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Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus

Abstract

Rhinoviruses (RVs) are the pathogens most often responsible for the common cold, and are a frequent cause of exacerbations in asthma, chronic obstructive pulmonary disease and cystic fibrosis. Here we report the discovery of IMP-1088, a picomolar dual inhibitor of the human N-myristoyltransferases NMT1 and NMT2, and use it to demonstrate that pharmacological inhibition of host-cell N-myristoylation rapidly and completely prevents rhinoviral replication without inducing cytotoxicity. The identification of cooperative binding between weak-binding fragments led to rapid inhibitor optimization through fragment reconstruction, structure-guided fragment linking and conformational control over linker geometry. We show that inhibition of the co-translational myristoylation of a specific virus-encoded protein (VP0) by IMP-1088 potently blocks a key step in viral capsid assembly, to deliver a low nanomolar antiviral activity against multiple RV strains, poliovirus and foot and-mouth disease virus, and protection of cells against virus-induced killing, highlighting the potential of host myristoylation as a drug target in picornaviral infections.

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Fig. 1: Proposed pathway for the generation of infectious RV particles in an infected host cell.
Fig. 2: Structure-guided discovery of potent human NMT inhibitors.
Fig. 3: Potent inhibitors of human NMTs inhibit RV myristoylation in infected cells.
Fig. 4: Novel human NMT inhibitors potently and efficiently block RV replication without cytotoxicity.
Fig. 5: IMP-1088 inhibits the production of infectious RV particles by blocking virus assembly.

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Acknowledgements

The authors gratefully acknowledge financial support from the Medical Research Council (MRC) of the UK (grant G0900278 and a confidence-in-concept award to Imperial College, MC-PC-14100), the EPSRC (grant EP/F500416/1), Cancer Research UK (grant C29637/A20183), MRC Asthma UK Centre in Allergic Mechanisms of Asthma (grant G1000758) and Imperial Innovations. A.M. is supported by an MRF/Asthma UK Research Grant (MRFAUK-2015-311). S.L.J. is supported by a Chair from Asthma UK (CH11SJ) and is a National Institute of Health Research (NIHR) Senior Investigator. The Pirbright Institute receives strategic funding from the Biotechnology and Biological Research Council of the UK. We thank Diamond Light Source for access to beamlines I04 and I04-1 (proposal nos mx12579, mx7864 and mx9948). We thank E. Cota (Imperial College London) for advice on structure determination, and S. Roberts for expert crystal handling. The authors thank K.-K. Conzelmann (Max von Pettenkofer-Institut) for permission to use the BSR-T7/5 cell line.

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Contributions

A.M. and D.P.S. designed and executed the RV infection experiments, with assistance from A.G. and R.S.; A.S.B. designed and synthesized the NMT inhibitors, with E.W.T., J.A.H. and R.J.L.; J.N., A.S.A. and T.J.T. undertook the PV and FMDV infections, and the sucrose gradient fractionation. J.M.-S. undertook chemical proteomics experiments and data analysis, with E.W.T.; I.P.-D., J.A.B. and A.J.W. undertook protein purification, X-ray crystallography and structure refinement. M.R. undertook cell viability and tagging experiments. S.W.R. and I.H.N. undertook SPR experiments and data analysis. S.L.J. provided advice on virus experiments, and access to essential facilities. E.W.T. and R.S. conceived the project and, with A.M. and A.B., directed the project. All of the authors contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Roberto Solari or Edward W. Tate.

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Competing interests

A.B., E.W.T., R.J.L., J.A.H. and J.A.B. are inventors on a patent application that describes NMT inhibitors that include IMP-1031 and IMP-1088 (Bell, A.S.; Tate, E.W.; Leatherbarrow, R.J.; Hutton, J.A.; Brannigan, J.A., Compounds and their use as inhibitors of N-myristoyl transferase, Patent Cooperation Treaty International Application (2017) WO 2017001812).

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Supplementary Figures 1–15, Table 1, Methods, NMR Spectra and References

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Mousnier, A., Bell, A.S., Swieboda, D.P. et al. Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nature Chem 10, 599–606 (2018). https://doi.org/10.1038/s41557-018-0039-2

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