Browsing by Subject "Molecular Structure"

Now showing 1 - 12 of 12

Open Access
A chemical method for labeling lysine methyltransferase substrates.
(Chembiochem : a European journal of chemical biology, 2011-01) Binda, Olivier; Boyce, Michael; Rush, Jason S; Palaniappan, Krishnan K; Bertozzi, Carolyn R; Gozani, Or
Several protein lysine methyltransferases (PKMTs) modify histones to regulate chromatin-dependent cellular processes, such as transcription, DNA replication and DNA damage repair. PKMTs are likely to have many additional substrates in addition to histones, but relatively few nonhistone substrates have been characterized, and the substrate specificity for many PKMTs has yet to be defined. Thus, new unbiased methods are needed to find PKMT substrates. Here, we describe a chemical biology approach for unbiased, proteome-wide identification of novel PKMT substrates. Our strategy makes use of an alkyne-bearing S-adenosylmethionine (SAM) analogue, which is accepted by the PKMT, SETDB1, as a cofactor, resulting in the enzymatic attachment of a terminal alkyne to its substrate. Such labeled proteins can then be treated with azide-functionalized probes to ligate affinity handles or fluorophores to the PKMT substrates. As a proof-of-concept, we have used SETDB1 to transfer the alkyne moiety from the SAM analogue onto a recombinant histone H3 substrate. We anticipate that this chemical method will find broad use in epigenetics to enable unbiased searches for new PKMT substrates by using recombinant enzymes and unnatural SAM cofactors to label and purify many substrates simultaneously from complex organelle or cell extracts.
Open Access
Chemical inhibitor of nonapoptotic cell death with therapeutic potential for ischemic brain injury.
(Nature chemical biology, 2005-07) Degterev, Alexei; Huang, Zhihong; Boyce, Michael; Li, Yaqiao; Jagtap, Prakash; Mizushima, Noboru; Cuny, Gregory D; Mitchison, Timothy J; Moskowitz, Michael A; Yuan, Junying
The mechanism of apoptosis has been extensively characterized over the past decade, but little is known about alternative forms of regulated cell death. Although stimulation of the Fas/TNFR receptor family triggers a canonical 'extrinsic' apoptosis pathway, we demonstrated that in the absence of intracellular apoptotic signaling it is capable of activating a common nonapoptotic death pathway, which we term necroptosis. We showed that necroptosis is characterized by necrotic cell death morphology and activation of autophagy. We identified a specific and potent small-molecule inhibitor of necroptosis, necrostatin-1, which blocks a critical step in necroptosis. We demonstrated that necroptosis contributes to delayed mouse ischemic brain injury in vivo through a mechanism distinct from that of apoptosis and offers a new therapeutic target for stroke with an extended window for neuroprotection. Our study identifies a previously undescribed basic cell-death pathway with potentially broad relevance to human pathologies.
Open Access
Conductive junctions with parallel graphene sheets.
(J Chem Phys, 2010-03-21) Zheng, Xiao; Ke, San-Huang; Yang, Weitao
The establishment of conductive graphene-molecule-graphene junction is investigated through first-principles electronic structure calculations and quantum transport calculations. The junction consists of a conjugated molecule connecting two parallel graphene sheets. The effects of molecular electronic states, structure relaxation, and molecule-graphene contact on the conductance of the junction are explored. A conductance as large as 0.38 conductance quantum is found achievable with an appropriately oriented dithiophene bridge. This work elucidates the designing principles of promising nanoelectronic devices based on conductive graphene-molecule-graphene junctions.
Open Access
HRP-mediated polymerization forms tough nanocomposite hydrogels with high biocatalytic performance.
(Chemical communications (Cambridge, England), 2013-09) Su, Teng; Zhang, Da; Tang, Zhou; Wu, Qing; Wang, Qigang
This communication describes the mild and quick construction of tough nanocomposite hydrogels via a horseradish peroxidase-mediated radical polymerization for effectively immobilizing enzymes to attain high catalytic performance in various solvents.
Open Access
Identification of select glucocorticoids as Smoothened agonists: potential utility for regenerative medicine.
(Proc Natl Acad Sci U S A, 2010-05-18) Wang, Jiangbo; Lu, Jiuyi; Bond, Michael C; Chen, Minyong; Ren, Xiu-Rong; Lyerly, H Kim; Barak, Larry S; Chen, Wei
Regenerative medicine holds the promise of replacing damaged tissues largely by stem cell activation. Hedgehog signaling through the plasma membrane receptor Smoothened (Smo) is an important process for regulating stem cell proliferation. The development of Hedgehog-related therapies has been impeded by a lack of US Food and Drug Administration (FDA)-approved Smo agonists. Using a high-content screen with cells expressing Smo receptors and a beta-arrestin2-GFP reporter, we identified four FDA-approved drugs, halcinonide, fluticasone, clobetasol, and fluocinonide, as Smo agonists that activate Hedgehog signaling. These drugs demonstrated an ability to bind Smo, promote Smo internalization, activate Gli, and stimulate the proliferation of primary neuronal precursor cells alone and synergistically in the presence of Sonic Hedgehog protein. Halcinonide, fluticasone, clobetasol, and fluocinonide provide an unprecedented opportunity to develop unique clinical strategies to treat Hedgehog-dependent illnesses.
Open Access
Leukocyte and Dried Blood Spot Arylsulfatase A Assay by Tandem Mass Spectrometry.
(Analytical chemistry, 2020-05) Hong, Xinying; Kumar, Arun Babu; Daiker, Jessica; Yi, Fan; Sadilek, Martin; De Mattia, Fabiola; Fumagalli, Francesca; Calbi, Valeria; Damiano, Roberta; Della Bona, Maria; la Marca, Giancarlo; Vanderver, Adeline L; Waldman, Amy T; Adang, Laura; Sherbini, Omar; Woidill, Sarah; Suhr, Teryn; Kurtzberg, Joanne; Beltran-Quintero, Maria L; Escolar, Maria; Aiuti, Alessandro; Finglas, Alan; Olsen, Amber; Gelb, Michael H
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays were developed to measure arylsulfatase A (ARSA) activity in leukocytes and dried blood spots (DBS) using deuterated natural sulfatide substrate. These new assays were highly specific and sensitive. Patients with metachromatic leukodystrophy (MLD) and multiple sulfatase deficiency (MSD) displayed a clear deficit in the enzymatic activity and could be completely distinguished from normal controls. The leukocyte assay reported here will be important for diagnosing MLD and MSD patients and for monitoring the efficacy of therapeutic treatments. ARSA activity was measured in DBS for the first time without an antibody. This new ARSA DBS assay can serve as a second-tier test following the sulfatide measurement in DBS for newborn screening of MLD. This leads to an elimination of most of the false positives identified by the sulfatide assay.
Open Access
Modulating unimolecular charge transfer by exciting bridge vibrations.
(J Am Chem Soc, 2009-12-23) Lin, Zhiwei; Lawrence, Candace M; Xiao, Dequan; Kireev, Victor V; Skourtis, Spiros S; Sessler, Jonathan L; Beratan, David N; Rubtsov, Igor V
Ultrafast UV-vibrational spectroscopy was used to investigate how vibrational excitation of the bridge changes photoinduced electron transfer between donor (dimethylaniline) and acceptor (anthracene) moieties bridged by a guanosine-cytidine base pair (GC). The charge-separated (CS) state yield is found to be lowered by high-frequency bridge mode excitation. The effect is linked to a dynamic modulation of the donor-acceptor coupling interaction by weakening of H-bonding and/or by disruption of the bridging base-pair planarity.
Open Access
Multivalent benzoboroxole functionalized polymers as gp120 glycan targeted microbicide entry inhibitors.
(Mol Pharm, 2010-02-01) Jay, Julie I; Lai, Bonnie E; Myszka, David G; Mahalingam, Alamelu; Langheinrich, Kris; Katz, David F; Kiser, Patrick F
Microbicides are women-controlled prophylactics for sexually transmitted infections. The most important class of microbicides target HIV-1 and contain antiviral agents formulated for topical vaginal delivery. Identification of new viral entry inhibitors that target the HIV-1 envelope is important because they can inactivate HIV-1 in the vaginal lumen before virions can come in contact with CD4+ cells in the vaginal mucosa. Carbohydrate binding agents (CBAs) demonstrate the ability to act as entry inhibitors due to their ability to bind to glycans and prevent gp120 binding to CD4+ cells. However, as proteins they present significant challenges in regard to economical production and formulation for resource-poor environments. We have synthesized water-soluble polymer CBAs that contain multiple benzoboroxole moieties. A benzoboroxole-functionalized monomer was synthesized and incorporated into linear oligomers with 2-hydroxypropylmethacrylamide (HPMAm) at different feed ratios using free radical polymerization. The benzoboroxole small molecule analogue demonstrated weak affinity for HIV-1BaL gp120 by SPR; however, the 25 mol % functionalized benzoboroxole oligomer demonstrated a 10-fold decrease in the K(D) for gp120, suggesting an increased avidity for the multivalent polymer construct. High molecular weight polymers functionalized with 25, 50, and 75 mol % benzoboroxole were synthesized and tested for their ability to neutralize HIV-1 entry for two HIV-1 clades and both R5 and X4 coreceptor tropism. All three polymers demonstrated activity against all viral strains tested with EC(50)s that decrease from 15000 nM (1500 microg mL(-1)) for the 25 mol % functionalized polymers to 11 nM (1 microg mL(-1)) for the 75 mol % benzoboroxole-functionalized polymers. These polymers exhibited minimal cytotoxicity after 24 h exposure to a human vaginal cell line.
Open Access
Pretargeting and Bioorthogonal Click Chemistry-Mediated Endogenous Stem Cell Homing for Heart Repair.
(ACS nano, 2018-12) Li, Zhenhua; Shen, Deliang; Hu, Shiqi; Su, Teng; Huang, Ke; Liu, Feiran; Hou, Lei; Cheng, Ke
Stem cell therapy is one of the promising strategies for the treatment of ischemic heart disease. However, the clinical application of stem cells transplantation is limited by low cell engraftment in the infarcted myocardium. Taking advantage of pretargeting and bioorthogonal chemistry, we engineered a pretargeting and bioorthogonal chemistry (PTBC) system to capture endogenous circulating stem cells and target them to the injured heart for effective repair. Two bioorthogonal antibodies were i.v. administrated with a pretargeting interval (48 h). Through bioorthogonal click reaction, the two antibodies are linked in vivo, engaging endogenous stem cells with circulating platelets. As a result, the platelets redirect the stem cells to the injured heart. In vitro and in vivo studies demonstrated that bioorthogonal click reaction was able to induce the conjugation of platelets and endothelial progenitor cells (EPCs) and enhance the binding of EPCs to collagen and injured blood vessels. More importantly, in a mouse model of acute myocardial infarction, the in vivo results of cardiac function, heart morphometry, and immunohistochemistry assessment all confirmed effective heart repair by the PTBC system.
Open Access
Reductive ligation mediated one-step disulfide formation of S-nitrosothiols.
(Org Lett, 2010-09-17) Zhang, Jiming; Li, Sheng; Zhang, Dehui; Wang, Hua; Whorton, A Richard; Xian, Ming
A one-step reductive ligation mediated disulfide formation of S-nitrosothiols was developed. This reaction involves the reaction of the S-nitroso group with phosphine-thioesters to form sulfenamide and thiolate intermediates, which then undergo a fast intermolecular disulfide formation to form stable conjugates. This reaction can be used to design new biosensors of S-nitrosated proteins.
Open Access
The manganese(III) porphyrin MnTnHex-2-PyP5+ modulates intracellular ROS and breast cancer cell migration: Impact on doxorubicin-treated cells.
(Redox biology, 2019-01) Flórido, Ana; Saraiva, Nuno; Cerqueira, Sara; Almeida, Nuno; Parsons, Maddy; Batinic-Haberle, Ines; Miranda, Joana P; Costa, João G; Carrara, Guia; Castro, Matilde; Oliveira, Nuno G; Fernandes, Ana S
Manganese(III) porphyrins (MnPs) are superoxide dismutase (SOD) mimics with demonstrated beneficial effects in cancer treatment in combination with chemo- and radiotherapy regimens. Despite the ongoing clinical trials, little is known about the effect of MnPs on metastasis, being therefore essential to understand how MnPs affect this process. In the present work, the impact of the MnP MnTnHex-2-PyP5+ in metastasis-related processes was assessed in breast cancer cells (MCF-7 and MDA-MB-231), alone or in combination with doxorubicin (dox). The co-treatment of cells with non-cytotoxic concentrations of MnP and dox altered intracellular ROS, increasing H2O2. While MnP alone did not modify cell migration, the co-exposure led to a reduction in collective cell migration and chemotaxis. In addition, the MnP reduced the dox-induced increase in random migration of MDA-MB-231 cells. Treatment with either MnP or dox decreased the proteolytic invasion of MDA-MB-231 cells, although the effect was more pronounced upon co-exposure with both compounds. Moreover, to explore the cellular mechanisms underlying the observed effects, cell adhesion, spreading, focal adhesions, and NF-κB activation were also studied. Although differential effects were observed according to the endpoints analysed, overall, the alterations induced by MnP in dox-treated cells were consistent with a therapeutically favorable outcome.
Open Access
Total synthesis of cyanolide A and confirmation of its absolute configuration.
(Org Lett, 2010-06-18) Kim, Hyoungsu; Hong, Jiyong
The tandem allylic oxidation/oxa-Michael reaction promoted by the gem-disubstituent effect and the 2-methyl-6-nitrobenzoic anhydride (MNBA)-mediated dimerization were explored for the efficient and facile synthesis of cyanolide A.