-Throughput Sequencing–Fluorescent Ligand Interaction Profiling (HiTS-FLIP), we identified specific singlestranded DNA aptamers that enhanced nsP2pro activity. Additionally, both random single-stranded DNA and single-stranded RNA were found to stimulate protease activity, whereas double-stranded DNA showed no such effect. Circular dichroism spectroscopy and secondary structure predictions confirmed that the identified aptamers adopt stable folded conformations. Similarly, structured RNA sequences were also capable of promoting protease activity. The observed stimulatory effect depended on the nucleic acid strand type, length, and buffer conditions, suggesting the involvement of electrostatic interactions. NMR experiments demonstrated that nsP2pro interacts with single-stranded DNA, accompanied by changes in its conformational dynamics upon binding. Molecular dynamic simulations of nsP2pro-RNA and -DNA complexes revealed that these nucleic acids interact specifically with the nsP2pro methyltransferase domain and induce an opening process in the protease active site. Our findings provide novel insights into the regulation of nsP2pro, enhancing our understanding of CHIKV replication mechanisms, and may guide future antiviral development strategies.

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Contributing Institute(s):

1. Strukturbiochemie (IBI-7)

Research Program(s):

1. 5241 - Molecular Information Processing in Cellular Systems (POF4-524) (POF4-524)

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Database coverage:
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