Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals
Dengue viruses (DENVs) infect approximately 400 million people each year, and currently, there are no effective therapeutics available. To explore potential starting points for antiviral drug development, we conducted a large-scale crystallographic fragment screen targeting the RNA-dependent RNA polymerase (RdRp) domain of the nonstructural protein 5 (NS5) from DENV serotype 2. Our screening, which involved 1108 fragments, identified 60 hit compounds across various known binding sites, including the active site, N pocket, and RNA tunnel. Additionally, we discovered a novel binding site and a fragment-binding hot spot in thumb site II. These structural findings open amenable avenues for developing non-nucleoside inhibitors and offer valuable insights for future structure-based drug design aimed at DENV and other flaviviral RdRps.
Authors
- Blake Balcomb (ORCID: https://orcid.org/0000-0001-7599-8467)
- Francesc X. Ruiz (ORCID: https://orcid.org/0000-0002-0457-0030)
- Anu V. Chandran (ORCID: https://orcid.org/0000-0001-9942-2614)
- Ashima Chopra (ORCID: https://orcid.org/0000-0001-7867-1507)
- F. von Delft (ORCID: https://orcid.org/0000-0003-0378-0017)
- J.C. Aschenbrenner (ORCID: https://orcid.org/0000-0002-4318-0481)
- Manisha Saini (ORCID: https://orcid.org/0000-0003-2242-3218)
- Eddy Arnold (ORCID: https://orcid.org/0000-0003-2612-9622)
- D. Fearon (ORCID: https://orcid.org/0000-0003-3529-7863)
- Peter Marples (ORCID: https://orcid.org/0000-0002-8787-7969)
Institutions
- Rutgers, The State University of New Jersey (US)
- Nuffield Orthopaedic Centre (GB)
- Diamond Light Source (GB)
- Advanced Pharma (US)
- Research Complex at Harwell (GB)
Publication Details
- Journal
- Journal of Medicinal Chemistry
- Published
- 2025-09-02
- DOI
- https://doi.org/10.1021/acs.jmedchem.5c01014
- Citations
- 1
- Primary Topic
- Mosquito-borne diseases and control
- Type
- article
- Field-Weighted Citation Impact
- 1.88
Funders
- Diamond Light Source
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases