Crystallographic determination of the structures of human α‐thrombin complexed with BMS‐186282 and BMS‐189090

• Published in: Protein science 1996-02, Vol.5 (2), p.221-228
• Main Authors: Malley, Mary F., Sack, John S., Tabernero, Lydia, Chang, Chiehying Y., Ohringer, Shari L., Roberts, Daniel G. M., Das, Jagabandhu
• Format: Article
• Language: English
• Subjects: Amino Acid Chloromethyl Ketones - pharmacology; Amino Acid Sequence; Binding Sites - drug effects; Chemical Phenomena; Chemistry, Physical; crystallography; Crystallography, X-Ray; Guanidines - chemistry; Guanidines - metabolism; Guanidines - pharmacology; human α‐thrombin‐inhibitor complexes; Humans; Models, Molecular; Molecular Sequence Data; Nipecotic Acids - chemistry; Nipecotic Acids - metabolism; Nipecotic Acids - pharmacology; Protein Binding; Protein Structure, Secondary; Serine - analogs & derivatives; Serine - chemistry; Serine - metabolism; Serine - pharmacology; structure‐based drug design; Thrombin - antagonists & inhibitors; Thrombin - chemistry; Thrombin - metabolism; Thrombin - pharmacology
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.5560050205

The crystallographic structures of the ternary complexes of human α‐thrombin with hirugen (a sulfated hirudin fragment) and the small‐molecule active site thrombin inhibitors BMS‐186282 and BMS‐189090 have been determined at 2.6 and 2.8 Å. In both cases, the inhibitors, which adopt very‐similar bound conformations, bind in an antiparallel β‐strand arrangement relative to the thrombin main chain in a manner like that reported for PPACK, D‐Phe‐Pro‐Arg‐CH2Cl. They do, however, exhibit differences in the binding of the alkyl guanidine moiety in the specificity pocket. Numerous hydrophilic and hydrophobic interactions serve to stabilize the inhibitors in the binding pocket. Although PPACK forms covalent bonds to both serine and the histidine of the catalytic triad of thrombin, neither BMS‐186282 nor BMS‐189090 bind covalently and only BMS‐186282 forms a hydrogen bond to the serine of the catalytic triad. Both inhibitors bind with high affinity (Ki = 79 nM and 3.6 nM, respectively) and are highly selective for thrombin over trypsin and other serine proteases.