scholarly journals A moving target: structure and disorder in pursuit of Myc inhibitors

2017 ◽  
Vol 45 (3) ◽  
pp. 709-717 ◽  
Author(s):  
Richard Bayliss ◽  
Selena G. Burgess ◽  
Eoin Leen ◽  
Mark W. Richards
Keyword(s):  
Protein Interaction ◽  
Kinase Inhibitors ◽  
Kinase Domain ◽  
Transactivation Domain ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Molecular Scaffold ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
And Function

The Myc proteins comprise a family of ubiquitous regulators of gene expression implicated in over half of all human cancers. They interact with a large number of other proteins, such as transcription factors, chromatin-modifying enzymes and kinases. Remarkably, few of these interactions have been characterized structurally. This is at least in part due to the intrinsically disordered nature of Myc proteins, which adopt a defined conformation only in the presence of binding partners. Owing to this behaviour, crystallographic studies on Myc proteins have been limited to short fragments in complex with other proteins. Most recently, we determined the crystal structure of Aurora-A kinase domain bound to a 28-amino acid fragment of the N-Myc transactivation domain. The structure reveals an α-helical segment within N-Myc capped by two tryptophan residues that recognize the surface of Aurora-A. The kinase domain acts as a molecular scaffold, independently of its catalytic activity, upon which this region of N-Myc becomes ordered. The binding site for N-Myc on Aurora-A is disrupted by certain ATP-competitive inhibitors, such as MLN8237 (alisertib) and CD532, and explains how these kinase inhibitors are able to disrupt the protein–protein interaction to affect Myc destabilization. Structural studies on this and other Myc complexes will lead to the design of protein–protein interaction inhibitors as chemical tools to dissect the complex pathways of Myc regulation and function, which may be developed into Myc inhibitors for the treatment of cancer.

scholarly journals Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase–TPX2 protein–protein interaction

2017 ◽  
Vol 53 (67) ◽  
pp. 9372-9375 ◽  
Author(s):  
Daniel J. Cole ◽  
Matej Janecek ◽  
Jamie E. Stokes ◽  
Maxim Rossmann ◽  
John C. Faver ◽  
...  
Keyword(s):  
Free Energy ◽  
Small Molecule ◽  
Protein Interaction ◽  
Small Molecule Inhibitors ◽  
Binding Free Energy ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Protein Protein Interaction ◽  
Important Protein

Computational binding free energy predictions were validated against experiment and used to design new inhibitors of an important protein–protein interaction.

scholarly journals Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1690
Author(s):  
Louise Pinet ◽  
Nadine Assrir ◽  
Carine van Heijenoort
Keyword(s):  
Tyrosine Kinases ◽  
Kinase Domain ◽  
Cellular Motility ◽  
Dynamic Features ◽  
Sh2 Domains ◽  
Intrinsically Disordered ◽  
Src Homology ◽  
Regulation Functions ◽  
And Function

ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features.

Benzo[e]pyrimido[5,4-b][1,4]diazepin-6(11H)-one derivatives as Aurora A kinase inhibitors: LQTA-QSAR analysis and detailed systematic validation of the developed model

2015 ◽  
Vol 19 (4) ◽  
pp. 965-974 ◽  
Author(s):  
Ashish M. Kanhed ◽  
Radha Charan Dash ◽  
Nishant Parmar ◽  
Tarun Kumar Das ◽  
Rajani Giridhar ◽  
...  
Keyword(s):  
Kinase Inhibitors ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Qsar Analysis

ChemInform Abstract: Single Step Synthesis of New Fused Pyrimidine Derivatives and Their Evaluation as Potent Aurora-A Kinase Inhibitors.

ChemInform ◽  
2011 ◽  
Vol 43 (4) ◽  
pp. no-no
Author(s):  
Mohamed R. Shaaban ◽  
Tamer S. Saleh ◽  
Abdelrahman S. Mayhoub ◽  
Ahmad M. Farag
Keyword(s):  
Kinase Inhibitors ◽  
Single Step ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Pyrimidine Derivatives

scholarly journals Classification of Nonenzymatic Homologues of Protein Kinases

2009 ◽  
Vol 2009 ◽  
pp. 1-17 ◽  
Author(s):  
K. Anamika ◽  
K. R. Abhinandan ◽  
K. Deshmukh ◽  
N. Srinivasan
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Protein Interaction ◽  
Transmembrane Domain ◽  
Homo Sapiens ◽  
Interaction Domain ◽  
Protein Protein Interaction ◽  
Domain 3 ◽  
Eukaryotic Organisms ◽  
And Function

Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely,Homo sapiens,Mus musculus,Rattus norvegicus, andDrosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes which would be helpful in deciphering their roles in cellular processes.

scholarly journals Structure-Based Discovery and Bioactivity Evaluation of Novel Aurora-A Kinase Inhibitors as Anticancer Agents via Docking-Based Comparative Intermolecular Contacts Analysis (dbCICA)

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 6003
Author(s):  
Majd S. Hijjawi ◽  
Reem Fawaz Abutayeh ◽  
Mutasem O. Taha
Keyword(s):  
Anticancer Agents ◽  
Cell Cycle Progression ◽  
Kinase Inhibitors ◽  
Epithelial Mesenchymal Transition ◽  
Resonance Energy ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Characteristic Analysis ◽  
Mesenchymal Transition ◽  
Intermolecular Contacts

Aurora-A kinase plays a central role in mitosis, where aberrant activation contributes to cancer by promoting cell cycle progression, genomic instability, epithelial-mesenchymal transition, and cancer stemness. Aurora-A kinase inhibitors have shown encouraging results in clinical trials but have not gained Food and Drug Administration (FDA) approval. An innovative computational workflow named Docking-based Comparative Intermolecular Contacts Analysis (dbCICA) was applied—aiming to identify novel Aurora-A kinase inhibitors—using seventy-nine reported Aurora-A kinase inhibitors to specify the best possible docking settings needed to fit into the active-site binding pocket of Aurora-A kinase crystal structure, in a process that only potent ligands contact critical binding-site spots, distinct from those occupied by less-active ligands. Optimal dbCICA models were transformed into two corresponding pharmacophores. The optimal one, in capturing active hits and discarding inactive ones, validated by receiver operating characteristic analysis, was used as a virtual in-silico search query for screening new molecules from the National Cancer Institute database. A fluorescence resonance energy transfer (FRET)-based assay was used to assess the activity of captured molecules and five promising Aurora-A kinase inhibitors were identified. The activity was next validated using a cell culture anti-proliferative assay (MTT) and revealed a most potent lead 85(NCI 14040) molecule after 72 h of incubation, scoring IC50 values of 3.5–11.0 μM against PANC1 (pancreas), PC-3 (prostate), T-47D and MDA-MB-231 (breast)cancer cells, and showing favorable safety profiles (27.5 μM IC50 on fibroblasts). Our results provide new clues for further development of Aurora-A kinase inhibitors as anticancer molecules.

scholarly journals Estrogen-related receptor alpha directly binds to p53 and cooperatively controls colon cancer growth through the regulation of mitochondrial biogenesis and function

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Humberto De Vitto ◽  
Joohyun Ryu ◽  
Ali Calderon-Aparicio ◽  
Josh Monts ◽  
Raja Dey ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Protein Interaction ◽  
Mitochondrial Biogenesis ◽  
P53 Protein ◽  
Selection Criterion ◽  
In Vivo Studies ◽  
Clear Understanding ◽  
Protein Protein Interaction ◽  
Mutational Status ◽  
And Function

Abstract Background Of the genes that control mitochondrial biogenesis and function, ERRα emerges as a druggable metabolic target to be exploited for cancer therapy. Of the genes mutated in cancer, TP53 remains the most elusive to target. A clear understanding of how mitochondrial druggable targets can be accessed to exploit the underlying mechanism(s) explaining how p53-deficient tumors promote cell survival remains elusive. Methods We performed protein-protein interaction studies to demonstrate that ERRα binds to p53. Moreover, we used gene silencing and pharmacological approaches in tandem with quantitative proteomics analysis by SWATH-MS to investigate the role of the ERRα/p53 complex in mitochondrial biogenesis and function in colon cancer. Finally, we designed in vitro and in vivo studies to investigate the possibility of targeting colon cancers that exhibit defects in p53. Results Here, we are the first to identify a direct protein-protein interaction between the ligand-binding domain (LBD) of ERRα and the C-terminal domain (CTD) of p53. ERRα binds to p53 regardless of p53 mutational status. Furthermore, we show that the ERRα and p53 complex cooperatively control mitochondrial biogenesis and function. Targeting ERRα creates mitochondrial metabolic stresses, such as production of reactive oxygen species (ROS) and mitochondrial membrane permeabilization (MMP), leading to a greater cytotoxic effect that is dependent on the presence of p53. Pharmacological inhibition of ERRα impairs the growth of p53-deficient cells and of p53 mutant patient-derived colon xenografts (PDX). Conclusions Therefore, our data suggest that by using the status of the p53 protein as a selection criterion, the ERRα/p53 transcriptional axis can be exploited as a metabolic vulnerability.

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