amTCO, a new trans-cyclooctene derivative to study drug-target interactions in cells

2021 ◽  
Vol 57 (14) ◽  
pp. 1814-1817
Author(s):  
Cécile Echalier ◽  
Anna Rutkowska ◽  
Ana Kojic ◽  
Douglas W. Thomson ◽  
Lee J. Edwards ◽  
...  
Keyword(s):  
Click Chemistry ◽  
Drug Target ◽  
Study Drug ◽  
Drug Binding ◽  
Binding Assays ◽  
Intact Cells ◽  
In Cells

We provide a new tagging entity for click chemistry to perform improved drug binding assays in intact cells.

Monitoring Drug Target Engagement in Cells and Tissues Using the Cellular Thermal Shift Assay

Science ◽  
2013 ◽  
Vol 341 (6141) ◽  
pp. 84-87 ◽  
Author(s):  
Daniel Martinez Molina ◽  
Rozbeh Jafari ◽  
Marina Ignatushchenko ◽  
Takahiro Seki ◽  
E. Andreas Larsson ◽  
...  
Keyword(s):  
Drug Target ◽  
Drug Transport ◽  
Drug Binding ◽  
Target Engagement ◽  
Tissue Samples ◽  
Target Proteins ◽  
Thermal Shift Assay ◽  
Cellular Thermal Shift Assay ◽  
Thermal Shift ◽  
In Cells

The efficacy of therapeutics is dependent on a drug binding to its cognate target. Optimization of target engagement by drugs in cells is often challenging, because drug binding cannot be monitored inside cells. We have developed a method for evaluating drug binding to target proteins in cells and tissue samples. This cellular thermal shift assay (CETSA) is based on the biophysical principle of ligand-induced thermal stabilization of target proteins. Using this assay, we validated drug binding for a set of important clinical targets and monitored processes of drug transport and activation, off-target effects and drug resistance in cancer cell lines, as well as drug distribution in tissues. CETSA is likely to become a valuable tool for the validation and optimization of drug target engagement.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3339-3349 ◽  
Author(s):  
Indrani Bera ◽  
Pavan V. Payghan
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Simulations ◽  
Drug Target ◽  
Structural Information ◽  
Drug Binding ◽  
Structure Based Drug Design ◽  
Drug Designing ◽  
Target Binding ◽  
Dynamics Simulations

Background: Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process. Objective: The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design. Method: This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained. Results: This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations. Conclusion: The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

scholarly journals A Novel H+ Conductance in Eosinophils

1999 ◽  
Vol 190 (2) ◽  
pp. 183-194 ◽  
Author(s):  
Botond Bánfi ◽  
Jacques Schrenzel ◽  
Oliver Nüsse ◽  
Daniel P. Lew ◽  
Erzsébet Ligeti ◽  
...  
Keyword(s):  
Nadph Oxidase ◽  
The Novel ◽  
Experimental Conditions ◽  
Intact Cells ◽  
Electrophysiological Studies ◽  
Dependent Signal ◽  
Low Threshold ◽  
Nadph Oxidase Activation ◽  
In Cells

Efficient mechanisms of H+ ion extrusion are crucial for normal NADPH oxidase function. However, whether the NADPH oxidase—in analogy with mitochondrial cytochromes—has an inherent H+ channel activity remains uncertain: electrophysiological studies did not find altered H+ currents in cells from patients with chronic granulomatous disease (CGD), challenging earlier reports in intact cells. In this study, we describe the presence of two different types of H+ currents in human eosinophils. The “classical” H+ current had properties similar to previously described H+ conductances and was present in CGD cells. In contrast, the “novel” type of H+ current had not been described previously and displayed unique properties: (a) it was absent in cells from gp91- or p47-deficient CGD patients; (b) it was only observed under experimental conditions that allowed NADPH oxidase activation; (c) because of its low threshold of voltage activation, it allowed proton influx and cytosolic acidification; (d) it activated faster and deactivated with slower and distinct kinetics than the classical H+ currents; and (e) it was ∼20-fold more sensitive to Zn2+ and was blocked by the histidine-reactive agent, diethylpyrocarbonate (DEPC). In summary, our results demonstrate that the NADPH oxidase or a closely associated protein provides a novel type of H+ conductance during phagocyte activation. The unique properties of this conductance suggest that its physiological function is not restricted to H+ extrusion and repolarization, but might include depolarization, pH-dependent signal termination, and determination of the phagosomal pH set point.

Regulation of cell shape in Euglena gracilis. III. Involvement of stable microtubules

1985 ◽  
Vol 74 (1) ◽  
pp. 219-237
Author(s):  
C.L. Lachney ◽  
T.A. Lonergan
Keyword(s):  
Euglena Gracilis ◽  
Cell Shape ◽  
Microtubule Assembly ◽  
Live Cells ◽  
Microtubule Depolymerization ◽  
Cytoplasmic Microtubule ◽  
Intact Cells ◽  
Calmodulin Antagonist ◽  
Cell Shapes ◽  
In Cells

The role of cytoplasmic microtubules in a recently reported biological clock-controlled rhythm in cell shape of the alga Euglena gracilis (strain Z) was examined using indirect immunofluorescence microscopy. The resulting fluorescent patterns indicated that, unlike many other cell systems, Euglena cells apparently change from round to long to round cell shape without associated cytoplasmic microtubule assembly and disassembly. Instead, the different cell shapes were correlated with microtubule patterns, which suggested that movement of stable microtubules to accomplish cell shape changes. In live intact cells, these microtubules were demonstrated by immunofluorescence to be stable to lowered temperature and elevated intracellular Ca2+ levels, treatments that are commonly used to depolymerize microtubules. In cells extracted in detergent at low temperature or in the presence of elevated Ca2+ levels, the fluorescent image of the microtubules was disrupted. Transmission electron microscopy confirmed the loss of one subset of pellicle microtubules. The difference in microtubule stability to these agents between live intact cells and cells extracted in detergent suggested the presence of a microtubule-stabilizing factor in live cells, which is released from the cell by extraction with detergent, thereby permitting microtubule depolymerization by Ca2+ or lowered temperature. The calmodulin antagonist trifluoperazine prevented the Ca2+-induced disruption of the fluorescent microtubule pattern in cells extracted in detergent. These results implied the involvement of calmodulin in the sensitivity to Ca2+ of the microtubules of cells extracted in detergent.

scholarly journals Structural basis for strand-transfer inhibitor binding to HIV intasomes

Science ◽  
2020 ◽  
Vol 367 (6479) ◽  
pp. 810-814 ◽  
Author(s):  
Dario Oliveira Passos ◽  
Min Li ◽  
Ilona K. Jóźwik ◽  
Xue Zhi Zhao ◽  
Diogo Santos-Martins ◽  
...  
Keyword(s):  
High Resolution ◽  
Drug Target ◽  
Antiretroviral Drugs ◽  
Drug Binding ◽  
Structural Basis ◽  
Strand Transfer ◽  
Cryo Electron Microscopy ◽  
Integrase Strand Transfer Inhibitors ◽  
Transfer Inhibitor ◽  
Host Chromatin

The HIV intasome is a large nucleoprotein assembly that mediates the integration of a DNA copy of the viral genome into host chromatin. Intasomes are targeted by the latest generation of antiretroviral drugs, integrase strand-transfer inhibitors (INSTIs). Challenges associated with lentiviral intasome biochemistry have hindered high-resolution structural studies of how INSTIs bind to their native drug target. Here, we present high-resolution cryo–electron microscopy structures of HIV intasomes bound to the latest generation of INSTIs. These structures highlight how small changes in the integrase active site can have notable implications for drug binding and design and provide mechanistic insights into why a leading INSTI retains efficacy against a broad spectrum of drug-resistant variants. The data have implications for expanding effective treatments available for HIV-infected individuals.

Kinetics of Drug Binding and Residence Time

2019 ◽  
Vol 70 (1) ◽  
pp. 143-171 ◽  
Author(s):  
Mattia Bernetti ◽  
Matteo Masetti ◽  
Walter Rocchia ◽  
Andrea Cavalli
Keyword(s):  
Computational Methods ◽  
Residence Time ◽  
Drug Target ◽  
Early Stage ◽  
Kinetic Constant ◽  
Theoretical Background ◽  
Drug Binding ◽  
Binding Kinetics ◽  
Kinetics Of

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.

Glycan-Mediated, Ligand-Controlled Click Chemistry for Drug-Target Identification

ChemBioChem ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 150-154 ◽  
Author(s):  
Henning Stöckmann ◽  
Violeta L. Marin ◽  
Paul Nimmer ◽  
Corina M. Balut ◽  
Donald J. Davidson ◽  
...  
Keyword(s):  
Click Chemistry ◽  
Drug Target ◽  
Target Identification ◽  
Drug Target Identification

scholarly journals Peptide Deformylase as an Antibacterial Drug Target: Assays for Detection of Its Inhibition in Escherichia coli Cell Homogenates and Intact Cells

2001 ◽  
Vol 45 (4) ◽  
pp. 1053-1057 ◽  
Author(s):  
Christian M. Apfel ◽  
Stefan Evers ◽  
Christian Hubschwerlen ◽  
Wolfgang Pirson ◽  
Malcolm G. P. Page ◽  
...  
Keyword(s):  
Drug Target ◽  
Peptide Deformylase ◽  
Translation System ◽  
Antibacterial Drug ◽  
Bacterial Cells ◽  
Methionine Aminopeptidase ◽  
Intact Cells ◽  
Physiological Conditions ◽  
A Cell ◽  
Antibacterial Drug Target

ABSTRACT An assay was developed to determine the activity of peptide deformylase (PDF) inhibitors under conditions as close as possible to the physiological situation. The assay principle is the detection of N-terminal [35S]methionine labeling of a protein that contains no internal methionine. If PDF is active, the deformylation of the methionine renders the peptide a substrate for methionine aminopeptidase, resulting in the removal of the N-terminal methionine label. In the presence of a PDF inhibitor, the deformylation is blocked so that the N-formylated peptide is not processed and the label is detected. Using this assay, it is possible to determine the PDF activity under near-physiological conditions in a cell-free transcription-translation system as well as in intact bacterial cells.

Recent Advances in NMR Diffusion Techniques for Studying Drug Binding

2003 ◽  
Vol 56 (9) ◽  
pp. 855 ◽  
Author(s):  
William S. Price
Keyword(s):  
Drug Development ◽  
Study Drug ◽  
Drug Binding ◽  
Model Systems ◽  
Aqueous Samples ◽  
Recent Advances ◽  
Physiological Relevance ◽  
Nmr Diffusion

Characterizing the binding of ligands to macromolecular receptors in solution is important to many areas of chemistry, biology, and nanobiotechnology, but perhaps most notably to drug development. NMR has proven to be particularly useful for such studies, but the systems studied have generally been restricted to model systems with dubious physiological relevance. This paper reviews the use of NMR diffusion measurements to study drug binding and two recent advances that enable measurements to be conducted in more sensitive higher-field NMR spectrometers in non-deuterated aqueous samples.

Sign in / Sign up

Export Citation Format

Share Document