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Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine


Designing selective inhibitors of proteases has proven problematic, in part because pharmacophores that confer potency exploit the conserved catalytic apparatus. We developed a fundamentally different approach by designing irreversible inhibitors that target noncatalytic cysteines that are structurally unique to a target in a protein family. We have successfully applied this approach to the important therapeutic target HCV protease, which has broad implications for the design of other selective protease inhibitors.

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Figure 1: Compounds rationally designed to covalently bond to a conserved HCVP cysteine.
Figure 2: Covalent NS3/4A inhibitor selectively modifies the target cysteine and gains potency through covalent modification.
Figure 3: Sustained inhibition of NS3/4A self-cleavage activity correlates with target occupancy, and the covalent compound shows a high degree of selectivity in cell lysates.

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We thank the following for critical reading of the manuscript: A. Whitty, B. Lindenbach, S. Witowski and N. Mahanthappa. We also thank R. Bartenschlager for helpful conversations. We thank Proteros Biostructures for help with X-ray crystallographic studies and A. Prasad for help with figures.

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Authors and Affiliations



M.H., T.S.M., M.P.S., M.T.L., H.B., R.M.K. and P.C. performed experiments; D.N., L.Q., J.S. and R.C.P. designed and generated chemical compounds; Z.Z. and J.S. performed molecular modeling; M.N., W.F.W., R.C.P. and J.S. supervised the project; M.H., M.N., R.C.P. and J.S. wrote the manuscript.

Corresponding author

Correspondence to Juswinder Singh.

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Competing interests

All authors are employees and shareholders of Avila Therapeutics, except H.B. who is a former employee.

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Supplementary Methods, Supplementary Schemes 1–4, Supplementary Figures 1–11 and Supplementary Tables 1–3 (PDF 1372 kb)

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Hagel, M., Niu, D., St Martin, T. et al. Selective irreversible inhibition of a protease by targeting a noncatalytic cysteine. Nat Chem Biol 7, 22–24 (2011).

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