Identification and X‐ray Co‐crystal Structure of a Small‐Molecule Activator of LFA‐1‐ICAM‐1 Binding

Hintersteiner, Martin; Kallen, Joerg; Schmied, Mario; Gräf, Christine; Jung, Thomas; Mudd, Gemma; Shave, Steven; Gstach, Hubert; Auer, Manfred

doi:10.1002/anie.201310240

Cited by 15 publications

(23 citation statements)

References 34 publications

(28 reference statements)

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“…Remarkably, clusters of residues were identified in both systems that form continuous pathways spreading from the allosteric site to the orthosteric site and to regions known to be important for protein function (Figure 9(a)). Finally, predicted free energies of cooperativity for binding of the allosteric and orthosteric ligands to LFA‐1 revealed a nonadditive stabilization in agreement with the experimentally confirmed mechanisms of negative and positive cooperativity …”

Section: Applicationssupporting

confidence: 73%

Rigidity theory for biomolecules: concepts, software, and applications

Hermans

Pfleger

Nutschel

et al. 2017

WIREs Comput Mol Sci

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The mechanical heterogeneity of biomolecular structures is intimately linked to their diverse biological functions. Applying rigidity theory to biomolecules identifies this heterogeneous composition of flexible and rigid regions, which can aid in the understanding of biomolecular stability and long-ranged information transfer through biomolecules, and yield valuable information for rational drug design and protein engineering. We review fundamental concepts in rigidity theory, ways to represent biomolecules as constraint networks, and methodological and algorithmic developments for analyzing such networks and linking the results to biomolecular function. Software packages for performing rigidity analyses on biomolecules in an efficient, automated way are described, as are rigidity analyses on biomolecules including the ribosome, viruses, or transmembrane proteins. The analyses address questions of allosteric mechanisms, mutation effects on (thermo-)stability, protein (un-)folding, and coarse-graining of biomolecules. We advocate that the application of rigidity theory to biomolecules has matured in such a way that it could be broadly applied as a computational biophysical method to scrutinize biomolecular function from a structure-based point of view and to complement approaches focused on biomolecular dynamics. We discuss possibilities to improve constraint network representations and to perform large-scale and prospective studies.

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Section: Applicationssupporting

confidence: 73%

Rigidity theory for biomolecules: concepts, software, and applications

Hermans

Pfleger

Nutschel

et al. 2017

WIREs Comput Mol Sci

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“…Based on SAR information obtained from on-bead screens of tagged one-bead one-compound combinatorial libraries, a novel α L β 2 ligand acting as agonist was identified [ 71 ]. The small molecule 19, named IBE-667 ( Figure 7 ), increased the binding of biotinylated soluble ICAM-1 to activated T-cells, thus acting as an ICAM-1 binding enhancer for LFA-1.…”

Section: Leukocyte Integrinsmentioning

confidence: 99%

Can Integrin Agonists Have Cards to Play against Cancer? A Literature Survey of Small Molecules Integrin Activators

Tolomelli

Galletti

Baiula

et al. 2017

Cancers

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The ability of integrins to activate and integrate intracellular communication illustrates the potential of these receptors to serve as functional distribution hubs in a bi-directional signal transfer outside-in and inside-out of the cells. Tight regulation of the integrin signaling is paramount for normal physiological functions such as migration, proliferation, and differentiation, and misregulated integrin activity could be associated with several pathological conditions. Because of the important roles of integrins and their ligands in biological development, immune responses, leukocyte traffic, haemostasis, and cancer, their potential as therapeutic tools is now widely recognized. Nowadays extensive efforts have been made to discover and develop small molecule ligands as integrin antagonists, whereas less attention has been payed to agonists. In recent years, it has been recognized that integrin agonists could open up novel opportunities for therapeutics, which gain benefits to increase rather than decrease integrin-dependent adhesion and transductional events. For instance, a significant factor in chemo-resistance in melanoma is a loss of integrin-mediated adhesion; in this case, stimulation of integrin signaling by agonists significantly improved the response to chemotherapy. In this review, we overview results about small molecules which revealed an activating action on some integrins, especially those involved in cancer, and examine from a medicinal chemistry point of view, their structure and behavior.

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“…The confocal scanning technology (CONA) was originally developed to enable screening of combinatorial chemical libraries directly on the solid bead-based support, which in effect serves as a nanoscale assay compartment [ 6 – 11 ]. The confocal sectioning of a monolayer of ~ 100-μm-sized beads imaged on a fluorescence microscope equipped with a scanning stage enables the high-throughput, highly sensitive detection of binding events between a bead-linked small molecule and a fluorescently labeled target protein in solution [ 6 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

et al. 2018

Self Cite

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BackgroundThe ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging.ResultsUPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme.ConclusionsAs a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.Electronic supplementary materialThe online version of this article (10.1186/s12915-018-0554-z) contains supplementary material, which is available to authorized users.

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Identification and X‐ray Co‐crystal Structure of a Small‐Molecule Activator of LFA‐1‐ICAM‐1 Binding

Cited by 15 publications

References 34 publications

Rigidity theory for biomolecules: concepts, software, and applications

Rigidity theory for biomolecules: concepts, software, and applications

Can Integrin Agonists Have Cards to Play against Cancer? A Literature Survey of Small Molecules Integrin Activators

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

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