Crystal structure of an Aurora-A mutant that mimics Aurora-B bound to MLN8054: insights into selectivity and drug design

2010 ◽  
Vol 427 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Charlotte A. Dodson ◽  
Magda Kosmopoulou ◽  
Mark W. Richards ◽  
Butrus Atrash ◽  
Vassilios Bavetsias ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Rational Design ◽  
Kinase Inhibitors ◽  
Protein Kinase Inhibitors ◽  
Structural Basis ◽  
Cancer Drug ◽  
Aurora B ◽  
Aurora A ◽  
Point Mutant

The production of selective protein kinase inhibitors is often frustrated by the similarity of the enzyme active sites. For this reason, it is challenging to design inhibitors that discriminate between the three Aurora kinases, which are important targets in cancer drug discovery. We have used a triple-point mutant of Aurora-A (AurAx3) which mimics the active site of Aurora-B to investigate the structural basis of MLN8054 selectivity. The bias toward Aurora-A inhibition by MLN8054 is fully recapitulated by AurAx3in vitro. X-ray crystal structures of the complex suggest that the basis for the discrimination is electrostatic repulsion due to the T217E substitution, which we have confirmed using a single-point mutant. The activation loop of Aurora-A in the AurAx3–MLN8054 complex exhibits an unusual conformation in which Asp274 and Phe275 side chains point into the interior of the protein. There is to our knowledge no documented precedent for this conformation, which we have termed DFG-up. The sequence requirements of the DFG-up conformation suggest that it might be accessible to only a fraction of kinases. MLN8054 thus circumvents the problem of highly homologous active sites. Binding of MLN8054 to Aurora-A switches the character of a pocket within the active site from polar to a hydrophobic pocket, similar to what is observed in the structure of Aurora-A bound to a compound that induces DFG-out. We propose that targeting this pocket may be a productive route in the design of selective kinase inhibitors and describe the structural basis for the rational design of these compounds.

Atomically dispersed Ni as the active site towards selective hydrogenation of nitroarenes

2019 ◽  
Vol 21 (3) ◽  
pp. 704-711 ◽  
Author(s):  
Fan Yang ◽  
Minjian Wang ◽  
Wei Liu ◽  
Bin Yang ◽  
Ying Wang ◽  
...  
Keyword(s):  
Noble Metal ◽  
Catalytic Hydrogenation ◽  
Selective Hydrogenation ◽  
Porous Carbon ◽  
Active Site ◽  
Active Sites ◽  
Rational Design ◽  
Metal Free

Noble-metal-free catalytic hydrogenation of nitroarenes is achieved through the rational design of atomically dispersed Ni sites on N-doped porous carbon. The outstanding activity of the catalyst originates from the atomic dispersion of Ni active sites with a high Ni–N3 content.

scholarly journals The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5053
Author(s):  
Alina K. Bakunova ◽  
Alena Yu. Nikolaeva ◽  
Tatiana V. Rakitina ◽  
Tatiana Y. Isaikina ◽  
Maria G. Khrenova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structural Analysis ◽  
Active Site ◽  
Active Sites ◽  
Structural Basis ◽  
Active Site Residues ◽  
Type Iv ◽  
Fold Type ◽  
Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

scholarly journals Rational Design of Potential Bcr-Abl Tyrosine Kinase Inhibitors by the Methods of Molecular Modeling

2020 ◽  
Vol 15 (2) ◽  
pp. 396-415
Author(s):  
A.M. Anrdrianov ◽  
Yu.V. Kornoushenko ◽  
A.D. Karpenko ◽  
I.P. Bosko ◽  
Zh.V. Ignatovich ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Tyrosine Kinase ◽  
Rational Design ◽  
Kinase Inhibitors ◽  
Calculated Data ◽  
Protein Kinase Inhibitors ◽  
Modeling Tools ◽  
Abl Tyrosine Kinase ◽  
Anti Cancer ◽  
Derivatives Of

Discovery of the nature of inhibiting cancer processes by small organic molecules has changed the principles of the development of drug compounds for antitumor therapy. Recent achievements in this area are associated with the design of small-molecule protein kinase inhibitors, organic compounds exhibiting directed pathogenetic action. In this study, in silico design of 38 potential anti-cancer compounds with multikinase profile was carried out based on the derivatives of 2-arylaminopyrimidine. Evaluation of inhibitory activity potential of these compounds against the native and mutant (T315I) forms of Bcr-Abl tyrosine kinase, an enzyme that plays a key role in the pathogenesis of chronic myeloid leukemia characterized by uncontrolled growth myeloid cells in peripheral blood and bone marrow, was performed using molecular modeling tools. As a result, 5 top-ranking compounds that exhibit, according to the calculated data, a high-affinity binding to the native and mutant Bcr-Abl tyrosine kinase were identified. The designed compounds were shown to form good scaffolds for the development of novel potent antitumor drugs.

scholarly journals MOLECULAR DOCKING STUDIES ON THIADIAZOLE DERIVATIVES AS PROTEIN KINASE INHIBITORS

2018 ◽  
Vol 10 (12) ◽  
pp. 70
Author(s):  
D. Sivakumar ◽  
G. Geetha
Keyword(s):  
Protein Kinase ◽  
Active Sites ◽  
Kinase Inhibitors ◽  
Three Dimensional ◽  
Docking Study ◽  
Docking Studies ◽  
Protein Kinase Inhibitors ◽  
Protein Kinase G ◽  
Dimensional Structure ◽  
Thiadiazole Derivatives

Objective: In the present study, a novel series of 1, 3, 4-thiadiazole derivatives were docked against the mycobacterium tuberculosis protein kinase G. 1, 3, 4–thiadiazole derivatives with a modified primary amine group at 5th position were used for docking studies.Methods: The three-dimensional structure of the protein was obtained from PDB, and its active sites were predicted. The structures of all the compounds were drawn using chemdraw software version 8.0. The docking studies were done by using schrödinger software against the enzyme protein kinase G. Totally eighteen compounds was synthesized based on glide scoreResults: In this Docking study the thiadiazole analogues were showing good binding energy. The amino acids residues GLU588, SER412, GLY410 and GLU 628 in the kinase domain active site form hydrogen bonds with the ligand.Conclusion: The compounds D34, D16, D7, D25, D15, and D27 showed better interaction with protein kinase G (pknG) more than the other drug molecules

scholarly journals Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases

Science ◽  
2019 ◽  
Vol 366 (6461) ◽  
pp. 109-115 ◽  
Author(s):  
Yasushi Kondo ◽  
Jana Ognjenović ◽  
Saikat Banerjee ◽  
Deepti Karandur ◽  
Alan Merk ◽  
...  
Keyword(s):  
Drug Targets ◽  
Active Sites ◽  
Kinase Inhibitors ◽  
Distal Segment ◽  
Kinase Domain ◽  
Terminal Segment ◽  
Cancer Drug ◽  
Active Conformation ◽  
Raf Kinase ◽  
Cryo Electron Microscopy

Raf kinases are important cancer drug targets. Paradoxically, many B-Raf inhibitors induce the activation of Raf kinases. Cryo–electron microscopy structural analysis of a phosphorylated B-Raf kinase domain dimer in complex with dimeric 14-3-3, at a resolution of ~3.9 angstroms, shows an asymmetric arrangement in which one kinase is in a canonical “active” conformation. The distal segment of the C-terminal tail of this kinase interacts with, and blocks, the active site of the cognate kinase in this asymmetric arrangement. Deletion of the C-terminal segment reduces Raf activity. The unexpected asymmetric quaternary architecture illustrates how the paradoxical activation of Raf by kinase inhibitors reflects an innate mechanism, with 14-3-3 facilitating inhibition of one kinase while maintaining activity of the other. Conformational modulation of these contacts may provide new opportunities for Raf inhibitor development.

scholarly journals High-Resolution Crystal Structure of the Subclass B3 Metallo-β-Lactamase BJP-1: Rational Basis for Substrate Specificity and Interaction with Sulfonamides

2010 ◽  
Vol 54 (10) ◽  
pp. 4343-4351 ◽  
Author(s):  
Jean-Denis Docquier ◽  
Manuela Benvenuti ◽  
Vito Calderone ◽  
Magdalena Stoczko ◽  
Nicola Menciassi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Bradyrhizobium Japonicum ◽  
Active Sites ◽  
Structural Diversity ◽  
Binding Pocket ◽  
Structural Basis ◽  
Side Chain ◽  
Functional Heterogeneity ◽  
Hydrophobic Binding

ABSTRACT Metallo-β-lactamases (MBLs) are important enzymatic factors in resistance to β-lactam antibiotics that show important structural and functional heterogeneity. BJP-1 is a subclass B3 MBL determinant produced by Bradyrhizobium japonicum that exhibits interesting properties. BJP-1, like CAU-1 of Caulobacter vibrioides, overall poorly recognizes β-lactam substrates and shows an unusual substrate profile compared to other MBLs. In order to understand the structural basis of these properties, the crystal structure of BJP-1 was obtained at 1.4-Å resolution. This revealed significant differences in the conformation and locations of the active-site loops, determining a rather narrow active site and the presence of a unique N-terminal helix bearing Phe-31, whose side chain binds in the active site and represents an obstacle for β-lactam substrate binding. In order to probe the potential of sulfonamides (known to inhibit various zinc-dependent enzymes) to bind in the active sites of MBLs, the structure of BJP-1 in complex with 4-nitrobenzenesulfonamide was also obtained (at 1.33-Å resolution), thereby revealing the mode of interaction of these molecules in MBLs. Interestingly, sulfonamide binding resulted in the displacement of the side chain of Phe-31 from its hydrophobic binding pocket, where the benzene ring of the molecule is now found. These data further highlight the structural diversity shown by MBLs but also provide interesting insights in the structure-function relationships of these enzymes. More importantly, we provided the first structural observation of MBL interaction with sulfonamides, which might represent an interesting scaffold for the design of MBL inhibitors.

scholarly journals Inhibition of Aurora A and Aurora B Is Required for the Sensitivity of HPV-Driven Cervical Cancers to Aurora Kinase Inhibitors

2017 ◽  
Vol 16 (9) ◽  
pp. 1934-1941 ◽  
Author(s):  
David Martin ◽  
Sora Fallaha ◽  
Martina Proctor ◽  
Alexander Stevenson ◽  
Lewis Perrin ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Aurora Kinase ◽  
Aurora B ◽  
Aurora A ◽  
Cervical Cancers ◽  
Aurora Kinase Inhibitors

scholarly journals Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors

2016 ◽  
Vol 113 (48) ◽  
pp. 13726-13731 ◽  
Author(s):  
Mark W. Richards ◽  
Selena G. Burgess ◽  
Evon Poon ◽  
Anne Carstensen ◽  
Martin Eilers ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Catalytic Domain ◽  
Neuroblastoma Cells ◽  
Direct Interaction ◽  
Cancer Therapeutics ◽  
Structural Basis ◽  
Aurora A ◽  
Polyubiquitin Chains ◽  
Ubiquitin Proteasome ◽  
A Site

Myc family proteins promote cancer by inducing widespread changes in gene expression. Their rapid turnover by the ubiquitin–proteasome pathway is regulated through phosphorylation of Myc Box I and ubiquitination by the E3 ubiquitin ligase SCFFbxW7. However, N-Myc protein (the product of theMYCNoncogene) is stabilized in neuroblastoma by the protein kinase Aurora-A in a manner that is sensitive to certain Aurora-A–selective inhibitors. Here we identify a direct interaction between the catalytic domain of Aurora-A and a site flanking Myc Box I that also binds SCFFbxW7. We determined the crystal structure of the complex between Aurora-A and this region of N-Myc to 1.72-Å resolution. The structure indicates that the conformation of Aurora-A induced by compounds such as alisertib and CD532 is not compatible with the binding of N-Myc, explaining the activity of these compounds in neuroblastoma cells and providing a rational basis for the design of cancer therapeutics optimized for destabilization of the complex. We also propose a model for the stabilization mechanism in which binding to Aurora-A alters how N-Myc interacts with SCFFbxW7to disfavor the generation of Lys48-linked polyubiquitin chains.

scholarly journals NMPylation and de-NMPylation of SARS-CoV-2 Nsp9 by the NiRAN domain

2021 ◽  
Author(s):  
Bing Wang ◽  
Dmitri Svetlov ◽  
Irina Artsimovitch
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Rational Design ◽  
Rna Synthesis ◽  
Rna Binding ◽  
Catalytic Reactions ◽  
Mechanistic Studies ◽  
Rna Dependent Rna Polymerase ◽  
Nucleotide Analogs ◽  
Nucleotidyl Transferase

Nsp12, the catalytic subunit of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), contains two active sites that catalyze nucleotidyl-monophosphate (NMP) transfer (NMPylation). RNA synthesis is mediated by the RdRp active site that is conserved among all RNA viruses and has been a focus of mechanistic studies and drug discovery. The second active site resides in a Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. Both catalytic reactions are essential for viral replication, but the mechanism and targets of NiRAN are poorly characterized. One recent study showed that NiRAN transfers NMP to the first residue of RNA-binding protein Nsp9. Another study reported a structure of SARS-CoV-2 replicase with an extended Nsp9 in the NiRAN active site but observed NMP transfer to RNA instead. We show that SARS-CoV-2 Nsp12 efficiently and reversibly NMPylates the native but not the extended Nsp9. Substitutions of the invariant NiRAN residues abolish NMPylation, whereas a substitution of a catalytic RdRp Asp residue does not. NMPylation is inhibited by nucleotide analogs, pyrophosphate, and bisphosphonates, suggesting a path for rational design of NiRAN inhibitors. We hypothesize that Nsp9 remodels both active sites of Nsp12 to support initiation of RNA synthesis by RdRp and subsequent capping of the product RNA by the NiRAN domain.

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