Crystal structure of the retroviral protease‐like domain of a protozoal DNA damage‐inducible 1 protein

Abstract

DNA damage‐inducible 1 (Ddi1) is a multidomain protein with one of the domains being retropepsin‐like. HIV ‐1 protease inhibitors were found to reduce opportunistic infections caused by pathogens like Leishmania and Plasmodium , and some of them were shown to inhibit the growth of these parasites. In Leishmania , Ddi1 was identified as a likely target of the inhibitors. We report the crystal structure of the retropepsin‐like domain of Ddi1 from Leishmania major as a dimer with clear density for the critical ‘flap’ region. We have characterized binding with one of the HIV ‐1 protease inhibitors in solution using bio‐layer interferometry and by docking. Further, we have performed molecular dynamics ( MD ) simulation studies that show that the protein undergoes a conformational change from open to semi‐open and closed forms with the closing of the flexible flap over the active site.

Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

“…In Ddi PRs, these regions-corresponding to the flaps of HIV-1 PR-adopt less-ordered conformational loops and exhibit higher flexibility; consequently, only one or none of the loops is visible in the known structures [5][6][7][8]. Contact maps proved that both the residue number and area of the interface are higher in the closed conformation.…”

“…This region, which adopts an α-helical conformation, is located in the flap elbow, near the conserved active site motif (Figure 1). The structural role of this additional helix has been revealed by molecular dynamics simulations suggesting its determinant role in the flexibility of the flaps [8]. Despite the relatively higher rigidity of flap movement, the tips of the flaps have high flexibility in Ddi PRs, and thus, they are not defined fully in most structures by electron density maps.…”

“…Despite the low sequence identity, retropepsins exhibit high structural similarity, suggesting that the eukaryotic homologs may also share their overall fold and main features with retropepsins. Substantial structural information is available for DNA damage-inducible protein 1 and 2 (Ddi1 and Ddi2, respectively), which are eukaryotic proteins containing a retroviral-like aspartic protease domain [5][6][7][8].…”

“…Despite the low sequence identity between the target and template structures, retroviral and retroviral-like PRs exhibit high structural similarity [5], which makes the homology modeling of retroviral-like PRs possible. Before the deposition of the first Ddi1-Lm crystal structure to the PDB in 2017 [8], model structures were previously prepared for Ddi1-like PR of L. major [5,12,13], and the PRs of Schistosoma mansoni and Hymenolepis microstoma [13]. Numerous eukaryotic organisms have been found to express homologs of retrovirus and retroelement PRs, which evolved from their ancestors and which were retained during their evolution [3,4].…”

HIV Protease Inhibitor Nelfinavir Targets Human DDI2 and Potentiates Proteasome Inhibitor-based Chemotherapy

“…1a). The RVP domain is highly conserved in DDI2's orthologs and retroviral proteases such as HIV protease [30][31][32] . When spatially aligned, RVP domain structures of DDI2 and HIV protease largely overlapped, indicating that these two structures shared high degree of similarity ( Fig.…”