The de novo folate synthesis pathway is an attractive target for the design of antimicrobials, as
humans lack this pathway and only derive folate from their diets. In an attempt to combat resistance against
standard antimicrobials targeting the folate synthesis pathway in E.coli, compound CD 15-3 was designed
to inhibit the activity of dihydrofolate reductase (DHFR), in both its wild-type and evolved mutant strains.
The purpose of this study was to investigate potential off-target interactions of the drug CD 15-3.
In the first phase of the study, molecular docking was employed to assess the binding of the small molecule
to 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK), using the online docking service
SwissDock. Structural analysis of the protein-small molecule complexes showed an abundance of
interactions between CD 15-3 and residues TYR 53 and PHE 123 of HPPK. Afterwards, more precise
docking using Maestro, a dedicated drug discovery software, rendered a binding mode of CD 15-3 in which
the small molecule is “sandwiched” in between residues TYR 53 and PHE 123 of HPPK through pi-stacking
interactions. A docking score of -9.7 kcal/mol for the competitive binding in the pterin binding site of HPPK
was obtained.
Moreover, CD 15-3 appears to bind more favorably to HPPK, and not to DHFR, as it was
previously assumed. Further, molecular dynamics (MD) and anisotropic network model (ANM)
simulations would elucidate the binding interactions between the small molecule CD 15-3 and the flexible
chain of the protein HPPK.