Design and Synthesis of a Series of Potent and Orally Bioavailable Noncovalent Thrombin Inhibitors That Utilize Nonbasic Groups in the P1 Position

Abstract

As part of an ongoing effort to prepare therapeutically useful orally active thrombin inhibitors, we have synthesized a series of compounds that utilize nonbasic groups in the P1 position. The work is based on our previously reported lead structure, compound 1, which was discovered via a resin-based approach to varying P1. By minimizing the size and lipophilicity of the P3 group and by incorporating hydrogen-bonding groups on the N-terminus or on the 2-position of the P1 aromatic ring, we have prepared a number of derivatives in this series that exhibit subnanomolar enzyme potency combined with good in vivo antithrombotic and bioavailability profiles. The oxyacetic amide compound 14b exhibited the best overall profile of in vitro and in vivo activity, and crystallographic studies indicate a unique mode of binding in the thrombin active site.

Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study

“…[51] The two competing effects nearly cancel each other and the selectivi- [a] Experimental data given as K i values for all the complexes. [27,28] For direct comparison to calculated affinities, conversion to DG was estimated by DG = ÀRTlnK i . www.chemeurj.org ty of binding is thus dominated by the favorable van der Waals energy and nonpolar solvation free energy.…”

“…As such, many pharmaceutical companies have invested significant efforts to identify less basic and neutral mimics to try to improve the pharmacokinetic properties of these compounds. [25] In this study, molecular dynamics (MD) simulations followed by molecular mechanics generalized Born surface area (MM-GBSA) [26] analyses have been carried out to study the selectivity of two neutral and weakly basic P1 group inhibitors (177 [27] and CDA [28] ) with thrombin and trypsin. Both inhibitors exhibit excellent selectivity of thrombin versus trypsin despite the lack of a strong interaction with the specificity pocket.…”

“…Thus, the study would be advantageous to produce small-molecule scaffolds of neutral and weakly basic P1 groups with greater intrinsic specificity toward thrombin and against anti-targets such as trypsin. [27,28] The structures of the two inhibitors are shown in Scheme 1. Protons were added to the system by using the Leap module of AMBER9.…”

Small, noncovalent serine protease inhibitors

“…The bound structure of 29 showed that, compared to the cyclohexylamine of 22, the dichlorophenyl group is rotated in S1 with one of the chlorines sitting over the aromatic group of tyr-228. 71,72 The second chlorine points away from S1 towards bulk solvent without making contact with the enzyme and deletion of this second chlorine results in only a modest drop in potency.…”

“…In an effort to improve the efficacy without sacrificing oral bioavailability, and using a finding from prior P3 optimization studies, 69 the less lipophilic residue D-cyclohexylglycine was incorporated in the P3 position to give essentially equipotent compound 30. 72 The potency was then enhanced by filling the previously described lipophilic region bounded by the P1 substituent, the aliphatic portion of Glu-192 and the Cys-200/Cys-191 disulfide. This could be accomplished by appending the extra substituent either to the N terminus in the manner of compound 23, or to the 2-position of the P1 group via an ether link.…”