1,721,077 research outputs found
Strategie computazionali per lo studio delle interazioni tra macromolecole e per la ricerca di nuovi inibitori di proteine chinasi
No full textThe concept of "druggable genome" limits the molecular targets for which commercially viable compounds can be developed. In humans, whose genome accounts for about 30,000 genes, it has been calculated that a subset of no more than 3,000 genes express proteins able to bind drug-like molecules. This limit derives from the fact that the ability of a protein to bind a small molecule with the appropriate chemical properties does not necessarily make it a potential drug target, this latter feature being only applied to proteins that are also linked to disease. Among these, it has become evident that the proteins participating in intra- or intercellular communication represent the largest family with about 20-25% of the druggable genome consisting of kinases followed by G-protein coupled receptors (15%) and cation channels (5%), three of the fundamental groups of proteins implicated in signal transduction. For this reason, protein kinases have turned out to be one of the richest target mines, since drugs inhibiting specific kinases are in constant development, and some of them are currently investigated in clinical trials such as Gleevec and Iressa. Most of the structural information currently available about protein kinases is resulting from the continuously growing number of crystallographic structures solved. These studies suggest that the overall architecture of the kinases is quite similar, however, since the ATP-binding site possesses some distinct subsites, different kinases can be targeted by quite selective drugs. Two main objectives will be pursued: a) a search for new potent and selective inhibitors and b) an analysis of the interactions between kinases and related substrates.
a) Our laboratory has a long-lasting expertise in targeting the human kinome, especially the protein kinase CK1, CK2 and Aurora-A, all implicated in carcinogenesis; we performed a new virtual screening approach searching for new potent and selective scaffolds against the three kinases. Virtual screening involves the rapid assessment of large libraries of chemical structures in order to guide the selection of potential drug candidates. The results obtained was really encouraging; in fact new good inhibitors for all the three kinases where obtained from the virtual screening strategy.
b) The interaction of protein kinases with their substrates and/or effectors represents a key event in the overall picture of cellular regulation. In the case of CK2 more than 300 substrates have been identified the majority of which are phosphorylated both in vitro and in vivo. Our purpose is to highlight the molecular features underlying the interaction between CK2 and its peptides or protein substrates by using our protein-protein docking approach. Protein-protein docking is a computational tool for the prediction of three-dimensional structure of protein complexes from the coordinates of the component's structure
The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design
Full text linkCasein kinase II (CK2) is an ubiquitous and pleiotropic serine/threonine protein kinase able to phosphorylate hundreds of substrates. Being implicated in several human diseases, from neurodegeneration to cancer, the biological roles of CK2 have been intensively studied. Upregulation of CK2 has been shown to be critical to tumor progression, making this kinase an attractive target for cancer therapy. Several CK2 inhibitors have been developed so far, the first being discovered by “trial and error testing”. In the last decade, the development of in silico rational drug design has prompted the discovery, de novo design and optimization of several CK2 inhibitors, active in the low nanomolar range. The screening of big chemical libraries and the optimization of hit compounds by Structure Based Drug Design (SBDD) provide telling examples of a fruitful application of rational drug design to the development of CK2 inhibitors. Ligand Based Drug Design (LBDD) models have been also applied to CK2 drug discovery, however they were mainly focused on methodology improvements rather than being critical for de novo design and optimization. This manuscript provides detailed description of in silico methodologies whose applications to the design and development of CK2 inhibitors proved successful and promising
Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery
No full textThe search for new compounds with a given biological activity requires enormous effort in terms of manpower and cost. This effort arises from the large number of compounds that need to be synthesized and subsequently biologically evaluated. For this reason the pharmaceutical industry has shown great interest in theoretical methods that enable the rational design of pharmaceutical agents. In the last years bioinformatics has experienced a great evolution due to the development of specialized software and to the increasing computer power. The codification of the structural information of molecules through molecular descriptors and the subsequent data analysis allow establishing QSAR models (Quantitative Structure-Activity Relationship) that can be applied to the design and the virtual screening of new drugs. The development of sophisticated Docking methodologies also allows a more accurate predict of the biological activity of molecules. Moreover, through this type of computational techniques and theoretical approaches, it is possible to develop explanatory hypothesis on the mechanism of action of drugs. This work provides a brief description of a series of studies implemented in the software MOE (Molecular Operating Environment) with particular attention to the medicinal chemistry aspects
Kinase CK2 Inhibition: An Update
No full textProtein kinase CK2 (Casein Kinase 2) is an essential, ubiquitous and highly pleiotropic protein kinase, implicated in several human diseases. In the last decade, several inhibitors of CK2, have been discovered and characterized to be ATP-competitive compounds. However, only one of them, CX-4945, has recently completed Phase I clinical trial as potential anticancer drug. In this review, we report all chemical classes of CK2 inhibitors available in literature, focusing our attention on conventional ATP-competitive and on non ATP-competitive inhibitors, which could represent a new frontier in CK2 inhibition and, consequently, a promising field of study in discovering new drug candidates. © 2013 Bentham Science Publishers
Protein Kinase CK2 Inhibitors: Emerging Anticancer Therapeutic Agents?
No full textProtein kinase CK2 is a ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. A number of structurally unrelated CK2 inhibitors, tested on a variety of cells derived from tumours, including lymphomas, leukaemias, multiple myeloma and prostate carcinoma, display a pro-apoptotic effect which is roughly proportional to their in vitro inhibitory potency. In the present review we summarize the most recent discovery of potent and selective CK2 inhibitors and their prospective as future anticancer agents
The acidophilic kinases PLK2 and PLK3: structure, substrate targeting and inhibition
No full textPLK2 and PLK3 are two closely related acidophilic kinases belonging to the Polo-like kinases (PLKs), a family of five members in mammals with a central role in cell cycle and related events. PLK1 is the most investigated enzyme from both physiological and pharmaceutical points of view, however, several specialized cellular functions of PLK2 and PLK3 have been recently discovered paving the way to deepened studies on their biological roles and their feasible selection as future therapeutic targets. Our review aims to provide a summarized view of the current knowledge regarding PLK2 and PLK3 kinases, including substrate specificity and signaling pathways directly affected by these kinases. Finally, an overview of PLK2 and PLK3 pharmacological regulation and perspectives in future achievements are proposed
A novel glucosyltransferase from Catharanthus roseus cell suspensions
No full textThe potential applications of glycosyltransferases in glycoconjugate synthesis have attracted considerable interest from the biotechnology community in recent years. In this work, we present a novel glucosyltransferase from Catharanthus roseus cell cultures. The enzyme was purified to one spot in SDS-polyacrylamide gel electrophoresis, and its molecular weight was about 51 kDa. The optimum temperature was 35 °C, and the optimum pH was 7.6. Sodium ion has weak effect on enzyme activity, whereas divalent ions inhibit enzyme activity strongly. The Km values were 0.112, 0.077, 0.064 and 1.0 mM for scopoletin, 5,7-dihydroxyflavone, 5,7-dihydroxyflavanone and UDPG, respectively. Substrate screening with the purified enzyme was performed against a range of phenolic compounds using UDPG as sugar donor. The enzyme showed activity towards a number of coumarins including umbelliferone, scopoletin, isoscopoletin and esculetin, and flavonoids including a flavone, a flavanone and chalcones. No activity was detected with compounds characterized by a single aromatic ring, i.e. simple and acidic phenols. The substrate specificity and the regioselectivity suggest enzyme structural features that are different from those of other glucosyltransferase
The Selectivity of CK2 Inhibitor Quinalizarin: A Reevaluation
Full text linkMany polyphenolic compounds have been reported to inhibit protein kinases, with special reference to CK2, a pleiotropic serine/threonine kinase, implicated in neoplasia, neurodegenerative disease, and viral infections. In general however these compounds are not endowed with stringent selectivity. Among them quinalizarin (1,2,5,8-tetrahydroxyanthraquinone) turned out to be particularly potent (Ki = 0.058 μM) and quite selective as judged by profiling it on a small panel of 70 protein kinases. Here, by profiling quinalizarin on a larger panel of 140 kinases we reach the conclusion that quinalizarin is one of the most selective inhibitors of CK2, superior to the first-in-class CK2 inhibitor, CX-4945, now in clinical trials for the treatment of cancer. Moreover here we show that quinalizarin is able to discriminate between the isolated CK2 catalytic subunit (CK2α) and CK2 holoenzyme (CK2α2 β2), consistent with in silico and in vitro analyses
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