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Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design

  • Perspectives
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Perspectives in Drug Discovery and Design

Summary

The wealth of structural information now available on thrombin, its precursors, its substrates and its inhibitors allows a rationalization of its many roles. α-Thrombin exhibits an unusually deep and narrow active-site cleft, formed by loop insertions that are characteristic of thrombin. This canyon structure is one of the prime causes for the narrow specificity of thrombin. As a result of the conjunction of amino acid residues with similar properties such as charge or hydrophobicity, thrombin can be divided up into a number of functional regions. The apposition of the active site to a hydrophobic pocket (the apolar binding site) on one side and a basic patch (the fibrinogen recognition exosite) on the other allows for a fine-tuning of enzymatic activity, as seen for fibrinogen. These two sites are also optimally used by the leech-derived inhibitor hirudin, allowing the very tight binding observed; thrombin inhibition is effected by blocking access to the active site. Interactions with antithrombin III are tightened with the help of heparin, which binds to a second basic site (the heparin binding site). Non-proteolytic cellular properties are attributed to the rigid insertion loop at Tyr60A. The observed rigidity of the thrombin molecule in its complexes makes thrombin ideal for structure-based drug design. Thrombin can be inhibited either at the active site or at the fibrinogen recognition exosite, or both. Structural information shows that binding at the former is enhanced by good fit of aromatic moieties to the aryl and S2 binding sites (the apolar binding site). Binding at the fibrinogen recognition exosite is facilitated by negatively charged groups. The unpredictable nature of inhibitor binding underlines the importance of experimental monitoring of structures of thrombin inhibitors in the drug design process.

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    Milton T. Stubbs & Wolfram Bode

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Stubbs, M.T., Bode, W. Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design. Perspectives in Drug Discovery and Design 1, 431–452 (1994). https://doi.org/10.1007/BF02171858

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