Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors

Evgenii M Osipov; Ali H Munawar; Steven Beelen; Daren Fearon; Alice Douangamath; Conor Wild; Stephen D Weeks; Arthur Van Aerschot; Frank von Delft; Sergei V Strelkov

doi:10.1039/d2cb00052k

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors

RSC Chem Biol. 2022 Apr 29;3(8):1013-1027. doi: 10.1039/d2cb00052k. eCollection 2022 Aug 3.

Authors

Evgenii M Osipov¹, Ali H Munawar^{1

2

3}, Steven Beelen¹, Daren Fearon^{4

5}, Alice Douangamath^{4

5}, Conor Wild^{6

7}, Stephen D Weeks^{1

3}, Arthur Van Aerschot⁸, Frank von Delft^{4

5

6

9

10}, Sergei V Strelkov¹

Affiliations

¹ Biocrystallography, KU Leuven Herestraat 49 Leuven Belgium sergei.strelkov@kuleuven.be.
² Orthogon Therapeutics LLC 45 Dan Road Suite 126 Canton MA 02021 USA.
³ Pledge Tx B.V. Gaston Geenslaan 1 Leuven Belgium.
⁴ Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot UK.
⁵ Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK.
⁶ Centre for Medicines Discovery, University of Oxford South Parks Road Headington OX3 7DQ UK.
⁷ Department of Statistics, University of Oxford 29 St Giles' Oxford OX1 3LB UK.
⁸ Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven Herestraat 49 Leuven Belgium.
⁹ Structural Genomics Consortium, University of Oxford Old Road Campus Roosevelt Drive Headington OX3 7DQ UK.
¹⁰ Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa.

Abstract

Polyomaviruses are a family of ubiquitous double-stranded DNA viruses many of which are human pathogens. These include BK polyomavirus which causes severe urinary tract infection in immunocompromised patients and Merkel cell polyomavirus associated with aggressive cancers. The small genome of polyomaviruses lacks conventional drug targets, and no specific drugs are available at present. Here we focus on the main structural protein VP1 of BK polyomavirus which is responsible for icosahedral capsid formation. To provide a foundation towards rational drug design, we crystallized truncated VP1 pentamers and subjected them to a high-throughput screening for binding drug-like fragments through a direct X-ray analysis. To enable a highly performant screening, rigorous optimization of the crystallographic pipeline and processing with the latest generation PanDDA2 software were necessary. As a result, a total of 144 binding hits were established. Importantly, the hits are well clustered in six surface pockets. Three pockets are located on the outside of the pentamer and map on the regions where the 'invading' C-terminal arm of another pentamer is attached upon capsid assembly. Another set of three pockets is situated within the wide pore along the five-fold axis of the VP1 pentamer. These pockets are situated at the interaction interface with the minor capsid protein VP2 which is indispensable for normal functioning of the virus. Here we systematically analyse the three outside pockets which are highly conserved across various polyomaviruses, while point mutations in these pockets are detrimental for viral replication. We show that one of the pockets can accommodate antipsychotic drug trifluoperazine. For each pocket, we derive pharmacophore features which enable the design of small molecules preventing the interaction between VP1 pentamers and therefore inhibiting capsid assembly. Our data lay a foundation towards a rational development of first-in-class drugs targeting polyomavirus capsid.