skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Small molecule inhibitors of mesotrypsin from a structure-based docking screen

Abstract

PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active site residues, and commercial availability. Diminazene (C1D22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (Ki) of 3.6±0.3 pM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.

Authors:
 [1];  [2];  [3];  [4];  [2];  [2]; ORCiD logo [1]
  1. Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL (United States). Department of Cancer Biology
  2. University of Minnesota, Austin, MN (United States). The Hormel Institute
  3. Brookhaven National Lab. (BNL), Upton, NY (United States). Photon Sciences Directorate
  4. Mayo Clinic College of Medicine, Jacksonville, FL (United States). Department of Neuroscience
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH)
OSTI Identifier:
1430883
Report Number(s):
BNL-203390-2018-JAAM
Journal ID: ISSN 1932-6203
Grant/Contract Number:  
SC0012704
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 12; Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; mesotrypsin; trypsin; serine protease; protease inhibitor; drug discovery; structure-based docking; in-silico screening; virtual screening; crystal structure; x-ray crystallography

Citation Formats

Kayode, Olumide, Huang, Zunnan, Soares, Alexei S., Caulfield, Thomas R., Dong, Zigang, Bode, Ann M., and Radisky, Evette S. Small molecule inhibitors of mesotrypsin from a structure-based docking screen. United States: N. p., 2017. Web. doi:10.1371/journal.pone.0176694.
Kayode, Olumide, Huang, Zunnan, Soares, Alexei S., Caulfield, Thomas R., Dong, Zigang, Bode, Ann M., & Radisky, Evette S. Small molecule inhibitors of mesotrypsin from a structure-based docking screen. United States. doi:10.1371/journal.pone.0176694.
Kayode, Olumide, Huang, Zunnan, Soares, Alexei S., Caulfield, Thomas R., Dong, Zigang, Bode, Ann M., and Radisky, Evette S. Tue . "Small molecule inhibitors of mesotrypsin from a structure-based docking screen". United States. doi:10.1371/journal.pone.0176694. https://www.osti.gov/servlets/purl/1430883.
@article{osti_1430883,
title = {Small molecule inhibitors of mesotrypsin from a structure-based docking screen},
author = {Kayode, Olumide and Huang, Zunnan and Soares, Alexei S. and Caulfield, Thomas R. and Dong, Zigang and Bode, Ann M. and Radisky, Evette S.},
abstractNote = {PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active site residues, and commercial availability. Diminazene (C1D22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (Ki) of 3.6±0.3 pM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.},
doi = {10.1371/journal.pone.0176694},
journal = {PLoS ONE},
number = 5,
volume = 12,
place = {United States},
year = {2017},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

A trypanosome oligopeptidase as a target for the trypanocidal agents pentamidine, diminazene and suramin
journal, August 1998


Structural binding evidence of the trypanocidal drugs Berenil® and Pentacarinate® active principles to a serine protease model
journal, June 2010

  • Perilo, Cecília Steinberg; Pereira, Márcio Tadeu; Santoro, Marcelo Matos
  • International Journal of Biological Macromolecules, Vol. 46, Issue 5
  • DOI: 10.1016/j.ijbiomac.2010.03.006

Keratinocytes Synthesize Enteropeptidase and Multiple Forms of Trypsinogen during Terminal Differentiation
journal, April 2010

  • Nakanishi, Jotaro; Yamamoto, Mami; Koyama, Junichi
  • Journal of Investigative Dermatology, Vol. 130, Issue 4
  • DOI: 10.1038/jid.2009.364

Flexible ligand docking using conformational ensembles
journal, April 1998


Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Multiple pathways are involved in DNA degradation during keratinocyte terminal differentiation
journal, April 2014

  • Yamamoto-Tanaka, M.; Makino, T.; Motoyama, A.
  • Cell Death & Disease, Vol. 5, Issue 4
  • DOI: 10.1038/cddis.2014.145

Crystal structure reveals basis for the inhibitor resistance of human brain trypsin
journal, February 2002

  • Katona, Gergely; Berglund, Gunnar I.; Hajdu, Janos
  • Journal of Molecular Biology, Vol. 315, Issue 5
  • DOI: 10.1006/jmbi.2001.5305

Extra Precision Glide:  Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
journal, October 2006

  • Friesner, Richard A.; Murphy, Robert B.; Repasky, Matthew P.
  • Journal of Medicinal Chemistry, Vol. 49, Issue 21
  • DOI: 10.1021/jm051256o

Conformation-Based Restrictions and Scaffold Replacements in the Design of Hepatitis C Virus Polymerase Inhibitors: Discovery of Deleobuvir (BI 207127)
journal, November 2013

  • LaPlante, Steven R.; Bös, Michael; Brochu, Christian
  • Journal of Medicinal Chemistry, Vol. 57, Issue 5
  • DOI: 10.1021/jm4011862

Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin
journal, December 2007

  • Salameh, Moh'd A.; Soares, Alexei S.; Hockla, Alexandra
  • Journal of Biological Chemistry, Vol. 283, Issue 7
  • DOI: 10.1074/jbc.M708268200

Cis−Trans Isomerization of Organic Molecules and Biomolecules:  Implications and Applications
journal, July 2003

  • Dugave, Christophe; Demange, Luc
  • Chemical Reviews, Vol. 103, Issue 7
  • DOI: 10.1021/cr0104375

Mesotrypsin Has Evolved Four Unique Residues to Cleave Trypsin Inhibitors as Substrates
journal, July 2015

  • Alloy, Alexandre P.; Kayode, Olumide; Wang, Ruiying
  • Journal of Biological Chemistry, Vol. 290, Issue 35
  • DOI: 10.1074/jbc.M115.662429

Mesotrypsin and Caspase-14 Participate in Prosaposin Processing: POTENTIAL RELEVANCE TO EPIDERMAL PERMEABILITY BARRIER FORMATION
journal, May 2014

  • Yamamoto-Tanaka, Mami; Motoyama, Akira; Miyai, Masashi
  • Journal of Biological Chemistry, Vol. 289, Issue 29
  • DOI: 10.1074/jbc.M113.543421

Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
journal, March 2004

  • Friesner, Richard A.; Banks, Jay L.; Murphy, Robert B.
  • Journal of Medicinal Chemistry, Vol. 47, Issue 7
  • DOI: 10.1021/jm0306430

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Combinatorial protein engineering of proteolytically resistant mesotrypsin inhibitors as candidates for cancer therapy
journal, May 2016

  • Cohen, Itay; Kayode, Olumide; Hockla, Alexandra
  • Biochemical Journal, Vol. 473, Issue 10
  • DOI: 10.1042/BJ20151410

A New Generation of Crystallographic Validation Tools for the Protein Data Bank
journal, October 2011


Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109
journal, December 2009

  • Hockla, Alexandra; Radisky, Derek C.; Radisky, Evette S.
  • Breast Cancer Research and Treatment, Vol. 124, Issue 1
  • DOI: 10.1007/s10549-009-0699-0

The Future of Peptide-based Drugs
journal, December 2012

  • Craik, David J.; Fairlie, David P.; Liras, Spiros
  • Chemical Biology & Drug Design, Vol. 81, Issue 1
  • DOI: 10.1111/cbdd.12055

Discovery of XEN907, a spirooxindole blocker of NaV1.7 for the treatment of pain
journal, June 2011

  • Chowdhury, Sultan; Chafeev, Mikhail; Liu, Shifeng
  • Bioorganic & Medicinal Chemistry Letters, Vol. 21, Issue 12
  • DOI: 10.1016/j.bmcl.2011.04.088

Human Mesotrypsin Is a Unique Digestive Protease Specialized for the Degradation of Trypsin Inhibitors
journal, September 2003

  • Szmola, Richárd; Kukor, Zoltán; Sahin-Tóth, Miklós
  • Journal of Biological Chemistry, Vol. 278, Issue 49
  • DOI: 10.1074/jbc.M310301200

Activity of recombinant trypsin isoforms on human proteinase-activated receptors (PAR): mesotrypsin cannot activate epithelial PAR-1, -2, but weakly activates brain PAR-1
journal, December 2005

  • Grishina, Zoryana; Ostrowska, Ewa; Halangk, Walter
  • British Journal of Pharmacology, Vol. 146, Issue 7
  • DOI: 10.1038/sj.bjp.0706410

The P2′ residue is a key determinant of mesotrypsin specificity: engineering a high-affinity inhibitor with anticancer activity
journal, October 2011

  • Salameh, Moh'd A.; Soares, Alexei S.; Hockla, Alexandra
  • Biochemical Journal, Vol. 440, Issue 1
  • DOI: 10.1042/BJ20110788

The Amyloid Precursor Protein/Protease Nexin 2 Kunitz Inhibitor Domain Is a Highly Specific Substrate of Mesotrypsin
journal, November 2009

  • Salameh, Moh'd A.; Robinson, Jessica L.; Navaneetham, Duraiswamy
  • Journal of Biological Chemistry, Vol. 285, Issue 3
  • DOI: 10.1074/jbc.M109.057216

Trypsin IV or Mesotrypsin and p23 Cleave Protease-activated Receptors 1 and 2 to Induce Inflammation and Hyperalgesia
journal, July 2007

  • Knecht, Wolfgang; Cottrell, Graeme S.; Amadesi, Silvia
  • Journal of Biological Chemistry, Vol. 282, Issue 36
  • DOI: 10.1074/jbc.M703840200

Keratinocyte-Specific Mesotrypsin Contributes to the Desquamation Process via Kallikrein Activation and LEKTI Degradation
journal, June 2014

  • Miyai, Masashi; Matsumoto, Yuuko; Yamanishi, Haruyo
  • Journal of Investigative Dermatology, Vol. 134, Issue 6
  • DOI: 10.1038/jid.2014.3

Ligand Bioactive Conformation Plays a Critical Role in the Design of Drugs That Target the Hepatitis C Virus NS3 Protease
journal, November 2013

  • LaPlante, Steven R.; Nar, Herbert; Lemke, Christopher T.
  • Journal of Medicinal Chemistry, Vol. 57, Issue 5
  • DOI: 10.1021/jm401338c

Sequence and Conformational Specificity in Substrate Recognition: SEVERAL HUMAN KUNITZ PROTEASE INHIBITOR DOMAINS ARE SPECIFIC SUBSTRATES OF MESOTRYPSIN
journal, October 2014

  • Pendlebury, Devon; Wang, Ruiying; Henin, Rachel D.
  • Journal of Biological Chemistry, Vol. 289, Issue 47
  • DOI: 10.1074/jbc.M114.609560

PRSS3 promotes tumour growth and metastasis of human pancreatic cancer
journal, October 2010


Molecular replacement with MOLREP
journal, December 2009

  • Vagin, Alexei; Teplyakov, Alexei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042589

Trypsinogen 4 boosts tumor endothelial cells migration through proteolysis of tissue factor pathway inhibitor-2
journal, July 2015


Synthesis of Rigidified eIF4E/eIF4G Inhibitor-1 (4EGI-1) Mimetic and Their in Vitro Characterization as Inhibitors of Protein–Protein Interaction
journal, June 2014

  • Mahalingam, Poornachandran; Takrouri, Khuloud; Chen, Ting
  • Journal of Medicinal Chemistry, Vol. 57, Issue 12
  • DOI: 10.1021/jm401733v

The Protein Data Bank
journal, January 2000


Autocrine Extra-Pancreatic Trypsin 3 Secretion Promotes Cell Proliferation and Survival in Esophageal Adenocarcinoma
journal, October 2013


Discovery of benzothiazole guanidines as novel inhibitors of thrombin and trypsin IV
journal, July 2012

  • Karle, Michael; Knecht, Wolfgang; Xue, Yafeng
  • Bioorganic & Medicinal Chemistry Letters, Vol. 22, Issue 14
  • DOI: 10.1016/j.bmcl.2012.05.046

Determinants of Affinity and Proteolytic Stability in Interactions of Kunitz Family Protease Inhibitors with Mesotrypsin
journal, September 2010

  • Salameh, Moh'd A.; Soares, Alexei S.; Navaneetham, Duraiswamy
  • Journal of Biological Chemistry, Vol. 285, Issue 47
  • DOI: 10.1074/jbc.M110.171348

Kinetic Studies on the Thermal Cis−Trans Isomerization of 1,3-Diphenyltriazene in Aqueous Solution. Effects of Acids and Bases
journal, September 2000

  • Barra, Mónica; Chen, Nan
  • The Journal of Organic Chemistry, Vol. 65, Issue 18
  • DOI: 10.1021/jo000599l

S100 Family Members and Trypsinogens Are Predictors of Distant Metastasis and Survival in Early-Stage Non-Small Cell Lung Cancer
journal, August 2004


PRSS3 expression is associated with tumor progression and poor prognosis in epithelial ovarian cancer
journal, June 2015


PRSS3/Mesotrypsin Is a Therapeutic Target for Metastatic Prostate Cancer
journal, December 2012