Current Pharmaceutical Design - Volume 18, Issue 20, 2012

Protein kinases (PKs) play key roles in signal transduction pathways. Therefore, aberrant PK activity can cause significant alterations in many important cellular processes such as transcription, proliferation, differentiation, angiogenesis, and inhibition of apoptosis, thereby contributing to a variety of illnesses including cancer, metabolic disorders, inflammation, autoimmune diseases, diabetes, etc [1]. More than 1000 X-ray crystal structures indicate that all PKs share certain structural similarities, comprising a small N-terminal lobe and a larger Cterminal lobe, with a highly conserved catalytic domain. ATP adjusts perfectly in a cleft between the lobes, and the protein substrate binds at the entrance of the cleft. PKs catalyze the transfer of the terminal γ-phosphate of the ATP to the hydroxyl group on the side chains of tyrosine, serine, or threonine residues of the substrate proteins. Phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. The discovery of PK inhibitors has attracted growing interest for novel drugs research and development [2]. The success of smallmolecule such as imatinib, nilotinib, and dasatinib for the treatment of chronic myelogenous leukemia, sunitinib and sorafenib for the treatment of renal cell carcinoma, gefitinib and erlotinib for the treatment of non-small-cell lung cancer, and lapatinib for the treatment of breast cancer and other solid tumours, confirm that ATP-competitive inhibitors are effective [3-5]. The discovery of ATP-competitive PK inhibitors has increased exponentially in the last years. Emerging knowledge of the both structure and the mechanism of action and modulation of PKs provided clues for the development of the new inhibition strategies. The design of ATP-competitive PK inhibitors faces a challenging selectivity problem because of the high structural homology between the ATP-binding site of PKs. Therefore, some novel strategies have been identified to explote other functionally critical binding sites. These approaches include substrate competitive inhibitors and targeting of allosteric sites that stabilize inactive conformations, and non-catalytic domains [6]....

Protein kinases are enzymes that catalyze the transfer of the γ-phosphate group from ATP to the hydroxyl groups in side chains of tyrosine, serine, or threonine. Protein kinases are divided in two classes: tyrosine kinases (TKs) and serine/threonine kinases (STKs). Overexpression or activation of protein tyrosine kinases (PTKs) has been found to be responsible for the development of many diseases, including cancer, inflammation, and many cardiovascular and neurodegenerative disorders. Thus, the design of PTK inhibitors (PTKIs) has become a subject of a major interest for the pharmaceutical industry. A number of marketed PTKIs that target conserved ATP binding site of PTKs were found to demonstrate toxicity (e.g., imitanib and sorafenib) or to generate resistance (e.g., imitanib and vemurafenib in chronic myeloid leukemia and metastatic melanoma, respectively). Thus, alternative strategies are urgently required for designing novel PTKIs. Linear peptides designed based on the natural protein substrates of PTKs have been introduced to target unique and non conserved PTK regions, such as substrate binding site. These compounds are more specific than the small molecules that usually target conserved ATP binding site. On the other hand, linear peptides are susceptible to hydrolysis by endogenous peptidases. Cyclization of linear peptides has led to generation of diverse conformationally constrained structures as PTKIs. Introduction of the conformational constraints enhances the stability towards proteases, the free energy upon binding, and binding affinity, but reduces the conformational entropy penalty upon receptor binding. Herein, design strategies for conformationally constrained peptides and their application as PTKIs are discussed.

The vascular endothelial growth factor (VEGF) is a key regulator of neovascularization and an elevated level of VEGF is known to correlate with increased metastatic invasion. Anti-angiogenic therapies focus on targeted inhibition of overexpressed growth factors with the aim of suppressing tumor proliferation, one approach is the attempt to block the intracellular tyrosine kinase at the adenosine triphosphate (ATP) binding site with small molecule inhibitors. For most effective treatment these targeted tumor therapies are accompanied with a more sensitive need for dose optimization and monitoring the therapeutic response. Direct non-invasive molecular imaging of tumor vascularization and of the angiogenic process in vivo would facilitate the selection of patients and help to evaluate the efficacy of an anti-angiogenic therapy. Radionuclide-based imaging technologies like PET and SPECT are progressively affecting the clinical diagnosis and treatment of cancer. A non-invasive and a reliable quantitative method to determine in vivo the levels of VEGFR expression using radiolabeled small molecules would help to develop a customized VEGFR-targeted chemotherapy. This review will give an overview on radiolabeled derivatives of small molecule VEGFR inhibitors basing on lead structures that have been approved or have reached clinical trials. It is covering aspects of the radiosynthesis as well the results of radiopharmacological and biological evaluation.

Protein kinases play central roles in cellular signaling pathways and their abnormal phosphorylation activity is inseparably linked with various human diseases. Therefore, modulation of kinase activity using potent inhibitors is an attractive strategy for the treatment of human disease. While most protein kinase inhibitors in clinical development are mainly targeted to the highly conserved ATP-binding sites and thus likely promiscuously inhibit multiple kinases including kinases unrelated to diseases, protein substratecompetitive inhibitors are more selective and expected to be promising therapeutic agents. Most substrate-competitive inhibitors mimic peptides derived from substrate proteins, or from inhibitory domains within kinases or inhibitor proteins. In addition, bisubstrate inhibitors are generated by conjugating substrate-competitive peptide inhibitors to ATP-competitive inhibitors to improve affinity and selectivity. Although structural information on protein kinases provides invaluable guidance in designing substrate-competitive inhibitors, other strategies including bioinformatics, computational modeling, and high-throughput screening are often employed for developing specific substrate-competitive kinase inhibitors. This review focuses on recent advances in the design and discovery of substrate-competitive inhibitors of protein kinases.

Deregulation of cyclin-dependent kinases (CDKs) has been associated with many cancer types and has evoked an interest in chemical inhibitors with possible therapeutic benefit. While most known inhibitors display broad selectivity towards multiple CDKs, recent work highlights CDK9 as the critical target responsible for the anticancer activity of clinically evaluated drugs. In this review, we discuss recent findings provided by structural biologists that may allow further development of highly specific inhibitors of CDK9 towards applications in cancer therapy. We also highlight the role of CDK9 in inflammatory processes and diseases.

In the last decade kinase inhibitors have emerged as a new class of very potent and relatively safe anticancer drugs. However, despite their success, off-target toxicities and induction of rapid resistance are major drawbacks that highly compromise successful longterm administration. In the current review, we provide an overview of the approaches that have been undertaken to overcome these issues by conjugation of these agents to carriers that enable their cellular and/or intracellular targeted delivery. Eventually, targeting kinase inhibitors will provide powerful treatment options not only for cancer, but also for other less-life threatening diseases that involve deregulated kinase signaling pathways.

The insulin-like growth factors (IGF) and their receptors play pivotal roles in cellular signaling transduction and thus regulate cell growth, differentiation, apoptosis, transformation and other important physiological progresses. The insulin-like growth factor 1 receptor (IGF-1R) mainly engages in the Ras/mitogen-activated protein kinase (MAPK) pathway and the phosphoinositide 3-kinase/protein kinase B (PI3K/AKT) pathway, and also forms cross-talk with the epidermal growth factor receptor (EGFR) pathway. Currently, it draws more attention since its overexpression has been demonstrated in various human cancers, such as colorectal cancer, breast cancer, prostate cancer and lung tumors, thus the strategy targeting the IGF-1R would be promising in treatment of these cancers. There are already dozens of agents developed for the inhibition of IGF-1R, which are categorized into monoclonal antibodies, small molecule inhibitors and so on. While in this review, small molecule inhibitors would be the focus for detailed discussion. Herein, we updated previously reported research papers and reviews in this field and summarized developments of small molecule inhibitors up to 2011. Finally, we proposed the application of network pharmacology methods to reconsider the clinical use of inhibitors with concomitant IR inhibition or other kinases inhibition, hoping that more optimal combinations would be obtained for cancer therapy.

Protein kinases are potential targets of drugs to treat many human diseases. Intensive efforts have been made to develop protein kinase inhibitors, but a major challenge is achieving specificity. Exploiting regulatory elements outside the ATP binding pocket, such as the substrate binding site, may provide an alternative that allows generation of competitive inhibitors with improved selectivity. Indepth understanding of substrate recognition by protein kinase is essential for design and refinement of competitive inhibitors. Here we described strategies for specifically targeting protein kinases and highlight our current progress in the development of substrate competitive inhibitors for glycogen synthase kinase-3 (GSK-3).

Angiogenesis and vasculogenesis, regulated by VEGF/VEGFR signaling pathways, play key roles in tumor growth and metastasis. Selective inhibition of VEGFR kinase has been explored as a highly successful clinical strategy in cancer treatment. A number of VEGFR inhibitors have been approved in clinical use and many more are in various stages of drug development. This paper reviews selective small-molecule VEGFR inhibitors in clinical uses and in clinical trials, with particular focus on in vitro, in vivo and clinical trial results of these inhibitors. The VEGF/VEGFR genes and signaling pathways involved in tumor angiogenesis, and the strategies for accessing and improving the therapeutic efficacy of VEGFR inhibitors are also discussed.

Over the past decade, therapeutics that target subsets of the 518 human protein kinases have played a vital role in the fight against cancer. Protein kinases are typically targeted at the adenosine triphosphate (ATP) binding cleft by type I and II inhibitors, however, the high sequence and structural homology shared by protein kinases, especially at the ATP binding site, inherently leads to polypharmacology. In order to discover or design truly selective protein kinase inhibitors as both pharmacological reagents and safer therapeutic leads, new efforts are needed to target kinases outside the ATP cleft. Recent advances include the serendipitous discovery of type III inhibitors that bind a site proximal to the ATP pocket as well as the truly allosteric type IV inhibitors that target protein kinases distal to the substrate binding pocket. These new classes of inhibitors are often selective but usually display moderate affinities. In this review we will discuss the different classes of inhibitors with an emphasis on bisubstrate and bivalent inhibitors (type V) that combine different inhibitor classes. These inhibitors have the potential to couple the high affinity and potency of traditional active site targeted small molecule inhibitors with the selectivity of inhibitors that target the protein kinase surface outside ATP cleft.

Protein kinases (PKs) are key components of protein phosphorylation based signaling networks in eukaryotic cells. They have been identified as being implicated in many diseases. High-resolution X-ray crystallographic data exist for many PKs and, in many cases, these structures are co-complexed with inhibitors. Although this valuable information confirms the precise structure of PKs and their complexes, it ignores the dynamic movements of the structures which are relevant to explain the affinities and selectivity of the ligands, to characterize the thermodynamics of the solvated complexes, and to derive predictive models. Atomistic molecular dynamics (MD) simulations present a convenient way to study PK-inhibitor complexes and have been increasingly used in recent years in structure-based drug design. MD is a very useful computational method and a great counterpart for experimentalists, which helps them to derive important additional molecular information. That enables them to follow and understand structure and dynamics of protein-ligand systems with extreme molecular detail on scales where motion of individual atoms can be tracked. MD can be used to sample dynamic molecular processes, and can be complemented with more advanced computational methods (e.g., free energy calculations, structure-activity relationship analysis). This review focuses on the most commonly applications to study PK-inhibitor complexes using MD simulations. Our aim is that researchers working in the design of PK inhibitors be aware of the benefits of this powerful tool in the design of potent and selective PK inhibitors.

The small GTPase RhoA and its downstream effector, Rho kinase (ROCK), appear to mediate numerous pathophysiological signals, including smooth muscle cell contraction, actin cytoskeleton organization, cell adhesion and motility, proliferation, differentiation and the expression of several genes. Clinical interest in the RhoA/ROCK pathway has increased, due to emerging evidence that this signaling pathway is involved in the pathogenesis of several diseases, including hypertension, coronary vasospasm, stroke, atherosclerosis, heart failure and diabetes; ROCK is considered an important future therapeutic target. Several pharmaceutical companies are already actively engaged in the development of ROCK inhibitors as the next generation of therapeutic agents for these diseases. This review discusses the relationship between diabetes and hyperglycemia-induced RhoA/ROCK activation, highlights recent findings on the roles of ROCK inhibitors from experimental models of diabetes and clinical studies in cardiovascular patients, and elucidates major challenges for developing more selective ROCK inhibitors. Accumulating evidence suggests the potential of ROCK inhibitors as therapeutic agents for diabetes and its complications.

Roscovitine is a synthetic inhibitor of cyclin-dependent kinases that is currently undergoing clinical trials as a candidate drug for some oncological indications. Its discovery prompted many research teams to further optimize its structure or to initiate their own related but independent studies. This article reviews known roscovitine bioisosteres that have been prepared as CDK inhibitors using different core heterocycles. The individual bioisostere types have been described and explored to a different extent, which complicates direct comparisons of their biochemical activity - only six direct analogs containing different purine bioisosteres have been prepared and evaluated side by side with roscovitine. Only four types of bioisosteres have demonstrated improved biological properties, namely pyrazolo[ 1,5-a]-1,3,5-triazines, pyrazolo[1,5-a]pyrimidines, pyrazolo[1,5-a]pyridines and pyrazolo[4,3-d]pyrimidines.

Thymidine kinase 2 (TK2), encoded on chromosome 16q22 of the human genome, is a deoxynucleoside kinase (dNK) that catalyzes the phosphorylation of the pyrimidine deoxynucleosides 2’-deoxythymidine (dThd), 2’-deoxyuridine (dUrd) and 2’- deoxycytidine (dCyd) to the corresponding deoxynucleoside 5’-monophosphate derivatives. In contrast to the S-phase-specific thymidine kinase 1 (TK1), TK2 is constitutively expressed in the mitochondria and plays an important role in providing dNTPs for the replication and maintenance of mitochondrial DNA (mtDNA). The severe mitochondrial DNA depletion syndrome (MDS) has been associated with mutations in TK2, resulting in mtDNA depletion, isolated skeletal myopathy, and death of the individual at an early stage of life. Some antiviral nucleoside analogs, such as 3’-azido-dThd (AZT) that is targeting the human immunodeficiency virus (HIV)-encoded reverse transcriptase, are substrates for TK2 and it has been proposed that the mitochondrial toxicity observed after prolonged treatment with such drugs could be due to their interaction with TK2. Therefore, the design of specific TK2 inhibitors may be useful to investigate the role of TK2 in the maintenance and homeostasis of mitochondrial dNTP pools and its contribution to the mitochondrial toxicity of several antiviral and anticancer drugs. Since 2000, several potent and selective TK2 inhibitors have been described. Besides bringing together previously reported inhibitors, special attention will be paid in this review to the new families of TK2 inhibitors more recently described, together with modeling studies and biological assays. Moreover, the last section will be focused on several recent investigations that suggest that depletion of mtDNA can take place both in tumorigenesis and during cancer treatment with certain nucleoside analogues.