Allosteric inhibition and kinetic characterization of Klebsiella pneumoniae CysE: An emerging drug target

• Published in: International journal of biological macromolecules Vol. 151; pp. 1240 - 1249
• Main Authors: Verma, Deepali, Gupta, Sunita, Saxena, Rahul, Kaur, Punit, R., Rachana, Srivastava, Sudha, Gupta, Vibha
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.05.2020
• Subjects: Allosteric inhibitor; Allosteric Regulation - drug effects; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - pharmacology; Cloning, Molecular; Crystal structure; CysE; Enzyme Stability; Gene Expression; Humans; Kinetics; Klebsiella pneumoniae; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - enzymology; Klebsiella pneumoniae - genetics; Molecular Conformation; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular dynamics simulations; Protein Denaturation; Quercetin; Recombinant Proteins - genetics; Recombinant Proteins - isolation & purification; Serine O-Acetyltransferase - antagonists & inhibitors; Serine O-Acetyltransferase - chemistry; Serine O-Acetyltransferase - genetics; Serine O-Acetyltransferase - isolation & purification; Structure-Activity Relationship; CysE; Allosteric inhibitor; Molecular dynamics simulations; Klebsiella pneumoniae; Quercetin; Crystal structure
• ISSN: 0141-8130; 1879-0003
• DOI: 10.1016/j.ijbiomac.2019.10.170

•Cloning, purification and biochemical characterization of CysE from Klebsiella pneumoniae•3-D crystal structure of Kpn CysE complexed with L-cysteine at 2.8 Å•In silico identification and in vitro validation of inhibitory potential of quercetin•Identification of an allosteric site at the trimer-trimer interface in the hexameric CysE The emergence and spread of multidrug-resistant strains of Klebsiella pneumoniae is a major concern that necessitates the development of unique therapeutics. The essential requirement of serine acetyltransferase (SAT/CysE) for survival of several human pathogens makes it a very promising target for inhibitor designing and drug discovery. In this study, as an initial step to structure-based drug discovery, CysE from K. pneumonia was structurally and biochemically characterized. Subsequently, blind docking of selected natural products into the X-ray crystallography determined 3D structure of the target was carried out. Experimental validation of the inhibitory potential of the top-scorers established quercetin as an uncompetitive inhibitor of Kpn CysE. Molecular dynamics simulations carried out to elucidate the binding mode of quercetin reveal that this small molecule binds at the trimer-trimer interface of hexameric CysE, a site physically distinct from the active site of the enzyme. Detailed analysis of conformational differences incurred in Kpn CysE structure on binding to quercetin provides mechanistic understanding of allosteric modulation. Binding of quercetin to CysE leads to conformation changes in the active site loops and proximal loops that affect its internal dynamics and consequently its affinity for substrate/co-factor binding, justifying the reduced enzyme activity.