NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors.
Staphylococcus aureus is a leading cause of hospital-acquired infections in the USA and is a major health concern as methicillin-resistant S. aureus and other antibiotic-resistant strains are common. Compounds that inhibit the S. aureus sortase (SrtA) cysteine transpeptidase may function as potent anti-infective agents as this enzyme attaches virulence factors to the bacterial cell wall. While a variety of SrtA inhibitors have been discovered, the vast majority of these small molecules have not been optimized using structure-based approaches. Here we have used NMR spectroscopy to determine the molecular basis through which pyridazinone-based small molecules inhibit SrtA. These inhibitors covalently modify the active cysteine thiol and partially mimic the natural substrate of SrtA by inducing the closure of an active site loop. Computational and synthetic chemistry methods led to second-generation analogues that are ~70-fold more potent than the lead molecule. These optimized molecules exhibit broad-spectrum activity against other types of class A sortases, have reduced cytotoxicity, and impair SrtA-mediated protein display on S. aureus cell surface. Our work shows that pyridazinone analogues are attractive candidates for further development into anti-infective agents, and highlights the utility of employing NMR spectroscopy and solubility-optimized small molecules in structure-based drug discovery.
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.|UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.|Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Albert H
http://orcid.org/0000-0001-5809-8483
AH
Chan
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Sung Wook
SW
Yi
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.|UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.|Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Ethan M
EM
Weiner
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.|UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.|Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Brendan R
BR
Amer
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Christopher K
CK
Sue
Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, USA.
Jeff
J
Wereszczynski
Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Carly A
CA
Dillen
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Silvia
S
Senese
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Jorge Z
JZ
Torres
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.|Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA.|Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
J Andrew
JA
McCammon
Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Lloyd S
LS
Miller
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
Michael E
ME
Jung
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.|UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA.|Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
Robert T
RT
Clubb
D019881:Aminoacyltransferases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000494:pharmacology / Q000633:toxicity; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D002470:Cell Survival / Q000187:drug effects; D002473:Cell Wall / Q000201:enzymology; D003546:Cysteine Endopeptidases / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology / Q000633:toxicity; D031541:Fluorescence Resonance Energy Transfer; D006367:HeLa Cells; D006801:Humans; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D013058:Mass Spectrometry; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011724:Pyridazines / Q000737:chemistry* / Q000494:pharmacology / Q000633:toxicity; D013211:Staphylococcus aureus / Q000187:drug effects / Q000201:enzymology*; D013329:Structure-Activity Relationship
D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D011724:Pyridazines; D019881:Aminoacyltransferases; C120542:sortase A; D003546:Cysteine Endopeptidases

NMR
; 
Staphylococcus aureus
; Sortase; SrtA; molecular docking; molecular dynamics; protein structure; protein-inhibitor complex; transpeptidase