Questions and Answers (17) View all

  • Answer added in Simulation and Modeling
    8 Protein model optimization in order to get a proper Ramachandran plot.
    By Prerna Jha · University of Queensland 
    David Reichert · Washington University in St. Louis
    I've had pretty good look using the program ModRefiner, for improving the quality of homology models. Its freely available from the University of Mich... [more]
  • Answer added in Computational Chemistry
    5 Is there any way to minimize (energy minimization) specific residue in a given protein ?
    By Pankaj Pandey · University of Mississippi
    David Reichert · Washington University in St. Louis
    As noted it does depend on the program that you are using, often you have the option to freeze or ignore atoms. In those cases you would freeze all of... [more]
  • Answer added in Cheminformatics
    21 Is it possible to make a structure based virtual screening with one ligand against thousands of multi-targets with Glide or Gold?
    By Abdurrahman Olğaç · Gazi University
    David Reichert · Washington University in St. Louis
    Just from a practical standpoint you would be hard pressed to cross dock more than a handful of protein sites at once. Remember protein structures pul... [more]
  • Answer added in DLPOLY
    15 Atomistic NVE MD run with temperature problem.
    By German Sastre · Research Scientist
    David Reichert · Washington University in St. Louis
    I agree with Stéphane's opinion as well. Make sure that the system is well equilibrated at 300K then gradually increase the temp, probably with long ... [more]

Publications (42) View all

  • Article: Evaluation of N-phenyl homopiperazine analogs as potential dopamine D3 receptor selective ligands.
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    ABSTRACT: A series of N-(2-methoxyphenyl)homopiperazine analogs was prepared and their affinities for dopamine D2, D3, and D4 receptors were measured using competitive radioligand binding assays. Several ligands exhibited high binding affinity and selectivity for the D3 dopamine receptor compared to the D2 receptor subtype. Compounds 11a, 11b, 11c, 11f, 11j and 11k had Ki values ranging from 0.7 to 3.9nM for the D3 receptor with 30- to 170-fold selectivity for the D3 versus D2 receptor. Calculated logP values (logP=2.6-3.6) are within the desired range for passive transport across the blood-brain barrier. When the binding and the intrinsic efficacy of these phenylhomopiperazines was compared to those of previously published phenylpiperazine analogues, it was found that (a) affinity at D2 and D3 dopamine receptors generally decreased, (b) the D3 receptor binding selectivity (D2:D3Ki value ratio) decreased and, (c) the intrinsic efficacy, measured using a forskolin-dependent adenylyl cyclase inhibition assay, generally increased.
    Bioorganic & medicinal chemistry 04/2013; · 2.82 Impact Factor
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    Article: Microfluidic radiolabeling of biomolecules with PET radiometals.
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    ABSTRACT: INTRODUCTION: A robust, versatile and compact microreactor has been designed, fabricated and tested for the labeling of bifunctional chelate conjugated biomolecules (BFC-BM) with PET radiometals. METHODS: The developed microreactor was used to radiolabel a chelate, either 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) or 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) that had been conjugated to cyclo(Arg-Gly-Asp-DPhe-Lys) peptide, with both (64)Cu and (68)Ga respectively. The microreactor radiolabeling conditions were optimized by varying temperature, concentration and residence time. RESULTS: Direct comparisons between the microreactor approach and conventional methods showed improved labeling yields and increased reproducibility with the microreactor under identical labeling conditions, due to enhanced mass and heat transfer at the microscale. More importantly, over 90% radiolabeling yields (incorporation of radiometal) were achieved with a 1:1 stoichiometry of bifunctional chelate biomolecule conjugate (BFC-BM) to radiometal in the microreactor, which potentially obviates extensive chromatographic purification that is typically required to remove the large excess of unlabeled biomolecule in radioligands prepared using conventional methods. Moreover, higher yields for radiolabeling of DOTA-functionalized BSA protein (Bovine Serum Albumin) were observed with (64)Cu/(68)Ga using the microreactor, which demonstrates the ability to label both small and large molecules. CONCLUSIONS: A robust, reliable, compact microreactor capable of chelating radiometals with common chelates has been developed and validated. Based on our radiolabeling results, the reported microfluidic approach overall outperforms conventional radiosynthetic methods, and is a promising technology for the radiometal labeling of commonly utilized BFC-BM in aqueous solutions.
    Nuclear Medicine and Biology 10/2012; · 3.02 Impact Factor
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    Article: Microfluidic labeling of biomolecules with radiometals for use in nuclear medicine.
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    ABSTRACT: Radiometal-based radiopharmaceuticals, used as imaging and therapeutic agents in nuclear medicine, consist of a radiometal that is bound to a targeting biomolecule (BM) using a bifunctional chelator (BFC). Conventional, macroscale radiolabeling methods use an excess of the BFC-BM conjugate (ligand) to achieve high radiolabeling yields. Subsequently, to achieve maximal specific activity (minimal amount of unlabeled ligand), extensive chromatographic purification is required to remove unlabeled ligand, often resulting in longer synthesis times and loss of imaging sensitivity due to radioactive decay. Here we describe a microreactor that overcomes the above issues through integration of efficient mixing and heating strategies while working with small volumes of concentrated reagents. As a model reaction, we radiolabel 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) conjugated to the peptide cyclo(Arg-Gly-Asp-DPhe-Lys) with (64)Cu(2+). We show that the microreactor (made from polydimethylsiloxane and glass) can withstand 260 mCi of activity over 720 hours and retains only minimal amounts of (64)Cu(2+) (<5%) upon repeated use. A direct comparison between the radiolabeling yields obtained using the microreactor and conventional radiolabeling methods shows that improved mixing and heat transfer in the microreactor leads to higher yields for identical reaction conditions. Most importantly, by using small volumes (~10 µL) of concentrated solutions of reagents (>50 µM), yields of over 90% can be achieved in the microreactor when using a 1:1 stoichiometry of radiometal to BFC-BM. These high yields eliminate the need for use of excess amounts of often precious BM and obviate the need for a chromatographic purification process to remove unlabeled ligand. The results reported here demonstrate the potential of microreactor technology to improve the production of patient-tailored doses of radiometal-based radiopharmaceuticals in the clinic.
    Lab on a Chip 10/2010; 10(24):3387-96. · 5.67 Impact Factor
  • Article: Subtype selectivity of dopamine receptor ligands: insights from structure and ligand-based methods.
    Qi Wang, Robert H Mach, Robert R Luedtke, David E Reichert
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    ABSTRACT: Subtype selective dopamine receptor ligands have long been sought after as therapeutic and/or imaging agents for the treatment and monitoring of neurologic disorders. We report herein on a combined structure- and ligand-based approach to explore the molecular mechanism of the subtype selectivity for a large class of D₂-like dopamine receptor ligands (163 ligands in total). Homology models were built for both human D(₂L) and D₃ receptors in complex with haloperidol. Other ligands, which included multiple examples of substituted phenylpiperazines, were aligned against the binding conformations of haloperidol, and three-dimensional quantitative structure activity relationship (3D-QSAR) analyses were carried out. The receptor models show that although D₂ and D₃ share highly similar folds and 3D conformations, the slight sequence differences at their extracellular loop regions result in the binding cavity in D₂ being comparably shallower than in D₃, which may explain why some larger ligands bind with greater affinity at D₃ compared to D₂ receptors. The QSAR models show excellent correlation and high predictive power even when evaluated by the most stringent criteria. They confirm that the origins of subtype selectivity for the ligands arise primarily due to differences in the contours of the two binding sites. The predictive models suggest that while both steric and electrostatic interactions contribute to the compounds' binding affinity, the major contribution arises from hydrophobic interactions, with hydrogen bonding conferring binding specificity. The current work provides clues for the development of more subtype selective dopamine receptor ligands. Furthermore, it demonstrates the possibility of being able to apply similar modeling methods to other subtypes or classes of receptors to study GPCR receptor-ligand interactions at a molecular level.
    Journal of Chemical Information and Modeling 10/2010; 50(11):1970-85. · 4.68 Impact Factor
  • Article: Neurosteroid analogues. 17. Inverted binding orientations of androsterone enantiomers at the steroid potentiation site on γ-aminobutyric acid type A receptors.
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    ABSTRACT: The enantiomer pair androsterone and ent-androsterone are positive allosteric modulators of γ-aminobutyric acid (GABA) type A receptors. Each enantiomer was shown to bind at the same receptor site. Binding orientations of the enantiomers at this site were deduced using enantiomer pairs containing OBn substituents at either C-7 or C-11. 11β-OBn-substituted steroids and 7α-OBn-substituted ent-steroids potently displace [(35)S]-tert-butylbicyclophosphorothionate, augment GABA currents, and anesthetize tadpoles. In contrast, 7β-OBn-substituted steroids and 11α-OBn-substituted ent-steroids have diminished actions. The results suggest that the binding orientations of the active analogues are inverted relative to each other with the 7α- and 11β-substituents similarly located on the edges of the molecules not in contact with the receptor surface. Analogue potentiation of the GABA current was abrogated by an α(1) subunit Q241L mutation, indicating that the active analogues act at the same sites in α(1)β(2)γ(2L) receptors previously associated with positive neurosteroid modulation.
    Journal of Medicinal Chemistry 12/2011; 55(3):1334-45. · 4.80 Impact Factor

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