Advances in the structural biology, design and clinical development of Bcr-Abl kinase inhibitors for the treatment of chronic myeloid leukaemia

The constitutively activated Abl tyrosine kinase domain of the chimeric Bcr-Abl oncoprotein is responsible for the transformation of haematopoietic stem cells and the symptoms of chronic myeloid leukaemia (CML). Imatinib targets the tyrosine kinase activity of Bcr-Abl and is a first-line therapy for this malignancy. Although highly effective in chronic phase CML, patients who have progressed to the advanced phase of the disease frequently fail to respond to imatinib or develop resistance to therapy and relapse. This is often due to the emergence of clones expressing mutant forms of Bcr-Abl, which exhibit a decreased sensitivity towards inhibition by imatinib. Considerable progress has recently been made in understanding the structural biology of Abl and the molecular basis for resistance, facilitating the discovery and development of second generation drugs designed to combat mutant forms of Bcr-Abl. The first of these compounds to enter clinical development were BMS-354825 (BristolMyersSquibb) and AMN107 (Novartis Pharma) and, from Phase I results, both of these promise a breakthrough in the treatment of imatinib-resistant CML. Recent advances with these and other promising classes of new CML drugs are reviewed.     

Ontogeny and regulation of IL-7-expressing thymic epithelial cells

Epithelial cells in the thymus produce IL-7, an essential cytokine that promotes the survival, differentiation, and proliferation of thymocytes. We identified IL-7-expressing thymic epithelial cells (TECs) throughout ontogeny and in the adult mouse thymus by in situ hybridization analysis. IL-7 expression is initiated in the thymic fated domain of the early primordium by embryonic day 11.5 and is expressed in a Foxn1-independent pathway. Marked changes occur in the localization and regulation of IL-7-expressing TECs during development. IL-7-expressing TECs are present throughout the early thymic rudiment. In contrast, a major population of IL-7-expressing TECs is localized to the medulla in the adult thymus. Using mouse strains in which thymocyte development is arrested at various stages, we show that fetal and postnatal thymi differ in the frequency and localization of IL-7-expressing TECs. Whereas IL-7 expression is initiated independently of hemopoietic-derived signals during thymic organogenesis, thymocyte-derived signals play an essential role in regulating IL-7 expression in the adult TEC compartment. Moreover, different thymocyte subsets regulate the expression of IL-7 and keratin 5 in adult cortical epithelium, suggesting that despite phenotypic similarities, the cortical TEC compartments of wild-type and RAG-1(-/-) mice are developmentally and functionally distinct.     

Abnormalities of caudal pharyngeal pouch development in Pbx1 knockout mice mimic loss of Hox3 paralogs

Pbx1 is a TALE-class homeodomain protein that functions in part as a cofactor for Hox class homeodomain proteins. Previous analysis of the in vivo functions of Pbx1 by targeted mutagenesis in mice has revealed roles for this gene in skeletal patterning and development and in the organogenesis of multiple systems. Both RNA expression and protein localization studies have suggested a possible role for Pbx1 in pharyngeal region development. As several Hox mutants have distinct phenotypes in this region, we investigated the potential requirement for Pbx1 in the development of the pharyngeal arches and pouches and their organ derivatives. Pbx1 homozygous mutants exhibited delayed or absent formation of the caudal pharyngeal pouches, and disorganized patterning of the third pharyngeal pouch. Formation of the third pouch-derived thymus/parathyroid primordia was also affected, with absent or hypoplastic primordia, delayed expression of organ-specific differentiation markers, and reduced proliferation of thymic epithelium. The fourth pouch and the fourth pouch-derived ultimobranchial bodies were usually absent. These phenotypes are similar to those previously reported in Hoxa3(-/-) single mutants and Hoxa1(-/-);Hoxb1(-/-) or Hoxa3(+/-);Hoxb3(-/-);Hoxd3(-/-) compound mutants, suggesting that Pbx1 acts together with multiple Hox proteins in the development of the caudal pharyngeal region. However, some aspects of the Pbx1 mutant phenotype included specific defects that were less severe than those found in known Hox mutant mice, suggesting that some functions of Hox proteins in this region are Pbx1-independent.     

Allosteric inhibitors of Bcr-abl-dependent cell proliferation

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized at the molecular level by the expression of Bcr-abl, a 210-kDa fusion protein with deregulated tyrosine kinase activity. Encouraged by the clinical validation of Bcr-abl as the target for the treatment of CML by imatinib, we sought to identify pharmacological agents that could target this kinase by a distinct mechanism. We report the discovery of a new class of Bcr-abl inhibitors using an unbiased differential cytotoxicity screen of a combinatorial kinase-directed heterocycle library. Compounds in this class (exemplified by GNF-2) show exclusive antiproliferative activity toward Bcr-abl-transformed cells, with potencies similar to imatinib, while showing no inhibition of the kinase activity of full-length or catalytic domain of c-abl. We propose that this new class of compounds inhibits Bcr-abl kinase activity through an allosteric non-ATP competitive mechanism.     

The Glycoprotein B Disintegrin-Like Domain Binds Beta 1 Integrin To Mediate Cytomegalovirus Entry

Cellular integrins were identified as human cytomegalovirus (HCMV) entry receptors and signaling mediators in both fibroblasts and endothelial cells. The goal of these studies was to determine the mechanism by which HCMV binds to cellular integrins to mediate virus entry. HCMV envelope glycoprotein B (gB) has sequence similarity to the integrin-binding disintegrin-like domain found in the ADAM (a disintegrin and metalloprotease) family of proteins. To test the ability of this region to bind to cellular integrins, we generated a recombinant soluble version of the gB disintegrin-like domain (gB-DLD). The gB-DLD protein bound to human fibroblasts in a specific, dose-dependent and saturable manner that required the expression of an intact β1 integrin ectodomain. Furthermore, a physical association between gB-DLD and β1 integrin was demonstrated through in vitro pull-down assays. The function of this interaction was shown by the ability of cell-bound gB-DLD to efficiently block HCMV entry and the infectivity of multiple in vivo target cells. Additionally, rabbit polyclonal antibodies raised against gB-DLD neutralized HCMV infection. Mimicry of the ADAM family disintegrin-like domain by HCMV gB represents a novel mechanism for integrin engagement by a virus and reveals a unique therapeutic target for HCMV neutralization. The strong conservation of the DLD across beta- and gammaherpesviruses suggests that integrin recognition and utilization may be a more broadly conserved feature throughout the Herpesviridae.Like many other herpesviruses, human cytomegalovirus (HCMV) is an opportunistic pathogen that is able to asymptomatically infect the human population with high incidence throughout the world. Primary infection is followed by a life-long latent phase that may reactivate and cause disease during the immunosuppression experienced by AIDS patients and organ transplant recipients (14, 52). HCMV disease is also a cause of significant morbidity and mortality during primary congenital infections (66). Currently there is no effective HCMV vaccine, and HCMV antiviral therapies, such as ganciclovir, are highly toxic and unsuitable for treating pregnant women in the congenital setting (92).HCMV disease can manifest itself in most organ systems and tissue types. Pathology from HCMV-infected individuals reveals that HCMV can infect most cell types, including fibroblasts, endothelial cells, epithelial cells, smooth muscle cells, stromal cells, monocytes/macrophages, neutrophils, neuronal cells, and hepatocytes (20, 25, 77, 83, 87). The broad intrahost organ and tissue tropism of HCMV is paralleled in vitro with the virus'' ability to bind and fuse with nearly every vertebrate cell type tested (40, 62, 78). However, full productive infection is limited to secondary strains of fibroblasts and endothelial cells. The ability of HCMV to enter such a diverse range of cell types is indicative of multiple cell-specific receptors, broadly expressed receptors, or a complex entry pathway in which a combination of both cell-specific and broadly expressed cellular receptors are utilized.The genes that encode envelope glycoprotein B (gB) and gH are essential (37), play several key roles during virus entry and egress, and are conserved throughout the Herpesviridae (reviewed in reference 80). A soluble form of gB truncated at the transmembrane domain (gBs) binds to permissive cells specifically, blocks virus entry, and is sufficient to trigger signal transduction events that result in the activation of an interferon-responsive pathway that is also activated by HCMV virions (10, 12, 13).HCMV entry requires initial tethering of virions to cell surface heparan sulfate proteoglycans (HSPGs) (22, 80). The HCMV envelope contains at least two separate glycoprotein complexes with affinities for heparan sulfate: gB (22) and the gM/gN complex (48). The gM/gN complex is more abundant than gB within the envelope (88) and binds heparin with higher affinity (49). Thus, the gM/gN complex is thought to be the primary heparin-binding component of the HCMV envelope.Virus-cell tethering via HSPGs is followed by a more stable interaction and subsequent signal transduction cascades. This interaction was proposed to be mediated via cell surface epidermal growth factor receptor (EGFR) (17, 95). These data, however, conflicted with more recent reports that demonstrate EGFR is not explicitly required for infection (21, 42). Platelet-derived growth factor receptor (PDGFR) has also been reported to function as an attachment receptor that functions to activate signaling cascades required for infection (79). The relative contribution of signaling and virus-host cell attachment for each of these growth factor receptors remains to be further characterized. The possibility also exists that additional attachment receptors still remain unidentified.Integrins are expressed on the cell surfaces of all vertebrate cells, a characteristic that parallels the promiscuity of HCMV entry. Additionally, β1 integrins are capable of mediating many of the same signal transduction pathways that are triggered during HCMV entry into host cells. Upon binding and fusing with host cell surfaces, HCMV triggers changes in Ca²⁺ homeostasis (36) and the activation of phospholipases C and A2, as well as an increased release of arachidonic acid and its metabolites (2). Additionally, mitogen-activated protein kinase (MAPK) (44, 45), phosphatidylinositol-3-OH kinase (PI3-K) (46), and G proteins are activated (73). Indeed, it was shown that HCMV entry led to an activation of integrin signaling pathways that reorganized the actin cytoskeleton (31) and phosphorylated β1 and β3 integrin cytoplasmic domains (31), focal adhesion kinase (FAK) (31), and Src (94). Integrin antibody blocking studies in combination with HCMV infectivity assays in β1 integrin-null GD25 cells identified α2β1, α6β1, and αVβ3 integrins as HCMV “postattachment” entry receptors (31). Certain integrin signaling events could be triggered by both HCMV and a soluble version of gB and require the expression of β1 integrin, identifying this specific viral ligand in integrin engagement (31).ADAM family members are multifunctional proteins that contain a metalloproteinase domain involved in ectodomain shedding and a disintegrin module of approximately 90 amino acids that confers RGD-independent integrin binding (43, 81, 99). The minimum component of the disintegrin module required for integrin engagement is the 12- to 13-amino-acid disintegrin loop, for which a consensus sequence has been described: RX₆DLXXF (29). The 20-amino-acid stretch encompassing the gB disintegrin-like domain is highly conserved, with greater than 98% amino acid identity among HCMV clinical isolates. Additionally, this domain is present in most gammaherpesviruses and all betaherpesviruses, suggesting that integrin engagement may be a conserved feature for most of the Herpesviridae. Synthetic peptides of the gB disintegrin loop block virus fusion (tegument delivery) but not virus attachment (31). This fact suggests a disintegrin-mediated molecular mechanism of herpesvirus-integrin engagement. Glycoprotein H (gH) has also been identified as an αVβ3 integrin ligand (94). However, gH contains no previously identified integrin recognition motifs, and the αVβ3 integrin heterodimer does not typically engage ADAM family proteins.Herein, we explore the molecular mechanism of integrin engagement by HCMV envelope gB. We provide multiple lines of evidence that demonstrate a physical interaction between the gB disintegrin module with β1 integrin. Furthermore, this interaction has significant consequences to the viral life cycle, since a soluble version of the gB disintegrin module efficiently blocks HCMV infection at a postattachment step during entry into multiple in vivo cell targets. Similarly, polyclonal antibodies directed against the gB disintegrin-like domain neutralize HCMV infectivity. These data identify the molecular mechanism of an HCMV ligand-receptor interaction required for virus-host fusion.     

Genotypic effects of calpain 1 and calpastatin on the tenderness of cooked M. longissimus dorsi steaks from Jersey x Limousin, Angus and Hereford-cross cattle

Single nucleotide polymorphisms (SNPs) in the calpain 1 (CAPN1) and calpastatin (CAST) genes were studied to determine their effects on meat tenderness in Bos taurus cattle. Strip loins (M. longissimus dorsi) were removed from cattle in four resource populations after slaughter (n = 1042), aged under controlled conditions until fixed times after rigor mortis, cooked and measured using a tenderometer. Animals were genotyped for the CAPN1 SNP c.947C>G (p.Ala316Gly; AF252504) and for the CAST SNP c.2959A>G (AF159246). Frequencies of CAPN1 C alleles ranged from 23% to 68%, and CAST A alleles from 84% to 99.5%. From all data combined, the CAPN1 CC genotype (compared with the GG genotype) was associated with a 20.1 +/- 1.7% reduced average shear force at intermediate stages of ageing (P < 0.001) and with a 9.5 +/- 1.3% reduction near ultimate tenderness (P < 0.001). The heterozygote was intermediate. For CAST, corresponding values for AA compared with AG genotypes were reductions of 8.6 +/- 2.0% and 5.1 +/- 1.6% respectively (both P < 0.001), but there were too few GG genotypes for comparison. There were small interactions between the CAPN1 and CAST genotypes. For the CAPN1 and CAST genotypes combined, the maximal genotype effect in average shear force was 25.7 +/- 5.5% (P < 0.001) at intermediate stages and 15.2 +/- 4.8% near ultimate tenderness (P < 0.01).     

A comparative study on the antimutagenic properties of aqueous extracts of Aspalathus linearis (rooibos), different Cyclopia spp. (honeybush) and Camellia sinensis teas

Antimutagenic activity of aqueous extracts of the South African herbal teas, Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush) was compared with that of Camellia sinensis (black, oolong and green) teas in the Salmonella mutagenicity assay using aflatoxin B(1) (AFB(1)) and 2-acetylaminofluorene (2-AAF) as mutagens. The present study presents the first investigation on antimutagenic properties of C. subternata, C. genistoides and C. sessiliflora. The herbal teas demonstrated protection against both mutagens in the presence of metabolic activation, with the exception of "unfermented" (green/unoxidised) C. genistoides against 2-AAF, which either protected or enhanced mutagenesis depending on the concentration. Antimutagenic activity of "fermented" (oxidised) rooibos was significantly (P<0.05) less than that of Camellia sinensis teas against AFB(1), while for 2-AAF it was less (P<0.05) than that of black tea and similar (P>0.05) to that of oolong and green teas. Antimutagenic activity of unfermented C. intermedia and C. subternata exhibited a similar protection as fermented rooibos against AFB(1). Against 2-AAF, fermented rooibos exhibited similar protective properties than unfermented C. intermedia and C. sessiliflora. Unfermented rooibos was less effective than the C. sinensis teas and fermented rooibos, but had similar (P>0.05) antimutagenicity to that of fermented C. sessiliflora against AFB(1) and fermented C. subternata against 2-AAF. Fermented C. intermedia and C. genistoides exhibited the lowest protective effect against 2-AAF, while fermented C. intermedia exhibited the lowest protection when utilising AFB(1) as mutagen. Aspalathin and mangiferin, major polyphenols in rooibos and Cyclopia spp., respectively, exhibited weak to moderate protective effects when compared to the major green tea catechin, (-)epigallocatechin gallate (EGCG). Antimutagenic activity of selected herbal tea phenolic compounds indicated that they contribute towards (i) observed antimutagenic activity of the aqueous extracts against both mutagens and (ii) enhancement of the mutagenicity of 2-AAF by unfermented C. genistoides. Antimutagenic activity of the South African herbal teas was mutagen-specific, affected by fermentation and plant material, presumably due to changes and variation in phenolic composition.     

Parkin and Mitofusins Reciprocally Regulate Mitophagy and Mitochondrial Spheroid Formation

Mitochondrial homeostasis via mitochondrial dynamics and quality control is crucial to normal cellular functions. Mitophagy (mitochondria removed by autophagy) stimulated by a mitochondrial uncoupler, carbonyl cyanide m-chlorophenylhydrazone (CCCP), requires Parkin, but it is not clear why Parkin is crucial to this process. We found that in the absence of Parkin, carbonyl cyanide m-chlorophenylhydrazone induced the formation of mitochondrial spheroids. Mitochondrial spheroid formation is also induced in vivo in the liver by acetaminophen overdose, a condition causing severe oxidative mitochondrial damages and liver injury. Mitochondrial spheroids could undergo a maturation process by interactions with acidic compartments. The formation of this new structure required reactive oxygen species and mitofusins. Parkin suppressed these mitochondrial dynamics by promoting mitofusin degradation. Consistently, genetic deletion of mitofusins without concomitant expression of Parkin was sufficient to prevent mitochondrial spheroid formation and resumed mitophagy. Mitochondrial spheroid formation and mitophagy could represent different strategies of mitochondrial homeostatic response to oxidative stress and are reciprocally regulated by mitofusins and Parkin.     

NMR insights into protein allostery

Allosterism is one of nature's principal methods for regulating protein function. Allosterism utilizes ligand binding at one site to regulate the function of the protein by modulating the structure and dynamics of a distant binding site. In this review, we first survey solution NMR techniques and how they may be applied to the study of allostery. Subsequently, we describe several examples of application of NMR to protein allostery and highlight the unique insight provided by this experimental technique.     

Growth characteristics of three Fusarium species evaluated by near-infrared hyperspectral imaging and multivariate image analysis

Colony growth of three Fusarium spp. on potato dextrose agar was followed by collecting near-infrared (NIR) hyperspectral images of the colonies at regular intervals after inoculation up to 55?h. After principal component analysis (PCA), two clusters were apparent in the score plot along principal component 1. Using the brushing technique, these clusters were divided into four groups of pixels with similar score values. These could be visualised as growth zones within the colonies in the corresponding score image. Three spectral bands, i.e. 1,166, 1,380 and 1,918?nm, were prominent in the multiplicative scatter corrected and Savitzky?CGolay second derivative spectra. These indicated chemical changes, associated with carbohydrates (1,166 and 1,380?nm) and protein (1,918?nm), that occurred as the mycelium grew and matured. The protein band was more prominent in the mature fungal material while the carbohydrate band was less pronounced. The younger material and the agar were characterised by the carbohydrate spectral band. Integrating whole mycelium colonies as the sum of pixels over time made it possible to construct curves that resembled growth curves; this included the lag phase, active growth phase, deceleration phase and phase of constant growth. Growth profiles constructed from individual growth zones indicated more detailed growth characteristics. The use of NIR hyperspectral imaging and multivariate image analysis (MIA) allowed one to visualise radial growth rings in the PCA score images. This would not have been possible with bulk spectroscopy. Interpreting spectral data enabled better understanding of microbial growth characteristics on agar medium. NIR hyperspectral imaging combined with MIA is a powerful tool for the evaluation of growth characteristics of fungi.