From Substrate to Fragments to Inhibitor Active In Vivo against Staphylococcus aureus

Abstract

Antibiotic resistance is a worldwide threat due to the decreasing supply of new antimicrobials. Novel targets and innovative strategies are urgently needed to generate pathbreaking drug compounds. NAD kinase (NADK) is essential for growth in most bacteria, as it supports critical metabolic pathways. Here, we report the discovery of a new class of antibacterials that targets bacterial NADK. We generated a series of small synthetic adenine derivatives to screen those harboring promising substituents in order to guide efficient fragment linking. This led to NKI1, a new lead compound inhibiting NADK that showed in vitro bactericidal activity against Staphylococcus aureus. In a murine model of infection, NKI1 restricted survival of the bacteria, including methicillin-resistant S. aureus. Collectively, these findings identify bacterial NADK as a potential drug target and NKI1 as a lead compound in the treatment of staphylococcal infections.

New Chemical Probe Targeting Bacterial NAD Kinase

“…The introduction of an aminoalkyl chain at position 6 of the adenosine residue located in the N subsite (compounds 2 and 3 ) led to sharp decrease in inhibitory potency ( Figure 5 ). This finding is consistent with our previous work describing the affinity drop induced by the introduction of a N6-cyclopropylamino group on the adenosine residue located in the subsite N [ 18 ]. Introduction of the spacer arm at the 5’-end of the diadenosine derivative (compound 4 ) resulted in a slightly reduced inhibitory potency as compared to that of inhibitor 1 ( NKI1 ).…”

“…We checked the binding properties of these new di-adenosine derivatives by determining their complex with crystallized Lm NADK1. The soaking procedure described previously for inhibitor 1 [ 18 ] was used to obtain crystals of the target in complex with compounds 2-5 . The X-ray structures were solved by molecular replacement using PDB6RGC [ 18 ] as a starting template and refined to 2.2–2.4 Å resolution.…”

“…The soaking procedure described previously for inhibitor 1 [ 18 ] was used to obtain crystals of the target in complex with compounds 2-5 . The X-ray structures were solved by molecular replacement using PDB6RGC [ 18 ] as a starting template and refined to 2.2–2.4 Å resolution. The resulting structures showed the same overall mode of binding to Lm NADK1, the ligands occupying both sub-sites A and N of the NAD binding pocket ( Figure 4 ).…”

“…Following a fragment-based approach, we identified a series of diadenosine derivatives with low micromolar inhibitory potencies against recombinant Lm NADK1 and S. aureus NADK [ 16 , 17 ]. We subsequently discovered the first NAD kinase inhibitor (namely NKI1 , Figure 1 ) active in mice infected with S. aureus , including antibiotic-resistant strains [ 18 ].…”

“…Here, we describe the synthesis of a series of functionalized diadenosine derivatives based on the chemical structure of NKI1 [ 18 ]. Short aminoalkyl chains were introduced at each flanking region or middle region of the diadenosine motif ( Figure 2 ) that could be used for coupling with a NHS-activated matrix.…”