Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics

Blake T. Riley, Olga Ilyichova, Mauricio G. S. Costa, Benjamin T. Porebski, Simon J. de Veer, Joakim E. Swedberg, Itamar Kass, Jonathan M. Harris, David E. Hoke, Ashley M. Buckle

Research output: Contribution to journalArticleResearchpeer-review

Abstract

The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (∼1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.

Original languageEnglish
Article number35385
Number of pages14
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 21 Oct 2016

Keywords

  • enzyme mechanisms
  • nanocrystallography

Cite this

Riley, Blake T. ; Ilyichova, Olga ; Costa, Mauricio G. S. ; Porebski, Benjamin T. ; de Veer, Simon J. ; Swedberg, Joakim E. ; Kass, Itamar ; Harris, Jonathan M. ; Hoke, David E. ; Buckle, Ashley M. / Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics. In: Scientific Reports. 2016 ; Vol. 6.
@article{7c218eeb8f9747cc979780ce28b4fedc,
title = "Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics",
abstract = "The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (∼1 {\AA}) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.",
keywords = "enzyme mechanisms, nanocrystallography",
author = "Riley, {Blake T.} and Olga Ilyichova and Costa, {Mauricio G. S.} and Porebski, {Benjamin T.} and {de Veer}, {Simon J.} and Swedberg, {Joakim E.} and Itamar Kass and Harris, {Jonathan M.} and Hoke, {David E.} and Buckle, {Ashley M.}",
year = "2016",
month = "10",
day = "21",
doi = "10.1038/srep35385",
language = "English",
volume = "6",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",

}

Riley, BT, Ilyichova, O, Costa, MGS, Porebski, BT, de Veer, SJ, Swedberg, JE, Kass, I, Harris, JM, Hoke, DE & Buckle, AM 2016, 'Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics' Scientific Reports, vol. 6, 35385. https://doi.org/10.1038/srep35385

Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics. / Riley, Blake T.; Ilyichova, Olga; Costa, Mauricio G. S.; Porebski, Benjamin T.; de Veer, Simon J.; Swedberg, Joakim E.; Kass, Itamar; Harris, Jonathan M.; Hoke, David E.; Buckle, Ashley M.

In: Scientific Reports, Vol. 6, 35385, 21.10.2016.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics

AU - Riley, Blake T.

AU - Ilyichova, Olga

AU - Costa, Mauricio G. S.

AU - Porebski, Benjamin T.

AU - de Veer, Simon J.

AU - Swedberg, Joakim E.

AU - Kass, Itamar

AU - Harris, Jonathan M.

AU - Hoke, David E.

AU - Buckle, Ashley M.

PY - 2016/10/21

Y1 - 2016/10/21

N2 - The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (∼1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.

AB - The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (∼1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.

KW - enzyme mechanisms

KW - nanocrystallography

UR - http://www.scopus.com/inward/record.url?scp=84992322878&partnerID=8YFLogxK

U2 - 10.1038/srep35385

DO - 10.1038/srep35385

M3 - Article

VL - 6

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

M1 - 35385

ER -