scholarly journals Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kyle G. Kroeck ◽  
Michael D. Sacco ◽  
Emmanuel W. Smith ◽  
Xiujun Zhang ◽  
Daniel Shoun ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Small Molecule ◽  
Conformational Changes ◽  
Lipid A ◽  
Acyl Carrier Protein ◽  
Structural Features ◽  
X Ray ◽  
X Ray Crystallography ◽  
Small Molecule Ligands ◽  
Lipid A Biosynthesis

Abstract The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.

scholarly journals ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Mark F. Mabanglo ◽  
Elisa Leung ◽  
Siavash Vahidi ◽  
Thiago V. Seraphim ◽  
Bryan T. Eger ◽  
...  
Keyword(s):  
Small Molecule ◽  
Conformational Changes ◽  
Electrostatic Interaction ◽  
Structural Changes ◽  
Structural Heterogeneity ◽  
Interaction Networks ◽  
Structural Basis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bacterial Cell Death

Abstract Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.

scholarly journals Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway

2015 ◽  
Vol 71 (10) ◽  
pp. 1205-1214 ◽  
Author(s):  
Lauren Sartor ◽  
Charmaine Ibarra ◽  
Ahmad Al-Mestarihi ◽  
Brian O. Bachmann ◽  
Jessica L. Vey
Keyword(s):  
Substrate Specificity ◽  
Natural Product ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography

The anthracyclines are a class of highly effective natural product chemotherapeutics and are used to treat a range of cancers, including leukemia. The toxicity of the anthracyclines has stimulated efforts to further diversify the scaffold of the natural product, which has led to renewed interest in the biosynthetic pathway responsible for the formation and modification of this family of molecules. DnmZ is an N-hydroxylating flavin monooxygenase (a nitrososynthase) that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of L-daunosamine observed in the anthracycline baumycin. Here, X-ray crystallography was used to elucidate the three-dimensional structure of DnmZ. Two crystal structures of DnmZ were yielded: that of the enzyme alone, solved to 3.00 Å resolution, and that of the enzyme in complex with thymidine diphosphate, the nucleotide carrier portion of the substrate, solved to 2.74 Å resolution. These models add insights into the structural features involved in substrate specificity and conformational changes involved in thymidine diphosphate binding by the nitrososynthases.

scholarly journals Integrative x-ray structure and molecular modeling for the rationalization of procaspase-8 inhibitor potency and selectivity

2019 ◽  
Author(s):  
Janice H. Xu ◽  
Jerome Eberhardt ◽  
Brianna Hill-Payne ◽  
Gonzalo E. González-Páez ◽  
José Omar Castellón ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Small Molecules ◽  
Small Molecule ◽  
Conformational Changes ◽  
Active Sites ◽  
Structural Similarity ◽  
X Ray ◽  
X Ray Crystallography ◽  
Molecule Inhibitor ◽  
High Structural Similarity

AbstractCaspases are a critical class of proteases involved in regulating programmed cell death and other biological processes. Selective inhibitors of individual caspases, however, are lacking, due in large part to the high structural similarity found in the active sites of these enzymes. We recently discovered a small-molecule inhibitor, 63-R, that covalently binds the zymogen, or inactive precursor (pro-form), of caspase-8, but not other caspases, pointing to an untapped potential of procaspases as targets for chemical probes. Realizing this goal would benefit from a structural understanding of how small molecules bind to and inhibit caspase zymogens. There have, however, been very few reported procaspase structures. Here, we employ x-ray crystallography to elucidate a procaspase-8 crystal structure in complex with 63-R, which reveals large conformational changes in active-site loops that accommodate the intramolecular cleavage events required for protease activation. Combining these structural insights with molecular modeling and mutagenesis-based biochemical assays, we elucidate key interactions required for 63-R inhibition of procaspase-8. Our findings inform the mechanism of caspase activation and its disruption by small molecules, and, more generally, have implications for the development of small molecule inhibitors and/or activators that target alternative (e.g., inactive precursor) protein states to ultimately expand the druggable proteome.

scholarly journals Unusual Conformational Changes in 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase as Revealed by X-ray Crystallography and NMR

2001 ◽  
Vol 276 (43) ◽  
pp. 40274-40281 ◽  
Author(s):  
Bing Xiao ◽  
Genbin Shi ◽  
Jinhai Gao ◽  
Jaroslaw Blaszczyk ◽  
Qin Liu ◽  
...  
Keyword(s):  
Conformational Changes ◽  
X Ray ◽  
X Ray Crystallography

Two new zinc(II) and mercury(II) complexes based on N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide): synthesis, crystal structures and antibacterial activities

2020 ◽  
Vol 76 (5) ◽  
pp. 476-482
Author(s):  
Al-Ameen Bariz OmarAli ◽  
Ahmed Jasim M. Al-Karawi ◽  
Adil A. Awad ◽  
Necmi Dege ◽  
Sevgi Kansız ◽  
...  
Keyword(s):  
Organic Ligand ◽  
Antibacterial Activities ◽  
Structural Features ◽  
Bacterial Strains ◽  
Tetrahedral Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Growth Inhibitory ◽  
The Difference

Reaction of N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide), C20H18F2N4O2, (LF ), with zinc chloride and mercury(II) chloride produced different types and shapes of neutral coordination complexes, namely, dichlorido[N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide)-κ2 N,O]zinc(II), [ZnCl2(C20H18F2N4O2)], (1), and dichlorido[N,N′-(cyclohexane-1,2-diylidene)bis(4-fluorobenzohydrazide)-κ4 O,N,N′,O′]mercury(II), [HgCl2(C20H18F2N4O2)], (2). The organic ligand and its metal complexes are characterized using various techniques: IR, UV–Vis and nuclear magnetic resonance (NMR) spectroscopies, in addition to powder X-ray diffraction (PXRD), single-crystal X-ray crystallography and microelemental analysis. Depending upon the data from these analyses and measurements, a typical tetrahedral geometry was confirmed for zinc complex (1), in which the ZnII atom is located outside the bis(benzhydrazone) core. The HgII atom in (2) is found within the core and has a common octahedral structure. The in vitro antibacterial activities of the prepared compounds were evaluated against two different bacterial strains, i.e. gram positive Bacillus subtilis and gram negative Pseudomonas aeruginosa bacteria. The prepared compounds exhibited differentiated growth-inhibitory activities against these two bacterial strains based on the difference in their lipophilic nature and structural features.

scholarly journals Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

FEBS Open Bio ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 557-570 ◽  
Author(s):  
Mikiya Satoh ◽  
Hajime Saburi ◽  
Tomoyuki Tanaka ◽  
Yoshinori Matsuura ◽  
Hisashi Naitow ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Small Molecule ◽  
Dynamics Simulation ◽  
Binding Modes ◽  
X Ray ◽  
X Ray Crystallography ◽  
Multiple Binding

scholarly journals Exploring ribozyme conformational changes with X-ray crystallography

Methods ◽  
2009 ◽  
Vol 49 (2) ◽  
pp. 87-100 ◽  
Author(s):  
Robert C. Spitale ◽  
Joseph E. Wedekind
Keyword(s):  
Conformational Changes ◽  
X Ray ◽  
X Ray Crystallography

PLP undergoes conformational changes during the course of an enzymatic reaction

2014 ◽  
Vol 70 (2) ◽  
pp. 596-606 ◽  
Author(s):  
Ho-Phuong-Thuy Ngo ◽  
Nuno M. F. S. A. Cerqueira ◽  
Jin-Kwang Kim ◽  
Myoung-Ki Hong ◽  
Pedro Alexandrino Fernandes ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Catalytic Mechanism ◽  
Enzymatic Reaction ◽  
Nucleophilic Attack ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography ◽  
Starting Point ◽  
High Level

Numerous enzymes, such as the pyridoxal 5′-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.

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