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A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods

Author

Listed:
  • Marko Novinec

    (University of Zurich
    Faculty of Chemistry and Chemical Technology, University of Ljubljana)

  • Matevž Korenč

    (Faculty of Chemistry and Chemical Technology, University of Ljubljana)

  • Amedeo Caflisch

    (University of Zurich)

  • Rama Ranganathan

    (Green Center for Systems Biology, UT Southwestern Medical Center)

  • Brigita Lenarčič

    (Faculty of Chemistry and Chemical Technology, University of Ljubljana
    Jožef Stefan Institute)

  • Antonio Baici

    (University of Zurich)

Abstract

Allosteric modifiers have the potential to fine-tune enzyme activity. Therefore, targeting allosteric sites is gaining increasing recognition as a strategy in drug design. Here we report the use of computational methods for the discovery of the first small-molecule allosteric inhibitor of the collagenolytic cysteine peptidase cathepsin K, a major target for the treatment of osteoporosis. The molecule NSC13345 is identified by high-throughput docking of compound libraries to surface sites on the peptidase that are connected to the active site by an evolutionarily conserved network of residues (protein sector). The crystal structure of the complex shows that NSC13345 binds to a novel allosteric site on cathepsin K. The compound acts as a hyperbolic mixed modifier in the presence of a synthetic substrate, it completely inhibits collagen degradation and has good selectivity for cathepsin K over related enzymes. Altogether, these properties qualify our methodology and NSC13345 as promising candidates for allosteric drug design.

Suggested Citation

  • Marko Novinec & Matevž Korenč & Amedeo Caflisch & Rama Ranganathan & Brigita Lenarčič & Antonio Baici, 2014. "A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods," Nature Communications, Nature, vol. 5(1), pages 1-10, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4287
    DOI: 10.1038/ncomms4287
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    Cited by:

    1. Ahmed Abdul Quadeer & David Morales-Jimenez & Matthew R McKay, 2018. "Co-evolution networks of HIV/HCV are modular with direct association to structure and function," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-29, September.
    2. Marko Novinec, 2017. "Computational investigation of conformational variability and allostery in cathepsin K and other related peptidases," PLOS ONE, Public Library of Science, vol. 12(8), pages 1-22, August.

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