Current Topics in Medicinal Chemistry - Volume 11, Issue 11, 2011

The present issue of CTMC aims at updating biological information of some important protein kinases (PKs) as basis for drug discovery, and frontline design and synthesis of novel compounds and biologics. Since discovery of staurosporine, an ATP-competitive non-selective kinase inhibitor, research on PK inhibitors has increased exponentially. A beautiful fruit of these efforts is imanitib, a small molecule PK inhibitor for the treatment of chronic myelogenous leukemia and gastrointestinal stromal tumors. Imatinib is an inhibitor of the tyrosine kinases BCR-ABL, c-KIT, and the platelet-derived growth factor receptor (PDGF) TK. Human genome encodes more than 500 PKs [1]. Protein kinases catalyse protein phosphorylation, an important means by which cell functions are regulated [2]. Aberrant expression of PKs, usually producing overactivity of a PK, leads to disease processes, e.g. the development of cancer. PKs are also major players in the signalling of cytokines and other mediators of inflammation. PK structures in non-mammalian cells such as in certain parasites (e.g. Leishmania sp.) differ from mammalian ones [3] and they are therefore most interesting targets for PK inhibitors. Degenerative brain diseases such as Alzheimer’s disease may in the future be therapeutic target for drugs acting on PKs. Thus, drugs affecting PKs (or more widely protein phosphorylation) may be of great importance in future treatment strategies of a large variety of diseases. Biologics, such as trastuzumab, are effective drugs acting on receptor tyrosine kinases (RTKs). However, most of the PKs are intracellular and biologicals are not able to enter the cell. Therefore, most of the effort has been used to develop small molecules that would penetrate the cell membranes and affect the intracellular PKs including intracellular domains of RTKs. Virtually all PK-inhibitors in clinical use today are targeted on the ATP binding site in the catalytic domain of the PKs. It is surprising that many of the drugs show rather good selectivity, although the ATP binding site in PKs is rather similar. Also allosteric inhibitors of PKs have been discovered that apparently is a way to overcome the structural similarity of the ATPbinding pocket [4]. Other possibilities to modify PK activity include regulatory domains of certain kinases such as PKA and PKC. PKCregulatory domain is unique to PKC and is not found in other PKs. The C1-domain of PKC is the binding site of DAG, the physiological activator of the enzyme. The C1-domain of various PKC-isoenzymes is an attractive drug-target, since the drugs would probably have specificity for PKCs over other kinases and it would also be possible to discover PKC-isozyme-selective inhibitors. The catalytic domain of various PKs is highly conserved, especially the ATP binding site. On the other hand, the region surrounding the sensu stricto ATP binding site is quite variable from one kinase to another and can be exploited for the specific binding of ligands that will act as selective inhibitors competing with ATP [5]. Anchoring proteins, such as the receptors for activated C-kinase, RACK1 and RACK2, bind to PKC?? and translocate it to the site of catalytic activity [6]. Several peptides inhibit the binding of PKCε to RACK1 or RACK2 [7]. The PKCε-derived octapeptide HDAPIGYD has been shown to be a PKCε agonist and prevents the heart from ischemic damage [8]. It is obvious that we need compounds that are rather selective to one or several kinases. Opposite to a major pharmacological principle, protein kinase inhibitors may not necessarily need to be specific to a single PK but, rather, could inhibit several “correct” kinases simultaneously. This is of course a major challenge to a rational and structure-based drug discovery and, indeed, there is an increasing need for better in vitro and in vivo models of diseases to test such compounds.

In recent years the development of small organic molecules modulating protein-protein interactions (P-PIs) has drawn major attention in both academic and industrial research. Despite the appreciable progress being made, targeting such extensive interaction areas with comparatively small, drug-like agents has proven to be an ambitious objective. This review highlights the reasons rendering this task highly challenging and provides an overview on the latest developments in rational design approaches for P-PI modulators. The significance, scope and limitations of computational methods in this particular field of research are analyzed. Recent successfully identified and designed P-PI modulators are discussed. Thereby, particular focus is taken on small organic molecules disrupting protein-protein interfaces of protein kinases.

Paullones are a class of molecules structurally based on the 7,12-dihydroindolo[3,2-d][1]benzazepin-6(5H)-one parent scaffold. Many of these structures are inhibitors of certain protein kinases, namely cyclin-dependent kinases and glycogen synthase kinase-3. Being well referenced in the literature on the one hand and commercially available on the other hand, paullones have been used as biochemical tools in basic research and drug development for more than a decade. This review gives an overview over the published reports regarding chemistry, biological activity and pharmacological applications of paullone derivatives.

Many of the protein kinase activators and inhibitors presently under investigation are natural products or are derivatives of natural products. Since over 500 kinases are encoded by the human genome, the task is to discover modulatory compounds which have high specificity for a single enzyme. Many different low molecular weight compounds have been studied for activity. These come from various sources, such as plants, marine organisms, microorganisms and cyanobacteria. The search for specific inhibitors is mainly performed in cell-based assays.

CK2 denotes a pleiotropic, constitutively active protein kinase whose abnormally high level in many cancer cells is held as an example of “non oncogene addiction”. A wide spectrum of cell permeable, fairly specific ATP sitedirected CK2 inhibitors are currently available which are proving useful to dissect its biological functions and which share the property of inducing apoptosis of cancer cells with no comparable effect on their “normal” counterparts. One of these, CX-4945, has recently entered clinical trials for the treatment of advanced solid tumors, Castelman's disease and multiple myeloma. The solution of a wide range of 3D structures of inhibitors bound to the catalytic subunits of CK2 reveals that their efficacy substantially relies on hydrophobic interactions within a cavity which is smaller than in other protein kinases. Accordingly the potency of tetra-halogenated benzimidazoles increases upon replacement of chlorine by bromine and, even more, by iodine, and decreases if two unique bulky side chains on CK2 (Val66 and Ile174) are mutated to alanines. Many CK2 inhibitors have been tested on a panel of more than 60 kinases providing Promiscuity Scores useful to evaluate their selectivity, the lowest value (9.47), denoting highest selectivity, being displayed by quinalizarin. The observation that CK2 inhibitors with medium/high promiscuity scores share the ability to inhibit a group of protein kinases as effectively as CK2 discloses the possibility of using their scaffolds for the rational development of selective inhibitors of these kinases, with special reference to PIMs, DYRKs, HIPK2, PKD and ERK8.

Signaling through protein kinases is an evolutionary conserved, widespread language of biological regulation. The eukaryotic type serine-threonine protein kinases (STPKs) found in normal human microbiote and in pathogenic bacteria play a key role in regulation of microbial survival, virulence and pathogenicity. Therefore, down-regulation of bacterial STPKs emerges as an attractive approach to cure infections. In this review we focused on actinobacterial STPKs to demonstrate that these enzymes can be used for crystal structure studies, modeling of 3D structure, construction of test systems and design of novel chemical libraries of low molecular weight inhibitors. In particular, the prototypic pharmacological antagonists of Mycobacterium tuberculosis STPKs are perspective for development of a novel generation of drugs to combat the socially important disease. These inhibitors may modulate both actinobacterial and host STPKs and trigger programmed death of pathogenic bacteria.

The second messenger diacylglycerol (DAG) plays a central role in the signal transduction of G-protein coupled receptors and receptor tyrosine kinases by binding to C1 domain of effector proteins. C1 domain was first identified in protein kinase C (PKC) which comprises a family of ten isoforms that play roles in diverse cellular processes such as proliferation, apoptosis and differentiation. Aberrant signaling through PKC isoforms and other C1 domain-containing proteins has been implicated in several pathological disorders. Drug discovery concerning C1 domains has exploited both natural products and rationally designed compounds. Currently, molecules from several classes of C1 domain-binding compounds are in clinical trials; however, still more have the potential to enter the drug development pipeline. This review gives a summary of the recent developments in C1 domain-binding compounds.

The prototype second messenger cAMP and its major mediator, the cAMP-dependent protein kinase (PKA), is able to control simultaneously multiple processes within the same cell. This appears to be achieved through its unique dissociative regulation and the spatiotemporal regulation of both cAMP and PKA. The widespread tissue distribution and physiological function of this pathway makes it an attractive, but challenging pharmacological target. We will discuss current progress in manipulating the fine-tuning of PKA, and outline so far underexploited possibilities for therapy, such as novel ways to target specific substrates and catalytic cycle intermediates of PKA. An attractive strategy to achieve a more focused pharmacological treatment is to combine more traditional targeting of extracellular receptors or ligands with that of intracellular signaling pathway components. The cAMP signaling pathway provides a variety of possibilities for such an approach.

Anaplastic Lymphoma Kinase (ALK) is a receptor tyrosine kinase that belongs to the Insulin receptor subfamily involved as full length receptor in neural development. Even if the expression of ALK protein is down-regulated in the adults, the ALK full length is expressed in different types of tumors. Moreover, chromosomal rearrangements, involving the alk gene, can occur leading to the formation of different ALK fusion proteins characterized by the kinase domain of ALK fused to several partners that determine cellular localization. Structural investigation and characterization of the ALK kinase domain in absence of its crystal structure constituted the basis of development of ALK small molecule inhibitors. Here, we described normal function of the ALK receptor and its role in tumors; formation of the constitutively activated ALK fusion proteins and we reported an update of developed small molecule inhibitors of the ALK kinase activity.