Discovery and Computer Aided Potency Optimization of a Novel Class of Small Molecule CXCR4 Antagonists

Vinader, V.; Ahmet, Djevdet S.; Ahmed, Mohaned; Patterson, Laurence H.; Afarinkia, K.

doi:10.1371/journal.pone.0078744

Cited by 6 publications

(6 citation statements)

References 63 publications

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“…Specifically, our results suggest that chemotaxis was observed in the study by Vinader et al 14 because the chemoattractant concentration was close to the K d for CXCL12-CXCR4. Conversely, as the chemoattractant concentration near the spot was much higher than the K d for EGF-EGFR, it is unlikely that true chemotaxis was observed by Wiggins and Rappoport.…”

Section: Discussionsupporting

confidence: 82%

“…The solution is generalizable for different chemoattractants and initial concentrations, but for concreteness, we focus here on cases matching the conditions used in the studies carried out by Wiggins and Rappoport 11 and by Vinader et al 14 The significant experimental parameters that were different between the two studies were the type and concentration of chemoattractant used. Wiggins and Rappoport used 5 μ M EGF; Vinader et al used 125 nM CXCL12.…”

Section: Resultsmentioning

confidence: 99%

“…However, when the dish is moved, mixing would occur in the medium, leading to disruption of the gradient. Moreover, in some studies, 11,14 cells are plated and allowed to adhere for 4 h in 10% FCS, after which the medium is changed to 0.1% FCS to enhance direction sensing and reduce proliferation. If the medium is changed at 4 h after plating the cells, the chemoattractant concentration is subsequently about 10% of what it would be otherwise (data not shown).…”

Section: Discussionmentioning

confidence: 99%

“…Previously measured values of the diffusion coefficients and dissociation constants for EGF and CXCL12 are used to apply model results to the particular cases of MDAMB-231 breast cancer cells migrating in gradients of EGF (as in the study by Wiggins and Rappoport 11 ) and CXCL12 (as in the study by Vinader et al 14 ). Additionally, the gradients generated in the assay are compared with the gradients needed to induce chemotaxis in MDA-MB-231 cells, as estimated from experimental results.…”

Section: Methodsmentioning

confidence: 99%

“…This assay is inexpensive, simple to set up, and amenable to multiplexing, making it a valuable complement to more expensive and laborious methods such as microfluidic assays. The assay has been used to study cancer cell signaling and motility, 12–14 effects of Vitamin D3 on macrophage chemotaxis, 15 dental pulp cell migration in wound healing, 16 and neural crest cell movement during development. 17 A disadvantage to the assay is that it can only sustain gradients that cells can sense for a limited duration.…”

Section: Introductionmentioning

confidence: 99%

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Improving the design of the agarose spot assay for eukaryotic cell chemotaxis

2014

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Migration of cells along gradients of effector molecules, i.e., chemotaxis, is necessary in immune response and is involved in development and cancer metastasis. The experimental assessment of chemotaxis thus is of high interest. The agarose spot assay is a simple tissue culture system used to analyze chemotaxis. Although direction sensing requires gradients to be sufficiently steep, how the chemical gradients developed in this assay change over time, and thus, under what conditions chemotaxis is plausible, has not yet been determined. Here, we use numerical solution of the diffusion equation to determine the chemoattractant gradient produced in the assay. Our analysis shows that, for the usual spot size, the lifetime of the assay is optimized if the chemoattractant concentration in the spot is initially 30 times the dissociation constant of the chemoattractant-receptor bond. This result holds regardless of the properties of the chemoattractant. With this initial concentration, the chemoattractant gradient falls to the minimum threshold for directional sensing at the same time that the concentration drops to the optimal level for detecting gradient direction. If a higher initial chemoattractant concentration is used, the useful lifetime of the assay is likely to be shortened because receptor saturation may decrease the cells’ sensitivity to the gradient; lower initial concentrations would result in too little chemoattractant for the cells to detect. Moreover, chemoattractants with higher diffusion coefficients would sustain gradients for less time. Based on previous measurements of the diffusion coefficients of the chemoattractants EGF and CXCL12, we estimate that the assay will produce gradients that cells can sense for a duration of 10 h for EGF and 5 h for CXCL12. These gradient durations are comparable to what can be achieved with the Boyden chamber assay. The analysis presented in this work facilitates determination of suitable parameters for the assay, and can be used to assess whether observed cell motility is likely due to chemotaxis or chemokinesis.

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Section: Discussionsupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Improving the design of the agarose spot assay for eukaryotic cell chemotaxis

2014

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Aspartate‐Based CXCR4 Chemokine Receptor Binding of Cross‐Bridged Tetraazamacrocyclic Copper(II) and Zinc(II) Complexes

Maples

Cain

Burke

et al. 2016

Chemistry A European J

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The CXCR4 chemokine receptor is implicated in a number of diseases including HIV infection and cancer development and metastasis. Previous studies have demonstrated that configurationally restricted bis-tetraazamacrocyclic metal complexes are high-affinity CXCR4 antagonists. Here, we present the synthesis of Cu2+ and Zn2+ acetate complexes of six cross-bridged tetraazamacrocycles to mimic their coordination interaction with the aspartate side chains known to bind them to CXCR4. X-ray crystal structures for three new Cu2+ acetate complexes and two new Zn2+ acetate complexes, demonstrate metal-ion dependent differences in the mode of binding the acetate ligand concomitantly with the requisite cis-V configured cross-bridged tetraazamacrocyle. Concurrent density functional theory molecular modelling studies produced an energetic rationale for the unexpected [Zn(OAc)(H2O)]+ coordination motif present in all of the Zn2+ cross-bridged tetraazamacrocycle crystal structures, which differs from the chelating acetate [Zn(OAc)]+ structures of known unbridged and side-bridged tetraazamacrocyclic Zn2+ containing CXCR4 antagonists.

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