Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei

Abstract

Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series.

Molecular Recognition in Chemical and Biological Systems

“…c) Overlay of ten Ec IspF crystal structures showing the high flexibility of pocket II (PDB IDs: 1GX1, 1JY8, 1KNJ, 1KNK, 1U3L, 1U3P, 1U40, 1U43, 1YQN, 2GZL) 99. c) Binding mode of ligands 27 and 28 in complex with B pIspF ( 27 : 2.05 Å resolution, PDB ID: 3KE1; 28 : 1.75 Å resolution, PDB ID: 3Q8H) 102c. Color code: C ligand( 27 )+water molecule hot pink, C enzyme( 27 ) old pink, C ligand( 28 ) dark blue, C enzyme( 28 ) cyan.…”

(Z)-4-Chloro-N-{3-[(4-chlorophenyl)sulfonyl]-2,3-dihydrobenzo[d]thiazol-2-ylidene}benzenesulfonamide

“…Inhibition of enzymes from this pathway has tremendous potential to generate new anti-infective agents or herbicides (Frank & Groll, 2017; Witschel et al ., 2013). The enzyme 2-methylerythritol 2,4-cyclodiphosphate synthase (IspF) is present in the MEP pathway (Zhang et al ., 2013, Geist et al ., 2010, Crane et al ., 2006). Recently, bis-sulfonamides of ortho -phenylenediamine have been shown to have micromolar inhibitory activity against IspF from Arabidopsis thaliana , Plasmodium falciparum , or Burkholderia pseudomallei (Thelemann et al ., 2015).…”

Aryl Bis‐Sulfonamide Inhibitors of IspF from Arabidopsis thaliana and Plasmodium falciparum

“…Thus, the T5 coordination to the catalytic zinc ion of AtIspF,p redicted by GOLD,i sp ossible. It was recently well established that binding to the Zn 2 + ion of IspF from different speciesu nder replacement of the fourth (water) ligand only yields aw eakly enhanced binding affinity; [7,35] in other words, the SO 2 group as weaklyb inding ligand is ag ood possibility.…”

“…Despite the reported poor gain in binding affinity upon substituting the fourth water coordination site to the Zn 2 + ligand by other donor ligands, [7,35] we wanted to probe this once more with inhibitors that feature as terically unencumbered primary sulfonamidea sz inc binding group linked to ac ytosine derivative that docks into Pocket III of the active site.…”

“…Several IspF inhibitors have been reported,i ncluding substrate analogue ligands with dissociation constants (K d )o f 15 mm against IspF from Escherichia coli [6] and 70 mm against IspF of Burkholderia pseudomallei (BpIspF). [7] We previously reported thiazolopyrimidine-derived PfIspF inhibitors, discovered by high-throughput screening (HTS), with IC 50 (median inhibitory concentration)v alues as low as 9.6 mm. [8] Herein we report work on aryl bis-sulfonamides, an ew class of IspF inhibitors, which were identified following the same HTS approach.…”