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Ligand-conjugated quantum dots for fast sub-diffraction protein tracking in acute brain slices.
Thal LB, Mann VR, Sprinzen D, McBride JR, Reid KR, Tomlinson ID, McMahon DG, Cohen BE, Rosenthal SJ
(2020) Biomater Sci 8: 837-845
MeSH Terms: Animals, Brain, Brain Chemistry, Ligands, Mice, Microscopy, Fluorescence, Microtomy, Proteins, Quantum Dots, Selenium Compounds, Staining and Labeling, Zinc Compounds
Show Abstract · Added March 18, 2020
Semiconductor quantum dots (QDs) have demonstrated utility in long-term single particle tracking of membrane proteins in live cells in culture. To extend the superior optical properties of QDs to more physiologically relevant cell platforms, such as acute brain slices, we examine the photophysics of compact ligand-conjugated CdSe/CdS QDs using both ensemble and single particle analysis in brain tissue media. We find that symmetric core passivation is critical for both photostability in oxygenated media and for prolonged single particle imaging in brain slices. We then demonstrate the utility of these QDs by imaging single dopamine transporters in acute brain slices, achieving 20 nm localization precision at 10 Hz frame rates. These findings detail design requirements needed for new QD probes in complex living environments, and open the door to physiologically relevant studies that capture the utility of QD probes in acute brain slices.
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12 MeSH Terms
Kinetic Modeling of Steady-State Situations in Cytochrome P450 Enzyme Reactions.
Guengerich FP
(2019) Drug Metab Dispos 47: 1232-1239
MeSH Terms: Computer Simulation, Cytochrome P-450 Enzyme Inhibitors, Cytochrome P-450 Enzyme System, Humans, Kinetics, Ligands
Show Abstract · Added March 3, 2020
In the course of investigations of the kinetics of individual reactions of cytochrome P450 (P450) enzymes, a number of points about the complexity of P450 enzyme kinetics have become apparent. Several of these are of particular relevance to work with P450 enzymes in the course of drug development and lead optimization, particularly with regard to estimating in vitro kinetic parameters and dealing with enzyme inhibitors. Modern simulation modeling has been applied to situations involving issues of preincubation time with moderate strength and strong inhibitors, inhibition by tightly bound ligands that have been identified in P450 enzymes, extensive substrate depletion, P450 reactions with a rate-limiting step after product formation, and the consumption of an inhibitor during a reaction by either a P450 enzyme being monitored or another one in a mixture. The results all follow from first principles, and simulations reveal the extent of their significance in various settings. The order of addition of substrate and inhibitors can change the apparent outcome (inhibition constant, ), and the effect of the order is more pronounced with a stronger inhibitor. Substrate depletion alters parameters (Michaelis constant, ) and can generate apparently sigmoidal plots. A rate-limiting step after product formation lowers the apparent and distorts Consumption of an inhibitor during a reaction affects and differs depending on which enzyme is involved. The results are relevant with P450 enzymes and other enzymes as well. SIGNIFICANCE STATEMENT: Kinetic simulations have been used to address several potential problems in enzyme kinetic analysis. Although the simulations done here are general for enzyme reactions, several problems addressed here are particularly relevant to cytochrome P450 reactions encountered in drug development work.
Copyright © 2019 by The American Society for Pharmacology and Experimental Therapeutics.
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6 MeSH Terms
A unified structural model of the mammalian translocator protein (TSPO).
Xia Y, Ledwitch K, Kuenze G, Duran A, Li J, Sanders CR, Manning C, Meiler J
(2019) J Biomol NMR 73: 347-364
MeSH Terms: Animals, Bacterial Proteins, Ligands, Mammals, Mice, Mitochondrial Membrane Transport Proteins, Models, Molecular, Molecular Imaging, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Protein Conformation, Receptors, GABA
Show Abstract · Added March 21, 2020
The translocator protein (TSPO), previously known as the peripheral benzodiazepine receptor (PBR), is a membrane protein located on the outer mitochondrial membrane. Experimentally-derived structures of mouse TSPO (mTSPO) and its homologs from bacterial species have been determined by NMR spectroscopy and X-ray crystallography, respectively. These structures and ligand interactions within the TSPO binding pocket display distinct differences. Here, we leverage experimental and computational studies to derive a unified structural model of mTSPO in the presence and absence of the TSPO ligand, PK11195, and study the effects of DPC detergent micelles on the TSPO structure and ligand binding. From this work, we conclude that that the lipid-mimetic system used to solubilize mTSPO for NMR studies thermodynamically destabilizes the protein, introduces structural perturbations, and alters the characteristics of ligand binding. Furthermore, we used Rosetta to construct a unified mTSPO model that reconciles deviating features of the mammalian and bacterial TSPO. These deviating features are likely a consequence of the detergent system used for structure determination of mTSPO by NMR. The unified mTSPO model agrees with available experimental NMR data, appears to be physically realistic (i.e. thermodynamically not frustrated as judged by the Rosetta energy function), and simultaneously shares the structural features observed in sequence-conserved regions of the bacterial proteins. Finally, we identified the binding site for an imaging ligand VUIIS8310 that is currently positioned for clinical translation using NMR spectroscopy and propose a computational model of the VUIIS8310-mTSPO complex.
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MeSH Terms
Human cytochrome P450 enzymes bind drugs and other substrates mainly through conformational-selection modes.
Guengerich FP, Wilkey CJ, Phan TTN
(2019) J Biol Chem 294: 10928-10941
MeSH Terms: Catalysis, Cytochrome P-450 CYP2D6, Cytochrome P-450 CYP2E1, Cytochrome P-450 CYP3A, Cytochrome P-450 Enzyme Inhibitors, Cytochrome P-450 Enzyme System, Humans, Kinetics, Lauric Acids, Ligands, Molecular Conformation, Oxidation-Reduction, Palmitic Acid, Protein Binding, Protein Conformation, Spiro Compounds, Substrate Specificity
Show Abstract · Added March 3, 2020
Cytochrome P450 (P450) enzymes are major catalysts involved in the oxidations of most drugs, steroids, carcinogens, fat-soluble vitamins, and natural products. The binding of substrates to some of the 57 human P450s and other mammalian P450s is more complex than a two-state system and has been proposed to involve mechanisms such as multiple ligand occupancy, induced-fit, and conformational-selection. Here, we used kinetic analysis of binding with multiple concentrations of substrates and computational modeling of these data to discern possible binding modes of several human P450s. We observed that P450 2D6 binds its ligand rolapitant in a mechanism involving conformational-selection. P450 4A11 bound the substrate lauric acid via conformational-selection, as did P450 2C8 with palmitic acid. Binding of the steroid progesterone to P450 21A2 was also best described by a conformational-selection model. Hexyl isonicotinate binding to P450 2E1 could be described by either a conformational-selection or an induced-fit model. Simulation of the binding of the ligands midazolam, bromocriptine, testosterone, and ketoconazole to P450 3A4 was consistent with an induced-fit or a conformational-selection model, but the concentration dependence of binding rates for varying both P450 3A4 and midazolam concentrations revealed discordance in the parameters, indicative of conformational-selection. Binding of the P450s 2C8, 2D6, 3A4, 4A11, and 21A2 was best described by conformational-selection, and P450 2E1 appeared to fit either mode. These findings highlight the complexity of human P450-substrate interactions and that conformational-selection is a dominant feature of many of these interactions.
© 2019 Guengerich et al.
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17 MeSH Terms
BCL::Mol2D-a robust atom environment descriptor for QSAR modeling and lead optimization.
Vu O, Mendenhall J, Altarawy D, Meiler J
(2019) J Comput Aided Mol Des 33: 477-486
MeSH Terms: Algorithms, Drug Design, Drug Discovery, Humans, Ligands, Quantitative Structure-Activity Relationship, Small Molecule Libraries
Show Abstract · Added March 21, 2020
Comparing fragment based molecular fingerprints of drug-like molecules is one of the most robust and frequently used approaches in computer-assisted drug discovery. Molprint2D, a popular atom environment (AE) descriptor, yielded the best enrichment of active compounds across a diverse set of targets in a recent large-scale study. We present here BCL::Mol2D descriptors that outperformed Molprint2D on nine PubChem datasets spanning a wide range of protein classes. Because BCL::Mol2D records the number of AEs from a universal AE library, a novel aspect of BCL::Mol2D over the Molprint2D is its reversibility. This property enables decomposition of prediction from machine learning models to particular molecular substructures. Artificial neural networks with dropout, when trained on BCL::Mol2D descriptors outperform those trained on Molprint2D descriptors by up to 26% in logAUC metric. When combined with the Reduced Short Range descriptor set, our previously published set of descriptors optimized for QSARs, BCL::Mol2D yields a modest improvement. Finally, we demonstrate how the reversibility of BCL::Mol2D enables visualization of a 'pharmacophore map' that could guide lead optimization for serine/threonine kinase 33 inhibitors.
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7 MeSH Terms
Biotinylated-spiperone ligands for quantum dot labeling of the dopamine D2 receptor in live cell cultures.
Tomlinson ID, Kovtun O, Crescentini TM, Rosenthal SJ
(2019) Bioorg Med Chem Lett 29: 959-964
MeSH Terms: Biotin, Dopamine D2 Receptor Antagonists, HEK293 Cells, Humans, Ligands, Microscopy, Fluorescence, Quantum Dots, Receptors, Dopamine D2, Spiperone, Streptavidin
Show Abstract · Added March 26, 2019
We have synthesized 3 analogs of the dopamine D2 receptor (D2 DR) antagonist spiperone that can be conjugated to streptavidin-coated quantum dots via a pegylated biotin derivative. Using fluorescent imaging we demonstrate that substitution on the spiro position is tolerated, whilst the length and rigidity of a spacer arm attached to spiperone is important in controlling specific labeling as well as minimizing nonspecific labeling to cells and the surface of cell culture dishes. The ligand with the most rigid linker IDT772 (4) had the best binding profile and had high specific binding to D2 DR expressing HEK-293T cells with low nonspecific binding to plates and HEK-293T cells that lacked the D2 DR.
Copyright © 2019. Published by Elsevier Ltd.
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10 MeSH Terms
BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.
Brown BP, Mendenhall J, Meiler J
(2019) J Chem Inf Model 59: 689-701
MeSH Terms: Cheminformatics, Ligands, Molecular Docking Simulation, Monte Carlo Method, Protein Conformation, Small Molecule Libraries
Show Abstract · Added March 21, 2020
Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .
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Novel M positive allosteric modulators derived from questioning the role and impact of a presumed intramolecular hydrogen-bonding motif in β-amino carboxamide-harboring ligands.
Poslusney MS, Salovich JM, Wood MR, Melancon BJ, Bollinger KA, Luscombe VB, Rodriguez AL, Engers DW, Bridges TM, Niswender CM, Conn PJ, Lindsley CW
(2019) Bioorg Med Chem Lett 29: 362-366
MeSH Terms: Allosteric Regulation, Amides, Dose-Response Relationship, Drug, Humans, Hydrogen Bonding, Ligands, Molecular Structure, Receptor, Muscarinic M4, Structure-Activity Relationship
Show Abstract · Added March 3, 2020
This letter describes a focused exercise to explore the role of the β-amino carboxamide moiety found in all of the first generation M PAMs and question if the NH group served solely to stabilize an intramolecular hydrogen bond (IMHB) and enforce planarity. To address this issue (and to potentially find a substitute for the β-amino carboxamide that engendered P-gp and contributed to solubility liabilities), we removed the NH, generating des-amino congeners and surveyed other functional groups in the β-position. These modifications led to weak M PAMs with poor DMPK properties. Cyclization of the β-amino carboxamide moiety by virtue of a pyrazole ring re-enforced the IMHB, led to potent (and patented) M PAMs, many as potent as the classical bicyclic β-amino carboxamide analogs, but with significant CYP1A2 inhibition. Overall, this exercise indicated that the β-amino carboxamide moiety most likely facilitates an IMHB, and is essential for M PAM activity within classical bicyclic M PAM scaffolds.
Copyright © 2018 Elsevier Ltd. All rights reserved.
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Discovery of 4-alkoxy-6-methylpicolinamide negative allosteric modulators of metabotropic glutamate receptor subtype 5.
Felts AS, Bollinger KA, Brassard CJ, Rodriguez AL, Morrison RD, Scott Daniels J, Blobaum AL, Niswender CM, Jones CK, Conn PJ, Emmitte KA, Lindsley CW
(2019) Bioorg Med Chem Lett 29: 47-50
MeSH Terms: Allosteric Regulation, Animals, Dose-Response Relationship, Drug, Drug Discovery, Humans, Ligands, Molecular Structure, Picolinic Acids, Rats, Receptor, Metabotropic Glutamate 5, Structure-Activity Relationship
Show Abstract · Added March 3, 2020
This letter describes the further chemical optimization of VU0424238 (auglurant), an mGlu NAM clinical candidate that failed in non-human primate (NHP) 28 day toxicology due to accumulation of a species-specific aldehyde oxidase (AO) metabolite of the pyrimidine head group. Here, we excised the pyrimidine moiety, identified the minimum pharmacophore, and then developed a new series of saturated ether head groups that ablated any AO contribution to metabolism. Putative back-up compounds in this novel series provided increased sp character, uniform CYP-mediated metabolism across species, good functional potency and high CNS penetration. Key to the optimization was a combination of matrix and iterative libraries that allowed rapid surveillance of multiple domains of the allosteric ligand.
Copyright © 2018 Elsevier Ltd. All rights reserved.
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Structural basis of ligand binding modes at the neuropeptide Y Y receptor.
Yang Z, Han S, Keller M, Kaiser A, Bender BJ, Bosse M, Burkert K, Kögler LM, Wifling D, Bernhardt G, Plank N, Littmann T, Schmidt P, Yi C, Li B, Ye S, Zhang R, Xu B, Larhammar D, Stevens RC, Huster D, Meiler J, Zhao Q, Beck-Sickinger AG, Buschauer A, Wu B
(2018) Nature 556: 520-524
MeSH Terms: Arginine, Binding Sites, Crystallography, X-Ray, Dihydropyridines, Diphenylacetic Acids, Humans, Inositol Phosphates, Ligands, Molecular Docking Simulation, Mutant Proteins, Mutation, Neuropeptide Y, Nuclear Magnetic Resonance, Biomolecular, Phenylurea Compounds, Protein Binding, Receptors, Neuropeptide Y, Structure-Activity Relationship, Substrate Specificity
Show Abstract · Added March 21, 2020
Neuropeptide Y (NPY) receptors belong to the G-protein-coupled receptor superfamily and have important roles in food intake, anxiety and cancer biology . The NPY-Y receptor system has emerged as one of the most complex networks with three peptide ligands (NPY, peptide YY and pancreatic polypeptide) binding to four receptors in most mammals, namely the Y, Y, Y and Y receptors, with different affinity and selectivity . NPY is the most powerful stimulant of food intake and this effect is primarily mediated by the Y receptor (YR) . A number of peptides and small-molecule compounds have been characterized as YR antagonists and have shown clinical potential in the treatment of obesity , tumour and bone loss . However, their clinical usage has been hampered by low potency and selectivity, poor brain penetration ability or lack of oral bioavailability . Here we report crystal structures of the human YR bound to the two selective antagonists UR-MK299 and BMS-193885 at 2.7 and 3.0 Å resolution, respectively. The structures combined with mutagenesis studies reveal the binding modes of YR to several structurally diverse antagonists and the determinants of ligand selectivity. The YR structure and molecular docking of the endogenous agonist NPY, together with nuclear magnetic resonance, photo-crosslinking and functional studies, provide insights into the binding behaviour of the agonist and for the first time, to our knowledge, determine the interaction of its N terminus with the receptor. These insights into YR can enable structure-based drug discovery that targets NPY receptors.
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