Common Drug Targets Research Articles

GATA Factor-G-Protein-Coupled Receptor Circuit Suppresses Hematopoiesis.

SummaryHematopoietic stem cells (HSCs) originate from hemogenic endothelium within the aorta-gonad-mesonephros (AGM) region of the mammalian embryo. The relationship between genetic circuits controlling stem cell genesis and multi-potency is not understood. A Gata2 cis element (+9.5) enhances Gata2 expression in the AGM and induces the endothelial to HSC transition. We demonstrated that GATA-2 rescued hematopoiesis in +9.5−/− AGMs. As G-protein-coupled receptors (GPCRs) are the most common targets for FDA-approved drugs, we analyzed the GPCR gene ensemble to identify GATA-2-regulated GPCRs. Of the 20 GATA-2-activated GPCR genes, four were GATA-1-activated, and only Gpr65 expression resembled Gata2. Contrasting with the paradigm in which GATA-2-activated genes promote hematopoietic stem and progenitor cell genesis/function, our mouse and zebrafish studies indicated that GPR65 suppressed hematopoiesis. GPR65 established repressive chromatin at the +9.5 site, restricted occupancy by the activator Scl/TAL1, and repressed Gata2 transcription. Thus, a Gata2 cis element creates a GATA-2-GPCR circuit that limits positive regulators that promote hematopoiesis.

Effects of dipotassium-trioxohydroxytetrafluorotriborate, K2[B3O3F4OH], on cell viability and gene expression of common human cancer drug targets in a melanoma cell line

Recently it was found that dipotassium-trioxohydroxytetrafluorotriborate, K2(B3O3F4OH), is a potent and highly specific inhibitor of precancerous cell processes. We conducted gene expression profiling of human melanoma cells before and after treatment with two concentrations (0.1 and 1 mM) of this boron inorganic derivative in order to assess its effects on deregulation of genes associated with tumor pathways. Parallel trypan blue exclusion assay was performed to assess the cytotoxicity effects of this chemical. Treatment with K2(B3O3F4OH) induced a significant decrease of cell viability in melanoma cellline at both tested concentrations. Furthermore, these treatments caused deregulation of more than 30 genes known as common anti-tumor drug targets. IGF-1 and hTERT were found to be significantly downregulated and this result may imply potential use of K2(B3O3F4OH) as an inhibitor or human telomerase and insulin-like growth factor 1, both of which are associated with various tumor pathways.

In Silico Study of Variable Surface Proteins in Plasmodium Species: Perspectives in Drug Design.

The variable surface proteins expressed by P. falciparum and P. vivax are transported to the surface of infected erythrocyte and are exposed to the host immune system. The possibility of using variable surface proteins as a common drug target has been analyzed in both the Plasmodium species. Sequence analysis of variable surface proteins showed a low-level conservation within as well as between the species. Amino acid composition analysis revealed higher frequency of hydrophilic amino acids as compared with that of hydrophobic residues. In order to gain more insight into their diverse functional role, the three-dimensional structure was predicted using comparative modeling approach. These models were evaluated and validated by checking stereochemistry of underlying amino acids. Structural alignment of variable surface proteins by superimposing them shows less conservation. Due to differences at sequence as well as structural level, the variable surface proteins are expected to show difference in their degree of invasiveness. These differences were also cross-examined by evolutionary study, and the results obtained were in accordance with the aforesaid study. The existence of structural differences noticed in the present study showed that the variable surface proteins could not be used as a common drug target in both the malarial species. Therefore, species-specific strategy may be followed for drug targeting against variable surface proteins of P. falciparum and P. vivax.

Identification of Putative Drug Targets and Vaccine Candidates for Pathogens Causing Atherosclerosis

Atherosclerosis is a chronic inflammatory artery disease, responsible for both cardiovascular (heart) and cerebrovascular (brain) stroke with high morbidity and mortality worldwide. Infectious pathogens such as Chlamydophila pneumoniae, Porphyromonas gingivalis and Helicobacter pylori are shown to be associated with the disease in recent epidemiological studies. Therefore, identification of common drug targets and vaccine candidates against these three pathogens would be vital towards therapy and management of atherosclerosis. Chlamydophila pneumonia was selected as a reference organism due to its predominant role in atherosclerosis. Implementing comparative genomic approach, subtractive genomic approach, metabolic pathway analysis, non-homologous gut flora analysis and domain search analysis, 35 common putative drug targets were identified against pathogens of atherosclerosis. Subcellular localization studies were performed and identified UvrABC protein as vaccine candidate. Metabolic pathway analysis has showed that, out of 35 drug targets, 14 enzymes were participating in key pathways linked to pathogen’s survival, proliferation and pathogenesis without any alternative mechanism to synthesize the product. The gut microbiota analysis was performed to identify the drug targets which do not affect the microbiota in the humans. Domain search was performed for the identified 14 drug targets using Pfam and SMART databases and protein network analysis was carried out using STRING and Cytoscape v3.2.0. The drug targets and vaccine candidates proposed in the present study would serve as basis to design potent inhibitors and subunit vaccines through in silico approach for combating atherosclerosis caused by infectious pathogens.

Thioredoxin-interacting Protein as a Common Regulation Target for Multiple Drugs in Clinical Therapy/Application

Initially identified in HL60 cells treated with Vitamin D3, thioredoxin-interacting protein (TXNIP) is considered as a major redox regulator and a potential connector between cellular redox state and metabolism. TXNIP plays an important role in the control of glucose and lipid metabolism, and it has been defined as a tumor suppressor gene in various solid tumors and hematological malignancies. This review gives an overview of the mechanism of various medicines including Lycium barbarum polysaccharide, Quercetin, trans-resveratrol, metformin, purple sweet potato color, nobiletin, taurine, suberoylanilide hydroxamic acid, and Theophylline, and their potential applications in the clinical treatment of many diseases.

Dihydromyricetin induces mouse hepatoma Hepal-6 cell apoptosis via the transforming growth factor-β pathway.

Dihydromyricetin (DHM) is a flavonoid compound which possesses potent antitumor activity. In the present study, it was demonstrated that DHM significantly inhibited proliferation and induced apoptosis in mouse hepatocellular carcinoma Hepal-6 cells. Transforming growth factor β (TGF-β) is recognized as a major profibrogenic cytokine and is therefore a common target for drugs in the treatment of liver disease. The present study aimed to investigate whether TGF-β was involved in DHM-triggered cell-viability inhibition and apoptosis induction. An MTT assay was used to evaluate the viability of Hepal-6 cells following DHM treatment. TGF-β signalling is mediated by Smads and nicotinamide adenine dinucleotide phosphate oxidase 4 (NOX4) is a crucial regulator of reactive oxygen species ROS production. TGF-β, Smad3, phosphorylated (p)-Smad2/3 and NOX4 protein expression levels were evaluated by western blot analysis. TGF-β and NOX4 gene expression levels were determined by quantitative polymerase chain reaction. The results indicated that DHM downregulated TGF-β, Smad3, p-Smad2/3 and NOX4 in a concentration-dependent manner. A cell counting assay indicated that DHM also inhibited Hepal-6 cell growth in a concentration-dependent manner. TGF-β expression was significantly decreased following DHM treatment. In conclusion, the results of the present study defined and supported a novel function for DHM, indicating that it induced cell apoptosis by downregulating ROS production via the TGF-β/Smad3 signaling pathway in mouse hepatocellular carcinoma Hepal-6 cells.

Abstract 411: Targeted PF1, JARID1B inhibition induces epigenetic reprogramming in triple negative breast cancer

Abstract Triple Negative Breast cancer (TNBC) is an aggressive subtype of breast cancer associated with early recurrence and poor prognosis. The treatment options are limited due to lack of expression of common drug targets: estrogen receptor (ER), Progesterone receptor (PR) and Epidermal growth factor receptor 2 (Her2). Epigenetic programs can generate aberrant transcription contributing to TNBC progression; however the dynamic and reversible nature of epigenetic changes offers the possibility to reprogram cancer cells to re-express targets that can render TNBC sensitive to targeted therapies like tamoxifen. Envisioning such ‘epidrugs’, we previously published that targeting PAH2 domain of the master transcriptional scaffold Sin3 by stable expression of 13-mer peptide corresponding to a specific motif called SID (mSin3A interaction domain) disrupts its interaction with a small group of SID-containing transcription factors. This interference reverts the expression of important breast cancer-associated genes and impairs tumor growth in vivo. We have now extended our study towards the evaluation of a cell penetrating SID peptide (pSID) in in vitro and in vivo models to establish parameters for the design of targeted epigenetic therapy for TNBC. pSID co-localizes with Sin3A and interference with PAH2-mediated Sin3A functions by pSID is shown by disruption of Sin3A-MAD1 interactions in Co-IP and Duo-Link assays. pSID treatment in MDA-MB 231 cells results in functional re-expression of CDH1 and ER along with increased H3K4 and decreased H3K27 methylation on their promoters. We also show reduction in the tumorsphere formation by pSID-pretreated MDA-MB-231 cells indicating possible epigenetic reprogramming of tumor initiating stem cells towards a differentiated phenotype. Support to this hypothesis is added by the 50% reduction in tumor growth and re-expression of CDH1 observed in FVB mice injected with pSID-pretreated MMTV-myc cells. Moreover, microarray expression analysis indicates pSID-induced EMT reversal, increased cell adhesion and reduced cell migration. Intriguingly, upon further dissection of the mechanism of epigenetic regulation by pSID we show dissociation of two important chromatin readers/modifiers from the Sin3 complex: histone H3K4Me3/2 demethylase JARID1B and H3K4Me0 binding PHD-like domain containing protein PF1; both with significantly correlated overexpression in invasive breast carcinoma. We also observe loss of recruitment of JARID1B but not Sin3A from the CDH1 promoter. Currently studies are underway to understand the cooperative role between JARID1B and PF1 in potentiating the aberrant transcription regulation by Sin3 at important breast cancer-associated promoters that can be selectively reprogrammed by SID decoys. We believe this selectivity can limit the otherwise adverse affects that may be observed by the use of generic HDAC inhibitors and demethylating agents. Citation Format: Rossitza Christova, Kevin Petrie, Nidhi Bansal, Boris Leibovitch, Louise Howell, Veronica Gil, Ming-Ming Zhou, Edgardo Ariztia, Eduardo Farias, Arthur Zelent, Samuel Waxman. Targeted PF1, JARID1B inhibition induces epigenetic reprogramming in triple negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 411. doi:10.1158/1538-7445.AM2014-411

Cytochrome P450 monooxygenase CYP53 family in fungi: comparative structural and evolutionary analysis and its role as a common alternative anti-fungal drug target.

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins whose role as a drug target against pathogenic microbes has been explored because of their stereo- and regio-specific oxidation activity. We aimed to assess the CYP53 family's role as a common alternative drug target against animal (including human) and plant pathogenic fungi and its role in fungal-mediated wood degradation. Genome-wide analysis of fungal species revealed the presence of CYP53 members in ascomycetes and basidiomycetes. Basidiomycetes had a higher number of CYP53 members in their genomes than ascomycetes. Only two CYP53 subfamilies were found in ascomycetes and six subfamilies in basidiomycetes, suggesting that during the divergence of phyla ascomycetes lost CYP53 P450s. According to phylogenetic and gene-structure analysis, enrichment of CYP53 P450s in basidiomycetes occurred due to the extensive duplication of CYP53 P450s in their genomes. Numerous amino acids (103) were found to be conserved in the ascomycetes CYP53 P450s, against only seven in basidiomycetes CYP53 P450s. 3D-modelling and active-site cavity mapping data revealed that the ascomycetes CYP53 P450s have a highly conserved protein structure whereby 78% amino acids in the active-site cavity were found to be conserved. Because of this rigid nature of ascomycetes CYP53 P450s' active site cavity, any inhibitor directed against this P450 family can serve as a common anti-fungal drug target, particularly toward pathogenic ascomycetes. The dynamic nature of basidiomycetes CYP53 P450s at a gene and protein level indicates that these P450s are destined to acquire novel functions. Functional analysis of CYP53 P450s strongly supported our hypothesis that the ascomycetes CYP53 P450s ability is limited for detoxification of toxic molecules, whereas basidiomycetes CYP53 P450s play an additional role, i.e. involvement in degradation of wood and its derived components. This study is the first report on genome-wide comparative structural (gene and protein structure-level) and evolutionary analysis of a fungal P450 family.

Concerted versus stepwise mechanism in thymidylate synthase.

Thymidylate synthase (TSase) catalyzes the intracellular de novo formation of thymidylate (a DNA building block) in most living organisms, making it a common target for chemotherapeutic and antibiotic drugs. Two mechanisms have been proposed for the rate-limiting hydride transfer step in TSase catalysis: a stepwise mechanism in which the hydride transfer precedes the cleavage of the covalent bond between the enzymatic cysteine and the product and a mechanism where both happen concertedly. Striking similarities between the enzyme-bound enolate intermediates formed in the initial and final step of the reaction supported the first mechanism, while QM/MM calculations favored the concerted mechanism. Here, we experimentally test these two possibilities using secondary kinetic isotope effect (KIE), mutagenesis study, and primary KIEs. The findings support the concerted mechanism and demonstrate the critical role of an active site arginine in substrate binding, activation of enzymatic nucleophile, and the hydride transfer studied here. The elucidation of this reduction/substitution sheds light on the critical catalytic step in TSase and may aid future drug or biomimetic catalyst design.

Voltage-gated sodium (NaV) channel blockade by plant cannabinoids does not confer anticonvulsant effects per se

Cannabidiol (CBD) is a non-psychoactive, well-tolerated, anticonvulsant plant cannabinoid, although its mechanism(s) of seizure suppression remains unknown. Here, we investigate the effect of CBD and the structurally similar cannabinoid, cannabigerol (CBG), on voltage-gated Na+ (NaV) channels, a common anti-epileptic drug target. CBG's anticonvulsant potential was also assessed in vivo. CBD effects on NaV channels were investigated using patch-clamp recordings from rat CA1 hippocampal neurons in brain slices, human SH-SY5Y (neuroblastoma) cells and mouse cortical neurons in culture. CBG effects were also assessed in SH-SY5Y cells and mouse cortical neurons. CBD and CBG effects on veratridine-stimulated human recombinant NaV1.1, 1.2 or 1.5 channels were assessed using a membrane potential-sensitive fluorescent dye high-throughput assay. The effect of CBG on pentyleneterazole-induced (PTZ) seizures was assessed in rat. CBD (10μM) blocked NaV currents in SH-SY5Y cells, mouse cortical neurons and recombinant cell lines, and affected spike parameters in rat CA1 neurons; CBD also significantly decreased membrane resistance. CBG blocked NaV to a similar degree to CBD in both SH-SY5Y and mouse recordings, but had no effect (50–200mg/kg) on PTZ-induced seizures in rat. CBD and CBG are NaV channel blockers at micromolar concentrations in human and murine neurons and recombinant cells. In contrast to previous reports investigating CBD, CBG had no effect upon PTZ-induced seizures in rat, indicating that NaV blockade per se does not correlate with anticonvulsant effects.

Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease

Alzheimer's disease (AD) is an incurable neurodegenerative disorder. Much effort has been devoted to developing effective therapeutic agents. Recently, targeting microRNAs (miRNAs) with small molecules has become a novel therapy for human diseases. In this study, we present a systematic computational approach to construct a bioactive Small molecule and miRNA association Network in AD (SmiRN-AD), which is based on the gene expression signatures of bioactive small molecule perturbation and AD-related miRNA regulation. We also performed topological and functional analysis of the SmiRN-AD from multiple perspectives. At the significance level of p ≤ 0.01, 496 small molecule-miRNA associations, including 25 AD-related miRNAs and 275 small molecules, were recognized and used to construct the SmiRN-AD. The drugs that were connected with the same miRNA tended to share common drug targets (p = 1.72 × 10(-4)) and belong to the same therapeutic category (p = 4.22 × 10(-8)). The miRNAs that were linked to the same small molecule regulated more common miRNA targets (p = 6.07 × 10(-3)). Further analysis of the positive connections (quinostatin and miR-148b, amantadine and miR-15a) and the negative connections (melatonin and miR-30e-5p) indicated that our large-scale predictions afforded specific biological insights into AD pathogenesis and therapy. This study proposes a holistic strategy for deciphering the associations between small molecules and miRNAs in AD, which may be helpful for developing a novel effective miRNA-associated therapeutic strategy for AD. A comprehensive database for the SmiRN-AD and the differential expression patterns of the miRNA targets in AD is freely available at http://bioinfo.hrbmu.edu.cn/SmiRN-AD/.

Combination of site directed mutagenesis and secondary structure analysis predicts the amino acids essential for stability of M. leprae MurE

The life-threatening infections caused by Mycobacterium leprae (Mle) remain a major challenge in developing countries as well as globe and there is a need to design potent anti-leprosy drugs. In our previous studies, ATP-dependent Mle-MurE ligase involved in biosynthesis of peptidoglycan was identified as one of the common drug targets, homology modeled and reported. In this work in silico site directed mutagenesis study was carried out on the homology modeled Mle-MurE ligase. This predicted the amino acids essential for stability. In addition, the distribution of these residues in different secondary structures and in active sites was analyzed. Finally, the role of the conserved residues in stability and function was analyzed. The availability of Mle-MurE ligase built model together with insights gained from stability studies and docking studies will promote the rational design of potent and selective Mle-MurE ligase inhibitors as anti-leprosy therapeutics.

Block of Na+ Currents and Suppression of Action Potentials in Cultured Hippocampal Neurons by Gs-458967

Voltage-gated Na+ channels (NaChs) are common targets for anti-epileptic drugs due to their role in the initiation and propagation of action potentials in central neurons. NaCh blocking agents, such as phenytoin and lamotrigine, act by blocking peak Na+ current (INa) in voltage- and frequency- dependent manner. A recent study showed that GS-458967 (GS967) is a potent blocker of cardiac INa. However, the effects of GS967 on neuronal INa and action potentials were not examined. Thus, using isolated rat cultured hippocampal neurons, effects of GS967 on neuronal INa and excitability were determined. GS967 (10-1000 nM) caused a voltage- (−60 mV) and frequency (10 Hz)-dependent block of INa with IC50 values of 40.6±4.0 (n=4, at each concentration) and 477.0±53.0 nM (n=4, at each concentration), respectively. However, tonic block of INa was minimal (7.6±0.5 % at 1000 nM, n= 4). GS967 decreased the sustained repetitive firing (SRF) in response to a 1-sec depolarizing current injection with an IC50 value of 47.8±2.8 nM (n=3-4, at each concentration). Consistent with minimal tonic block of INa, the compound had no effect on the amplitude of the first action potential during SRF (2.2±0.8 % at 300 nM). Furthermore, GS967 reversibly reduced the epileptiform activity induced by NMDA activation (removal of extracellular Mg2+) with an IC50 value of 50.7±1.4 nM (n=3-5, at each concentration). In addition, the effects of GS967 on ligand-gated ion channels that are essential for synaptic inhibition or excitation were tested. GS967 (1000 nM) had no effect on GABA-activated currents (4.2±3.4%, n=8). At 1000 nM, GS967 inhibited NMDA-activated currents by 18.2±6.2% (n=5). Taken together, these findings provide preliminary evidence that GS967 could be effective in controlling abnormal neuronal firing.

Computational Design of Peptide Vaccine against Acinetobacter Baumannii Infection using Comparative Genomic Approach

The bacterial species Acinetobacter baumannii is a major cause of hospital acquired infection throughout the world and it is increasing public health concern. Infection caused by multidrug resistant A. baumannii is currently among the most difficult to treat due to propensity to acquire mobile genetic element. To date there is no vaccine or specific drug available for its treatment, this necessitate the need for the identification of therapeutic target enzyme and vaccine. Pharmacogenomic and computational biology represent an attractive alternative approach for the identification of common drug target and peptide-vaccine candidates in the pathogen. Vaccine designing is shifted from entire pathogen or whole antigen to peptide or epitope based-vaccines that are specific, safe and easy to produce. Comparative genomic approach was used to identify conserved protein signatures among five genomes. Three outer membrane proteins conserved among the genomes with high vaxijen scores were used to produce both B-cell and T-cell mediated immunity. Propred and propred1 were used to predict promiscuos helper T-Lymphocytes (HTL), Cytotoxic T-Lymphocyte (CTL) epitopes and MHCPred for their binding affinity.Three T-cell epitopes derived from identified B-cells bind to maximum number of MHC class I and class II alleles and specifically bind to HLA alleles such as DRB1*0101 and DRB1*0401.The epitopes are YEKLAAGPS, FYTSQPEDS and YVTGNPLGL with high potential to induce humoral and cell mediated immune responses. These predicted epitopes (small peptide) might be promising candidates for vaccine design against A. baumannii infection, though experimental validation.

CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins?

Glioblastoma (GBM) is the malignant form of glioma, and the interplay of different pathways working in concert in GBM development and progression needs to be fully understood. Wnt signaling and sonic hedgehog (SHH) signaling pathways, having basic similarities, are among the major pathways aberrantly activated in GBM, and hence, need to be targeted. It becomes imperative, therefore, to explore the functioning of these pathways in context of each other in GBM. An integrative approach may help provide new biological insights, as well as solve the problem of identifying common drug targets for simultaneous targeting of these pathways. The beauty of this approach is that it can recapitulate several known facts, as well as decipher new emerging patterns, identifying those targets that could be missed when relying on one type of data at a time. This approach can be easily extended to other systems to discover key patterns in the functioning of signaling molecules. Studies were designed to assess the relationship between significant differential expression of genes of the Wnt (Wnt/β-catenin canonical and Wnt non-canonical) and SHH signaling pathways and their connectivity patterns in interaction and signaling networks. Further, the aim was to decipher underlying mechanistic patterns that may be involved in a more specific way and to generate a ranked list of genes that can be used as markers or drug targets. These studies predict that Wnt pathway plays a relatively more pro-active role than the SHH pathway in GBM. Further, CTNNB1, CSNK1A1, and Gli2 proteins may act as key drug targets common to these pathways. While CTNNB1 is a widely studied molecule in the context of GBM, the likely roles of CSNK1A1 and Gli2 are found to be relatively novel. It is surmised that Gli2 may be antagonistic to CSNK1A1, preventing the phosphorylation of CTNNB1 and SMO proteins in Wnt and SHH signaling pathway, respectively, by CSNK1A1, and thereby, aberrant activation. New insights into the possible behavior of these pathway molecules relative to each other in GBM reveal some key interesting patterns.

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

Cell-surface receptors are the most common target for therapeutic drugs. The design and optimization of next generation synthetic drugs require a detailed understanding of the interaction with their corresponding receptors. Mathematical approximations to study ligand-receptor systems based on reaction kinetics strongly simplify the spatial constraints of the interaction, while full atomistic ligand-receptor models do not allow for a statistical many-particle analysis, due to their high computational requirements. Here we present a generic coarse-grained model for ligand-receptor systems that accounts for the essential spatial characteristics of the interaction, while allowing statistical analysis. The model captures the main features of ligand-receptor kinetics, such as diffusion dependence of affinity and dissociation rates. Our model is used to characterize chimeric compounds, designed to take advantage of the receptor over-expression phenotype of certain diseases to selectively target unhealthy cells. Molecular dynamics simulations of chimeric ligands are used to study how selectivity can be optimized based on receptor abundance, ligand-receptor affinity and length of the linker between both ligand subunits. Overall, this coarse-grained model is a useful approximation in the study of systems with complex ligand-receptor interactions or spatial constraints.

Antibody-Based Imaging of HER-2: Moving into the Clinic

Human epidermal growth factor receptor-2 (HER-2) mediates a number of important cellular activities, and is up-regulated in a diverse set of cancer cell lines, especially breast cancer. Accordingly, HER-2 has been regarded as a common drug target in cancer therapy. Antibodies can serve as ideal candidates for targeted tumor imaging and drug delivery, due to their inherent affinity and specificity. Advanced by the development of a wide variety of imaging techniques, antibody-based imaging of HER-2 can allow for early detection and localization of tumors, as well as monitoring of drug delivery and tissue's response to drug treatment. In this review article, antibody-based imaging of HER-2 are summarized and discussed, with an emphasis on the involved imaging methods.

Prevalence of mutation and phenotypic expression associated with sulfadoxine-pyrimethamine resistance in Plasmodium falciparum and Plasmodium vivax

Therapeutic efficacy of sulfadoxine-pyrimethamine (SP), which is commonly used to treat falciparum malaria, was assessed in isolates of Plasmodium falciparum (Welch, 1897) and Plasmodium vivax (Grassi et Feletti, 1890) ofAligarh, Uttar Pradesh, North India and Taif, Saudi Arabia during 2011-2012. Both the species showed mutations in dihydrofolate reductase (DHFR) enzyme as they have common biochemical drug targets. Mutation rate for pfdhfr was higher compared to pvdhfr because the drug was mainly given to treat falciparum malaria. Since both the species coexist, P. vivax was also exposed to SP due to faulty species diagnosis or medication without specific diagnosis. Low level of mutations against SP in P. falciparum of Saudi isolates indicates that the SP combination is still effective for the treatment of falciparum malaria. Since SP is used as first-line of treatment because of high level of resistance against chloroquine (CQ), it may result in spread of higher level of mutations resulting in drug resistance and treatment failure in near future. Therefore, to avoid further higher mutations in the parasite, use of better treatment regimens such as artesunate combination therapy must be introduced against SP combination.

Comparative genomic studies and in-silco strategies on Leishmania brazilensis, Leishmania infantum and Leishmania major: Conserved features, putative functions and potential drug target

Leishmaniasis is a parasitic disease found largely in the tropics, which the World Health Organization has estimated infects 12 million people worldwide each year. More recently cases have been reported in Europe among intravenous drug users with HIV. At least 20 Leishmania species infect humans. New world parasite Leishmania. braziliensis is the causative agent of mucocutaneous Leishmaniasis. The old world species Leishmania. major and Leishmania. infantum, which are present in Africa, Europe and Asia, are parasites that cause cutaneous and visceral Leishmaniasis respectively. Aim of this Study is determination of major common genes and Protein identified Gene location on each of the chromosomes, and identification of a common protein drug target Promastigote surface antigen with available lead molecule acetylglucosamine (6-(acetylamino)-6-deoxyhexopyranose) and docking studies on those considered Leishmania species.DOI: http://dx.doi.org/10.3126/ijasbt.v1i2.8077 Int J Appl Sci Biotechnol, Vol. 1(2): 63-67

Combined whole genome copy number genotyping and multiplex somatic mutation profiling of FFPE brain tumor specimens for clinical diagnosis and trial selection.

2030 Background: Multi-dimensional cancer genotyping is increasingly needed for clinical diagnostics and trial selection. Whole genome copy number is relevant for glioblastoma and other brain tumors but routine prospective FFPE-based multiplex copy number and somatic mutation genotyping for clinical trials has not been achieved. Methods: Using novel DNA extraction protocols we implemented whole genome copy number (Agilent aCGH stock 1M feature arrays) and somatic mutation profiling (Oncomap v4.4 Sequenom) assays into a CLIA-certified laboratory setting. Twenty-three copy number aberrations (CNAs) relevant to brain tumors were reported from whole genome data and Oncomap results were reported for 471 cancer-related mutations in 41 genes. Results: During the initial eight months of our combined copy number and mutation-testing program, aCGH and Oncomap were performed prospectively on 239 and 157 brain tumor patients respectively. Copy number was reported in 90% of patients (214/239) and failures were due to insufficient DNA from small biopsies. GBMs (n = 94) harbored gains and losses at expected rates and included amplifications of common drug targets (EGFR, EGFRv3, MET, MDM2, MDM4, PDGFRA, CDK4, CDK6). Emerging candidate drug targets were identified including variant EGFR deletions (e.g. EGFRv2) and FGFR3-TACC3 gains for which other clinical tests are not available. Oncomap results for 78 GBMs revealed mutations in TP53, PTEN and IDH1. Less frequent mutations occurred in BRAF, RB1, PIK3CA, PIK3R1 and KRAS. We integrated copy number and mutation data for 27 GBMs, allowing for improved evaluation of tumor suppressor inactivation status (e.g. PTEN mutation with monosomy 10). In combination, our assays reported data on 10 clinically actionable drug targets relevant for 15 clinical trials open at the time of patient testing. Conclusions: We implemented complementary assays for efficiently detecting genome-wide CNAs and mutations on FFPE brain tumor samples in a CLIA-certified environment. Systematic integration of these results broadens the range of diagnostic and actionable data available to identify patients for trials of targeted therapeutics.