Soma Mandal

Rational drug design

In this article, current knowledge of drug design is reviewed and an approach of rational drug design is presented. The process of drug development is challenging, expensive, and time consuming, although this process has been accelerated due to the development of computational tools and methodologies. The current target based drug design approach is incomplete because most of the drugs developed by structure guided approaches have been shown to have serious toxic side effects. Otherwise these drugs would have been an ideal choice for the treatment of diseases. Hence, rational drug design would require a multidisciplinary approach. In this regard, incorporation of gene expression technology and bioinformatics tools would be indispensable in the structure based drug design. Global gene expression data and analysis of such data using bioinformatics tools will have numerous benefits such as efficiency, cost effectiveness, time saving, and will provide strategies for combination therapy in addition to overcoming toxic side effects. As a result of incorporation of gene expression data, partial benefit of the structure based drug design is slowly emerging and rapidly changing the approach of the drug development process. To achieve the full benefit of developing a successful drug, multidisciplinary approaches (approaches such as computational chemistry and gene expression analysis, as discussed in this article) would be necessary. In the future, there is adequate room for the development of more sophisticated methodologies.

Modeling of Molecular Interaction between Apoptin, BCR-Abl and CrkL - An Alternative Approach to Conventional Rational Drug Design

In this study we have calculated a 3D structure of apoptin and through modeling and docking approaches, we show its interaction with Bcr-Abl oncoprotein and its downstream signaling components, following which we confirm some of the newly-found interactions by biochemical methods. Bcr-Abl oncoprotein is aberrantly expressed in chronic myelogenous leukaemia (CML). It has several distinct functional domains in addition to the Abl kinase domain. The SH3 and SH2 domains cooperatively play important roles in autoinhibiting its kinase activity. Adapter molecules such as Grb2 and CrkL interact with proline-rich region and activate multiple Bcr-Abl downstream signaling pathways that contribute to growth and survival. Therefore, the oncogenic effect of Bcr-Abl could be inhibited by the interaction of small molecules with these domains. Apoptin is a viral protein with well-documented cancer-selective cytotoxicity. Apoptin attributes such as SH2-like sequence similarity with CrkL SH2 domain, unique SH3 domain binding sequence, presence of proline-rich segments, and its nuclear affinity render the molecule capable of interaction with Bcr-Abl. Despite almost two decades of research, the mode of apoptins action remains elusive because 3D structure of apoptin is unavailable. We performed in silico three-dimensional modeling of apoptin, molecular docking experiments between apoptin model and the known structure of Bcr-Abl, and the 3D structures of SH2 domains of CrkL and Bcr-Abl. We also biochemically validated some of the interactions that were first predicted in silico. This structure-property relationship of apoptin may help in unlocking its cancer-selective toxic properties. Moreover, such models will guide us in developing of a new class of potent apoptin-like molecules with greater selectivity and potency.

Estrogen regulated expression of the p21 Waf1/Cip1 gene in estrogen receptor positive human breast cancer cells.

The cyclin‐dependent kinase inhibitor protein p21Waf1/Cip1 is a potent tumor suppressor. Here, we demonstrate that estradiol regulates the p21Waf1/Cip1 gene. Estradiol induces p21Waf1/Cip1 mRNA expression within 30–60 min independent of new protein synthesis in the estrogen receptor α (ERα) positive human breast cancer cell line MCF‐7. Similar to other estradiol responsive promoters, the p21Waf1/Cip1 upstream promoter region has several estrogen response element (ERE) half‐sites nestled in AP‐1 binding sites, which are positioned upstream to Sp1 binding sites. Using the chromatin immunoprecipitation (ChIP) assay, we show that estradiol stimulation resulted in the recruitment of transcription factors ERα, Sp1, and Sp3 to the p21Waf1/Cip1 upstream promoter element. The Sp1 inhibitor mithramycin A abrogated Sp1, and to a lesser extent Sp3 binding, and markedly reduced the estradiol stimulated p21Waf1/Cip1 gene expression. However, ERα binding was not affected in the mithramycin A and estradiol treated cells. On closer examination of the half‐site ERE/AP‐1 sites upstream to the Sp1 sites in a separate ChIP experiment, we found a pronounced association of ERα upon estradiol treatment compared to almost negligible binding of Sp1 or Sp3. Together these studies provide evidence that ERα is recruited to the half‐site ERE/AP‐1 sites in the p21Waf1/Cip1 upstream promoter element. Although Sp1/Sp3 is not involved in the recruitment of ERα to the promoter, Sp1 is necessary for estrogen‐induced p21Waf1/Cip1 promoter activity. J. Cell. Physiol. 224:28–32, 2010

The utility of cardiac biomarkers and echocardiography for the early detection of bevacizumab- and sunitinib-mediated cardiotoxicity

The recent introduction of novel anticancer therapies, including bevacizumab (BVZ) and sunitinib (SNT), is associated with an increased risk of cardiotoxicity. However, early identification of left ventricular (LV) systolic dysfunction may facilitate dose modification and avoid the development of advanced heart failure. Using a murine model of BVZ- and SNT-mediated cardiotoxicity, we investigated whether cardiac biomarkers and/or tissue velocity imaging (TVI) using echocardiography can detect early changes in cardiac function, before a decrease in LV ejection fraction is identified. A total of 75 wild-type C57Bl/6 male mice were treated with either 0.9% saline, BVZ, or SNT. Serial monitoring of blood pressure, high-sensitivity troponin I, and echocardiographic indexes were performed over a 14-day study period, after which the mice were euthanized for histological and biochemical analyses. Mice treated with either BVZ or SNT developed systemic hypertension as early as day 7, which increased by day 14. Cardiac biomarkers, specifically high-sensitivity troponin I, were not predictive of early LV systolic dysfunction. Although conventional LV ejection fraction values decreased at day 13 in mice treated with either BVZ or SNT, TVI confirmed early LV systolic dysfunction at day 8. Histological and biochemical analysis demonstrated loss of cellular integrity, increased oxidative stress, and increased cardiac apoptosis in mice treated with BVZ or SNT therapy at day 14. In a murine model of BVZ- or SNT-mediated cardiomyopathy, noninvasive assessment by TVI detected early LV systolic dysfunction before alterations in conventional echocardiographic indexes.

Role of MSK1 in the Malignant Phenotype of Ras-transformed Mouse Fibroblasts

Activated by the RAS-MAPK signaling pathway, MSK1 is recruited to immediate-early gene (IEG) regulatory regions, where it phosphorylates histone H3 at Ser-10 or Ser-28. Chromatin remodelers and modifiers are then recruited by 14-3-3 proteins, readers of phosphoserine marks, leading to the occupancy of IEG promoters by the initiation-engaged form of RNA polymerase II and the onset of transcription. In this study, we show that this mechanism of IEG induction, initially elucidated in parental 10T1/2 murine fibroblast cells, applies to metastatic Hras1-transformed Ciras-3 cells. As the RAS-MAPK pathway is constitutively activated in Ciras-3 cells, MSK1 activity and phosphorylated H3 steady-state levels are elevated. We found that steady-state levels of the IEG products AP-1 and COX-2 were also elevated in Ciras-3 cells. When MSK1 activity was inhibited or MSK1 expression was knocked down in Ciras-3 cells, the induction of IEG expression and the steady-state levels of COX-2, FRA-1, and JUN were greatly reduced. Furthermore, MSK1 knockdown Ciras-3 cells lost their malignant phenotype, as reflected by the absence of anchorage-independent growth.

An integrated analysis of genes and pathways exhibiting metabolic differences between estrogen receptor positive breast cancer cells

BackgroundThe sex hormone estrogen (E2) is pivotal to normal mammary gland growth and differentiation and in breast carcinogenesis. In this in silico study, we examined metabolic differences between ER(+)ve breast cancer cells during E2 deprivation.MethodsPublic repositories of SAGE and MA gene expression data generated from E2 deprived ER(+)ve breast cancer cell lines, MCF-7 and ZR75-1 were compared with normal breast tissue. We analyzed gene ontology (GO), enrichment, clustering, chromosome localization, and pathway profiles and performed multiple comparisons with cell lines and tumors with different ER status.ResultsIn all GO terms, biological process (BP), molecular function (MF), and cellular component (CC), MCF-7 had higher gene utilization than ZR75-1. Various analyses showed a down-regulated immune function, an up-regulated protein (ZR75-1) and glucose metabolism (MCF-7). A greater percentage of 77 common genes localized to the q arm of all chromosomes, but in ZR75-1 chromosomes 11, 16, and 19 harbored more overexpressed genes. Despite differences in gene utilization (electron transport, proteasome, glycolysis/gluconeogenesis) and expression (ribosome) in both cells, there was an overall similarity of ZR75-1 with ER(-)ve cell lines and ER(+)ve/ER(-)ve breast tumors.ConclusionThis study demonstrates integral metabolic differences may exist within the same cell subtype (luminal A) in representative ER(+)ve cell line models. Selectivity of gene and pathway usage for strategies such as energy requirement minimization, sugar utilization by ZR75-1 contrasted with MCF-7 cells, expressing genes whose protein products require ATP utilization. Such characteristics may impart aggressiveness to ZR75-1 and may be prognostic determinants of ER(+)ve breast tumors.

Toll-like receptor 2 dominance over Toll-like receptor 4 in stressful conditions for its detrimental role in the heart

It has been suggested that Toll-like receptor (TLR)4 promotes IL-10-mediated cardiac cell survival, whereas another receptor, TLR2, from the same family, is detrimental. Here, we examined the interactive role of these two innate signaling molecules under stressful conditions, including IL-10 knockout (IL-10-/-) mice, global ischemia-reperfusion (I/R) injury in rat hearts, and in vitro short hairpin RNA experimental models in the presence or absence of IL-10 (10 ng/ml). Circulating and myocardial levels of TNF-α as well as apoptosis and fibrosis were higher in IL-10-/- mice. The increase in TLR2 in IL-10-/- hearts indicated its negative regulation by IL-10. Ex vivo I/R also caused a marked upregulation of TLR2 and TNF-α as well as apoptotic and fibrotic signals. However, a 40-min reperfusion with IL-10 triggered an increase in TLR4 expression and improved recovery of cardiac function. The increase in IL-1 receptor-associated kinase (IRAK)-M and IRAK-2 activity during I/R injury suggested their role in TLR2 signaling. In vitro inhibition of TLR4 activity as a consequence of RNA inhibition-mediated suppression of myeloid differentiation gene (MyD)88 suggested MyD88-dependent activation of TLR4. The inclusion of IL-10 during reperfusion also downregulated the expression of IRAK-2, TNF-α receptor-associated factor 1-interacting protein (TRAIP) and apoptotic signals, caspase-3, and the Bax-to-Bcl-xL ratio. IL-10 reduced the TNF-α receptor-associated increase in TRAIP-induced apoptosis during I/R injury, which led to an increase in IL-1β to mitigate transforming growth factor-β receptor type I-mediated fibrosis. The IL-10 mitigation of these changes suggests that the stimulation through TLR4 signaling promotes IRAK-4 and phosphorylates IRAK-1 instead of IRAK-2 and may be an important therapeutic approach in restoring heart health in stress.NEW & NOTEWORTHY Under stress conditions such as downregulation of the IL-10 gene or ischemia-reperfusion injury, Toll-like receptor (TLR)4 and IL-1 receptor-associated kinase (IRAK)-1 activation is suppressed, along with the upregulation of TLR-2 and IRAK-2, resulting in fibrosis and apoptosis. It is suggested that IL-10 helps to maintain heart function during stress via myeloid differentiation gene 88/IRAK-4/IRAK-1-dependent TLR4 signaling.

Metabolomics and Transcriptional Responses in Estrogen Receptor Positive Breast Cancer Cells

Estrogen exposure is well recognized as a high risk factor of breast cancer, despite the fact that the hormone transcriptionally regulates the expression of tumor suppressor genes, like BRCA1 (Hockings et al., 2008). Estrogen acts through the estrogen receptor ┙ (ER┙) in target cells (Ali and Coombes, 2000). ER┙ overexpression occurs in about 70% of breast cancers, referred as “ER positive” (ER+) (Dickson and Lippman, 1988). ER┙ is a primary target for chemoprevention as well as other therapeutic interventions for breast cancer with the ER+ phenotype. Clinically, in pathological lesions such as women with benign breast tumors, who underwent surgery, presented with a high proportion of ER positivity than the control group. In such cases, logistic regression yielded an adjusted odds ratio of 6.5 for risk of development of breast cancer compared to 0.3 odds ratio for PR (progesterone receptor); there was an increased proportion of cells expressing ER┙ by immunohistochemical staining, thereby demonstrating the importance of ER┙ as a breast cancer risk marker (Khan et al., 1994). Estrogen or E2 mostly exerts its mitogenic effects by the modulation of metabolic responses and through the transcriptional induction of genes regulating crucial cellular processes like the cell cycle (Prall et al., 1998). Microarray and RNA interference studies suggest that the transcriptional regulation of about 60% of estrogen responsive genes (induced or repressed) is dependent upon ER┙ and Sp1/3 transcription factors (Bazley and Gullick, 2005). The basal expression of ER┙, in turn, is regulated by Sp1 in ER+ breast cancer cells (deGraffenried et al., 2002). Sp1 and Sp3 are ubiquitously expressed in mammalian cells and are abnormally expressed in various cancers, including breast (Li and Davie, 2010). Sp1 and Sp3 bind to the same DNA sequence defined as Sp1/3 sites, with similar affinity. Sp1 and Sp3 play important roles in regulating genes critical to the initiation and progression of breast cancers (Hirokawa, 1984; Lu and Archer, 2010). Targeting these proteins is a promising cancer therapeutic approach (Jia et al., 2010). In most cases, ER+ breast cancers present a better clinical prognosis than the ERbreast cancers. Moreover, it is an encouraging fact that the leading antiestrogenic drugs such as tamoxifen have effectively improved the overall survival of pre and postmenopausal women by the reduction of cancer incidence and formation of new tumors (Ferguson and Davidson, 1997; Muss, 2001). However, a major obstacle to breast cancer treatment is the development of drug resistance. Resistance is commonly associated with an increased expression of Erb

THE CARDIOPROTECTIVE ROLE OF NACA IN THE PREVENTION OF DOXORUBICIN AND TRASTUZUMAB MEDIATED CARDIAC DYSFUNCTION

was 149.7(13.6)/83.4(11.5) mm Hg at baseline. The intervention group had an adjusted mean (SE) reduction in systolic BP at 6 months of 18.0 (1.4) mm Hg compared with 11.0 (2.1) mm Hg in the control group (p1⁄40.005). CONCLUSION: Pharmacist prescribing for patients with uncontrolled hypertension resulted in a statistically and clinically significant reduction in systolic blood pressure when compared to usual care. CIHR, AIHS