Abstract
MALT1 paracaspase is central for lymphocyte antigen-dependent responses including NF-κB activation. We discovered nanomolar, selective allosteric inhibitors of MALT1 that bind by displacing the side chain of Trp580, locking the protease in an inactive conformation. Interestingly, we had previously identified a patient homozygous for a MALT1 Trp580-to-serine mutation who suffered from combined immunodeficiency. We show that the loss of tryptophan weakened interactions between the paracaspase and C-terminal immunoglobulin MALT1 domains resulting in protein instability, reduced protein levels and functions. Upon binding of allosteric inhibitors of increasing potency, we found proportionate increased stabilization of MALT1-W580S to reach that of wild-type MALT1. With restored levels of stable MALT1 protein, the most potent of the allosteric inhibitors rescued NF-κB and JNK signaling in patient lymphocytes. Following compound washout, MALT1 substrate cleavage was partly recovered. Thus, a molecular corrector rescues an enzyme deficiency by substituting for the mutated residue, inspiring new potential precision therapies to increase mutant enzyme activity in other deficiencies.
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Data availability
Data are available from the authors upon reasonable request. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD008421.
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Acknowledgements
We thank C.H. Régnier for helpful discussions. We gratefully acknowledge the contributions of C. Malinverni and J. Heng in the early part of this work. We acknowledge the Paul Scherrer Institut, Villigen, Switzerland for provision of synchrotron radiation beamtime at beamline PXII (X10/SA) of the SLS. We also thank the beamline staff, as well as J. Diez and his staff at Expose GmbH for their excellent help with data collection. We thank F. Sirokin for providing a model of the MALT1 complex with mepazine. We thank M. Shipp (Harvard University MA, USA) for providing the OCI-Ly3 B cell line. C.M.O. holds a Canada Research Chair in Protease Proteomics and Systems Biology (number: 950-20-3877). This work was supported by Canadian Institutes of Health Research grants (MOP-133691 to S.E.T. and FDN: 148408, MOP-37937 to C.M.O.), Natural Sciences and Engineering Research Council of Canada (RGPIN 435829-201 to S.E.T), the Michael Smith Foundation for Health Research to establish the British Columbia Proteomics Network (IN-NPG-00105-156 to C.M.O.) and the Canada Foundation for Innovation (31059 to C.M.O.).
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J.Q., A.S. and R.H. oversaw the discovery and synthesis of the compounds. T.K. and S.-Y.F. performed MALT1 stabilization, cleavage and signaling and functional experiments in B and T cells. T.K., S.Y.F., J.J.P. and S.K., performed experiments on expanded primary T cells. T.K., M.A.B. and R.I.V. performed kinetic experiments by TAILS, LC–MS/MS analysis and data analysis. J.K. synthesized the aldehyde polymer used for N-terminomic TAILS analyses, and T.K. analyzed proteomic data and made figures. M.R. conceived the crystallographic study, collected and analyzed crystallographic data, solved crystal structures and made figures. F.V. performed crystallization experiments. N.H. and P.E. designed and executed the SPR and DSF experiments. L.I. designed and executed the Trp580 quenching and enzymatic activity experiments. J.B. designed and oversaw the screening campaign and follow-up compound triage. J.Q., J.E., S.E.T., and C.M.O. conceived the research idea. J.Q., T.K., S.Y.F., S.E.T., F.B. and C.M.O. wrote the paper with contributions from all authors.
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J.Q., M.R., N.H., L.I., J.B., A.S., P.E., F.V., R.H., J.E., and F.B. are employees of the Novartis Institute of Biomedical Research. R.I.V. is and M.B. was an employee of Thermo Fisher Scientific, developer and distributor of the Orbitrap Fusion Lumos mass spectrometer.
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Quancard, J., Klein, T., Fung, SY. et al. An allosteric MALT1 inhibitor is a molecular corrector rescuing function in an immunodeficient patient. Nat Chem Biol 15, 304–313 (2019). https://doi.org/10.1038/s41589-018-0222-1
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DOI: https://doi.org/10.1038/s41589-018-0222-1