11 results on '"Ravi, Rajagopalan"'
Search Results
2. Regarding “Extension of saphenous thrombus into the femoral vein: a potential complication of new endovenous ablation techniques”
- Author
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Ravi, Rajagopalan, Rodriguez-Lopez, Julio, Ramaiah, Venkatesh, and Diethrich, Edward B.
- Published
- 2005
3. Endoluminal stent grafting of the thoracic aorta: Initial experience with the Gore Excluder
- Author
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Thompson, Charles S., Gaxotte, Virginia D., Rodriguez, Julio A., Ramaiah, Venkatesh G., Vranic, Mitar, Ravi, Rajagopalan, DiMugno, Leanne, Shafique, Shoaib, Olsen, Dawn, and Diethrich, Edward B.
- Published
- 2002
4. Preclinical Characterization and Human Microdose Pharmacokinetics of ITMN-8187, a Nonmacrocyclic Inhibitor of the Hepatitis C Virus NS3 Protease
- Author
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Scott D. Seiwert, Karl Kossen, John B. Nicholas, Jyanwei Liu, Caralee Schaefer, Brad O. Buckman, Lea Huang, Donald Ruhrmund, Sharlene Lim, Lisa Hooi, Leonid Beigelman, Lin Pan, Vladimir Serebryany, Sarah K. Stevens, Srikonda Sastry, Shawn Misialek, Sophia Yap, Ravi Rajagopalan, and Natalia Aleskovski
- Subjects
0301 basic medicine ,Simeprevir ,Hepatitis C virus ,Hepacivirus ,Viral Nonstructural Proteins ,Pharmacology ,medicine.disease_cause ,Antiviral Agents ,Mice ,03 medical and health sciences ,Dogs ,0302 clinical medicine ,MicroDose ,Pharmacokinetics ,medicine ,Animals ,Humans ,Potency ,Protease Inhibitors ,Pharmacology (medical) ,030212 general & internal medicine ,NS3 ,Binding Sites ,Molecular Structure ,business.industry ,virus diseases ,Haplorhini ,Hepatitis C ,medicine.disease ,Rats ,030104 developmental biology ,Infectious Diseases ,business ,Viral load - Abstract
The current paradigm for the treatment of chronic hepatitis C virus (HCV) infection involves combinations of agents that act directly on steps of the HCV life cycle. Here we report the preclinical characteristics of ITMN-8187, a nonmacrocyclic inhibitor of the NS3/4A HCV protease. X-ray crystallographic studies of ITMN-8187 and simeprevir binding to NS3/4A protease demonstrated good agreement between structures. Low nanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 1, 2b, 4, 5, and 6. In cell-based potency assays, half-maximal reduction of genotype 1a and 1b HCV replicon RNA was afforded by 11 and 4 nM doses of ITMN-8187, respectively. Combinations of ITMN-8187 with other directly acting antiviral agents in vitro displayed additive antiviral efficacy. A 30-mg/kg of body weight dose of ITMN-8187 administered for 4 days yielded significant viral load reductions through day 5 in a chimeric mouse model of HCV. A 3-mg/kg oral dose administered to rats, dogs, or monkeys yielded concentrations in plasma 16 h after dosing that exceeded the half-maximal effective concentration of ITMN-8187. Human microdose pharmacokinetics showed low intersubject variability and prolonged oral absorption with first-order elimination kinetics compatible with once-daily dosing. These preclinical characteristics compare favorably with those of other NS3/4A inhibitors approved for the treatment of chronic HCV infection.
- Published
- 2017
5. Preclinical Characteristics of the Hepatitis C Virus NS3/4A Protease Inhibitor ITMN-191 (R7227)
- Author
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Jin Hong, Christine Lemieux, Scott D. Seiwert, Shawn Misialek, Robert Rieger, Dylan P. Hartley, Lawrence M. Blatt, Sharlene R. Lim, Kevin Ronald Condroski, Antitsa Dimitrova Stoycheva, Lin Pan, Hua Tan, Gary P. Hingorani, Leonid Beigelman, Hailong Zhang, John A. Josey, Xiaoli Qin, Karl Kossen, P. T. Ravi Rajagopalan, Mary Geck Do, Vladimir Serebryany, Sarah K. Stevens, Andrews Steven W, and Jiang Yutong
- Subjects
viruses ,medicine.medical_treatment ,Hepatitis C virus ,Drug Evaluation, Preclinical ,Hepacivirus ,Interferon alpha-2 ,Viral Nonstructural Proteins ,Virus Replication ,medicine.disease_cause ,Antiviral Agents ,Polyethylene Glycols ,Viral Proteins ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Potency ,Protease Inhibitors ,Pharmacology (medical) ,Protease inhibitor (pharmacology) ,Replicon ,Pharmacology ,NS3 ,Protease ,biology ,Danoprevir ,Intracellular Signaling Peptides and Proteins ,Interferon-alpha ,virus diseases ,Drug Synergism ,Virology ,digestive system diseases ,Recombinant Proteins ,Rats ,Macaca fascicularis ,Infectious Diseases ,Liver ,Enzyme inhibitor ,biology.protein ,Carrier Proteins - Abstract
Future treatments for chronic hepatitis C virus (HCV) infection are likely to include agents that target viral components directly. Here, the preclinical characteristics of ITMN-191, a peptidomimetic inhibitor of the NS3/4A protease of HCV, are described. ITMN-191 inhibited a reference genotype 1 NS3/4A protein in a time-dependent fashion, a hallmark of an inhibitor with a two-step binding mechanism and a low dissociation rate. Under preequilibrium conditions, 290 pM ITMN-191 half-maximally inhibited the reference NS3/4A protease, but a 35,000-fold-higher concentration did not appreciably inhibit a panel of 79 proteases, ion channels, transporters, and cell surface receptors. Subnanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 4, 5, and 6, while single-digit nanomolar potency was observed against NS3/4A from genotypes 2b and 3a. Dilution of a preformed enzyme inhibitor complex indicated ITMN-191 remained bound to and inhibited NS3/4A for more than 5 h after its initial association. In cell-based potency assays, half-maximal reduction of genotype 1b HCV replicon RNA was afforded by 1.8 nM; 45 nM eliminated the HCV replicon from cells. Peginterferon alfa-2a displayed a significant degree of antiviral synergy with ITMN-191 and reduced the concentration of ITMN-191 required for HCV replicon elimination. A 30-mg/kg of body weight oral dose administered to rats or monkeys yielded liver concentrations 12 h after dosing that exceeded the ITMN-191 concentration required to eliminate replicon RNA from cells. These preclinical characteristics compare favorably to those of other inhibitors of NS3/4A in clinical development and therefore support the clinical investigation of ITMN-191 for the treatment of chronic hepatitis C.
- Published
- 2008
6. Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate
- Author
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Gordon G. Hammes, Zhiquan Zhang, Stephen J. Benkovic, P. T. Ravi Rajagopalan, and Tzvia Selzer
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chemistry.chemical_classification ,Conformational change ,Time Factors ,Multidisciplinary ,biology ,Chemistry ,Stereochemistry ,Substrate (chemistry) ,Biological Sciences ,Reductase ,Models, Biological ,Kinetics ,Tetrahydrofolate Dehydrogenase ,Folic Acid ,Enzyme ,Reaction rate constant ,Dihydrofolate reductase ,Kinetic isotope effect ,Escherichia coli ,biology.protein ,Conformational isomerism ,NADP - Abstract
The interaction of dihydrofolate (H 2 F) and NADPH with a fluorescent derivative of H 2 F reductase (DHFR) was studied by using transient and single-molecule techniques. The fluorescent moiety Alexa 488 was attached to the structural loop that closes over the substrates after they are bound. Fluorescence quenching was found to accompany the binding of both substrates and the hydride transfer reaction. For the binding of H 2 F to DHFR, the simplest mechanism consistent with the data postulates that the enzyme exists as slowly interconverting conformers, with the substrate binding preferentially to one of the conformers. At pH 7.0, the binding reaction has a bimolecular rate constant of 1.8 × 10 7 M -1 ·s -1 , and the formation of the initial complex is followed by a conformational change. The binding of NADPH to DHFR is more complex and suggests multiple conformers of the enzyme exist. NADPH binds to a different conformer than H 2 F with a bimolecular rate constant of 2.6–5.7 × 10 6 M -1 ·s -1 , with the former value obtained from single-molecule kinetics and the latter from stopped-flow kinetics. Single-molecule studies of DHFR in equilibrium with substrates and products revealed a reaction with ensemble average rate constants of 170 and 470 s -1 at pH 8.5. The former rate constant has an isotope effect of >2 when NADPD is substituted for NADPH and probably is associated with hydride transfer. The results from stopped-flow and single-molecule methods are complementary and demonstrate that multiple conformations of both the enzyme and enzyme–substrate complexes exist.
- Published
- 2004
7. MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
- Author
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Ralph A. Dean, Thomas K. Mitchell, Ravi Rajagopalan, Stanton L. Martin, Rod A. Wing, Douglas E Brown, Robert G. Sceeles, Sheila O. Denn, Barbara P. Blackmon, and Thomas D. Houfek
- Subjects
Genetic Markers ,Chromosomes, Artificial, Bacterial ,Relational database ,Information Storage and Retrieval ,Genomics ,Biology ,Genome ,Article ,Databases, Genetic ,Genetics ,Magnaporthe grisea ,Genomic library ,Plant Diseases ,Database engine ,Genomic Library ,Internet ,Base Sequence ,Contig ,Chromosome Mapping ,food and beverages ,Oryza ,biology.organism_classification ,Magnaporthe ,Genetic marker ,Database Management Systems ,Chromosomes, Fungal ,Genome, Fungal ,Forecasting - Abstract
We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.
- Published
- 2002
8. Interaction of dihydrofolate reductase with methotrexate: Ensemble and single-molecule kinetics
- Author
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Gordon G. Hammes, Stephen J. Benkovic, Mary A. Dwyer, P. T. Ravi Rajagopalan, Zhiquan Zhang, and Lynn McCourt
- Subjects
DNA, Bacterial ,Models, Molecular ,Conformational change ,Stereochemistry ,Protein Conformation ,Biotin ,chemistry.chemical_compound ,Protein structure ,Dihydrofolate reductase ,Escherichia coli ,Fluorescent Dyes ,chemistry.chemical_classification ,Multidisciplinary ,Quenching (fluorescence) ,biology ,Methotrexate binding ,Base Sequence ,Biological Sciences ,Dissociation constant ,Kinetics ,Tetrahydrofolate Dehydrogenase ,Enzyme ,Methotrexate ,chemistry ,Microscopy, Fluorescence ,Genes, Bacterial ,Mutation ,biology.protein ,Thermodynamics - Abstract
The thermodynamics and kinetics of the interaction of dihydrofolate reductase (DHFR) with methotrexate have been studied by using fluorescence, stopped-flow, and single-molecule methods. DHFR was modified to permit the covalent addition of a fluorescent molecule, Alexa 488, and a biotin at the N terminus of the molecule. The fluorescent molecule was placed on a protein loop that closes over methotrexate when binding occurs, thus causing a quenching of the fluorescence. The biotin was used to attach the enzyme in an active form to a glass surface for single-molecule studies. The equilibrium dissociation constant for the binding of methotrexate to the enzyme is 9.5 nM. The stopped-flow studies revealed that methotrexate binds to two different conformations of the enzyme, and the association and dissociation rate constants were determined. The single-molecule investigation revealed a conformational change in the enzyme-methotrexate complex that was not observed in the stopped-flow studies. The ensemble averaged rate constants for this conformation change in both directions is about 2–4 s −1 and is attributed to the opening and closing of the enzyme loop over the bound methotrexate. Thus the mechanism of methotrexate binding to DHFR involves multiple steps and protein conformational changes.
- Published
- 2002
9. Network of coupled promoting motions in enzyme catalysis
- Author
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Pratul K. Agarwal, Salomon R. Billeter, P. T. Ravi Rajagopalan, Sharon Hammes-Schiffer, and Stephen J. Benkovic
- Subjects
chemistry.chemical_classification ,Models, Molecular ,Multidisciplinary ,biology ,Kinetics ,Active site ,Sequence (biology) ,Biological Sciences ,Catalysis ,Protein Structure, Secondary ,Enzyme catalysis ,Molecular dynamics ,Tetrahydrofolate Dehydrogenase ,Enzyme ,chemistry ,Biochemistry ,Dihydrofolate reductase ,biology.protein ,Biophysics ,Animals ,Humans ,Quantum - Abstract
A network of coupled promoting motions in the enzyme dihydrofolate reductase is identified and characterized. The present identification is based on genomic analysis for sequence conservation, kinetic measurements of multiple mutations, and mixed quantum/classical molecular dynamics simulations of hydride transfer. The motions in this network span time scales of femtoseconds to milliseconds and are found on the exterior of the enzyme as well as in the active site. This type of network has broad implications for an expanded role of the protein fold in catalysis as well as ancillaries such as the engineering of altered protein function and the action of drugs distal to the active site.
- Published
- 2002
10. Oxygen-mediated inactivation of peptide deformylase
- Author
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Dehua Pei and P. T. Ravi Rajagopalan
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inorganic chemicals ,chemistry.chemical_classification ,Molecular Sequence Data ,Cell Biology ,Biochemistry ,Combinatorial chemistry ,Aminopeptidases ,Peptide Mapping ,In vitro ,Catalysis ,Amidohydrolases ,Oxygen ,Peptide deformylase ,Residue (chemistry) ,Enzyme ,chemistry ,Covalent bond ,Oxidizing agent ,Amino Acid Sequence ,Ferrous Compounds ,Molecular Biology ,Peptide sequence ,Oxidation-Reduction ,Cysteine - Abstract
Peptide deformylase catalyzes the removal of the N-formyl group from newly synthesized polypeptides in prokaryotes. Its essential character and unique presence in prokaryotes make it an attractive target for antibacterial chemotherapy. However, purification and characterization of the peptide deformylase have remained a major challenge because this enzyme is extraordinarily labile under a variety of conditions (t1/2 approximately 1 min at room temperature). In this work, we show that this unusual instability is because of oxidation of the catalytic Fe2+ ion of the deformylase into catalytically inactive Fe3+ ion by atmospheric oxygen. Oxidation of Fe2+ is accompanied by the conversion of O2 into a yet unidentified reactive species, which covalently modifies the deformylase protein, most likely by oxidizing cysteine-90, a ligand residue of the Fe2+ ion, into a cysteine sulfonic acid. Enzymatic exclusion of O2 from the deformylase assays renders the deformylase highly stable under otherwise identical conditions. An improved, readily reproducible purification procedure has been developed that produces approximately 10 mg of pure, fully active Fe2+ deformylase from a liter of cells. In addition, active peptide deformylase can be reconstituted in vitro from the denatured deformylase.
- Published
- 1998
11. Crystal Structure of the Escherichia coli Peptide Deformylase
- Author
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Chris M. Tsai, Weimin Gong, P. T. Ravi Rajagopalan, Michael K. Chan, Dehua Pei, and Bing Hao
- Subjects
Crystallography ,Materials science ,Crystal structure ,Biochemistry - Published
- 1998
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