2,205 results match your criteria: "The Skaggs Institute for Chemical Biology[Affiliation]"

There is an urgent need for monoclonal antibody (mAb) therapies that broadly protect against Ebola virus and other filoviruses. The conserved, essential interaction between the filovirus glycoprotein, GP, and its entry receptor Niemann-Pick C1 (NPC1) provides an attractive target for such mAbs but is shielded by multiple mechanisms, including physical sequestration in late endosomes. Here, we describe a bispecific-antibody strategy to target this interaction, in which mAbs specific for NPC1 or the GP receptor-binding site are coupled to a mAb against a conserved, surface-exposed GP epitope.

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Studies towards the improvement of an anti-cocaine monoclonal antibody for treatment of acute overdose.

Bioorg Med Chem Lett

October 2016

Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Immunology and Microbial Sciences, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Worm Institute of Medical Research (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

There is currently no clinically-approved antidote for cocaine overdose. Efforts to develop a therapy via passive immunization have resulted in a human monoclonal antibody, GNCgzk, with a high affinity for cocaine (K=0.18nM).

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Catalysis of Heterocyclic Azadiene Cycloaddition Reactions by Solvent Hydrogen Bonding: Concise Total Synthesis of Methoxatin.

J Am Chem Soc

September 2016

Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Although it has been examined for decades, no general approach to catalysis of the inverse electron demand Diels-Alder reactions of heterocyclic azadienes has been introduced. Typically, additives such as Lewis acids lead to nonproductive consumption of the electron-rich dienophiles without productive activation of the electron-deficient heterocyclic azadienes. Herein, we report the first general method for catalysis of such cycloaddition reactions by using solvent hydrogen bonding of non-nucleophilic perfluoroalcohols, including hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE), to activate the electron-deficient heterocyclic azadienes.

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Background: Early diagnosis of familial transthyretin (TTR) amyloid diseases remains challenging because of variable disease penetrance. Currently, patients must have an amyloid positive tissue biopsy to be eligible for disease-modifying therapies. Endomyocardial biopsies are typically amyloid positive when cardiomyopathy is suspected, but this disease manifestation is generally diagnosed late.

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The Kinetic Stability of a Full-Length Antibody Light Chain Dimer Determines whether Endoproteolysis Can Release Amyloidogenic Variable Domains.

J Mol Biol

October 2016

Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

Light chain (LC) amyloidosis (AL amyloidosis) appears to be caused by the misfolding, or misfolding and aggregation of an antibody LC or fragment thereof and is fatal if untreated. LCs are secreted from clonally expanded plasma cells, generally as disulfide-linked dimers, with each monomer comprising one constant and one variable domain. The energetic contribution of each domain and the role of endoproteolysis in AL amyloidosis remain unclear.

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Structures of Ebola virus GP and sGP in complex with therapeutic antibodies.

Nat Microbiol

August 2016

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

The Ebola virus (EBOV) GP gene encodes two glycoproteins. The major product is a soluble, dimeric glycoprotein (sGP) that is secreted abundantly. Despite the abundance of sGP during infection, little is known regarding its structure or functional role.

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Macrocyclization of Folded Diamines in Cavitands.

J Am Chem Soc

August 2016

Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.

Synthetic access to water-soluble cavitands and capsules has moved recognition events from organic solvents into aqueous media. Here we report the binding and reactivity of long-chain α,ω-diamines (C11 to C18) in cavitand hosts. The containers bind the diamines in folded conformations that bury the hydrocarbon chains and expose the amino groups to the aqueous medium.

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Approaches to improving the biological properties of natural products typically strive to modify their structures to identify the essential pharmacophore, or make functional group changes to improve biological target affinity or functional activity, change physical properties, enhance stability, or introduce conformational constraints. Aside from accessible semisynthetic modifications of existing functional groups, rarely does one consider using chemical synthesis to add molecular complexity to the natural product. In part, this may be attributed to the added challenge intrinsic in the synthesis of an even more complex compound.

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Robust anti-nociceptive effects of monoacylglycerol lipase inhibition in a model of osteoarthritis pain.

Br J Pharmacol

November 2016

Arthritis Research UK Pain Centre, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, UK.

Background And Purpose: Chronic pain is often a symptom of knee osteoarthritis (OA) for which current analgesics are either inadequate or are associated with serious side effects. The endocannabinoid system may offer alternative targets for pain relief. We evaluated the effects of a potent and selective monoacylglycerol (MAG) lipase inhibitor (MJN110) on OA pain behaviour, spinal mechanisms of action and joint histopathology in the rat.

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YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit.

Nucleic Acids Res

September 2016

Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario L8S4K1, Canada

YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.

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Water-soluble cavitands promote hydrolyses of long-chain diesters.

Proc Natl Acad Sci U S A

August 2016

Department of Chemistry, Fudan University, Shanghai 200433, China; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037

Water-soluble, deep cavitands serve as chaperones of long-chain diesters for their selective hydrolysis in aqueous solution. The cavitands bind the diesters in rapidly exchanging, folded J-shape conformations that bury the hydrocarbon chain and expose each ester group in turn to the aqueous medium. The acid hydrolyses in the presence of the cavitand result in enhanced yields of monoacid monoester products.

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Self-Assembly of the Cephalopod Protein Reflectin.

Adv Mater

October 2016

Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, 92697, USA.

Films from the cephalopod protein reflectin demonstrate multifaceted functionality as infrared camouflage coatings, proton transport media, and substrates for growth of neural stem cells. A detailed study of the in vitro formation, structural characteristics, and stimulus response of such films is presented. The reported observations hold implications for the design and development of advanced cephalopod-inspired functional materials.

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A Prominent Site of Antibody Vulnerability on HIV Envelope Incorporates a Motif Associated with CCR5 Binding and Its Camouflaging Glycans.

Immunity

July 2016

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA. Electronic address:

The dense patch of high-mannose-type glycans surrounding the N332 glycan on the HIV envelope glycoprotein (Env) is targeted by multiple broadly neutralizing antibodies (bnAbs). This region is relatively conserved, implying functional importance, the origins of which are not well understood. Here we describe the isolation of new bnAbs targeting this region.

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Ultraviolet (UV) light from the sun damages DNA by forming a cyclobutane pyrimidine dimer (CPD) and pyrimidine(6-4)pyrimidone photoproducts [(6-4) PP]. Photolyase (PHR) enzymes utilize near-UV/blue light for DNA repair, which is initiated by light-induced electron transfer from the fully reduced flavin adenine dinucleotide chromophore. Despite similar structures and repair mechanisms, the functions of PHR are highly selective; CPD PHR repairs CPD, but not (6-4) PP, and vice versa.

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At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code.

Cold Spring Harb Perspect Biol

September 2016

Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037.

The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.

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An Outbreak of Ebola Virus Disease in the Lassa Fever Zone.

J Infect Dis

October 2016

Department of Microbiology and Immunology Zalgen Labs, Germantown, Maryland.

Background: Kenema Government Hospital (KGH) has developed an advanced clinical and laboratory research capacity to manage the threat of Lassa fever, a viral hemorrhagic fever (VHF). The 2013-2016 Ebola virus (EBOV) disease (EVD) outbreak is the first to have occurred in an area close to a facility with established clinical and laboratory capacity for study of VHFs.

Methods: Because of its proximity to the epicenter of the EVD outbreak, which began in Guinea in March 2014, the KGH Lassa fever Team mobilized to establish EBOV surveillance and diagnostic capabilities.

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p53-Dependent DNA damage response sensitive to editing-defective tRNA synthetase in zebrafish.

Proc Natl Acad Sci U S A

July 2016

The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, La Jolla, CA 92037; Department of Cell and Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037; Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037; Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, FL 33458;

Brain and heart pathologies are caused by editing defects of transfer RNA (tRNA) synthetases, which preserve genetic code fidelity by removing incorrect amino acids misattached to tRNAs. To extend understanding of the broader impact of synthetase editing reactions on organismal homeostasis, and based on effects in bacteria ostensibly from small amounts of mistranslation of components of the replication apparatus, we investigated the sensitivity to editing of the vertebrate genome. We show here that in zebrafish embryos, transient overexpression of editing-defective valyl-tRNA synthetase (ValRS(ED)) activated DNA break-responsive H2AX and p53-responsive downstream proteins, such as cyclin-dependent kinase (CDK) inhibitor p21, which promotes cell-cycle arrest at DNA damage checkpoints, and Gadd45 and p53R2, with pivotal roles in DNA repair.

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More than 30 years ago, a calcium-dependent enzyme activity was described that generates N-acyl phosphatidylethanolamines (NAPEs), which are precursors for N-acyl ethanolamine (NAE) lipid transmitters, including the endocannabinoid anandamide. The identity of this calcium-dependent N-acyltransferase (Ca-NAT) has remained mysterious. Here, we use activity-based protein profiling to identify the poorly characterized serine hydrolase PLA2G4E as a mouse brain Ca-NAT and show that this enzyme generates NAPEs and NAEs in mammalian cells.

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Preparative scale and convenient synthesis of a water-soluble, deep cavitand.

Nat Protoc

August 2016

The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.

Cavitands are established tools of supramolecular chemistry and molecular recognition, and they are finding increasing application in sensing and sequestration of physiologically relevant molecules in aqueous solution. The synthesis of a water-soluble, deep cavitand is described. The route comprises six (linear) steps from commercially available precursors, and it relies on the fourfold oligomeric cyclization reaction of resorcinol with 2,3-dihydrofuran that leads to the formation of a shallow resorcinarene framework; condensation with aromatic panels, which deepens the hydrophobic binding cavity; construction of rigid urea functionalities on the upper rim; and the introduction of the water-solubilizing methylimidazolium groups on the lower rim.

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Synthesis of a Potent Vinblastine: Rationally Designed Added Benign Complexity.

J Am Chem Soc

July 2016

Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Many natural products, including vinblastine, have not been easily subjected to simplifications in their structures by synthetic means or modifications by late-stage semisynthetic derivatization in ways that enhance their biological potency. Herein, we detail a synthetic vinblastine that incorporates added benign complexity (ABC), which improves activity 10-fold, and is now accessible as a result of advances in the total synthesis of the natural product. The compound incorporates designed added molecular complexity but no new functional groups and maintains all existing structural and conformational features of the natural product.

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Dissecting AI-2-mediated quorum sensing through C5-analogue synthesis and biochemical analysis.

Tetrahedron

June 2015

Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.

Autoinducer-2 (AI-2)-mediated quorum sensing (QS) is utilised for both intra- and inter-species communication by a wide variety of bacteria. An understanding of the mechanism of this communication has the potential to elucidate new targets for antibacterial therapeutics. Herein, we report the synthesis of DPD analogues with modified dynamic equilibria and the evaluation of their behaviour in Gram-negative bacteria.

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Discriminative Stimulus Properties of the Endocannabinoid Catabolic Enzyme Inhibitor SA-57 in Mice.

J Pharmacol Exp Ther

August 2016

Department of Pharmacology and Toxicology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, Virginia (R.A.O., B.I.J., M.M., P.M.B., A.J., D.E.S., A.H.L.); RTI International, Research Triangle Park, North Carolina (J.L.W.); and The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California (M.J.N.; B.F.C.)

Whereas the inhibition of fatty acid amide hydrolase (FAAH) or monoacylglycerol lipase (MAGL), the respective major hydrolytic enzymes of N-arachidonoyl ethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), elicits no or partial substitution for Δ(9)-tetrahydrocannabinol (THC) in drug-discrimination procedures, combined inhibition of both enzymes fully substitutes for THC, as well as produces a constellation of cannabimimetic effects. The present study tested whether C57BL/6J mice would learn to discriminate the dual FAAH-MAGL inhibitor SA-57 (4-[2-(4-chlorophenyl)ethyl]-1-piperidinecarboxylic acid 2-(methylamino)-2-oxoethyl ester) from vehicle in the drug-discrimination paradigm. In initial experiments, 10 mg/kg SA-57 fully substituted for CP55,940 ((-)-cis-3-[2-hydroxy-4-(1,1-dimethylheptyl)phenyl]-trans-4-(3-hydroxypropyl)cyclohexanol), a high-efficacy CB1 receptor agonist in C57BL/6J mice and for AEA in FAAH (-/-) mice.

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Cavitands as Chaperones for Monofunctional and Ring-Forming Reactions in Water.

J Am Chem Soc

June 2016

Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China.

Cyclic processes involving medium-sized rings show low rates because internal strains-torsions and transannular interactions-are created during the reactions. High dilution is often used to slow the competing bi- and higher-molecular processes but cannot accelerate the desired cyclization reaction. Here we apply cavitands to the formation of medium- to large-sized rings through conversion of long-chain diisocyanates to cyclic ureas.

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The majority of reactions currently performed in the chemical industry take place in organic solvents, compounds that are generally derived from petrochemicals. To promote chemical processes in water, we examined the use of synthetic, deep water-soluble cavitands in the Staudinger reduction of long-chain aliphatic diazides (C8 , C10 , and C12 ). The diazide substrates are taken up by the cavitand in D2 O in folded, dynamic conformations.

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Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host.

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