Bound Structures of Novel P3−P1‘ β-Strand Mimetic Inhibitors of Thrombin

Charles, R. St; Matthews, John H.; Zhang, E; Tulinsky, A.

doi:10.1021/jm980052n

Cited by 47 publications

(44 citation statements)

References 38 publications

(95 reference statements)

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“…A d -Thr N - His57 NE2 interaction is observed as well, resembling that found in complexes of thrombin with active site inhibitors with benzothiazole [40] and ketothiazole [41] or with bivalent inhibitors with α-keto-amide [39] or 2-(4-aminobutyl)-hydrazyde (Abh) [37] at the P1′ position. Furthermore, d -Thr makes hydrophobic contacts with Trp60D, His57 and with the Cys42-Cys58 disulfide bond.…”

Section: Resultssupporting

confidence: 67%

Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors

et al. 2012

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The tremendous social and economic impact of thrombotic disorders, together with the considerable risks associated to the currently available therapies, prompt for the development of more efficient and safer anticoagulants. Novel peptide-based thrombin inhibitors were identified using in silico structure-based design and further validated in vitro. The best candidate compounds contained both l- and d-amino acids, with the general sequence d-Phe(P3)-Pro(P2)-d-Arg(P1)-P1′-CONH2. The P1′ position was scanned with l- and d-isomers of natural or unnatural amino acids, covering the major chemical classes. The most potent non-covalent and proteolysis-resistant inhibitors contain small hydrophobic or polar amino acids (Gly, Ala, Ser, Cys, Thr) at the P1′ position. The lead tetrapeptide, d-Phe-Pro-d-Arg-d-Thr-CONH2, competitively inhibits α-thrombin's cleavage of the S2238 chromogenic substrate with a Ki of 0.92 µM. In order to understand the molecular details of their inhibitory action, the three-dimensional structure of three peptides (with P1′ l-isoleucine (fPrI), l-cysteine (fPrC) or d-threonine (fPrt)) in complex with human α-thrombin were determined by X-ray crystallography. All the inhibitors bind in a substrate-like orientation to the active site of the enzyme. The contacts established between the d-Arg residue in position P1 and thrombin are similar to those observed for the l-isomer in other substrates and inhibitors. However, fPrC and fPrt disrupt the active site His57-Ser195 hydrogen bond, while the combination of a P1 d-Arg and a bulkier P1′ residue in fPrI induce an unfavorable geometry for the nucleophilic attack of the scissile bond by the catalytic serine. The experimental models explain the observed relative potency of the inhibitors, as well as their stability to proteolysis. Moreover, the newly identified direct thrombin inhibitors provide a novel pharmacophore platform for developing antithrombotic agents by exploring the conformational constrains imposed by the d-stereochemistry of the residues at positions P1 and P1′.

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Section: Resultssupporting

confidence: 67%

Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors

et al. 2012

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“…As is evident from their 3D structures in a ribbon model (Fig. 7, A and B), plasmin and thrombin share two ␣-helixes on the left side, four ␤-strands at the bottom, and a homologous active site at the center that consists of the identical catalytic triad residues (H622, D665, and S760 for plasmin; H406, D462, and S568 for thrombin) (21,22). Moreover, the space-filling models of both molecules show that many amino acid residues in the homologous regions are on the surface (Fig.…”

Section: Discussionmentioning

confidence: 93%

Identification of Anti-Plasmin Antibodies in the Antiphospholipid Syndrome That Inhibit Degradation of Fibrin

Yang

Hwang

Wang³

et al. 2004

The Journal of Immunology

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The combined presence of anti-phospholipid Ab (aPL) and thrombosis is recognized as the antiphospholipid syndrome (APS). The aPL represent a heterogeneous group of Ab that recognize various phospholipids (PL), PL-binding plasma proteins, and/or PL-protein complexes. Recently, we found the presence of antithrombin Ab in some APS patients and that some of these anti-thrombin Ab could inhibit thrombin inactivation by antithrombin. Considering that thrombin is homologous to plasmin, which dissolves fibrin, we hypothesize that some APS patients may have Ab that react with plasmin, and that some anti-plasmin Ab may interfere with the plasmin-mediated lysis of fibrin clots. To test this hypothesis, we searched for anti-plasmin Ab in APS patients and then studied those found for their effects on the fibrinolytic pathway. The results revealed that seven of 25 (28%) APS patients have IgG anti-plasmin Ab (using the mean OD plus 3 SD of 20 normal controls as the cutoff) and that six of six patient-derived IgG anti–thrombin mAb bind to plasmin with relative Kd values ranging from 5.6 × 10−8 to 1 × 10−6 M. These Kd values probably represent affinities in the higher ranges known for human IgG autoantibodies against protein autoantigens. Of these mAb, one could reduce the plasmin-mediated lysis of fibrin clots. These findings suggest that plasmin may be an important driving Ag for some aPL B cells in APS patients, and that the induced anti-plasmin Ab may act either directly, by binding to plasmin and inhibiting its fibrinolytic activity, or indirectly, by cross-reacting with other homologous proteins in the coagulation cascade to promote thrombosis.

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“…The Gap program uses a scoring matrix with matches scored as 1.5 and mismatches scored according to the evolutionary distance between the amino acids. The 3-D structures of thrombin and APC in the ribbon and space-filling models were generated based on the coordinates of human thrombin (1A5G) (18) and human APC (1AUT) (19), using RasMol software (version 2.7; Bernstein & Sons, Bellport, NY).…”

Section: Methodsmentioning

confidence: 99%

“…As can be seen in their 3-dimensional (3-D) structures in a ribbon model (Figures 2A and B), thrombin and APC share three ␣-helices on the left side, two ␤-sheets at the bottom side, and a homologous active site at the center that consists of the identical catalytic triad residues (H406, D462, S568 for thrombin and H253, D300, S405 for APC) (18,19). Moreover, the space-filling models of both molecules show that most of the amino acid residues in the highly homologous regions are on the surface (Figures 2C and D).…”

mentioning

confidence: 99%

A thrombin–cross‐reactive anticardiolipin antibody binds to and inhibits the anticoagulant function of activated protein C

Hwang¹,

Yang²,

Wang³

et al. 2003

Arthritis & Rheumatism

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ObjectiveTo test the hypotheses that some thrombin‐reactive anticardiolipin antibodies (aCL) may bind to protein C (PC) and/or activated PC (APC), and that some of the PC‐ and APC‐reactive aCL may inhibit PC activation and/or the function of APC.MethodsWe studied the reactivity of patient‐derived monoclonal aCL with PC and APC. We examined the effects of the reactive antibodies on PC activation and on the activity of APC in plasma coagulation.ResultsFive of 5 patient‐derived, thrombin‐reactive monoclonal aCL bound to PC and APC. In addition, 1 patient‐derived monoclonal antiprothrombin antibody (APT) that displayed aCL activity and reacted with thrombin also bound to PC and APC. Of these 6 PC‐ and APC‐reactive aCL/APT, all failed to inhibit PC activation, but 1 (CL15) shortened the plasma coagulation time in the presence of exogenous APC and thus inhibited the anticoagulant function of APC.ConclusionMost of the thrombin‐reactive aCL in patients with antiphospholipid syndrome may bind to PC and APC. Of the APC‐reactive aCL, some (like CL15) may inhibit the anticoagulant function of APC and are thus likely to be prothrombotic in the host.

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Bound Structures of Novel P3−P1‘ β-Strand Mimetic Inhibitors of Thrombin

Cited by 47 publications

References 38 publications

Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors

Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors

Identification of Anti-Plasmin Antibodies in the Antiphospholipid Syndrome That Inhibit Degradation of Fibrin

A thrombin–cross‐reactive anticardiolipin antibody binds to and inhibits the anticoagulant function of activated protein C

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