An unexpected dynamic binding mode between coagulation factor X and Rivaroxaban reveals importance of flexibility in drug binding

Abstract

Rivaroxaban (RIV) is a direct oral anticoagulant (DOAC) targeting activated coagulation factor X (FXa). An earlier study reported the F174A mutant of FXa resistant to a RIV‐like inhibitor, Apixaban. In current study, the detailed molecular mechanism of the resistance has been explored by molecular dynamics simulations on the impaired interactions between RIV and FXa in the damaged S4 pocket of F174A mutant. Besides, an unexpected relative stable binding mode of S1′S1 was revealed, which required dynamic motions of Gln192 and Gln61 to allow the morpholinone moiety of RIV to shift into the S1′ pocket and form strong interactions. These dynamic motions of RIV and critical residues might be important in drug design for direct inhibitors of coagulation factors.

Unexpected Dynamic Binding May Rescue the Binding Affinity of Rivaroxaban in a Mutant of Coagulation Factor X

“…At last, almost all residues in Y99A have relatively lower possibility to form H-bonds with RIV, which is consistent with the fact that RIV is rather released. However, Lys62 on the edge of the S1’ pocket is the only residue with occupancy increased to 8.1%, which may suggest that the half-released RIV is easier to bind to the half-exposed S1’ pocket, similar to what we discussed on the F174A mutant earlier ( Qu et al, 2019 ).…”

“…Considering that the R1 group should be more stably bound as discussed later, we chose to focus on the more dynamic distribution of the R4 group by superposition of the coordinates of the C3 atom on it. Conversely, a similar NOAC apixaban is much more rigid and compact, making it easier to be described, but at the same time, it may lose some possibility to bind FXa in alternative patterns as RIV, which may partially explain its lower binding affinity in some mutants, as discussed earlier ( Qu et al, 2019 ). From this example, we would again emphasize the recognition of the important influence of the flexibility of both the target protein and the drug molecule, which was often neglected in structure-based drug design and screening using static crystal structures but more and more considered in recent studies, especially in protein and antibody design ( Corbeil et al, 2021 ).…”

“…The procedure of molecular dynamics simulations is fairly same as that of our earlier studies ( Li et al, 2019 ; Qu et al, 2019 ; Qu and Xu, 2019 ). The package of GROMACS5.1.2 was used for the molecular dynamics simulations ( Abraham et al, 2015 ).…”

“…MD simulations also suggested the importance of flexibilities to the catalytic activity impacted by mutations in the S4 pocket and S1 pocket ( Abdel-Azeim et al, 2014 ) as well as the N-terminus of the serine protease domain ( Li et al, 2019 ). The dynamics lying behind drugs targeting the S1 and S4 binding sites of FX were also implemented, such as edoxaban, betrixaban ( Du et al, 2019 ), and rivaroxaban ( Qu et al, 2019 ).…”

“…A molecular model of the activated FX (FXa) with corresponding Y99C mutation in complex with rivaroxaban was then analyzed by molecular dynamics simulations. Unlike the Y99A mutant in which RIV is quickly released, this Y99C mutant is more like F174A and can have RIV dynamically bound with multiple patterns and unexpected strong affinity ( Qu et al, 2019 ; Qu and Xu, 2019 ). Therefore, we presume that the activated Tyr319Cys FX (Y99C FXa) mutant may not have a procoagulant function but may have the ability to bind the NOAC rivaroxaban and the potential to be developed into a novel reversal agent.…”