Structural Insights into a Unique Inhibitor Binding Pocket in Kinesin Spindle Protein

2013 ◽  
Vol 135 (6) ◽  
pp. 2263-2272 ◽  
Author(s):  
Venkatasubramanian Ulaganathan ◽  
Sandeep K. Talapatra ◽  
Oliver Rath ◽  
Andrew Pannifer ◽  
David D. Hackney ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Inhibitor Binding ◽  
Kinesin Spindle Protein ◽  
Structural Insights

scholarly journals Structural insights into the recognition of mono- and di-acetylated histones by the ATAD2B bromodomain

2018 ◽  
Author(s):  
Jonathan T. Lloyd ◽  
Kyle McLaughlin ◽  
Mulu Y. Lubula ◽  
Jamie C. Gay ◽  
Andrea Dest ◽  
...  
Keyword(s):  
Binding Pocket ◽  
List Type ◽  
Lysine Acetylation ◽  
Ligand Specificity ◽  
Inhibitor Binding ◽  
Functional Relationships ◽  
Functional Features ◽  
Key Residues ◽  
Structural Insights ◽  
Alternate Splice Variant

ABSTRACTBromodomains are chromatin reader modules that recognize acetylated lysine. Different bromodomains exhibit a preference for specific patterns of lysine acetylation marks on core and variant histone proteins, however, the functional relationships that exist between histone acetyllysine ligands and bromodomain recognition remain poorly understood. In this study, we examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralog in ATAD2. We show that the ATAD2B bromodomain selects for mono- and di-acetylated histones, and structural analysis identified key residues in the acetyllysine binding pocket that dictate ligand binding specificity. The X-ray crystal structure of the ATAD2B bromodomain in complex with an ATAD2 bromodomain inhibitor was solved at 2.4 Å resolution. This structure demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, and many of these residues play a dual role in acetyllysine recognition. We further characterized a variant of the ATAD2B bromodomain that through alternative splicing loses critical amino acids required for histone ligand and inhibitor coordination. Altogether our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism important for regulating the interaction of the ATAD2B protein with chromatin.HIGHLIGHTSThe ATAD2B bromodomain recognizes mono- and di-acetylated histone ligands.Chemical shift perturbations outline the ATAD2B bromodomain acetyllysine binding pocket.An ATAD2B bromodomain-inhibitor complex reveals important binding contacts.An alternate splice variant in the ATAD2B bromodomain abolishes histone and inhibitor binding.

Structural Insights into Azole-based Inhibitors of Heme Oxygenase-1: Development of Selective Compounds for Therapeutic Applications

2019 ◽  
Vol 25 (42) ◽  
pp. 5803-5821 ◽  
Author(s):  
Mona N. Rahman ◽  
Dragic Vukomanovic ◽  
Jason Z. Vlahakis ◽  
Walter A. Szarek ◽  
Kanji Nakatsu ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Competitive Inhibition ◽  
Cytochromes P450 ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Initial Study ◽  
Structural Basis ◽  
Heme Oxygenase 1 ◽  
Design Strategies ◽  
Inhibitor Binding

The development of isozyme-selective heme oxygenase (HO) inhibitors promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties with a role in several disease states; thus, it is an enticing therapeutic target. Historically, the metalloporphyrins have been used as competitive HO inhibitors based on their structural similarity to the substrate, heme. However, heme’s important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), results in non-selectivity being an unfortunate side effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort over a decade ago to develop novel compounds as potent, selective inhibitors of HO. The result was the creation of the first generation of non-porphyrin based, non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated and provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. Notably, HO-1 inhibitors are of particular interest for the treatment of hyperbilirubinemia and certain types of cancer. Key features based on this initial study have already been used by others to discover additional potential HO-1 inhibitors. Moreover, studies have begun to use selected compounds and determine their effects in some disease models.

Characterization of inhibitor binding to human kinesin spindle protein by site-directed mutagenesis

2009 ◽  
Vol 484 (1) ◽  
pp. 1-7 ◽  
Author(s):  
C. Gary Marshall ◽  
Maricel Torrent ◽  
Olusegun Williams ◽  
Kelly A. Hamilton ◽  
Carolyn A. Buser
Keyword(s):  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Inhibitor Binding ◽  
Kinesin Spindle Protein

scholarly journals Structural insights into human heme oxygenase-1 inhibition by potent and selective azole-based compounds

2013 ◽  
Vol 10 (78) ◽  
pp. 20120697 ◽  
Author(s):  
Mona N. Rahman ◽  
Dragic Vukomanovic ◽  
Jason Z. Vlahakis ◽  
Walter A. Szarek ◽  
Kanji Nakatsu ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Competitive Inhibition ◽  
Cytochromes P450 ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Potential Interaction ◽  
Structural Basis ◽  
Heme Oxygenase 1 ◽  
Design Strategies ◽  
Inhibitor Binding

The development of heme oxygenase (HO) inhibitors, especially those that are isozyme-selective, promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties and may play a role in several disease states, making it an enticing therapeutic target. Traditionally, the metalloporphyrins have been used as competitive HO inhibitors owing to their structural similarity with the substrate, heme. However, given heme's important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), non-selectivity is an unfortunate side-effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort to develop novel compounds as potent, selective inhibitors of HO. This resulted in the creation of non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated, which provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies.

scholarly journals Exploring the inhibitor binding pocket of respiratory complex I

2008 ◽  
Vol 1777 (7-8) ◽  
pp. 660-665 ◽  
Author(s):  
Uta Fendel ◽  
Maja A. Tocilescu ◽  
Stefan Kerscher ◽  
Ulrich Brandt
Keyword(s):  
Complex I ◽  
Binding Pocket ◽  
Inhibitor Binding ◽  
Respiratory Complex ◽  
Respiratory Complex I

scholarly journals Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding

2017 ◽  
Vol 61 (8) ◽  
Author(s):  
Susann Skagseth ◽  
Tony Christopeit ◽  
Sundus Akhter ◽  
Annette Bayer ◽  
Ørjan Samuelsen ◽  
...  
Keyword(s):  
Catalytic Efficiency ◽  
Kinetic Studies ◽  
Global Public Health ◽  
Equilibrium Dissociation Constant ◽  
Inhibitor Binding ◽  
Class A ◽  
Class D ◽  
Equilibrium Dissociation ◽  
Structural Insights

ABSTRACT Metallo-β-lactamases (MBLs) threaten the effectiveness of β-lactam antibiotics, including carbapenems, and are a concern for global public health. β-Lactam/β-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-β-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC50) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC50 levels of the new thiol-based inhibitors were 0.66 μM (inhibitor 2a) and 0.62 μM (inhibitor 2b), and the equilibrium dissociation constant (KD ) of inhibitor 2a was 1.6 μM; thus, both were more potent inhibitors than l-captopril (IC50 = 47 μM; KD = 25 μM). The crystal structure of TMB-1 was resolved to 1.75 Å. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped π-π stacking and R224 cation-π interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril.

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