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PDBsum entry 1gj6
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Engineering inhibitors highly selective for the s1 sites of ser190 trypsin-Like serine protease drug targets.
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Authors
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B.A.Katz,
P.A.Sprengeler,
C.Luong,
E.Verner,
K.Elrod,
M.Kirtley,
J.Janc,
J.R.Spencer,
J.G.Breitenbucher,
H.Hui,
D.Mcgee,
D.Allen,
A.Martelli,
R.L.Mackman.
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Ref.
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Chem Biol, 2001,
8,
1107-1121.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Involved or implicated in a wide spectrum of diseases, trypsin-like
serine proteases comprise well studied drug targets and anti-targets that can be
subdivided into two major classes. In one class there is a serine at position
190 at the S1 site, as in urokinase type plasminogen activator (urokinase or
uPA) and factor VIIa, and in the other there is an alanine at 190, as in tissue
type plasminogen activator (tPA) and factor Xa. A hydrogen bond unique to Ser190
protease-arylamidine complexes between O gamma(Ser190) and the inhibitor amidine
confers an intrinsic preference for such inhibitors toward Ser190 proteases over
Ala190 counterparts. RESULTS: Based on the structural differences between the S1
sites of Ser190 and Ala190 protease-arylamidine complexes, we amplified the
selectivity of amidine inhibitors toward uPA and against tPA, by factors as high
as 220-fold, by incorporating a halo group ortho to the amidine of a lead
inhibitor scaffold. Comparison of K(i) values of such halo-substituted and
parent inhibitors toward a panel of Ser190 and Ala190 proteases demonstrates
pronounced selectivity of the halo analogs for Ser190 proteases over Ala190
counterparts. Crystal structures of Ser190 proteases, uPA and trypsin, and of an
Ala190 counterpart, thrombin, bound by a set of ortho (halo, amidino) aryl
inhibitors and of non-halo parents reveal the structural basis of the exquisite
selectivity and validate the design principle. CONCLUSIONS: Remarkable
selectivity enhancements of exceptionally small inhibitors are achieved toward
the uPA target over the highly similar tPA anti-target through a single atom
substitution on an otherwise relatively non-selective scaffold. Overall
selectivities for uPA over tPA as high as 980-fold at physiological pH were
realized. The increase in selectivity results from the displacement of a single
bound water molecule common to the S1 site of both the uPA target and the tPA
anti-target because of the ensuing deficit in hydrogen bonding of the
arylamidine inhibitor when bound in the Ala190 protease anti-target.
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Figure 6.
Fig. 6. a: Structure and (2|F[o]|−|F[c]|), α[c] map
for uPA–APC-11092, 1.80 Å resolution. The long
N1–Oδ2[Asp189] and N2–Oδ2[Asp189] interactions (3.17
Å and 3.40 Å, respectively, at pH 6.5) are shown in
yellow and transparent light yellow, respectively. b: Structure
and (2|F[o]|−|F[c]|), α[c] map for uPA–APC-10950, 1.64
Å resolution. The H[2]O1[S1]–F hydrogen bond (2.76
Å) is formed at the expense of the H[2]O1[S1]–O[Trp215]
interaction, the length of which increases from 3.07 Å in
uPA–APC-8696 to 3.52 Å in uPA–APC-10950 (Table 3c).
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Figure 7.
Fig. 7. a: Structure and (2|F[o]|−|F[c]|), α[c] map of
trypsin–APC-11922, 1.50 Å resolution. For the major
inhibitor conformer (opaque sticks) there is a hydrogen bond
between the inhibitor phenol (O6′) and Nε2[His57], and a
short O6′–Oγ[Ser195] hydrogen bond. b: Structure and
(2|F[o]|−|F[c]|), α[c] map of uPA–APC-11421, 1.75 Å
resolution. In this and all other uPA complexes of the APC-7136
analogs in Fig. 2b, the phenol hydroxyl is at or near the
oxyanion hole, receiving hydrogen bonds from N[Gly193] and from
the inhibitor NH amide group. In many trypsin and thrombin
complexes the inhibitor is discretely disordered between the two
binding modes in (a) and (b).
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The above figures are
reprinted
by permission from Cell Press:
Chem Biol
(2001,
8,
1107-1121)
copyright 2001.
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