Enzyme Binding Selectivity Prediction: α-Thrombin vs Trypsin Inhibition

Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis

The high incidence of thrombembolic diseases justifies the development of new antithrombotics. The search for a direct inhibitor has resulted in the synthesis of a considerable number of low molecular weight molecules that inhibit human alpha-thrombin potently. However, efforts to develop an orally active drug remain in progress as the most active inhibitors with a highly basic P1 moiety exhibit an unsatisfactory bioavailability profile. In our previous work we solved several X-ray structures of human alpha-thrombin in complexes with (1) novel bicyclic arginine mimetics attached to the glycylproline amide and pyridinone acetamide scaffold and (2) inhibitors with a novel aza scaffold and with charged or neutral P1 moieties. In the present contribution, we correlate the structures of the complex between these inhibitors and the protein with the calculated free energy of binding. The energy of solvation was calculated using the Poisson-Boltzmann approach. In particular, the requirements for successful recognition of an inhibitor at the protein's active site pocket S1 are discussed.

Optimization algorithms and natural computing in drug discovery

Recent efforts in structural biology have lead to considerable growth in the number of structures available which are potential drug targets. Considerable progress in docking algorithms has enabled in silico screening as an attractive alternative to traditional screening for drug leads and optimization, because in vitro high-throughput screening of compounds is costly and relatively inefficient. In molecular modeling one is often confronted with hard problems, such as highly complicated energy landscapes in many dimensions and a combinatorial explosion of the number of possible solutions. Recently, however, several algorithms based on situations in nature have appeared and in this review we illustrate their strengths and weaknesses.: