Single-stranded nucleic acid binding enhances the in vitro catalytic activity of Chikungunya virus nsP2 protease

BBA Advances, vol. 10, pp. 100198

Abstract

Abstract Chikungunya virus (CHIKV) is an emerging arbovirus whose replication relies on the multifunctional nonstructural protein 2 (nsP2), particularly its viral protease (nsP2 pro ), which is essential for polyprotein processing. In this study, we investigated how interactions with nucleic acids influence nsP2 pro activity. Using high-throughput sequencing–fluorescent ligand interaction profiling, we identified specific single-stranded DNA aptamers that enhanced nsP2 pro 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. Molecular docking analyses further let us assume that these nucleic acids interact specifically with the nsP2 pro methyltransferase domain. Our findings provide novel insights into the regulation of nsP2 pro , enhancing our understanding of CHIKV replication mechanisms, and may guide future antiviral development strategies.

Authors 9

1. Mohammadamin Mastalipour

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

2. Mônika A. Coronado

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

3. Andrew J. Dingley

   Forschungszentrum Jülich · Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institut für Biologische Informationsprozesse (IBI-7), Forschungszentrum Jülich, Jülich, Germany

   Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

4. Ruth Anasthasia Siahaan Aachen Faculty of Chemistry and Biotechnology

   FH Aachen

   Affiliation as printed

   Faculty of Chemistry and Biotechnology, FH Aachen, Campus Jülich, Germany

5. Alissa Drees

   Universität Hamburg

   Affiliation as printed

   Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany

6. Christian Ahlers

   Universität Hamburg

   Affiliation as printed

   Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany

7. Markus J. Fischer

   Universität Hamburg

   Affiliation as printed

   Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Hamburg, Germany

8. Dieter Willbold

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany

9. Raphael J. Eberle corresponding

   Heinrich Heine University Düsseldorf

   Affiliation as printed

   Institut für Biochemische Pflanzenphysiologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany