Potent direct inhibitors of factor Xa based on the tetrahydroisoquinoline scaffold

Abstract

Direct inhibition of coagulation factor Xa (FXa) carries significant promise for developing effective and safe anticoagulants. Although a large number of FXa inhibitors have been studied, each can be classified as either possessing a highly flexible or a rigid core scaffold. We reasoned that an intermediate level of flexibility will provide high selectivity for FXa considering that its active site is less constrained in comparison to thrombin and more constrained as compared to trypsin. We studied several core scaffolds including 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid for direct FXa inhibition. Using a genetic algorithm-based docking and scoring approach, a promising candidate 23 was identified, synthesized, and found to inhibit FXa with a Ki of 28 μM. Optimization of derivative 23 resulted in the design of a potent dicarboxamide 47, which displayed a Ki of 135 nM. Dicarboxamide 47 displayed at least 1852-fold selectivity for FXa inhibition over other coagulation enzymes and doubled PT and aPTT of human plasma at 17.1 μM and 20.2 μM, respectively, which are comparable to those of clinically relevant agents. Dicarboxamide 47 is expected to serve as an excellent lead for further anticoagulant discovery.

Plasmin Regulation through Allosteric, Sulfated, Small Molecules

“…New NSGMs synthesized for the first time included 10 sulfated chalcones (1-10), six sulfated bis-quinazolinones homodimers (42)(43)(44)(45)(46)(47), four sulfated flavonoid-quinazolinone heterodimers (31)(32)(33)(34), and eight sulfated bis-flavonoid homodimers (48-55). The synthesis of the new NSGMs is described in detail in Supplementary Information (Schemes S1-S6).…”

“…Direct inhibition of thrombin and factor Xa by 31, 32, 52, and 54 was measured using a chromogenic substrate hydrolysis assay on a microplate reader (FlexStation III, Molecular Devices), as reported earlier [43]. Briefly, to each well of a 96-well microplate containing 185 μL of 20-50 mM Tris-HCl buffer, pH 7.4, containing 100-150 mM NaCl, 0.1% PEG8000 and 0.02% Tween80 at either 25 °C (thrombin) or 37 °C (factor Xa) was added 5 μL of 10-20 mM inhibitor (or vehicle) and 5 μL of the enzyme.…”

“…The monomeric scaffolds included chalcones (compounds 1-10), flavonoids (11)(12)(13)(14)(15)(16) [30][31][32], sucrose octasulfate (17) [40], quinazolinones (18 and 19) [37], and tetrahydro-isoquinolines (20)(21)(22)(23)(24)(25)(26)(27) [36], whereas the dimeric scaffolds comprised flavonoid-quinazolinone heterodimers (28)(29)(30)(31)(32)(33)(34) [37], bis-quinazolinones homodimers (35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47) [37], and bis-flavonoid homodimers (48-55). In addition to the inherent diversity of the scaffolds in this library, NSGMs also differed in the number (1 to 8) and orientation of the sulfate groups.…”

A Novel Fragment Recommendation Workflow using Direct and Indirect Transfer of SAR According to Integrated Similarities of Scaffold Motifs and SAR Trends: Application to Identifying Factor Xa Inhibitors

“…The scaffold of MMS R2 differed significantly from that of MMS Q1 (scaffold similarity = 0.36). MMS R3 [34] was the third most similar compared with MMS Q1 (MMS similarity = 0.48, entry 3 in Table 4.a). The resemblance between the two scaffolds of MMS Q1 and R3 yielded the highest scaffold similarity using our direct search protocol.…”

“…The MMS R3 and R5 [34] pair was a twin series with a combination of identical 2D-scaffold shapes and parallel SAR trends (MMS similarity = 1.00, entry 5 in Table 4.a). The MMS R4 and R6 [36] pair yielded an MMS similarity = 0.70 (entry 6 in Table 4.a).…”