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The crystal structures of human α‐thrombin complexed with active site‐directed diamino benzo[ b ] thiophene derivatives: A binding mode for a structurally novel class of inhibitors
Author(s) -
Chirgadze N.Y.,
Sall D.J.,
Briggs S.L.,
Clawson D.K.,
Zhang M.,
Smith G.F.,
Schevitz R.W.
Publication year - 2000
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.9.1.29
Subject(s) - active site , chemistry , stereochemistry , discovery and development of direct thrombin inhibitors , thiophene , binding site , hydrogen bond , thrombin , enzyme , molecule , biochemistry , organic chemistry , biology , platelet , immunology
The crystal structures of four active site‐directed thrombin inhibitors, 1–4, in a complex with human α‐thrombin have been determined and refined at up to 2.0 Å resolution using X‐ray crystallography. These compounds belong to a structurally novel family of inhibitors based on a 2,3‐disubstituted benzo[ b ]thiophene structure. Compared to traditional active‐site directed inhibitors, the X‐ray crystal structures of these complexes reveal a novel binding mode. Unexpectedly, the lipophilic benzo[ b ]thiophene nucleus of the inhibitor appears to bind in the S 1 specificity pocket. At the same time, the basic amine of the C‐3 side chain of the inhibitor interacts with the mostly hydrophobic proximal, S 2 , and distal, S 3 , binding sites. The second, basic amine side chain at C‐2 was found to point away from the active site, occupying a location between the S 1 and S' 1 sites. Together, the aromatic rings of the C‐2 and C‐3 side chains sandwich the indole ring of Trp60D contained in the thrombin S 2 insertion loop defined by the sequence “Tyr‐Pro‐Pro‐Trp.” [The thrombin residue numbering used in this study is equivalent to that reported for chymotrypsinogen (Hartley BS, Shotton DM, 1971, The enzymes , vol. 3. New York: Academic Press. pp 323–373).] In contrast to the binding mode of more classical thrombin inhibitors (D‐Phe‐Pro‐Arg‐H, NAPAP, Argatroban), this novel class of benzo[ b ]thiophene derivatives does not engage in hydrogen bond formation with Gly216 of the thrombin active site. A detailed analysis of the three‐dimensional structures not only provides a clearer understanding of the interaction of these agents with thrombin, but forms a foundation for rational structure‐based drug design. The use of the data from this study has led to the design of derivatives that are up to 2,900‐fold more potent than the screening hit 1.