Papers by jayakanth kankanala
Tyrosyl DNA phosphodiesterase II (TDP2) is a recently discovered enzyme that specifically repairs... more Tyrosyl DNA phosphodiesterase II (TDP2) is a recently discovered enzyme that specifically repairs DNA damages induced by topoisomerase II (Top2) poisons and causes resistance to these drugs. Inhibiting TDP2 is expected to enhance the efficacy of clinically important Top2-targeting anticancer drugs. However, TDP2 as a therapeutic target remains poorly understood. We report herein the discovery of isoquinoline-1,3-dione as a viable chemotype for selectively inhibiting TDP2. The initial hit compound 43 was identified by screening our in-house collection of synthetic compounds. Further structure-activity-relationship (SAR) studies identified numerous analogues inhibiting TDP2 in low micromolar range without appreciable inhibition against the homologous TDP1 at the highest testing concentration (111 M). The best compound 64 inhibited recombinant TDP2 with an IC50 of 1.9 µM. The discovery of this chemotype may provide a platform towards understanding TDP2 as a drug target.
Methods in Molecular Biology, 2015
The mammalian vascular endothelial growth factor receptor tyrosine kinases (VEGFRs) bind circulat... more The mammalian vascular endothelial growth factor receptor tyrosine kinases (VEGFRs) bind circulating growth factors and regulate the process of angiogenesis. The discovery of new small molecules that target the enzymatic activity of the VEGFR family as potential antiangiogenic drugs is of much commercial interest in the pharmaceutical sector. Here, we describe the use of a combined cell surface biotinylation and affinity isolation procedure to monitor ligand-stimulated VEGFR trafficking in endothelial cells, in which novel VEGFR inhibitors from chemical libraries can be identified by their ability to inhibit receptor internalization. Unlike a traditional cell-free enzyme activity assay, such a cell-based approach provides a physiologically relevant readout of inhibitor activity. In this example, we use the VEGF-A-VEGFR-2 axis and the well-characterized tyrosine kinase inhibitor sunitinib as a working model; however this technique is highly applicable for the identification of inhibitors to other receptor tyrosine kinases.
Journal of Thrombosis and Haemostasis
The Hepatitis C virus (HCV) p7 viroporin has emerged as a promising anti-viral target. p7 channel... more The Hepatitis C virus (HCV) p7 viroporin has emerged as a promising anti-viral target. p7 channel activity mediates a distinct stage of the virus life-cycle compared with licensed HCV antivirals, namely virion secretion, making it an attractive addition to the current repertoire. Our recently published p7 structure now renders the channel amenable to modern structure-guided drug design, and we have developed the first nanomolar-potency small molecules targeting the secretion of HCV particles as a result. To progress this series towards full drug development, we have capitalised upon a newly optimised, semi-automated method of quantifying HCV infectivity by indirect immunofluorescence using the IncuCyte ZOOM software. This has allowed the iterative characterisation of inhibitors binding to a defined, membrane exposed p7 site, informing the next wave of small molecule design. Resultant compounds display activity against both HCV genotype 1 and 3, making them highly relevant to the cli...
Copper-catalysed click reaction followed by either a palladium-catalysed cyclisation-cross coupli... more Copper-catalysed click reaction followed by either a palladium-catalysed cyclisation-cross coupling or a palladium catalysed cyclisation–carbonylation/amination process to 3,3-disubstituted oxindole derivatives occurred in good yields.
The potent pro-angiogenic growth factors VEGF-A and basic fibroblast growth factor (bFGF) exert t... more The potent pro-angiogenic growth factors VEGF-A and basic fibroblast growth factor (bFGF) exert their effects by binding VEGF receptor 2 and FGF receptor tyrosine kinases, respectively. Indolinones (e.g. SU5416 and Sutent) and anilinophthalazines (e.g. PTK787) are potent small molecule inhibitors of VEGFR2 and other tyrosine kinases, but their effects on VEGF-A- and bFGF-stimulated endothelial responses are unclear. Here we assess the ability of these compounds to inhibit pro-angiogenic responses through perturbation of receptor activity and endothelial function(s).
Vascular endothelial growth factor receptor 2 (VEGFR2) is an attractive therapeutic target for th... more Vascular endothelial growth factor receptor 2 (VEGFR2) is an attractive therapeutic target for the treatment of diseases such as cancer. Small-molecule VEGFR2 inhibitors of a variety of chemical classes are currently under development or in clinical use. In this study, we describe the de novo design of a new generation pyrazole-based molecule (JK-P3) that targets VEGFR2 kinase activity and angiogenesis.
Current interferon-based therapy for hepatitis C virus (HCV) infection is inadequate, prompting a... more Current interferon-based therapy for hepatitis C virus (HCV) infection is inadequate, prompting a shift toward combinations of direct-acting antivirals (DAA) with the first protease-targeted drugs licensed in 2012. Many compounds are in the pipeline yet primarily target only three viral proteins, namely, NS3/4A protease, NS5B polymerase, and NS5A. With concerns growing over resistance, broadening the repertoire for DAA targets is a major priority. Here we describe the complete structure of the HCV p7 protein as a monomeric hairpin, solved using a novel combination of chemical shift and nuclear Overhauser effect (NOE)-based methods. This represents atomic resolution information for a full-length virus-coded ion channel, or "viroporin," whose essential functions represent a clinically proven class of antiviral target exploited previously for influenza A virus therapy. Specific drug-protein interactions validate an allosteric site on the channel periphery and its relevance is demonstrated by the selection of novel, structurally diverse inhibitory small molecules with nanomolar potency in culture. Hit compounds represent a 10,000-fold improvement over prototypes, suppress rimantadine resistance polymorphisms at submicromolar concentrations, and show activity against other HCV genotypes.
Background: Protein kinases play a central role in tumor progression, regulating fundamental proc... more Background: Protein kinases play a central role in tumor progression, regulating fundamental processes such as angiogenesis, proliferation and metastasis. Such enzymes are an increasingly important class of drug target with small molecule kinase inhibitors being a major focus in drug development. However, balancing drug specificity and efficacy is problematic with off-target effects and toxicity issues.
West Nile virus (WNV) and Dengue virus (DENV) are important human pathogens for which there are p... more West Nile virus (WNV) and Dengue virus (DENV) are important human pathogens for which there are presently no vaccine or specific antivirals. We report herein a 5′-silylated nucleoside scaffold derived from 3′-azidothymidine (AZT) consistently and selectively inhibiting WNV and DENV at low micromolar concentrations. Further synthesis of various triazole bioisosteres demonstrated clear structure−activity relationships (SARs) in which the antiviral activity against WNV and DENV hinges largely on both the 5′-silyl group and the substituent of 3′-triazole or its bioisosteres. Particularly interesting is the 5′ silyl group which turns on the antiviral activity against WNV and DENV while abrogating the previously reported antiviral potency against human immunodeficiency virus (HIV-1). The antiviral activity was confirmed through a plaque assay where viral titer reduction was observed in the presence of selected compounds. Molecular modeling and competitive Sadenosyl-L-methionine (SAM) binding assay suggest that these compounds likely confer antiviral activity via binding to methyltransferase (MTase).
Receptor tyrosine kinases (RTKs) are membrane proteins that control the flow of information throu... more Receptor tyrosine kinases (RTKs) are membrane proteins that control the flow of information through signal transduction pathways, impacting on different aspects of cell function. RTKs are characterized by a ligand-binding ectodomain, a single transmembrane α-helix, a cytosolic region comprising juxtamembrane and kinase domains followed by a flexible C-terminal tail. Somatic and germline RTK mutations can induce aberrant signal transduction to give rise to cardiovascular, developmental and oncogenic abnormalities. RTK overexpression occurs in certain cancers, correlating signal strength and disease incidence. Diverse RTK activation and signal transduction mechanisms are employed by cells during commitment to health or disease. Small molecule inhibitors are one means to target RTK function in disease initiation and progression. This review considers RTK structure, activation, and signal transduction and evaluates biological relevance to therapeutics and clinical outcomes.
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Papers by jayakanth kankanala