Crystal Structure Of Kinase Domain Research Articles

Eriodictyol Flavanones Based Virtual Screening of Bioactive Compounds from ChEMBL 2D Database with Classic 3-point Pharmacophore Screening Method for HER2 Inhibitors for Breast Cancer

Understanding binding interactions between flavanones and human epidermal growth factor receptor 2 (HER2) is an important step in developing effective treatments for breast cancer, and this study applies computational methods to do just that. This research presents a comprehensive computational methodology for identifying potential HER2 inhibitors with a focus on breast cancer treatment. The study leverages a combination of structural and pharmacophore-based approaches, starting with bioactive compound selection from the ChEMBL 2D database. The PDB-REDO refined crystal structure of Kinase domain of Human HER2 (erbB2) was used to conduct molecular docking simulations with the identified drugs. The Kleywegt-like plot analysis demonstrates the improved structural quality of the HER2 kinase domain after refinement, showing enhanced agreement with experimental data. Molecular docking simulations, conducted using the AutoDock tool, reveal the binding affinity and interaction patterns of selected compounds with the HER2 receptor. Virtual screening results highlight compounds with high binding affinity, favorable interaction patterns, and structural compatibility as potential lead candidates. To ensure safety and efficacy, ADMETox filtering was employed, providing insights into the compound’s toxicity profile and pharmacokinetic attributes. The selected compound, Eriodictyol (C20H20O6), exhibits a generally favorable safety profile, with predicted inactivity across multiple toxicity classifications and endpoints. While immunotoxicity is predicted, the overall low probabilities suggest a relatively low risk. Physicochemical and pharmacokinetic assessments indicate Eriodictyol’s potential for drug development. With a molecular weight of 356.37 g/mol, balanced lipophilicity, and high gastrointestinal absorption, the compound aligns with drug-likeness criteria. However, careful consideration is warranted due to its inhibitory effects on certain enzymes and alerts for catechol_A and isolated_alkene. In conclusion, this integrated computational approach streamlines the identification of potential HER2 inhibitors, offering a systematic strategy for drug discovery. Eriodictyol emerges as a promising candidate, demonstrating a favorable safety profile and pharmacokinetic attributes, paving the way for further in-depth studies and development as a potential therapeutic agent for breast cancer.

Crystal Structure of the Kinase Domain of ABL in Complex with a Potent Rationally-Designed Derivative of the PP1 Inhibitor, AB129

As part of our effort to understand the determinants of drug binding to the Abl tyrosine kinase, we determined the crystal structure of the Abl kinase domain bound to a derivative of the PP1 nucleoside analog. Just as the cancer drug imatinib selectively inhibits the tyrosine kinase activity of c-Abl, c-Kit, and the PDGF receptor, but is a poor inhibitor of the closely related Src kinases (1), PP1 is a selective inhibitor of the Src family (2), c-Kit (3), and PDGFR kinases but not of Abl tyrosine kinase activity (3, 4). In fact, PP1 is 1000X less effective at inhibiting Abl and Bcr-Abl kinases than at inhibiting the Src kinases (3, 4). We rationally designed a derivative of the PP1 compound to introduce hydrogen bonding between it and a strictly conserved lysine residue that coordinates the alpha and beta phosphate groups of ATP in protein kinases (5). By expanding the interactions between the inhibitor and Abl kinase, we sought to make the PP1 derivative, AB129, less selective. Our crystal structure of the Abl kinase domain bound to the AB129 inhibitor shows three important features. First, the compound binds to the kinase domain in the active conformation: alpha C helix is rotated inward facilitating a salt bridge between Lys271 and Glu286 and the conserved Asp-Phe-Gly (DFG) motif is oriented Asp-In. In contrast, the structure of PP1 bound to the Src family kinase Hck is in the inactive conformation (6). Second, the strictly conserved Glu286 residue, not Lys271, hydrogen bonds to the hydroxyl group of AB129. Third, the conformation of the phosphate binding loop (P-loop) is extended. We provide kinetic and calorimetric data to support our rationale for the observed conformational changes.

Structural Comparison of Human Mammalian Ste20-Like Kinases

BackgroundThe serine/threonine mammalian Ste-20 like kinases (MSTs) are key regulators of apoptosis, cellular proliferation as well as polarization. Deregulation of MSTs has been associated with disease progression in prostate and colorectal cancer. The four human MSTs are regulated differently by C-terminal regions flanking the catalytic domains.Principal FindingsWe have determined the crystal structure of kinase domain of MST4 in complex with an ATP-mimetic inhibitor. This is the first structure of an inactive conformation of a member of the MST kinase family. Comparison with active structures of MST3 and MST1 revealed a dimeric association of MST4 suggesting an activation loop exchanged mechanism of MST4 auto-activation. Together with a homology model of MST2 we provide a comparative analysis of the kinase domains for all four members of the human MST family.SignificanceThe comparative analysis identified new structural features in the MST ATP binding pocket and has also defined the mechanism for autophosphorylation. Both structural features may be further explored for inhibitors design.Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.

Structural Basis of Human p70 Ribosomal S6 Kinase-1 Regulation by Activation Loop Phosphorylation

p70 ribosomal S6 kinase (p70S6K) is a downstream effector of the mTOR signaling pathway involved in cell proliferation, cell growth, cell-cycle progression, and glucose homeostasis. Multiple phosphorylation events within the catalytic, autoinhibitory, and hydrophobic motif domains contribute to the regulation of p70S6K. We report the crystal structures of the kinase domain of p70S6K1 bound to staurosporine in both the unphosphorylated state and in the 3'-phosphoinositide-dependent kinase-1-phosphorylated state in which Thr-252 of the activation loop is phosphorylated. Unphosphorylated p70S6K1 exists in two crystal forms, one in which the p70S6K1 kinase domain exists as a monomer and the other as a domain-swapped dimer. The crystal structure of the partially activated kinase domain that is phosphorylated within the activation loop reveals conformational ordering of the activation loop that is consistent with a role in activation. The structures offer insights into the structural basis of the 3'-phosphoinositide-dependent kinase-1-induced activation of p70S6K and provide a platform for the rational structure-guided design of specific p70S6K inhibitors.

Structure and function in cell signalling

Acknowledgments. Preface. 1 The components and foundations of signalling. 1.1 Definition of terms used. 1.2 Historical foundations. 1.3 Early milestones in signal transduction research. 1.4 The discovery of receptors and G proteins. 1.5 cAMP pathways. 1.6 cAMP: ancient hunger signal - primitive signalling in amoebazoans and prokaryotes. References. 2 Enzymes and receptors - quantitative aspects. 2.1 Enzyme steady state assays - Michaelian enzymes. 2.2 Receptor equilibrium binding assays. 2.3 The receptor's environment. 2.4 Guanine nucleotides and the agonist 'affinity-shift' of 7-pass receptors. References. 3 Modules and motifs in transduction. 3.1 Src homology domains. 3.2 PH superfold modules: PH-, PTB- and PDZ-domains. 3.3 Bcr-homology (BcrH) domains. 3.4 Dbl homology (DH) domains - partners of PH domains. 3.5 Bcl-2 homology (BH) domains. 3.6 Ras binding domains. 3.7 Phosphoserine/phosphothreonine-binding domains. 3.8 EF-hands - calcium-sensing modules. 3.9 C1 and C2 domains - a Ca2p-activated, lipid-binding, module. References. 4 Protein kinase enzymes - activation and auto-inhibition. 4.1 The protein kinase fold. 4.2 Protein kinases activated by A-loop phosphorylation. 4.3 The insulin receptor kinase (IRK) - a 'gated' kinase. 4.4 Cyclin dependent kinases. 4.5 Secondary inhibition mechanisms - PKA. References. 5 7-pass receptors and the catabolic response. 5.1 7-pass receptor phylogeny. 5.2 Functional mechanisms of 7-pass receptors. 5.3 Amplification. 5.4 Adenylyl cyclase - signal limitation. 5.5 Adenylyl cyclase isoforms. 5.6 G proteins and the adenylyl cyclase effector isoforms. 5.7 Regulatory subunits of PKA and A-Kinase Anchoring Proteins. 5.8 Phosphorylase kinase. 5.9 Glycogen phosphorylase. 5.10 Glycogen synthase. 5.11 Remaining questions - scaffolds and alternate second messenger 'receptors'. 5.12 G protein coupled receptor kinases - downregulators, signal integrators. References. 6 Single pass growth factor receptors. 6.1 Receptor tyrosine kinases - ligands and signal transduction. 6.2 The PDGFR family - signal transduction. 6.3 PDGFR family autoinhibition: juxtamembrane and A-loop tyrosines. 6.4 Crystal structure of kinase domain of PDGFR family-A member: Flt-3. 6.5 The ErbB family. 6.6 ErbB-type receptor signal transduction particles. 6.7 Autoinhibition of EGFR and activation. References. 7 G proteins (I) - monomeric G proteins. 7.1 Classification. 7.2 ON and OFF states of Ras-like proteins. 7.3 Raf - a multi-domain serine/threonine kinase family of Ras effectors. 7.4 Ras protein structure and function. 7.5 The switch mechanism: hydrolysis-driven conformational change in Ras. 7.6 GTP hydrolysis. References. 8 G proteins (II) - heterotrimeric G proteins. 8.1 Classification and structural relationship with Ras. 8.2 Ga-subunits: the Ras-like core, G-boxes and switch regions. 8.3 GTP exchange, hydrolysis and switch movements. 8.4 b/g- and receptor-binding surfaces of a-subunits. 8.5 Modulators of G protein activity - the 'RGS' protein family. 8.6 Signal transduction by b/c subunits. References. 9 The insulin receptor and the anabolic response. 9.1 The insulin receptor - a pre-dimerised RTK with a unique substrate. 9.2 InsR and IGF-IR: differentiation leads differential tissue effects. 9.3 Features of metabolic control in key tissues. 9.4 InsR downstream signalling pathways. 9.5 The insulin receptor substrate - a surrogate signal transduction particle. 9.6 IRS-1/2 phosphorylation and PI-3-kinase activation. 9.7 Protein phosphatase-1 (PP-1). 9.8 Insulin reverses effects of adrenaline and/or glucagon. 9.9 PIP3 downstream effects - glycogen synthesis. 9.10 Many questions remain. References. 10 Mitogens and cell cycle progression. 10.1 The mitogenic response and the cell division cycle. 10.2 G0, competency, and the point of no return in G1 - the 'R-point'. 10.3 Oncogene products derived from growth factor pathway components. 10.4 Transcription and cyclins. 10.5 Cyclin dependent kinases. 10.6 Deactivation by cyclin destruction. 10.7 Cyclin dependent kinases - activation through cyclin synthesis. 10.8 Mitogenic pathway downstream of single pass tyrosine kinase receptors. 10.9 CyclinD/Cdk-4/6 - only important substrate is RB. 10.10 Retinoblastoma-related 'pocket proteins' - negative modulators of E2F. 10.11 De-repression of the cyclin E gene by cyclin D/Cdk-4/6. 10.12 Cyclin A/Cdk-2 - S-phase progression and termination. 10.13 The controlled process of mammalian DNA replication. 10.14 Cyclin B translocations and M-phase. 10.15 Cdk inhibitors. 10.16 p53 cell cycle arrest and apoptosis. 10.17 7-pass receptors and mitosis. 10.18 Concluding remarks and caveats. References. Appendix 1: Worked examples. A.1 Enzyme and receptor assays worked out from raw data examples. A.1.1 An alkaline phosphatase assay. Appendix 2: RasMol: installation and use. Index.

Crystal Structures of the Lyn Protein Tyrosine Kinase Domain in Its Apo- and Inhibitor-bound State

The Src-family protein-tyrosine kinase (PTK) Lyn is the most important Src-family kinase in B cells, having both inhibitory and stimulatory activity that is dependent on the receptor, ligand, and developmental context of the B cell. An important role for Lyn has been reported in acute myeloid leukemia and chronic myeloid leukemia, as well as certain solid tumors. Although several Src-family inhibitors are available, the development of Lyn-specific inhibitors, or inhibitors with reduced off-target activity to Lyn, has been hampered by the lack of structural data on the Lyn kinase. Here we report the crystal structure of the non-liganded form of Lyn kinase domain, as well as in complex with three different inhibitors: the ATP analogue AMP-PNP; the pan Src kinase inhibitor PP2; and the BCR-Abl/Src-family inhibitor Dasatinib. The Lyn kinase domain was determined in its "active" conformation, but in the unphosphorylated state. All three inhibitors are bound at the ATP-binding site, with PP2 and Dasatinib extending into a hydrophobic pocket deep in the substrate cleft, thereby providing a basis for the Src-specific inhibition. Analysis of sequence and structural differences around the active site region of the Src-family PTKs were evident. Accordingly, our data provide valuable information for the further development of therapeutics targeting Lyn and the important Src-family of kinases.

Crystal Structures of the Mnk2 Kinase Domain Reveal an Inhibitory Conformation and a Zinc Binding Site

Human mitogen-activated protein kinases (MAPK)-interacting kinases 1 and 2 (Mnk1 and Mnk2) target the translational machinery by phosphorylation of the eukaryotic initiation factor 4E (eIF4E). Here, we present the 2.1 A crystal structure of a nonphosphorylated Mnk2 fragment that encompasses the kinase domain. The results show Mnk-specific features such as a zinc binding motif and an atypical open conformation of the activation segment. In addition, the ATP binding pocket contains an Asp-Phe-Asp (DFD) in place of the canonical magnesium binding Asp-Phe-Gly (DFG) motif. The phenylalanine of this motif sticks into the ATP binding pocket and blocks ATP binding as observed with inhibitor bound and, thus, inactive p38 kinase. Replacement of the DFD by the canonical DFG motif affects the conformation of Mnk2, but not ATP binding and kinase activity. The results suggest that the ATP binding pocket and the activation segment of Mnk2 require conformational switches to provide kinase activity.