Crystallographic characterisation and development of bi-substrate inhibitors of coronavirus nsp14 methyltransferase
SARS-CoV-2 non-structural protein 14 (nsp14) is essential for viral mRNA cap guanine-N7 methylation and represents a promising but underexplored antiviral target. Herein we describe a structure-guided campaign based on a hit from a focussed SAM mimetic library. Systematic SAR exploration guided by six X-ray co-crystal structures in complex with SARS-CoV-2 led to compound 26, a bi-substrate inhibitor that bridges the SAM and RNA cap binding sites. Compound 26 achieved nanomolar potency against nsp14 from SARS-CoV-2 (IC<sub>50</sub> = 53 nM), SARS-CoV-1, and two alphacoronaviruses, with excellent selectivity over human RNMT and flaviviral MTase. In general, the compounds demonstrated favourable metabolic stability, passive permeability, and no HepG2 cytotoxicity. However, cellular antiviral activity was limited, revealing disconnects between enzyme inhibition and phenotypic response. These findings provide a structural framework for optimizing bi-substrate methyltransferase inhibitors against coronaviruses with a view for pan-coronaviral activity.
Authors
- Adrien Delpal (ORCID: https://orcid.org/0000-0003-0598-7679)
- Przemysław Grygier (ORCID: https://orcid.org/0000-0003-2022-0396)
- Craig D. Smith (ORCID: https://orcid.org/0000-0001-6465-7472)
- Sean O'Byrne
- Sk Akhtar Ahmad (ORCID: https://orcid.org/0000-0003-0025-2673)
- Ian H. Gilbert (ORCID: https://orcid.org/0000-0002-5238-1314)
- Jacek Plewka (ORCID: https://orcid.org/0000-0002-0307-0907)
- John Post (ORCID: https://orcid.org/0000-0002-2881-5821)
- Duncan E. Scott (ORCID: https://orcid.org/0000-0003-1917-9576)
- Nadya Urakova (ORCID: https://orcid.org/0000-0003-3499-8158)
- Alex Matsuda (ORCID: https://orcid.org/0000-0003-3264-7506)
- Anna Czarna (ORCID: https://orcid.org/0000-0003-1068-0671)
- Irene Georgiou (ORCID: https://orcid.org/0000-0002-6042-9816)
- Krzysztof Pyrć (ORCID: https://orcid.org/0000-0002-3867-7688)
- Patrick Wanningen (ORCID: https://orcid.org/0000-0002-6911-2030)
- Étienne Decroly (ORCID: https://orcid.org/0000-0002-6046-024X)
- T.C. Eadsforth (ORCID: https://orcid.org/0000-0002-6000-093X)
- Leanid Kresik (ORCID: https://orcid.org/0000-0002-7739-8358)
- Suzanne Norval (ORCID: https://orcid.org/0000-0002-9186-1994)
- Colin Robinson
- Kinga Wierzbicka
- Sandra O'Neill
- Kexin See
- Kumar Singh Saikatendu
- Mirjam Groenewold
- Eric J. Snijder
- Edcon Chang
Institutions
- Jagiellonian University (PL)
- Centre National de la Recherche Scientifique (FR)
- European Bioinformatics Institute (GB)
- University of Dundee (GB)
- Aix-Marseille Université (FR)
- Leiden University Medical Center (NL)
- Drug Discovery Laboratory (Norway) (NO)
- Takeda (United States) (US)
Publication Details
- Journal
- RSC Medicinal Chemistry
- Published
- 2026-01-01
- DOI
- https://doi.org/10.1039/d5md00896d
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Bill and Melinda Gates Foundation
- European Commission
- Fondation pour la Recherche Médicale