Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine

Castle, Brian T.; McCubbin, Seth; Prahl, L.; Bernens, Jordan N.; Sept, David; Odde, David J.

doi:10.1091/mbc.e16-08-0567

Cited by 63 publications

(92 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The progression of tubulin polymerization was examined by monitoring the increase in fluorescence emission at 420 nm (excitation wavelength is 360 nm) for 1 h at 37 °C. Vinblastine and paclitaxel, two known microtubule‐targeting agents acting as disassembly and assembly promoters, respectively, were used as controls . The effects on tubulin polymerization of three substances are shown in Figure (i.e., 4 as reference inhibitor and its biphenyl analogue 3 , as well as the potent antiproliferative compound 36 ).…”

Section: Resultsmentioning

confidence: 99%

“…Af urtheri nvestigation of the structure activity relationships was carried out by varying number andp osition of fluorine atoms (24 and 25)a nd replacing Fw ith OCH 3 (26 and 27)o n the distal phenyl ring. Within the limits of the chemical space examined, an et gain in the cell growth inhibition potency over compound 3 was observed with 4'-F (24)a nd 3'-OCH 3 (27)d erivatives. Ad ifferent spatialg eometry of the biphenyl moietyi n24 causedadrop of biological potency, as shown by the positional isomer 28 in which the distal 4'-F-phenyl is moved from para (in 24)t ometa positionrelative to NHCO.…”

Section: Resultsmentioning

confidence: 99%

“…Vinblastine and paclitaxel, two known microtubule-targeting agentsa cting as disassembly and assembly promoters, respectively,w ere used as controls. [27] The effectso ntubulin polymerization of three substancesa re shown in Figure 4( i.e., 4 as reference inhibitor and its biphenyl analogue 3,a sw ell as the potent antiproliferative compound 36).…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Investigating Structural Requirements for the Antiproliferative Activity of Biphenyl Nicotinamides

et al. 2017

View full text Add to dashboard Cite

A number of trimethoxybenzoic acid anilides, previously studied as permeability glycoprotein (P-gp) modulators, were screened with the aim of identifying new anticancer agents. One of these compounds, which showed antiproliferative activity against resistant MCF-7 cell line, was selected as the hit structure. Replacement of the trimethoxybenzoyl moiety with a nicotinoyl group, in order to overcome solubility issues, led to a new series of N-biphenyl nicotinoyl anilides, among which a nitro derivative, N-(3',5'-difluoro-3-nitro-[1,1'-biphenyl]-4-yl)nicotinamide (3), displayed antiproliferative activity against MCF-7 and MDA-MB-231 cells in the nanomolar range. The search for a bioisostere of the nitro group led to nitrile analogue N-(3-cyano-4'-fluoro-[1,1'-biphenyl]-4-yl)nicotinamide (36), which shows a strong increase in activity against MCF-7 and MDA-MB-231 cells. Compound 36 induced a dose-dependent accumulation of G - and M-phase MCF-7 cell populations, and a decrease in S-phase cells. Relative to vinblastine, a well-known potent antimitotic agent, compound 36 also induced G -phase arrest at low doses (20-40 nm), but did not inhibit in vitro tubulin polymerization.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Investigating Structural Requirements for the Antiproliferative Activity of Biphenyl Nicotinamides

et al. 2017

View full text Add to dashboard Cite

show abstract

“…This is in line with the results previously obtained (38) that longitudinal association is necessary to make the lateral bond stable. Hence, the combination of the lateral bond along with the longitudinal bond makes assembly dynamics feasible in a manner previously described in thermo-kinetic (TK) terms that predict cellular level (µm scale) dynamics at time scales of minutes (35,46). The TK modeling outputs, such as MT growth rate, shortening rate, catastrophe frequency, and rescue frequency, can be then used as inputs to cell-level models to predict dynamics and microtubule distributions associated with cell functions (47,(69)(70)(71)(72)(73)(74), which allows us to now connect MD to BD to TK to CL models ( Fig.…”

Section: Brownian Dynamics Simulations Of the Lateral Bond Potential mentioning

confidence: 99%

“…Considering the limits of current computational resources, capturing kinetic information from MD simulations at a time scale of ~ remains prohibitive, especially considering that multiple replicates are needed to sample the distribution of initial conditions. By contrast, coarse-grained Brownian dynamics (BD) with ~ms time scales at a cost of atomistic detail, and thermo-kinetic (TK) simulations with less detail allowing access to ~100s time scales, together enable recapitulation of the kinetic rates and microtubule tip structures consistent with those found in vitro and in vivo (35)(36)(37)(38). The interactions of particles in the BD simulations, here being the tubulin dimers, are modeled using an input potential, which can be dissimilar for tubulin as a function of its nucleotide state in different studies (7,(38)(39)(40)(41).…”

Section: Introductionmentioning

confidence: 99%

Multi-scale Computational Modeling of Tubulin-Tubulin Lateral Interaction

Hemmat

Castle

Sachs

et al. 2019

Preprint

View full text Add to dashboard Cite

Microtubules are multi-stranded polymers in eukaryotic cells that support key cellular functions such as chromosome segregation, motor-based cargo transport, and maintenance of cell polarity. Microtubules self-assemble via "dynamic instability," where the dynamic plus ends switch stochastically between alternating phases of polymerization and depolymerization. A key question in the field is what are the atomistic origins of this switching, i.e. what is different between the GTP-and GDP-tubulin states that enables microtubule growth and shortening, respectively? More generally, a major challenge in biology is how to connect theoretical frameworks across length-time scales, from atoms to cellular behavior. In this study, we describe a multi-scale model by linking atomistic molecular dynamics (MD), molecular Brownian dynamics (BD), and cellular-level thermokinetic (TK) modeling of microtubules. Here we investigated the underlying interaction energy landscape when tubulin dimers associate laterally by performing all-atom molecular dynamics simulations. We found that the lateral free energy is not significantly different among three nucleotide states of tubulin, GTP, GDP, and GMPCPP, and is estimated to be ≅-11 kBT. Furthermore, using MD potential energy in our BD simulations of tubulin dimers in solution confirms that the lateral bond is weak on its own with a mean lifetime of ~0.1 μs, implying that the longitudinal bond is required for microtubule assembly. We conclude that nucleotide-dependent lateral bond strength is not the key mediator microtubule dynamic instability, implying that GTP acts elsewhere to exert its stabilizing influence on microtubule polymer. Furthermore the estimated bond strength is well-aligned with earlier estimates based on thermokinetic (TK) modeling and light microscopy measurements (VanBuren et al., PNAS, 2002). Thus, we have computationally connected atomistic level structural information, obtained by cryoelectron microscopy, to cellular scale microtubule assembly dynamics using a combination of MD, BD, and TK models to bridge from Ångstroms to micrometers and from femtoseconds to minutes.

show abstract

Analysis of Microtubule Dynamics Heterogeneity in Cell Culture

Serikbaeva

Tvorogova

Kauanova

et al. 2018

Cellular Heterogeneity

View full text Add to dashboard Cite

Microtubules (MTs) are dynamic components of the cytoskeleton playing an important role in a large number of cell functions. Individual MTs in living cells undergo stochastic switching between alternate states of growth, shortening and attenuated phase, a phenomenon known as tempered dynamic instability. Dynamic instability of MTs is usually analyzed by labeling MTs with +TIPs, namely, EB proteins. Tracking of +TIP trajectories allows analyzing MT growth in cells with a different density of MTs. Numerous labs now use +TIP to track growing MTs in a variety of cell cultures. However, heterogeneity of MT dynamics is usually underestimated, and rather small sampling for the description of dynamic instability parameters is often used. The strategy described in this chapter is the method for repetitive quantitative analysis of MT growth rate within the same cell that allows minimization of the variation in MT dynamics measurement. We show that variability in MT dynamics within a cell when using repeated measurements is significantly less than between different cells in the same chamber. This approach allows better estimation of the heterogeneity of cells' responses to different treatments. To compare the effects of different MT inhibitors, the protocol using normalized values for MT dynamics and repetitive measurements for each cell is employed. This chapter provides detailed methods for analysis of MT dynamics in tissue cultures. We describe protocols for imaging MT dynamics by fluorescent microscopy, contrast enhancement technique, and MT dynamics analysis using triple color-coded display based on sequential subtraction analysis.

show abstract

Mechanisms of kinetic stabilization by the drugs paclitaxel and vinblastine

Cited by 63 publications

References 80 publications

Investigating Structural Requirements for the Antiproliferative Activity of Biphenyl Nicotinamides

Investigating Structural Requirements for the Antiproliferative Activity of Biphenyl Nicotinamides

Multi-scale Computational Modeling of Tubulin-Tubulin Lateral Interaction

Analysis of Microtubule Dynamics Heterogeneity in Cell Culture

Contact Info

Product

Resources

About