Studies of Benzothiophene Template as Potent Factor IXa (FIXa) Inhibitors in Thrombosis

Abstract

FIXa is a serine protease enzyme involved in the intrinsic pathway of the coagulation cascade. The upstream intervention of the coagulation cascade in selectively inhibiting FIXa would leave hemostasis intact via the extrinsic pathway, leading to an optimum combination of efficacy and safety with low incidence of bleeding. We have identified 2-amindinobenzothiophene template as a lead scaffold for FIXa inhibiton based on its homology with urokinase plasminogen activator (uPA). Subsequent SAR work on the template revealed a number of highly potent FIXa inhibitors, though with moderate selectivity against FXa. X-ray study with one of the analogues demonstrated active site binding interaction with the induced opening of the S1 beta pocket and a secondary binding at the S2-S4 sites, which is in direct contrast with the previous finding.

Investigation on the binding mode of benzothiophene analogues as potent factor IXa (FIXa) inhibitors in thrombosis by CoMFA, docking and molecular dynamic studies

“…These H-bonds at the P1 position could be found in all these benzothiophene analogues, which may be one classical characteristics for almost all FIXa inhibitors (including not only the benzothiophene-based ones) with an amidine tail in the P1 position. This investigation is consistent with the previous reports 1,11,12 and the X-ray result (PDB ID: 3LC5), and recent studies have demonstrated that in the absence of the amidine, for any of the serine proteases, they are completely lack of potency due to the loss of key interactions with Asp189 in the S1 pocket 8 . In P4 region, two big blue-coloured regions exist suggesting the possibility of increasing the potency by an introduction of electropositive substituent at the region.…”

“…Consequently, at the initiation stage of the cascade, the upstream inhibition of FIXa would represent a wonderful method for the development of anticoagulants with good selectivity and safety. Recently, several classes of compounds, such as 5-amidinoindoles 1 , pyrazole analogues 8,9 , 5-amidinobenzo[b]thiophenes 10 , benzothiophenes 11,12 and so on, have been reported as FIXa inhibitors. Among them, the benzothiophenes, designed on the basis of FIXa X-ray crystallography, illustrate high potential and selectivity for FIXa.…”

“…A diverse dataset of 84 benzothiophene analogues with the experimental values for the K i of the FIXa inhibitors were taken from literatures 11,12 that are published by the same research group. The activity of all the molecules was measured by the same assay on a recombinant form of human factor IX, which was prepared to overcome potential problems with the use of ethylene glycol in a factor IXa inhibition assay 11 .…”

“…The activity of all the molecules was measured by the same assay on a recombinant form of human factor IX, which was prepared to overcome potential problems with the use of ethylene glycol in a factor IXa inhibition assay 11 . Here, the converted molar pK i (−logK i ) values, ranging from 4.57 to 8.70 moles, were used as the dependent variables in the QSAR regression analysis to improve the normal distribution of the experimental data points.…”

FIXing Factor VIII inhibitors

“…1 A FIX protein designated FIX-ITV that contained 3 mutations (V181I, K265T, and I383V; see figure based on the wild-type FIX structure 6 ). FIX-ITV was demonstrated to promote coagulation in vitro in an aPTT assay when present at wild-type FIX levels in the absence of FVIII at ϳ 16% of the activity found when normal levels of wild-type FIX were present with normal levels of wild-type FVIII.…”