Fluorine Modulates Species Selectivity in the Triazolopyrimidine Class of Plasmodium falciparum Dihydroorotate Dehydrogenase Inhibitors

Abstract

Malaria is one of the most serious global infectious diseases. The pyrimidine biosynthetic enzyme Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) is an important target for antimalarial chemotherapy. We describe a detailed analysis of protein–ligand interactions between DHODH and a triazolopyrimidine-based inhibitor series to explore the effects of fluorine on affinity and species selectivity. We show that increasing fluorination dramatically increases binding to mammalian DHODHs, leading to a loss of species selectivity. Triazolopyrimidines bind Plasmodium and mammalian DHODHs in overlapping but distinct binding sites. Key hydrogen-bond and stacking interactions underlying strong binding to PfDHODH are absent in the mammalian enzymes. Increasing fluorine substitution leads to an increase in the entropic contribution to binding, suggesting that strong binding to mammalian DHODH is a consequence of an enhanced hydrophobic effect upon binding to an apolar pocket. We conclude that hydrophobic interactions between fluorine and hydrocarbons provide significant binding energy to protein–ligand interactions. Our studies define the requirements for species-selective binding to PfDHODH and show that the triazolopyrimidine scaffold can alternatively be tuned to inhibit human DHODH, an important target for autoimmune diseases.

A Triazolopyrimidine-Based Dihydroorotate Dehydrogenase Inhibitor with Improved Drug-like Properties for Treatment and Prevention of Malaria

“…DSM421 occupies the binding site adjacent to the flavin mononucleotide phosphate (FMN) cofactor in the same orientation and binding mode as previously solved X-ray structures of triazolopyrimidine analogs bound to DHODH. 18, 24–25 The binding mode is nearly identical to that observed for DSM265 and the two structures align with an RMSD of 0.19 Å (compared to PDB 4RX0). The DSM421 and DSM265 ligands in these structures are nearly superimposable, with only a slight tilt of the aniline rings relative to each other (Fig.…”

A long-duration dihydroorotate dehydrogenase inhibitor (DSM265) for prevention and treatment of malaria

“…Given the lack of species selectivity of DSM430, concentrations of this impurity will need to be carefully controlled in clinical batches of DSM265. The reduced selectivity of DSM430 relative to the mammalian enzymes mirrors that of analogs containing para CF 3 -aniline when combined with meta-fluorines (16). …”

SEDPHAT – A platform for global ITC analysis and global multi-method analysis of molecular interactions

“…SEDPHAT is a computational platform for global analysis of data from various biophysical techniques, including gITC, which has been widely adopted in ITC applications [11–14,15 ( this volume ),17,19,24,33–62]. Distinguishing aspects of SEDPHAT in comparison with other gITC platforms include the absence of data-specific or model-specific programming by the user, allowing for seamless combination of titration experiments in a graphical user interface, and offering many different pre-programmed multi-site models for two- and three-component systems [9].…”