ABSTRACT
As part of a fully integrated and comprehensive strategy to discover novel antibacterial agents, NMR- and mass spectrometry-based affinity selection screens were performed to identify compounds that bind to protein targets uniquely found in bacteria and encoded by genes essential for microbial viability. A biphenyl acid lead series emerged from an NMR-based screen with the Haemophilus influenzae protein HI0065, a member of a family of probable ATP-binding proteins found exclusively in eubacteria. The structure-activity relationships developed around the NMR-derived biphenyl acid lead were consistent with on-target antibacterial activity as the Staphylococcus aureus antibacterial activity of the series correlated extremely well with binding affinity to HI0065, while the correlation of binding affinity with B-cell cytotoxicity was relatively poor. Although further studies are needed to conclusively establish the mode of action of the biphenyl series, these compounds represent novel leads that can serve as the basis for the development of novel antibacterial agents that appear to work via an unprecedented mechanism of action. Overall, these results support the genomics-driven hypothesis that targeting bacterial essential gene products that are not present in eukaryotic cells can identify novel antibacterial agents.
Subject(s)
Adenosine Triphosphatases/metabolism , Anti-Bacterial Agents/chemistry , Bacterial Proteins/metabolism , Chemistry, Pharmaceutical/methods , Haemophilus influenzae/metabolism , Amino Acid Sequence , Animals , B-Lymphocytes/metabolism , Drug Design , Genome, Bacterial , Genomics , Magnetic Resonance Spectroscopy , Mass Spectrometry , Molecular Sequence Data , Protein Binding , Structure-Activity RelationshipABSTRACT
The D-Ala-D-Ala adding enzyme (MurF) from Streptococcus pneumoniae catalyzes the ATP-dependent formation of the UDP-MurNAc-pentapeptide, a critical component of the bacterial cell wall. MurF is a potential target for antibacterial design because it is unique to bacteria and performs an essential non-redundant function in the bacterial cell. The recent discovery and subsequent cocrystal structure determination of MurF in complex with a new class of inhibitors served as a catalyst to begin a medicinal chemistry program aimed at improving their potency. We report here a multidisciplinary approach to this effort that allowed for rapid generation of cocrystal structures, thereby providing the crystallographic information critical for driving the inhibitor optimization process. This effort resulted in the discovery of low-nanomolar inhibitors of this bacterial enzyme.
Subject(s)
Enzyme Inhibitors/chemistry , Peptide Synthases/antagonists & inhibitors , Structure-Activity Relationship , Crystallization , Crystallography, X-Ray , Enzyme Inhibitors/metabolism , Inhibitory Concentration 50 , Ligands , Magnetic Resonance Spectroscopy , Models, Molecular , Peptide Synthases/chemistry , Peptide Synthases/metabolism , Substrate Specificity , Sulfonamides/chemistry , Sulfonamides/metabolismABSTRACT
A novel class of MurF inhibitors was discovered and structure-activity relationship studies have led to several potent compounds with IC(50)=22 approximately 70 nM. Unfortunately, none of these potent MurF inhibitors exhibited significant antibacterial activity even in the presence of bacterial cell permeabilizers.