title: A double-headed cathepsin B inhibitor devoid of warhead.
abstract: Most synthetic inhibitors of peptidases have been targeted to the active site for inhibiting catalysis through reversible competition with the substrate or by covalent modification of catalytic groups. Cathepsin B is unique among the cysteine peptidase for the presence of a flexible segment, known as the occluding loop, which can block the primed subsites of the substrate binding cleft. With the occluding loop in the open conformation cathepsin B acts as an endopeptidase, and it acts as an exopeptidase when the loop is closed. We have targeted the occluding loop of human cathepsin B at its surface, outside the catalytic center, using a high-throughput docking procedure. The aim was to identify inhibitors that would interact with the occluding loop thereby modulating enzyme activity without the help of chemical warheads against catalytic residues. From a large library of compounds, the in silico approach identified [2-[2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethylamino]-2-oxoethyl] 2-(furan-2-carbonylamino) acetate, which fulfills the working hypothesis. This molecule possesses two distinct binding moieties and behaves as a reversible, double-headed competitive inhibitor of cathepsin B by excluding synthetic and protein substrates from the active center. The kinetic mechanism of inhibition suggests that the occluding loop is stabilized in its closed conformation, mainly by hydrogen bonds with the inhibitor, thus decreasing endoproteolytic activity of the enzyme. Furthermore, the dioxothiazolidine head of the compound sterically hinders binding of the C-terminal residue of substrates resulting in inhibition of the exopeptidase activity of cathepsin B in a physiopathologically relevant pH range.
authors.affiliation: Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
authors.forename: Patricia
authors.initials: P
authors.lastname: Schenker
authors.forename: Pietro
authors.initials: P
authors.lastname: Alfarano
authors.forename: Peter
authors.initials: P
authors.lastname: Kolb
authors.forename: Amedeo
authors.initials: A
authors.lastname: Caflisch
authors.forename: Antonio
authors.initials: A
authors.lastname: Baici
mesh_terms: D000595:Amino Acid Sequence; D001667:Binding, Competitive; D002401:Cathepsin B / Q000037:antagonists & inhibitors* / Q000378:metabolism*; D003198:Computer Simulation; D007700:Kinetics; D008969:Molecular Sequence Data; D019151:Peptide Library; D011480:Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D011485:Protein Binding; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D053778:Thiazolidines / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*
chemical_list: C534988:(2-(2-(2,4-dioxo-1,3-thiazolidin-3-yl)ethylamino)-2-oxoethyl) 2-(furan-2-carbonylamino)acetate; D019151:Peptide Library; D011480:Protease Inhibitors; D053778:Thiazolidines; D002401:Cathepsin B
references.citation: EMBO J. 1991 Sep;10(9):2321-30
references.pmid: 1868826
references.citation: Biochem J. 1980 Jul 1;189(1):17-25
references.pmid: 7458901
references.citation: Biochem J. 1983 Aug 1;213(2):467-71
references.pmid: 6351842
references.citation: Biol Chem Hoppe Seyler. 1988 May;369 Suppl:257-61
references.pmid: 3264507
references.citation: J Biol Chem. 1986 Jul 15;261(20):9375-81
references.pmid: 3522589
references.citation: Anal Biochem. 1973 Jun;53(2):484-90
references.pmid: 4716383
references.citation: J Biol Chem. 2000 Mar 17;275(11):8154-60
references.pmid: 10713138
references.citation: J Med Chem. 2005 Aug 11;48(16):5108-11
references.pmid: 16078830
references.citation: Biol Chem. 2003 Jul;384(7):1007-18
references.pmid: 12956417
references.citation: J Comput Chem. 2004 Feb;25(3):412-22
references.pmid: 14696075
references.citation: Biochemistry. 1999 Apr 20;38(16):5017-23
references.pmid: 10213604
references.citation: Biochem J. 1978 Jun 1;171(3):759-65
references.pmid: 666735
references.citation: Biol Chem. 2006 Aug;387(8):1017-21
references.pmid: 16895470
references.citation: Biol Chem. 1998 Aug-Sep;379(8-9):1007-18
references.pmid: 9792432
references.citation: Clin Cancer Res. 2005 May 1;11(9):3155-62
references.pmid: 15867207
references.citation: Anal Biochem. 2005 May 1;340(1):1-13
references.pmid: 15802124
references.citation: J Biol Chem. 1997 Jan 10;272(2):1197-202
references.pmid: 8995421
references.citation: J Am Chem Soc. 2006 Apr 26;128(16):5436-43
references.pmid: 16620115
references.citation: Eur J Biochem. 1995 Apr 15;229(2):533-9
references.pmid: 7744077
references.citation: Biochem J. 2002 Feb 1;361(Pt 3):613-9
references.pmid: 11802791
references.citation: Drug Discov Today. 2006 Jul;11(13-14):607-15
references.pmid: 16793529
references.citation: FEBS Lett. 2000 Dec 29;487(2):156-60
references.pmid: 11150500
references.citation: Biochemistry. 1997 Oct 14;36(41):12608-15
references.pmid: 9376367
references.citation: FEBS Lett. 1997 Dec 15;419(2-3):231-4
references.pmid: 9428640
references.citation: Proteins. 1999 Oct 1;37(1):88-105
references.pmid: 10451553
references.citation: Biochem J. 1980 Jun 1;187(3):909-12
references.pmid: 6897924
references.citation: Nat Rev Cancer. 2006 Oct;6(10):764-75
references.pmid: 16990854
references.citation: J Biol Chem. 2004 Sep 24;279(39):41012-7
references.pmid: 15262981
references.citation: FEBS Lett. 1993 Jun 21;324(3):325-30
references.pmid: 8405375
references.citation: Biochem J. 1996 Aug 1;317 ( Pt 3):901-5
references.pmid: 8760380
references.citation: J Chem Inf Model. 2005 Jan-Feb;45(1):177-82
references.pmid: 15667143
references.citation: Blood. 1984 Jan;63(1):88-95
references.pmid: 6418236
references.citation: Bioorg Chem. 2002 Aug;30(4):264-75
references.pmid: 12392705
references.citation: J Med Chem. 2008 Mar 13;51(5):1179-88
references.pmid: 18271520
references.citation: Biol Chem. 2001 Sep;382(9):1365-72
references.pmid: 11688719
references.citation: Curr Med Chem. 2006;13(19):2309-27
references.pmid: 16918357
references.citation: Ann Rheum Dis. 1995 Apr;54(4):289-97
references.pmid: 7763107
references.citation: Cancer Res. 2006 Jul 1;66(13):6699-707
references.pmid: 16818644
references.citation: Biol Chem. 2003 Jun;384(6):845-54
references.pmid: 12887051
references.citation: Biochem J. 1998 Nov 1;335 ( Pt 3):491-4
references.pmid: 9794785
references.citation: Biochim Biophys Acta. 1965 Jul 29;105(1):193-5
references.pmid: 4221326
references.citation: FEBS Lett. 1991 Mar 25;280(2):307-10
references.pmid: 2013328
references.citation: FEBS Lett. 1996 Apr 22;384(3):211-4
references.pmid: 8617355
references.citation: J Clin Invest. 2003 Jun;111(11):1733-45
references.pmid: 12782676
references.citation: FEBS Lett. 1998 Jan 23;422(1):61-4
references.pmid: 9475170
references.citation: Biopolymers. 1999;51(1):99-107
references.pmid: 10380357
references.citation: Anal Biochem. 2007 Dec 1;371(1):43-51
references.pmid: 17706587
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D160-4
references.pmid: 14681384
references.citation: Anal Biochem. 2004 Dec 15;335(2):244-52
references.pmid: 15556563
references.citation: Eur J Biochem. 1981 Sep;119(1):9-14
references.pmid: 7341250
references.citation: Biochem J. 1993 Sep 15;294 ( Pt 3):923-7
references.pmid: 8379946
references.citation: Histochem Cell Biol. 2003 Feb;119(2):93-101
references.pmid: 12610728
references.citation: Ann Rheum Dis. 1995 Apr;54(4):281-8
references.pmid: 7763106
references.citation: J Med Chem. 2006 Dec 14;49(25):7384-92
references.pmid: 17149868
references.citation: J Biol Chem. 2002 Jun 14;277(24):21389-96
references.pmid: 11932257
references.citation: Biochem Biophys Res Commun. 1967 Apr 20;27(2):157-62
references.pmid: 6035483
references.citation: Chem Rev. 1997 Feb 5;97(1):133-172
references.pmid: 11848867