School Of Basic And Applied Sciences
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Item In silico study of flavonoids as DPP-4 and α-glucosidase inhibitors(Bentham Science Publishers B.V., 2018) Kaur, J.; Singla, Ramit; Jaitak, VikasBackground: Diabetes being among the most prevalent disease is being studied widely to achieve most potent drug with lesser side-effects. Numerous targets have been explored and several drugs have been developed to combat type-2 diabetes. Worldwide scenario depicts an increase in the number of diabetics at an alarming rate. Due to this critical need in the current scenario, the focus has been shifted to natural products. Amongst which flavonoids have been extensively studied for their anti-diabetic potential. Among various targets inhibition of DPP-4, ?-glucosidase arose as an advantageous methodology for the management of type-2 diabetes. DPP-4 inhibitor helps to maintain the insulin levels in the body and ?-glucosidase inhibitor aids in the control of the postprandial glycemia. Methods: In the present study, the molecular modeling of 155 flavonoids has been performed using GLIDE against Dipeptidyl Peptidase-4 (DPP-4) (PDB ID:2ONC) and ?-glucosidase (PDB ID: 2QMJ) so as to achieve lead compounds that can be further used to develop a new drug. Results: Rutin and Theaflavin-3,3'-di-O-gallate were observed to possess the best docking score for ?-glucosidase and DPP-4 respectively. Conclusions: The top scoring flavonoids show promising results, but further studies are required to be carried out including the pharmacophore mapping, SAR and QSAR studies. The results illustrated that the hydrogen bonding plays a crucial role in the binding and positioning of the molecules into the active site. Further, the rescoring of the docking values mentioned as MMGB/SA also reconfirmed that these compounds show favorable results. ? 2018 Bentham Science Publishers.Item Genome-wide association study of 25(OH) Vitamin D concentrations in Punjabi Sikhs: Results of the Asian Indian diabetic heart study(Elsevier Ltd, 2016) Sapkota, B.R.; Hopkins, R.; Bjonnes, A.; Ralhan, S.; Wander, G.S.; Mehra, N.K.; Singh, J.R.; Blackett, P.R.; Saxena, R.; Sanghera, D.K.Vitamin D deficiency is implicated in multiple disease conditions and accumulating evidence supports that the variation in serum vitamin D (25(OH)D) levels, including deficiency, is under strong genetic control. However, the underlying genetic mechanism associated with vitamin 25(OH)D concentrations is poorly understood. We earlier reported a very high prevalence of vitamin D deficiency associated with an increased risk for type 2 diabetes and obesity in a Punjabi Sikh diabetic cohort as part of the Asian Indian diabetic heart study (AIDHS). Here we have performed the first genome-wide association study (GWAS) of serum 25(OH)D on 3538 individuals from this Punjabi Sikh population. Our discovery GWAS comprised of 1387 subjects followed by validation of 24 putative SNPs (P < 10-4) using an independent replication sample (n = 2151) from the same population by direct genotyping. A novel locus at chromosome 20p11.21 represented by rs2207173 with minor allele frequency (MAF) 0.29, [? = -0.13, p = 4.47 ? 10-9] between FOXA2 and SSTR4 was identified to be associated with 25(OH)D levels. Another suggestive association signal at rs11586313 (MAF 0.54) [? = 0.90; p = 1.36 ? 10-6] was found within the regulatory region of the IVL gene on chromosome 1q21.3. Additionally, our study replicated 3 of 5 known GWAS genes associated with 25(OH)D concentrations including GC (p = 0.007) and CYP2R1 (p = 0.019) reported in Europeans and the DAB1 (p = 0.003), reported in Hispanics. Identification of novel association signals in biologically plausible regions with 25(OH)D metabolism will provide new molecular insights on genetic drivers of vitamin D status and its implications in health disparities. ? 2015 Elsevier Ltd. All rights reserved.Item Chemical composition and antiproliferative, antioxidant, and proapoptotic effects of fruiting body extracts of the lingzhi or reishi medicinal mushroom, ganoderma lucidum (Agaricomycetes), from India(Begell House Inc., 2016) Gill, B.S.; Sharma, P.; Navgeet, Kumar, S.Ganoderma lucidum is a renowned medicinal mushroom exploited as a panacea because of the broad spectrum of its bioactivities, which give it invaluable nutritional and clinical implications. This research was implemented with an incentive to explore and quantify various macromolecules encompassed in the oriental fungus; these vary in concentration with respect to the development/growth phase, host plants, and geographic location of collection. Chemical profiling of G. lucidum confirmed the presence of myco-constituents, their amounts varying in response to extreme climatic conditions. G. lucidum extract exhibited elevated levels of all myco-constituents but flavonoids, which were more pronounced when in a parasitic relationship with their host plants. Proapoptotic efficiency portrayed by the extracts against a prostate cancer cell line (PC-3) was also found to be similar. The samples collected from the Bathinda region, with Azadirachta and Acacia trees as the host plants, showed several-fold augmentation in levels of G. lucidum gredients compared with other variants. Elevated levels of myco-constituents highlight their significance in inhibiting prostate cancer cell proliferation, reducing reactive oxygen species, suppressing invasive potential, and inducing apoptosis. It was thus concluded that G. lucidum grown on Azadirachta plants was more efficient in exhibiting potent biological activities than G. lucidum grown on other host plants. ? 2016 Begell House, Inc.Item Cellular uptake, intracellular trafficking and cytotoxicity of silver nanoparticles(2012) Singh, R.P.; Ramarao, P.Silver nanoparticles (Ag NPs) are used in consumer products and wound dressings due to their antimicrobial properties. However, in addition to toxic effects on microbes, Ag NPs can also induce stress responses as well as cytotoxicity in mammalian cells. We observed that Ag NPs are efficiently internalized via scavenger receptor-mediated phagocytosis in murine macrophages. Confocal and electron microscopy analysis revealed that internalized Ag NPs localize in the cytoplasm. Ag NPs cause mitochondrial damage, induce apoptosis and cell death. These effects were abrogated in presence of Ag ion-reactive, thiol-containing compounds suggesting the central of Ag ions in Ag NP toxicity. Quantitative image analysis revealed that intracellular dissolution of Ag NPs occurs about 50 times faster than in water. In conclusion, we demonstrate for the first time that Ag NPs are internalized by scavenger receptors, trafficked to cytoplasm and induce toxicity by releasing Ag ions. ? 2012 Elsevier Ireland Ltd.Item Chloroplast DNA phylogeography of holy basil (Ocimum tenuiflorum) in Indian subcontinent(2014) Bast, Felix; Rani, Pooja; Meena, DevendraOcimum tenuiflorum L., holy basil "Tulsi", is an important medicinal plant that is being grown and traditionally revered throughout Indian Subcontinent for thousands of years; however, DNA sequence-based genetic diversity of this aromatic herb is not yet known. In this report, we present our studies on the phylogeography of this species using trnL-trnF intergenic spacer of plastid genome as the DNA barcode for isolates from Indian subcontinent. Our pairwise distance analyses indicated that genetic heterogeneity of isolates remained quite low, with overall mean nucleotide p-distance of 5?10-4. However, our sensitive phylogenetic analysis using maximum likelihood framework was able to reveal subtle intraspecific molecular evolution of this species within the subcontinent. All isolates except that from North-Central India formed a distinct phylogenetic clade, notwithstanding low bootstrap support and collapse of the clade in Bayesian Inference. North-Central isolates occupied more basal position compared to other isolates, which is suggestive of its evolutionarily primitive status. Indian isolates formed a monophyletic and well-supported clade within O. tenuiflorum clade, which indicates a distinct haplotype. Given the vast geographical area of more than 3 million km 2 encompassing many exclusive biogeographical and ecological zones, relatively low rate of evolution of this herb at this locus in India is particularly interesting. ? 2014 Felix Bast et al.Item Homology modeling of chemokine CCR7, molecular docking, and in vitro studies evidenced plausible immunotherapeutic anticancer natural compounds(Birkhauser Boston, 2016) Singh, Pushpendra; Singh, Ravi Shankar; Rani, Alka; Bast, FelixThe chemokine receptor 7 is a G-protein coupled, receptors coordinates the migration of cancer cells towards CCL19 and CCL21 constitutively expressed lymphatic organs. Chemokine receptor 7 facilitates cancer progression by generating new lymphatic vessels that serve as conduits for tumor dissemination to lymph nodes. In this context, chemokine receptor 7 inhibitor recently caught an attention for cancer cell growth inhibitor. The 3-D crystalline structure of chemokine receptor 7 not available in protein data bank (PDB), first we predicted the 3-D structure of chemokine receptor 7 and then performed receptor-based molecular docking of chemokine receptor 7 against natural and marine compounds. Semiquantitative polymerase chain reaction (PCR) and quantitative real-time PCR were performed for mRNA expression of chemokine receptor 7 and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) used as internal control. The best-docked compounds have been selected for chemokine receptor 7 inhibitors by optimal energy value (Gscore), types of interactions, and conformations. CID6441009, 42607750, 72276, 6711419, 56835050, 65064, 23663412, 72277, 643668, 54679285 compound have a better binding energy ?11.35, ?10.51, ?10.16, ?9.98, ?9.95, ?9.86, ?9.83, ?9.57, ?9.47, and ?9.45 respectively against chemokine receptor 7. Protein?ligand interactions profile highlighted that amino acid Glu45, Lys50, Arg54, Lys57, Trp114, Met260, Glu205, Gln227, Gln276, and Asp309 involved in the hydrophobic, hydrogen bonding, and ?-? stacking interactions play a central role at the active site. Moreover, treatment with the Epigallocatechin gallate led to down-regulation of mRNA expression of chemokine receptor 7 in HepG2 and PC3 cells. This molecular docking study recapitulates the docking free energy, protein?ligands interactions profile, pharmacokinetic, and the pharmacodynamic parameter of lead molecules, which are extremely helpful to improve the activity of natural and marine compounds against chemokine receptor 7. ? 2016, Springer Science+Business Media New York.Item High-throughput virtual screening, identification and in vitro biological evaluation of novel inhibitors of signal transducer and activator of transcription 3(Birkhauser Boston, 2015) Singh, Pushpendra; Bast, FelixSignal transducer and activator of transcription (STAT) family, encompassing protein molecules that function as a second messenger and transcription factor, are famously known to regulate a multitude of cellular processes including inflammation, cell proliferation, invasion, angiogenesis, metastasis and immune system homeostasis. STAT3 is one of the six members of a family of transcription factors. STAT3 has proved themselves to be interesting candidates for anticancer therapy as they are over-expressed in most cancer cells. Thus, we studied receptor-based molecular docking of STAT3 against natural compounds and further validations of lead molecules in an array of cancer cells. In the present study, we screened approximately 50,000 natural compounds from the IBS. All natural compounds were docked with the X-ray crystal structure of STAT3 (PDB; 1BG1) retrieved from the protein data bank by using Maestro 9.6 (Schr?dinger Inc). First, we performed high-throughput virtual screening of IBS against the SH2 domain of STAT3. Further, best 20 compounds that possess minimal Gscore along with 85 natural compounds that had been reported in published literature as having anticancer properties were selected, and molecular docking was performed using the XP (extra precision) mode of GLIDE. We analyzed Gscore and protein-ligand interactions of top ranking compounds. It was discovered in this study, compounds CID252682, CID5281670 (Morin), CID5281672 (Myricetin), CID72277 (Epigallocatechol) and CID65064 (Epigallocatechin Gallate, EGCG) yielded the excellent dock score with the STAT3 concluded with the help of docking-free energy. Moreover, IBS STOCK1N-43090, STOCK1N-66505, STOCK1N-54303, STOCK1N-44634, STOCK1N-45027, STOCK1N-73784, STOCK1N-69597, STOCK1N-73062, STOCK1N-81915 and STOCK1N-70844 have better docking-free energy. Further, we chose EGCG and myricetin compounds, and their effect on biological activity such as cell proliferation, oxidative stress, colony formation, mRNA expression of STAT3, and cell number was reported after the 48 h treatments in cancer cell lines. EGCG and myricetin reduce the STAT3 mRNA expression confirmed by RTPCR. Moreover, EGCG and myricetin reduce cell proliferation and ROS generation after 48 h treatments. Interestingly, our result also indicates that the reduction in potential for colony formation enhances anti-metastasis activity of EGCG and myricetin. The information obtained from our study assisted us in drawing a more lucid picture regarding the existence STAT3 natural compounds inhibitor on diverse cancer cells. ? 2015 Springer Science+Business Media.Item Intracellular delivery of redox cycler-doxorubicin to the mitochondria of cancer cell by folate receptor targeted mitocancerotropic liposomes(2012) Malhi, Sarandeep Singh; Budhiraja, Abhishek; Arora, Sumit; Chaudhari, Kiran R.; Nepali, Kunal; Kumar, Raj; Sohi, Harmik; Murthy, Rayasa S.R.Cancer cells reflect higher level of ROS in comparison to the normal cell, so they become more vulnerable to further oxidative stress induced by exogenous ROS-generating agents. Through this a novel therapeutic strategy has evolved, which involves the delivery of redox cycler-doxorubicin (DOX) to the mitochondria of cancer cell where it acts as a source of exogenous ROS production. The purpose of this study is to develop a liposomal preparation which exhibits a propensity to selectively target cancer cell along with the potential of delivering drug to mitochondria of cell. We have rendered liposomes mitocancerotropic (FA-MTLs) by their surface modification with dual ligands, folic acid (FA) for cancer cell targeting and triphenylphosphonium (TPP) cations for mitochondria targeting. The cytotoxicity, ROS production and cell uptake of doxorubicin loaded liposomes were evaluated in FR (+) KB cells and found to be increased considerably with FA-MTLs in comparison to folic acid appended, mitochondria targeted and non-targeted liposomes. As confirmed by confocal microscopy, the STPP appended liposomes delivered DOX to mitochondria of cancer cell and also showed higher ROS production and cytotoxicity in comparison to folic acid appended and non-targeted liposomes. Most importantly, mitocancerotropic liposomes showed superior activity over mitochondria targeted liposomes which confirm the synergistic effect imparted by the presence of dual ligands - folic acid and TPP on the enhancement of cellular and mitochondrial delivery of doxorubicin in KB cells. ? 2012 Elsevier B.V. All rights reserved.Item Elevated level of acetylation of APE1 in tumor cells modulates DNA damage repair(Impact Journals LLC, 2016) Sengupta, S.; Mantha, Anil K.; Song, H.; Roychoudhury, S.; Nath, S.; Ray, S.; Bhakat, K.K.Apurinic/apyrimidinic (AP) sites are frequently generated in the genome by spontaneous depurination/depyrimidination or after removal of oxidized/modified bases by DNA glycosylases during the base excision repair (BER) pathway. Unrepaired AP sites are mutagenic and block DNA replication and transcription. The primary enzyme to repair AP sites in mammalian cells is AP endonuclease (APE1), which plays a key role in this repair pathway. Although overexpression of APE1 in diverse cancer types and its association with chemotherapeutic resistance are well documented, alteration of posttranslational modification of APE1 and modulation of its functions during tumorigenesis are largely unknown. Here, we show that both classical histone deacetylase HDAC1 and NAD+-dependent deacetylase SIRT1 regulate acetylation level of APE1 and acetylation of APE1 enhances its AP-endonuclease activity both in vitro and in cells. Modulation of APE1 acetylation level in cells alters AP site repair capacity of the cell extracts in vitro. Primary tumor tissues of diverse cancer types have higher level of acetylated APE1 (AcAPE1) compared to adjacent non-tumor tissue and exhibit enhanced AP site repair capacity. Importantly, in the absence of APE1 acetylation, cells accumulate AP sites in the genome and show increased sensitivity to DNA damaging agents. Together, our study demonstrates that elevation of acetylation level of APE1 in tumor could be a novel mechanism by which cells handle the elevated levels of DNA damages in response to genotoxic stress and maintain sustained proliferation.Item Human apurinic/apyrimidinic endonuclease (APE1) is acetylated at DNA damage sites in chromatin, and acetylation modulates its DNA repair activity(American Society for Microbiology, 2016) Roychoudhury, S.; Nath, S.; Song, H.; Hegde, M.L.; Bellot, L.J.; Mantha, Anil K.; Sengupta, S.; Ray, S.; Natarajan, A.; Bhakat, K.K.Apurinic/apyrimidinic (AP) sites, the most frequently formed DNA lesions in the genome, inhibit transcription and block replication. The primary enzyme that repairs AP sites in mammalian cells is the AP endonuclease (APE1), which functions through the base excision repair (BER) pathway. Although the mechanism by which APE1 repairs AP sites in vitro has been extensively investigated, it is largely unknown how APE1 repairs AP sites in cells. Here, we show that APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulated AP sites in the genome and showed higher sensitivity to DNA-damaging agents. Thus, mammalian cells, unlike Saccharomyces cerevisiae or Escherichia coli cells, require acetylation of APE1 for the efficient repair of AP sites and base damage in the genome. Our study reveals that APE1 acetylation is an integral part of the BER pathway for maintaining genomic integrity. ? 2017 Roychoudhury et al.