Molecular modeling: a search for a calpain inhibitor as a new treatment for cataractogenesis.

Studies of 17 analoges of 3 (SJA6017) in an in silico calpain model are reconciled to measured IC(50) values against ovine calpain. The studies validate the potential of the "model" and criteria established for inhibition as a tool to select structures for synthesis to test as calpain inhibitors. Using this screening methodology of virtual libraries led us to synthesize several inhibitors including macrocycle 33, which in vitro sheep eye lens culture experiments showed to substantially slow opacification.

[1]  M. Bogyo,et al.  Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries* , 2007, Journal of Biological Chemistry.

[2]  Z. Jia,et al.  Crystal structure of calpain reveals the structural basis for Ca2+‐dependent protease activity and a novel mode of enzyme activation , 1999, The EMBO journal.

[3]  D. E. Goll,et al.  A BODIPY fluorescent microplate assay for measuring activity of calpains and other proteases. , 2000, Analytical biochemistry.

[4]  T. Shearer,et al.  Characterization and Regulation of Lens-specific Calpain Lp82* , 2002, The Journal of Biological Chemistry.

[5]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[6]  D. Fairlie,et al.  Beta-strand mimicking macrocyclic amino acids: templates for protease inhibitors with antiviral activity. , 2002, Journal of medicinal chemistry.

[7]  S. Thrall,et al.  Chemical mechanism of a cysteine protease, cathepsin C, as revealed by integration of both steady-state and pre-steady-state solvent kinetic isotope effects. , 2008, Biochemistry.

[8]  M. Cygler,et al.  Structure of a calpain Ca2+-binding domain reveals a novel EF-hand and Ca2+-induced conformational changes , 1997, Nature Structural Biology.

[9]  F. Mackenzie,et al.  The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition. , 2007, Journal of molecular biology.

[10]  E. Melloni,et al.  Phosphorylation of rat brain calpastatins by protein kinase C , 1999, FEBS letters.

[11]  P. Yuen,et al.  Structure-activity relationship study and drug profile of N-(4-fluorophenylsulfonyl)-L-valyl-L-leucinal (SJA6017) as a potent calpain inhibitor. , 2003, Journal of medicinal chemistry.

[12]  D. Fairlie,et al.  Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. , 2000, Journal of medicinal chemistry.

[13]  E. Lunney,et al.  An alpha-mercaptoacrylic acid derivative is a selective nonpeptide cell-permeable calpain inhibitor and is neuroprotective. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[14]  R. Campbell,et al.  Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions. , 2008, Journal of medicinal chemistry.

[15]  A. Abell,et al.  Synthesis of macrocyclic beta-strand templates by ring closing metathesis. , 2009, The Journal of organic chemistry.

[16]  D. Fairlie,et al.  Designing supramolecular structures from models of cyclic peptide scaffolds with heterocyclic constraints. , 2003, Journal of molecular graphics & modelling.

[17]  R. Huber,et al.  The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[18]  O. Srivastava,et al.  Degradation of γD- and γs-Crystallins in Human Lenses , 1998 .

[19]  Z. Jia,et al.  Origins of the difference in Ca2+ requirement for activation of mu- and m-calpain. , 2002, The Biochemical journal.

[20]  N. Carragher.  Calpain inhibition: a therapeutic strategy targeting multiple disease states. , 2006, Current pharmaceutical design.

[21]  I. Donkor.  A survey of calpain inhibitors. , 2000, Current medicinal chemistry.

[22]  H. Mizuno,et al.  Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution. , 1993, The Journal of biological chemistry.

[23]  Christine Slingsby,et al.  The X-ray Crystal Structure of Human γS-crystallin C-terminal Domain* , 2002, The Journal of Biological Chemistry.

[24]  P. Davies,et al.  Calpastatin simultaneously binds four calpains with different kinetic constants , 2007, FEBS letters.

[25]  A. Abell,et al.  Synthesis, biological evaluation and molecular modelling of N-heterocyclic dipeptide aldehydes as selective calpain inhibitors. , 2008, Bioorganic & medicinal chemistry.

[26]  E. Defranchi,et al.  Association of Calpastatin with Inactive Calpain , 2006, Journal of Biological Chemistry.

[27]  R. Campbell,et al.  Calpain inhibition by alpha-ketoamide and cyclic hemiacetal inhibitors revealed by X-ray crystallography. , 2006, Biochemistry.

[28]  T. Shearer,et al.  Calpain may contribute to hereditary cataract formation in sheep. , 2005, Investigative ophthalmology & visual science.

[29]  J. Wiseman,et al.  Inhibition of the proteolysis of rat erythrocyte membrane proteins by a synthetic inhibitor of calpain. , 1988, Biochemical and biophysical research communications.

[30]  G. Duncan,et al.  Ion analyses of human cataractous lenses. , 1975, Experimental eye research.

[31]  A. Abell,et al.  Efficient Large-Scale Synthesis of CAT811, a Potent Calpain Inhibitor of Interest in the Treatment of Cataracts , 2009 .

[32]  G. Duncan,et al.  Calcium ionophore induced proteolysis and cataract: inhibition by cell permeable calpain antagonists. , 1996, Biochemical and biophysical research communications.

[33]  O. Srivastava,et al.  BetaB2-crystallin undergoes extensive truncation during aging in human lenses. , 2003, Biochemical and biophysical research communications.

[34]  E. Parker,et al.  Molecular modeling studies of peptide inhibitors highlight the importance of conformational prearrangement for inhibition of calpain. , 2010, Biochemistry.

[35]  I. Johnston,et al.  A newly classified vertebrate calpain protease, directly ancestral to CAPN1 and 2, episodically evolved a restricted physiological function in placental mammals. , 2010, Molecular biology and evolution.

[36]  Kalle Gehring,et al.  Concerted multi-pronged attack by calpastatin to occlude the catalytic cleft of heterodimeric calpains , 2008, Nature.

[37]  Z. Jia,et al.  A Ca2+ Switch Aligns the Active Site of Calpain , 2002, Cell.

[38]  D. Smith,et al.  The major in vivo modifications of the human water-insoluble lens crystallins are disulfide bonds, deamidation, methionine oxidation and backbone cleavage. , 2000, Experimental eye research.

[39]  W. Bode,et al.  Flexibility Analysis and Structure Comparison of Two Crystal Forms of Calcium-Free Human m-Calpain , 2002, Biological chemistry.

[40]  M. Maki,et al.  Amino-terminal conserved region in proteinase inhibitor domain of calpastatin potentiates its calpain inhibitory activity by interacting with calmodulin-like domain of the proteinase. , 1994, The Journal of biological chemistry.

[41]  B. Grigorenko,et al.  Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method , 2004 .

[42]  T. Shearer,et al.  Age-related changes in human lens crystallins identified by two-dimensional electrophoresis and mass spectrometry. , 1998, Experimental eye research.

[43]  S. Griffiths-Jones,et al.  Modulation of intrinsic phi,psi propensities of amino acids by neighbouring residues in the coil regions of protein structures: NMR analysis and dissection of a beta-hairpin peptide. , 1998, Journal of molecular biology.

[44]  R. Langridge,et al.  A simulation of the sulfur attack in catalytic pathway of papain using molecular mechanics and semiempirical quantum mechanics , 1990 .

[45]  W. Richards,et al.  Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: insights into the active site hydrogen-bonding network. , 2002, Journal of the American Chemical Society.

[46]  L. DeLucas,et al.  Crystal structure of calcium bound domain VI of calpain at 1.9 Å resolution and its role in enzyme assembly, regulation, and inhibitor binding , 1997, Nature Structural Biology.

[47]  T. Tsujinaka,et al.  Synthesis of a new cell penetrating calpain inhibitor (calpeptin). , 1988, Biochemical and biophysical research communications.

[48]  Robert Kiss,et al.  Local structural preferences of calpastatin, the intrinsically unstructured protein inhibitor of calpain. , 2008, Biochemistry.

[49]  Neer Asherie,et al.  High-resolution X-ray crystal structures of human gammaD crystallin (1.25 A) and the R58H mutant (1.15 A) associated with aculeiform cataract. , 2003, Journal of molecular biology.

[50]  R. F. Weaver,et al.  Molecular mode of action of a covalently inhibiting peptidomimetic on the human calpain protease core. , 2006, Biochemistry.

[51]  J. Morton,et al.  The involvement of calpains in opacification induced by Ca2+-overload in ovine lens culture. , 2008, Veterinary ophthalmology.

[52]  Terry Walsh,et al.  Countering cooperative effects in protease inhibitors using constrained beta-strand-mimicking templates in focused combinatorial libraries. , 2004, Journal of medicinal chemistry.

[53]  Jean B. Smith,et al.  Modifications of the Water-insoluble Human Lens α-Crystallins , 1996 .

[54]  Mika K Lindvall,et al.  Molecular modeling in cysteine protease inhibitor design. , 2002, Current pharmaceutical design.

[55]  M. Elder,et al.  Medical treatment of cataract , 2007, Clinical & experimental ophthalmology.

[56]  G. Lin,et al.  A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor. , 2003, Journal of molecular biology.

[57]  R. Payne,et al.  Peptidic aldehydes based on α- and β-amino acids: Synthesis, inhibition of m-calpain, and anti-cataract properties , 2004 .

[58]  N. Rawlings,et al.  Evolutionary Lines of Cysteine Peptidases , 2001, Biological chemistry.

[59]  A. Abell,et al.  Molecular modeling, synthesis, and biological evaluation of macrocyclic calpain inhibitors. , 2009, Angewandte Chemie.

[60]  E. Auerswald,et al.  Human -Calpain: Simple Isolation from Erythrocytes and Characterization of Autolysis Fragments , 2001 .

[61]  N. Katunuma,et al.  Inhibitory effect of di- and tripeptidyl aldehydes on calpains and cathepsins. , 1990, Journal of enzyme inhibition.

[62]  T. Shearer,et al.  Mass Measurements of C-terminally Truncated α-Crystallins from Two-dimensional Gels Identify Lp82 as a Major Endopeptidase in Rat Lens* , 2002, Molecular & Cellular Proteomics.

[63]  R. Campbell,et al.  Crystal structures of calpain-E64 and -leupeptin inhibitor complexes reveal mobile loops gating the active site. , 2004, Journal of molecular biology.

[64]  M. Maki,et al.  All four internally repetitive domains of pig calpastatin possess inhibitory activities against calpains I and II , 1987, FEBS letters.

[65]  Z. Jia,et al.  Calpain silencing by a reversible intrinsic mechanism , 2003, Nature Structural Biology.

[66]  R. Campbell,et al.  Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin , 2008, Nature.

[67]  A. Abell,et al.  Calpains: attractive targets for the development of synthetic inhibitors. , 2010, Current topics in medicinal chemistry.