High-throughput structural biology in drug discovery: protein kinases

A newly identified Hippo homologue from the oriental river prawn Macrobrachium nipponense is involved in the antimicrobial immune response

The Hippo signalling pathway plays a vital role in organ size control, cell proliferation, apoptosis, and immune regulation. In this study, a Hippo homologue with three isoforms (named MnHippo-a, MnHippo-b, and MnHippo-c) was isolated and characterized for the first time from the freshwater prawn Macrobrachium nipponense. The deduced amino acid sequences of MnHippo-a (698 aa), MnHippo-b (688 aa), and MnHippo-c (656 aa) were highly similar, and they all contained an N-terminal S_TKc (serine/threonine protein kinase catalytic) domain and a C-terminal Mst1_SARAH (Sav/Rassf/Hpo) domain. MnHippo-a and MnHippo-c were derived from alternative splicing. Phylogenetic analysis was performed, and the results revealed that MnHippo was a member of the clade containing STPK4 and Hippo of Penaeus vannamei. The expression distribution showed that MnHippo was constitutively expressed in various tissues of uninfected prawns and highly expressed in the hepatopancreas and intestine. In prawns challenged with Vibrio parahaemolyticus and Staphylococcus aureus, the expression of MnHippo in haemocytes was significantly upregulated. Furthermore, in MnHippo-knockdown prawns injected with V. parahaemolyticus or S. aureus, the transcription levels of five antimicrobial peptides were downregulated. MnHippo silencing weakened the clearance of V. parahaemolyticus and S. aureus in prawns. The survival rate of the MnHippo-dsRNA group was obviously decreased from 2 to 6 days post-injection with V. parahaemolyticus or S. aureus. Hence, MnHippo might be involved in the antibacterial immune defence of M. nipponense.

Manipulation of Focal Adhesion Signaling by Pathogenic Microbes

Focal adhesions (FAs) serve as dynamic signaling hubs within the cell. They connect intracellular actin to the extracellular matrix (ECM) and respond to environmental cues. In doing so, these structures facilitate important processes such as cell-ECM adhesion and migration. Pathogenic microbes often modify the host cell actin cytoskeleton in their pursuit of an ideal replicative niche or during invasion to facilitate uptake. As actin-interfacing structures, FA dynamics are also intimately tied to actin cytoskeletal organization. Indeed, exploitation of FAs is another avenue by which pathogenic microbes ensure their uptake, survival and dissemination. This is often achieved through the secretion of effector proteins which target specific protein components within the FA. Molecular mimicry of the leucine-aspartic acid (LD) motif or vinculin-binding domains (VBDs) commonly found within FA proteins is a common microbial strategy. Other effectors may induce post-translational modifications to FA proteins through the regulation of phosphorylation sites or proteolytic cleavage. In this review, we present an overview of the regulatory mechanisms governing host cell FAs, and provide examples of how pathogenic microbes have evolved to co-opt them to their own advantage. Recent technological advances pose exciting opportunities for delving deeper into the mechanistic details by which pathogenic microbes modify FAs.

Structure-activity relationships of Wee1 inhibitors: A review

Wee1 kinase plays an important role in regulating G2/M checkpoint and S phase, and the inhibition of it will lead to mitotic catastrophe in cancer cells with p53 mutation or deletion. Therefore, the mechanism of Wee1 kinase in cancer treatment and the development of its inhibitors have become a research hotspot. However, although a variety of Wee1 inhibitors with different scaffolds and considerable activity have been successfully identified, so far no one has systematically summarized the structure-activity relationships (SARs) of Wee1 inhibitors. Previous reviews mainly focused on its mechanism and clinical application. To facilitate the rational design and development of Wee1 inhibitors in the future, this paper systematically summarizes its structural types, SARs and binding modes according to the Wee1 inhibitors reported in scientific journals, and also summarizes the regulatory effect of Wee1 kinase on cell cycle and the progress of its inhibitors in clinical application.

Basic concepts and physical-chemical phenomena, that have conceptual meaning for the formation of systemic clinical thinking and formalization of the knowledge of systemic structural-functional organization of the human’s organism

From the point of view of perception and generalization processes there are complex, logic and conceptual forms of thinking. Its conceptual form is the highest result of interaction between thinking and speech. While realizing it, human uses the concept, which are logically formed thoughts, that are the meaning of representation in thinking of unity of meaningful features, relations of subjects or phenomena of objective reality. Special concepts, that are used in the science and technique are called terms. They perform a function of corresponding, special, precise marking of subjects and phenomena, their features and interactions. Scientific knowledge are in that way an objective representation of material duality in our consciousness. Certain complex of terms forms a terminological system, that lies in the basis of corresponding sphere of scientific knowledge and conditions a corresponding form and way of thinking. Clinical thinking is a conceptual form, that manifests and represents by the specialized internal speech with gnostic motivation lying in its basis. Its structural elements are corresponding definitions, terms and concepts. Cardinal features of clinical systems are consistency, criticality, justification and substantiation. Principles of perception and main concepts are represented in the article along with short descriptions of physical and chemical phenomena, that have conceptual meaning for the formation of systematic clinical thinking and formalization of systemic structural-functional organization of the human’s organism

Novel method to identify group-specific non-catalytic pockets of human kinome for drug design

Kinase proteins have been intensively investigated as drug targets for decades because of their crucial involvement in many biological pathways. We developed hybrid approach to identify non-catalytic pockets and will benefit the kinome drug design.

Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume

Prunus mume is an important ornamental woody plant that grows in tropical and subtropical regions. Freezing stress can adversely impact plant productivity and limit the expansion of geographical locations. Understanding cold-responsive genes could potentially bring about the development of new ways to enhance plant freezing tolerance. Members of the serine/threonine protein kinase (CIPK) gene family play important roles in abiotic stress. However, the function of CIPK genes in P. mume remains poorly defined. A total of 16 CIPK genes were first identified in P. mume. A systematic phylogenetic analysis was conducted in which 253 CIPK genes from 12 species were divided into three groups. Furthermore, we analysed the chromosomal locations, molecular structures, motifs and domains of CIPK genes in P. mume. All of the CIPK sequences had NAF domains and promoter regions containing cis-acting regulatory elements of the related stress response. Three PmCIPK genes were identified as Pmu-miR172/167-targeted sites. Transcriptome data showed that most PmCIPK genes presented tissue-specific and time-specific expression profiles. Nine genes were highly expressed in flower buds in December and January, and 12 genes were up-regulated in stems in winter. The expression levels of 12 PmCIPK genes were up-regulated during cold stress treatment confirmed by qRT-PCR. Our study improves understanding of the role of the PmCIPK gene family in the low temperature response in woody plants and provides key candidate genes and a theoretical basis for cold resistance molecular-assisted breeding technology in P. mume.

Targeting Receptor Kinases in Colorectal Cancer

Colorectal cancer is the third most common malignancy in men and the second most common cancer in women. Despite the success of screening programs and the development of adjuvant therapies, the global burden of colorectal cancer is expected to increase by 60% to more than 2.2 million new cases and 1.1 million deaths by 2030. In recent years, a great effort has been made to demonstrate the utility of protein kinase inhibitors for cancer treatment. Considering this heterogeneous disease is defined by mutations that activate different Receptor Tyrosine Kinases (RTKs) and affect downstream components of RTK-activated transduction pathways, in this review we analyze the potential utility of different kinase inhibitors for colorectal cancer treatment.

Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches

Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay.

Design, synthesis, and bioactivity evaluation of antitumor sorafenib analogues

Malignant tumors are a serious threat to human health and are generally treated with chemical therapy.

Structural features of human inositol phosphate multikinase rationalize its inositol phosphate kinase and phosphoinositide 3-kinase activities

Human inositol phosphate multikinase (HsIPMK) critically contributes to intracellular signaling through its inositol-1,4,5-trisphosphate (Ins(1,4,5)P₃) 3-kinase and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P₂) 3-kinase activities. This catalytic profile is not conserved; orthologs from Arabidopsis thaliana and Saccharomyces cerevisiae are predominantly Ins(1,4,5)P₃ 6-kinases, and the plant enzyme cannot phosphorylate PtdIns(4,5)P₂ Therefore, crystallographic analysis of the yeast and plant enzymes, without bound inositol phosphates, do not structurally rationalize HsIPMK activities. Here, we present 1.6-Å resolution crystal structures of HsIPMK in complex with either Ins(1,4,5)P₃ or PtdIns(4,5)P₂ The Ins(1,4,5)P₃ headgroup of PtdIns(4,5)P₂ binds in precisely the same orientation as free Ins(1,4,5)P₃ itself, indicative of evolutionary optimization of 3-kinase activities against both substrates. We report on nucleotide binding between the separate N- and C-lobes of HsIPMK. The N-lobe exhibits a remarkable degree of conservation with protein kinase A (root mean square deviation = 1.8 Å), indicating common ancestry. We also describe structural features unique to HsIPMK. First, we observed a constrained, horseshoe-shaped substrate pocket, formed from an α-helix, a 3₁₀ helix, and a recently evolved tri-proline loop. We further found HsIPMK activities rely on a preponderance of Gln residues, in contrast to the larger Lys and Arg residues in yeast and plant orthologs. These conclusions are supported by analyzing 14 single-site HsIPMK mutants, some of which differentially affect 3-kinase and 6-kinase activities. Overall, we structurally rationalize phosphorylation of Ins(1,4,5)P₃ and PtdIns(4,5)P₂ by HsIPMK.

Quinoxaline-Based Scaffolds Targeting Tyrosine Kinases and Their Potential Anticancer Activity

Quinoxaline derivatives, also called benzopyrazines, are an important class of heterocyclic compounds. Quinoxalines have drawn great attention due to their wide spectrum of biological activities. They are considered as an important basis for anticancer drugs due to their potential activity as protein kinase inhibitors. In this review, we focus on the chemistry of the quinoxaline derivatives, the strategies for their synthesis, their potential activities against various tyrosine kinases, and on the structure-activity relationship studies reported to date.

Mechanosensitivity and compositional dynamics of cell-matrix adhesions

Cells perceive information about the biochemical and biophysical properties of their tissue microenvironment through integrin-mediated cell-matrix adhesions, which connect the cytoskeleton with the extracellular matrix and thereby allow cohesion and long-range mechanical connections within tissues. The formation of cell-matrix adhesions and integrin signalling involves the dynamic recruitment and assembly of an inventory of proteins, collectively termed the 'adhesome', at the adhesive site. The recruitment of some adhesome proteins, most notably the Lin11-, Isl1- and Mec3-domain-containing proteins, depends on mechanical tension generated by myosin II-mediated contractile forces exerted on cell-matrix adhesions. When exposed to force, mechanosensitive adhesome proteins can change their conformation or expose cryptic-binding sites leading to the recruitment of proteins, rearrangement of the cytoskeleton, reinforcement of the adhesive site and signal transduction. Biophysical methods and proteomics revealed force ranges within the adhesome and cytoskeleton, and also force-dependent changes in adhesome composition. In this review, we provide an overview of the compositional dynamics of cell-matrix adhesions, discuss the most prevalent functional domains in adhesome proteins and review literature and concepts about mechanosensing mechanisms that operate at the adhesion site.

Prediction of the three-dimensional structure of serine/threonine protein kinase pto of Solanum lycopersicum by homology modelling

The resistant gene Pto of Solanum lycopersicum interacts with the avr Pto gene product of the bacterial pathogen Pseudomonas syringae pv tomato to launch a cascade of molecular events that triggers the hypersensitive disease-resistance response in tamato. The paper describes attempts to predict the structure of Pto encoding a serine/threonine protein kinase to understand the mechanism and function. A three-dimensional model based on the crystal structure of effect protein Avr ptob complexed with Kinase Pto and bacterial effector protein Avrpto was generated using Modeller9v7. We adopted different modelling approaches for our study, Intialy, we generated a model based on a single template protein and then a model based on multiple templates. The models generated through these approaches were further assessed with ANOLEA energy assessment, Ram Page server and PROCHECK for stereochemistry and geometry check. Comparative analysis suggested that the model generated was better than the templates. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in studying protein-protein interactions.

Polo-like kinases and DNA damage checkpoint: beyond the traditional mitotic functions

Polo-like kinases (Plks) are a family of serine-threonine kinases that play a pivotal role in cell cycle progression and in cellular response to DNA damage. The Plks are highly conserved from yeast to mammals. There are five Plk family members (Plk1-5) in humans, of which Plk1, is the best characterized. The Plk1 isoform is being aggressively pursued as a target for cancer therapy, following observations that this protein is overexpressed in human tumors and is actively involved in malignant transformation. The roles of Plks in mitotic entry, spindle pole functions and cytokinesis are well established and have been the subject of several recent reviews. In this review, we discuss functions of Plks other than their classical roles in mitotic progression. When cells incur DNA damage, they activate checkpoint mechanisms that result in cell cycle arrest and allow time for repair. If the damage is extensive and cannot be repaired, cells will undergo cell death by apoptosis. If the damage is repaired, cells can resume cycling, as part of the process known as checkpoint recovery. If the damage is not repaired or incompletely repaired, cells can override the checkpoint and resume cycling with damaged DNA, a process called checkpoint adaptation. The Plks play a role in all three outcomes and their involvement in these processes will be the subject of this review.

Enzymatic and functional analysis of a protein phosphatase, Pph3, from Myxococcus xanthus

A protein phosphatase, designated Pph3, from Myxococcus xanthus showed the enzymatic characteristics of PP2C-type serine/threonine protein phosphatases, which are metal ion-dependent, okadaic acid-insensitive protein phosphatases. The pph3 mutant under starvation conditions formed immature fruiting bodies and reduced sporulation.

Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening

The growing interest in the identification of kinase inhibitors, promising therapeutics in the treatment of many diseases, has created a demand for the structural characterization of the entire human kinome. At the outset of the drug development process, the lead-finding stage, approaches that enrich the screening library with bioactive compounds are needed. Here, protein structure based methods can play an important role, but despite structural genomics efforts, it is unlikely that the three-dimensional structures of the entire kinome will be available soon. Therefore, at the proteome level, structure-based approaches must rely on predicted models, with a key issue being their utility in virtual ligand screening. In this study, we employ the recently developed FINDSITE/Q-Dock ligand homology modeling approach, which is well-suited for proteome-scale applications using predicted structures, to provide extensive structural and functional characterization of the human kinome. Specifically, we construct structure models for the human kinome; these are subsequently subject to virtual screening against a library of more than 2 million compounds. To rank the compounds, we employ a hierarchical approach that combines ligand- and structure-based filters. Modeling accuracy is carefully validated using available experimental data with particularly encouraging results found for the ability to identify, without prior knowledge, specific kinase inhibitors. More generally, the modeling procedure results in a large number of predicted molecular interactions between kinases and small ligands that should be of practical use in the development of novel inhibitors. The data set is freely available to the academic community via a user-friendly Web interface at http://cssb.biology.gatech.edu/kinomelhm/ as well as at the ZINC Web site ( http://zinc.docking.org/applications/2010Apr/Brylinski-2010.tar.gz ).

Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach

Many drug candidates fail in clinical development due to their insufficient selectivity that may cause undesired side effects. Therefore, modern drug discovery is routinely supported by computational techniques, which can identify alternate molecular targets with a significant potential for cross-reactivity. In particular, the development of highly selective kinase inhibitors is complicated by the strong conservation of the ATP-binding site across the kinase family. In this paper, we describe X-React(KIN), a new machine learning approach that extends the modeling and virtual screening of individual protein kinases to a system level in order to construct a cross-reactivity virtual profile for the human kinome. To maximize the coverage of the kinome, X-React(KIN) relies solely on the predicted target structures and employs state-of-the-art modeling techniques. Benchmark tests carried out against available selectivity data from high-throughput kinase profiling experiments demonstrate that, for almost 70% of the inhibitors, their alternate molecular targets can be effectively identified in the human kinome with a high (>0.5) sensitivity at the expense of a relatively low false positive rate (<0.5). Furthermore, in a case study, we demonstrate how X-React(KIN) can support the development of selective inhibitors by optimizing the selection of kinase targets for small-scale counter-screen experiments. The constructed cross-reactivity profiles for the human kinome are freely available to the academic community at http://cssb.biology.gatech.edu/kinomelhm/ .

In vitro selection of a DNA-templated small-molecule library reveals a class of macrocyclic kinase inhibitors

DNA-templated organic synthesis enables the translation of DNA sequences into synthetic small-molecule libraries suitable for in vitro selection. Previously, we described the DNA-templated multistep synthesis of a 13,824-membered small-molecule macrocycle library. Here, we report the discovery of small molecules that modulate the activity of kinase enzymes through the in vitro selection of this DNA-templated small-molecule macrocycle library against 36 biomedically relevant protein targets. DNA encoding selection survivors was amplified by PCR and identified by ultra-high-throughput DNA sequencing. Macrocycles corresponding to DNA sequences enriched upon selection against several protein kinases were synthesized on a multimilligram scale. In vitro assays revealed that these macrocycles inhibit (or activate) the kinases against which they were selected with IC(50) values as low as 680 nM. We characterized in depth a family of macrocycles enriched upon selection against Src kinase, and showed that inhibition was highly dependent on the identity of macrocycle building blocks as well as on backbone conformation. Two macrocycles in this family exhibited unusually strong Src inhibition selectivity even among kinases closely related to Src. One macrocycle was found to activate, rather than inhibit, its target kinase, VEGFR2. Taken together, these results establish the use of DNA-templated synthesis and in vitro selection to discover small molecules that modulate enzyme activities, and also reveal a new scaffold for selective ATP-competitive kinase inhibition.

The novel mouse Polo-like kinase 5 responds to DNA damage and localizes in the nucleolus

Polo-like kinases (Plk1-4) are emerging as an important class of proteins involved in many aspects of cell cycle regulation and response to DNA damage. Here, we report the cloning of a fifth member of the polo-like kinase family named Plk5. DNA and protein sequence analyses show that Plk5 shares more similarities with Plk2 and Plk3 than with Plk1 and Plk4. Consistent with this observation, we show that mouse Plk5 is a DNA damage inducible gene. Mouse Plk5 protein localizes predominantly to the nucleolus, and deletion of a putative nucleolus localization signal (NoLS) within its N-terminal moiety disrupts its nucleolar localization. Ectopic expression of Plk5 leads to cell cycle arrest in G1, decreased DNA synthesis, and to apoptosis, a characteristic it shares with Plk3. Interestingly, in contrast to mouse Plk5 gene, the sequence of human Plk5 contains a stop codon that produces a truncated protein lacking part of the kinase domain.

Design and evaluation of hydroxamate derivatives as metal-mediated inhibitors of a protein tyrosine kinase

Protein tyrosine kinases use two Mg(2+) ions as cofactors in catalysis, one as the ATP-Mg complex (M1) and the other as an essential activator (M2). The M2-binding site has high affinity for transition metal cations such as cobalt and zinc. Taking advantage of this high affinity, we examined hydroxamates as metal-mediated inhibitors against C-terminal Src kinase (Csk), a protein tyrosine kinase. Of a small group of amino acid hydroxamates, tyrosine and phenylalanine hydroxamates inhibited Csk activity only in the presence of Co(2+). Four classes of phenylalanine and tyrosine hydroxamate derivatives were synthesized and evaluated as metal-mediated inhibitors of Csk, leading to improved inhibition and a better understanding of the structure-activity relationships. This study suggests that hydroxamates may serve as a general scaffold for developing metal-mediated inhibitors against protein tyrosine kinases. To the best of our knowledge, this is the first report of designing metal-mediated inhibitors against a protein tyrosine kinase by targeting a metal binding site.

Pyrazolo[3,4-d]pyrimidines as Potent Antiproliferative and Proapoptotic Agents toward A431 and 8701-BC Cells in Culture via Inhibition of c-Src Phosphorylation

We report here the synthesis of new pyrazolo[3,4-d]pyrimidine derivatives along with their biological properties as inhibitors of isolated Src and cell line proliferation (A431 and 8701-BC cells). Such compounds block the growth of cancer cells by interfering with the phosphorylation of Src, and they act as proapoptotic agents through the inhibition of the anti apoptotic gene BCL2. Several of them were found to be more active than the reference compound (1-(tert-butyl)-3-(4-chlorophenyl)-4-aminopyrazolo[3,4-d]pyrimidine, PP2) in inhibiting cell proliferation and in inducing apoptosis, and as active as PP2 in the inhibition of the phosphorylation of isolated Src. Moreover, molecular modeling simulations have been performed to hypothesize the way, at the molecular level, by which the inhibitors were able to act as antiproliferative agents.

Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validation

Kinases catalyze the phosphorylation of proteins, lipids, sugars, nucleosides, and other important cellular metabolites and play key regulatory roles in all aspects of eukaryotic cell physiology. Here, we describe the mining of public databases to collect the sequence information of all identified human kinase genes and the cloning of the corresponding ORFs. We identified 663 genes, 511 encoding protein kinases, and 152 encoding nonprotein kinases. We describe the successful cloning and sequence verification of 270 of these genes. Subcloning of this gene set in mammalian expression vectors and their use in high-throughput cell-based screens allowed the validation of the clones at the level of expression and the identification of previously uncharacterized modulators of the survivin promoter. Moreover, expressions of the kinase genes in bacteria, followed by autophosphorylation assays, identified 21 protein kinases that showed autocatalytic activity. The work described here will facilitate the functional assaying of this important gene family in phenotypic screens and their use in biochemical and structural studies.

Structure and function of Polo-like kinases

Polo-like kinases play critical roles during multiple stages of cell cycle progression. All Polo-like kinases contain an N-terminal Ser/Thr kinase catalytic domain and a C-terminal region that contains one or two Polo-boxes. For Polo-like kinase 1, 2, and 3, and their homologs, the entire C-terminal region, including both Polo-boxes, functions as a single modular phosphoserine/threonine-binding domain known as the Polo-box domain (PBD). In the absence of a bound substrate, the PBD inhibits the basal activity of the kinase domain. Phosphorylation-dependent binding of the PBD to its ligands releases the kinase domain, while simultaneously localizing Polo-like kinases to specific subcellular structures. These observations suggest two different models for how the PBD integrates signals arising from other mitotic kinases to target the activated kinase towards distinct substrates. The recent X-ray crystal structures of the PBD provide insights into the structural basis for PBD function and kinase regulation. Molecular modelling of the structure of the isolated kinase domain reveals a potential basis for motif-dependent substrate specificity.