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* Residue conservation analysis
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Enzyme class:
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Chains L, H:
E.C.3.4.21.5
- thrombin.
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Reaction:
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Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
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DOI no:
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Proc Natl Acad Sci U S A
90:8048-8052
(1993)
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PubMed id:
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Molecular basis for the inhibition of human alpha-thrombin by the macrocyclic peptide cyclotheonamide A.
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B.E.Maryanoff,
X.Qiu,
K.P.Padmanabhan,
A.Tulinsky,
H.R.Almond,
P.Andrade-Gordon,
M.N.Greco,
J.A.Kauffman,
K.C.Nicolaou,
A.Liu.
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ABSTRACT
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The macrocyclic peptide cyclotheonamide A (CtA), isolated from the marine sponge
Theonella sp., represents an unusual class of serine protease inhibitor. A
complex of this inhibitor with human alpha-thrombin, a protease central to the
bioregulation of thrombosis and hemostasis, was studied by x-ray
crystallography. This work (2.3-A resolution) confirms the structure of CtA and
reveals intimate details about its molecular recognition within the enzyme
active site. Interactions due to the "Pro-Arg motif" (Arg occupancy of
the S1 specificity pocket; formation of a hydrogen-bonded two-strand
antiparallel beta-sheet with Ser214-Gly216) and the alpha-keto amide group of
CtA are primarily responsible for binding to thrombin, with the alpha-keto amide
serving as a transition-state analogue. A special interaction with the
"insertion loop" of thrombin (Tyr60A-Thr60I) is manifested through
engagement of the hydroxyphenyl group of CtA with Trp60D as part of an
"aromatic stacking chain." Biochemical inhibition data (Ki values at
37 degrees C) were obtained for CtA with thrombin and a diverse collection of
serine proteases. Thus, CtA is just a moderate inhibitor of human alpha-thrombin
(Ki = 0.18 microM) but a potent inhibitor of trypsin (Ki = 0.023 microM) and
streptokinase (Ki = 0.035 microM). The relative lack of potency of CtA as a
thrombin inhibitor is discussed with respect to certain structural features of
the enzyme complex. We also report the total synthesis of CtA, by a convergent
fragment-condensation approach, to serve the preparation of
cyclotheonamide analogues for structure-function studies.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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G.G.Xu,
and
F.A.Etzkorn
(2010).
Convergent synthesis of alpha-ketoamide inhibitors of Pin1.
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Org Lett,
12,
696-699.
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N.Schaschke,
and
C.P.Sommerhoff
(2010).
Upgrading a Natural Product: Inhibition of Human beta-Tryptase by Cyclotheonamide Analogues.
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ChemMedChem,
5,
367-370.
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B.E.Maryanoff,
D.F.McComsey,
M.J.Costanzo,
S.C.Yabut,
T.Lu,
M.R.Player,
E.C.Giardino,
and
B.P.Damiano
(2006).
Exploration of potential prodrugs of RWJ-445167, an oxyguanidine-based dual inhibitor of thrombin and factor Xa.
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Chem Biol Drug Des,
68,
29-36.
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S.Butenas,
T.Orfeo,
M.Kalafatis,
and
K.G.Mann
(2006).
Peptidomimetic inhibitors for activated protein C: implications for hemophilia management.
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J Thromb Haemost,
4,
2411-2416.
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S.Cotesta,
and
M.Stahl
(2006).
The environment of amide groups in protein-ligand complexes: H-bonds and beyond.
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J Mol Model,
12,
436-444.
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D.Sipkema,
M.C.Franssen,
R.Osinga,
J.Tramper,
and
R.H.Wijffels
(2005).
Marine sponges as pharmacy.
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Mar Biotechnol (NY),
7,
142-162.
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E.Toyota,
H.Sekizaki,
Y.U.Takahashi,
K.Itoh,
and
K.Tanizawa
(2005).
Amidino-containing Schiff base copper(II) and iron(III) chelates as a thrombin inhibitor.
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Chem Pharm Bull (Tokyo),
53,
22-26.
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A.Lombardi,
G.De Simone,
S.Galdiero,
N.Staiano,
F.Nastri,
and
V.Pavone
(1999).
From natural to synthetic multisite thrombin inhibitors.
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Biopolymers,
51,
19-39.
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G.De Simone,
A.Lombardi,
S.Galdiero,
F.Nastri,
R.Della Morte,
N.Staiano,
C.Pedone,
M.Bolognesi,
and
V.Pavone
(1998).
Hirunorms are true hirudin mimetics. The crystal structure of human alpha-thrombin-hirunorm V complex.
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Protein Sci,
7,
243-253.
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PDB code:
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H.Kubinyi
(1998).
[Molecular similarity. 2. The structural basis of drug design]
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Pharm Unserer Zeit,
27,
158-172.
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S.Tada,
and
J.J.Blow
(1998).
The replication licensing system.
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Biol Chem,
379,
941-949.
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A.Caflisch
(1996).
Computational combinatorial ligand design: application to human alpha-thrombin.
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J Comput Aided Mol Des,
10,
372-396.
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P.D.Grootenhuis,
and
M.Karplus
(1996).
Functionality map analysis of the active site cleft of human thrombin.
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J Comput Aided Mol Des,
10,
1.
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R.Krishnan,
A.Tulinsky,
G.P.Vlasuk,
D.Pearson,
P.Vallar,
P.Bergum,
T.K.Brunck,
and
W.C.Ripka
(1996).
Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic.
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Protein Sci,
5,
422-433.
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PDB code:
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J.Vijayalakshmi,
K.P.Padmanabhan,
K.G.Mann,
and
A.Tulinsky
(1994).
The isomorphous structures of prethrombin2, hirugen-, and PPACK-thrombin: changes accompanying activation and exosite binding to thrombin.
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Protein Sci,
3,
2254-2271.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
