Current Medicinal Chemistry - Volume 18, Issue 19, 2011

Protein kinases are responsible for key events in the cells, and their hyperactivation, overexpression or mutations have been detected in several human cancers. Kinase inhibitors are currently one of the most important classes of anticancer drugs, and both one-target-selective and dual or politargeted compounds have been approved for therapy of haematological or solid malignancies in the last decade, representing new important tools for the fight against cancer. Inhibition of a single kinase (Bcr-Abl in chronic myeloid leukemia and Kit in gastrointestinal stromal tumors) led to the discovery of fundamental drugs, such as imatinib, that can cure these diseases. However several cases of drug resistance have been reported and prompted the search for new compounds able to act on mutated enzymes and/or in the real tumor microenvironment that is characterized by marked gradients in drug concentration and by regions of hypoxia and acidity, all of which can influence tumor cell sensitivity to drug treatment. Moreover systems-wide analyses of tumors have recently identified receptor tyrosine kinase (RTK) coactivation as an important mechanism by which cancer cells achieve chemoresistance and for this reason also the research of multitargeted kinase inhibitors that might target both receptor and cytoplasmatic kinases, is very active. Indeed experiments and clinical data in different tumors show that a better cancer therapy can be obtained with a polypharmacology approach, by blocking several tumor cell biochemical pathways at once, accurately selecting critical targets and adjusting drug dosages for the best results. A great debate also exists whether to use peptides or small molecules, being the field of cyclin-dependent kinases (CDKs) an important example. Peptides are more selective being derived by the linear protein sequences, indeed they should mimic the catalytic or the regulatory subunits of the cell cycle controller complexes, but on the other side they usually present poorer pharmacokinetic characteristics. In contrast, small molecules have better pharmacokinetic features but lower specificity because many protein kinases show high sequence similarity within the active site. Kinases are also involved in HIV-1 replication cycle at the nuclear level, both directly through their catalytic activity on viral proteins and indirectly being activated by the virus. Alternatively, kinases may act indirectly such as in the case of DNA repair factors activated following HIV-1 infection and demonstrated to regulate the viral life cycle. Finally, inhibition of cellular kinases interacting with HIV-1 at the nuclear level has been shown to severely affect the viral replication cycle, thus suggesting potential new therapeutic approaches. The ever-deepening study of kinome addressed the interest also in kinases not yet targeted until now for the synthesis of potential drugs, such as protein kinase CK2, an ubiquitous and constitutively active protein kinase, that catalyzes the phosphorylation of more than 300 substrates or two other cytoplasmatic kinases, Fes and Fyn, both involved in cancer development and the latter also in CNS degenerative pathologies, such as Alzheimer's disease. The common problems faced by the antiviral and anticancer fields needs the integration of structural, biochemical and in silico modelling approaches for the development of novel highly active kinase inhibitors. Particularly the knowledge of protein kinase three-dimensional structure is of great help in the rational design of specific ligands and kinase homology modeling techniques have been widely diffused. The research in the field of kinase inhibition is extremely active, also due the high number of protein kinases identified, as evidenced by the increasing number of publications that appear in the literature daily. For these reasons new updates are always needed and in this special issue some of the most exciting studies on this topic are reported.

Tyrosine kinase inhibitors are currently one of the most important classes of cancer drugs, essentially because many kinases and regulators are molecules related to frequently mutated oncogenes and tumor suppressors. Many experiments and clinical data in different tumors show that better cancer therapy can be obtained by blocking several tumor cell biochemical pathways at once, accurately selecting critical targets and adjusting drug dosages for the best results. Through our direct experience in experimental models of prostate cancer (PCa), we discuss in this review the issues of tyrosine kinase inhibition in neoplastic cells and illustrate the opportunities to extend cancer proliferation control to other key biological targets of clinical interest, aiming at the realization of better polypharmacology applications in cancer chemotherapy. Briefly, in this review the main experimental evidences on the efficacy of tyrosine kinase inhibitors (TKIs) on PCa are described, together with a reasoned analysis of biological data which may be useful for a general extension to other clinical areas of cancer multitargeted and possibly individualized polychemotherapy.

Protein phosphorylation is one of the major pathways used by eukaryotic cells to propagate signals to the final effectors, regulating multiple aspects of the living cell, such as metabolism, growth, differentiation, adhesion, motility, genome stability and death. In this context, tyrosine kinases (TKs) play a central role in signal transduction and their overexpression or disregulated activity has been implicated in tumor onset and malignancy progression. To date, eight TKs inhibitors have been approved by FDA for the treatment of specific tumors. In spite of their efficacy, insurgence of resistance is a common feature after prolonged administration. The selective pressure by these drugs, in fact, induces clonal expansion of subsets of cancer cells harboring TKs mutations, leading to decreased inhibition potency. Alternatively, resistance to TK inhibitors can be acquired through the activation of others, often unrelated, TKs. For this reason, while stringent target selectivity of TKs inhibitors has been always considered a desirable feature in order to limit toxicity, molecules targeting different TKs have been recently shown to be promising anti-cancer agents as well. Understanding the molecular mechanisms that confer resistance to TK inhibitors, through a combination of enzymatic, structural and cellular studies, is essential in the development of second generation inhibitors active also towards drug resistant tumors.

Protein kinases are key regulators of cell function that constitute one of the largest and most functionally diverse gene families, and knowledge of their three-dimensional structure could be of great help in the rational design of specific ligands. However, only about one quarter of human protein kinase structures has been experimentally defined; thus, kinase homology modeling techniques have been widely diffused. In this review, the most recent kinase homology models are reported, together with the most recent approaches and the main validation methods.

Cell cycle regulation involves processes crucial to the survival of a cell, including the detection and repair of genetic damage as well as the prevention of uncontrolled cell division. The molecular events that control cell cycle are ordered and directional. Cyclins and cyclin-dependent kinases (CDKs), determine cell progression through the cycle ensuring the orderly coordination of cellular events. Alterations of cell cycle controllers are among the main causes of cancer onset. In the past decades many efforts have been made to develop kinase inhibitors that are able to modulate cyclin and CDK complexes, either by mimicking the function of natural CDK inhibitors, such as p21, p16 and p27, or by modulating the cyclin-CDK complexes or their targets directly. The great debate is whether to use peptides or small molecules. Peptides are more selective being derived by the linear protein sequences, indeed they should mimic the catalytic or the regulatory subunits of the cell cycle controller complexes, but on the other side they usually present poorer pharmacokinetic characteristics. In contrast, small molecules have better pharmacokinetic features but lower specificity because many protein kinases show high sequence similarity within the active site. The purpose of this review article is to provide an overview of the main classes of CDK inhibitors focusing on structure-activity relationship (SAR) studies and discussing the pharmacological and therapeutic implications.

Casein kinase 2 (CK2) is a ubiquitous, highly pleiotropic and essential protein kinase whose abnormally high constitutive activity has been implicated in several human diseases. In the last decade, several ATP competitive inhibitors of CK2, characterized by an in vitro activity that ranges from micromolar to nanomolar, have been discovered. However, until now only one drug candidate has been entered in Phase I clinical trial as a potential anticancer drug. Why this constitutively active kinase is so undruggable? Can ATP competitive inhibitors be considered the most promising drug candidates for the near future? In this review, we would like to underline how targeting binding sites outside the conventional ATP-binding could represent a new promising strategy to inhibit CK2 activity and, consequently, bear a great potentiality in discovering new drug candidates.

The tumor microenvironment is characterized, not only by marked gradients in drug concentration, but also by gradients in the rate of cell proliferation and by regions of hypoxia and acidity, all of which can influence tumor cell sensitivity to drug treatment. Hypoxia is also an important environmental factor in chronic myeloid leukemia (CML), because bone marrow is intrinsically hypoxic in nature. Systems-wide analyses of tumors have recently identified receptor tyrosine kinase coactivation as an important mechanism by which cancer cells achieve chemoresistance. Recent work suggests that Src activation might play a prominent role in the response to hypoxia to promote cell survival, progression, and metastasis of a variety of human cancer. Other studies also established a functional link between Bcr-Abl and the Src family tyrosine kinases. It is well known that mutations can also cause some tyrosine kinases to become constitutively active, a nonstop functional state that may contribute to initiation or progression of cancer as in CML. Leukemic cells carrying chromosomal alteration, are sensitive to imatinib that induces complete remission in most patients. This inhibitor is a highly selective Bcr-Abl tyrosine kinase inhibitor (TKI). There is a considerable interest in understanding how activated signaling pathways enhance tumor cell survival under hypoxia, because this might lead to the introduction of more effective treatments to target these resistant subpopulations. For all these reasons it is important to identify new TKIs which are also active in hypoxia, the real tumor microenvironment, as possible alternative therapy.

Kit is a growth factor receptor of the type III tyrosine kinase family, whose gain-of-function mutations have been identified as driving causes of different kinds of tumours. It thus represents a viable drug target, and the development of Kit inhibitors has been shown to be a promising therapeutic concept. This review will focus on structural and signalling properties of both wild-type and mutant Kit, as well as its role in the development of human cancers. Special attention will be dedicated to gastrointestinal stromal tumours, GISTs. Progress in research on the aetiopathogenesis of GISTs and their therapeutic approaches will be fully discussed, focusing on the latest tendencies for the treatment of these kinds of tumours.

The central events of HIV-1 life cycle occur at the nuclear level where the viral genome is integrated into the host cellular DNA in order to be expressed and replicated. The viral pre-integration complexes (PICs) are actively transported in the nuclear compartment where integration occurs in specific regions of the cellular chromatin. Similar to all viruses, HIV-1 encodes for a limited number of proteins that are insufficient to produce new viral progenies. Several cellular pathways are thus hijacked by HIV-1 to efficiently complete the replication cycle. The majority of viral proteins are substrates for cellular kinases indicating a pivotal role of these cellular enzymes at multiple steps of the HIV-1 life cycle. The nuclear biology of the cell is highly controlled by kinases (nuclear transport, DNA replication, repair and transcription) and many of these kinases also sustain the viral nuclear events. This review summarizes our current knowledge on kinases that are involved in HIV-1 replication cycle at the nuclear level, both directly through their catalytic activity on viral proteins and indirectly being activated by the virus. Among viral proteins directly modified by kinases is integrase (IN) the factor that catalyzes the integration of HIV-1 in the cellular genome. Notably, this recent discovery may shed light onto mechanisms underlying the different susceptibility of the main cell types targeted by HIV-1 (CD-4+ T-cell) depending on their activation status. Alternatively, kinases may act indirectly such as in the case of DNA repair factors activated following HIV-1 infection and demonstrated to regulate the viral life cycle. Finally, inhibition of cellular kinases interacting with HIV-1 at the nuclear level has been shown to severely affect the viral replication cycle, thus suggesting potential new therapeutic approaches.

Non receptor protein tyrosine kinases are targets in the treatment of a number of diseases. This review focuses on the role of Fes tyrosine kinase and on the design of inhibitors of this protein. Fes and its homologously related protein Fer are the only two members of a distinct class of non receptor tyrosine kinases and they seem to play a role in cytoskeletal rearrangements and inside-out signalling associated with receptor-ligand, cell-matrix and cell-cell interactions. The knowledge of the three dimensional structure of this protein, in fact, has informed drug design, while at the same time it has helped to shed some light on the molecular mechanism at the basis of kinase activation and functions.

Fyn is a non-receptor tyrosine kinase belonging to the Src family kinases. It has been shown to play important roles in neuronal functions, including myelination and oligodendrocytes formation, and in inflammatory processes. It has also demonstrated its involvement in signaling pathways that lead to severe brain pathologies, such as Alzheimer's and Parkinson's diseases. Moreover, Fyn is upregulated in some malignancies. Experimental studies demonstrated that Fyn inhibition could be useful in the disruption of metabolic processes involved in cancer and in neurodegenerative diseases. Unfortunately no specific Fyn inhibitor has been discovered so far, being the reported compounds active also on other members of Src family or on different tyrosine kinases. However, multitargeted inhibitors might be endowed with therapeutic potential. Indeed, as increasingly reported, also a not completely selective inhibitor of a specific protein could be therapeutically useful, affecting a number of cell pathways involved especially in cancer development. In this review, we report some examples of small molecule tyrosine kinase inhibitors for which data on Fyn inhibition, both in enzymatic and in cell assays, have been reported, with the aim of giving information as starting point for the researchers working in this field.

Chronic myeloid leukemia (CML) is a myeloproliferative disease originating from a constitutively active tyrosine kinase, called BCR-ABL, expressed by an oncogene resulting from a reciprocal translocation between chromosome 9 and chromosome 22, coded as (t[9,22][q34;q11]). Inhibition of BCR-ABL with tyrosine kinase inhibitors (TKI) proved to be an efficient targeted therapy of Philadelphia-positive (Ph+) CML in the chronic phase. This review mainly addresses the synthetic pathways and process chemistry leading to the large scale preparation for pre-clinical demands and clinical supply of the three TKIs approved for Ph+ CML, i.e., imatinib, dasatinib and nilotinib and three more investigational drugs, i.e., bosutinib, ponatinib and bafetinib. Recent progress on the biochemical profiling of the six examined TKIs has been also reported.

The mammalian target of rapamycin (mTOR) is frequently activated in epithelial ovarian cancer, and is regarded as an attractive therapeutic target for therapy. Preclinical investigations using rapamycin and its analogs have demonstrated significant growthinhibitory effects on the growth of ovarian cancer both in the setting of monotherapy and in combination with cytotoxic agents. Based on promising preclinical data, mTOR inhibitors are currently being evaluated in several phase I/II trials in patients with ovarian cancer. In an effort to overcome resistance to rapamycin and its analogs, the novel ATP-competitive mTOR inhibitors have recently been developed. In this report, we review the scientific rationale and evidence for the potential clinical benefits provided by mTOR inhibitor therapy for patients with epithelial ovarian cancer.

The worldwide dissemination of «multi-drug resistant» (MDR) pathogens has severely reduced the efficacy of our antibiotic arsenal and increased the frequency of therapeutic failure. MDR bacteria over-express efflux pumps and this active mechanism can extrude all classes of antibiotics from the cell. It is necessary to clearly decipher the genetic, structural and functional aspects of this transport system in order to combat this polyselective mechanism. By understanding how efflux pumps work we may be able to develop a new group of antibacterial agents, collectively termed efflux reversals, including membrane permeabilisers, efflux pump inhibitors and flux-competitive agents, specific blockers, energy poisons, etc. Several chemical families of efflux pump inhibitors have been described and characterized. Among them several inhibitor compounds demonstrate efficient blocking of the efflux pump activity involved in the MDR phenotype as observed in many Gram-negative clinical isolates. This new family of molecules represents the first antibacterial class of compound specifically targeting active transport in the bacterial cell.