Modeling tubulin at interfaces. Immobilization of microtubules on self-assembled monolayers

A theoretical study of protein docking to self-assembled monolayers using a new approach is presented. Docking experiments based on space complementarity implemented in FTDock software were performed for three different proteins: tubulin dimer, cytochrome c, and lysozyme. The proteins were adsorbed on alkanethiol surfaces with different terminating groups and 50,000 best orientations of each protein were analyzed. For all systems three filters based on different chemical and biological approaches were applied. Correctly docked proteins for the cytochrome c and lysozyme systems were found in a list of the first 12 results after applying the geometrical and grouping filter and in a list of the first 3 results after applying the biological filter. We have found that alkanethiol monolayers with odd and even numbers of -CH2- groups have similar properties in terms of interactions with the two proteins. Docking of the tubulin dimer revealed that the orientation favored from the applicational point of view can be found in a list of the first 14 results for monolayers with different terminating groups and that there may be a noticeable difference in tubulin dimer interactions with alkanethiol chains of various length. The results for tubulin dimer docking combined with microtubules ability of reversible assembly suggest that these biological structures may become good candidates to serve as templates for fabrication of nanowires and other nanoscale electronic devices. The new method of theoretical docking presented may be used as a fast and reliable tool complementing other theoretical and experimental techniques of exploring other protein-surface interfaces.     

Interactions of halichondrin B and eribulin with tubulin

Compounds that modulate microtubule dynamics include highly effective anticancer drugs, leading to continuing efforts to identify new agents and improve the activity of established ones. Here, we demonstrate that [(3)H]-labeled halichondrin B (HB), a complex, sponge-derived natural product, is bound to and dissociated from tubulin rapidly at one binding site per αβ-heterodimer, with an apparent K(d) of 0.31 μM. We found no HB-induced aggregation of tubulin by high-performance liquid chromatography, even following column equilibration with HB. Binding of [(3)H]HB was competitively inhibited by a newly approved clinical agent, the truncated HB analogue eribulin (apparent K(i), 0.80 μM) and noncompetitively by dolastatin 10 and vincristine (apparent K(i)'s, 0.35 and 5.4 μM, respectively). Our earlier studies demonstrated that HB inhibits nucleotide exchange on β-tubulin, and this, together with the results presented here, indicated the HB site is located on β-tubulin. Using molecular dynamics simulations, we determined complementary conformations of HB and β-tubulin that delineated in atomic detail binding interactions of HB with only β-tubulin, with no involvement of the α-subunit in the binding interaction. Moreover, the HB model served as a template for an eribulin binding model that furthered our understanding of the properties of eribulin as a drug. Overall, these results established a mechanistic basis for the antimitotic activity of the halichondrin class of compounds.     

Electrochemical study on interaction of vincristine with tubulin

In Tris (0.005 mol/L)‐NaCl (0.05 mol/L) buffer solution (pH = 7.10), keeping temperature at 37°C, a highly sensitive reduction peak of the antitumor agent was obtained by linear sweep voltammetry. The peak potential is‐1.56 V (vs. SCE). The peak current is proportional to the concentration of vincristine over the range of 2.1 ± 10^?7‐4.2 ± 10^?6 mol/L with the detection limit of 1.0 ± 10^?7 mol/L. The behavior of the binding of vincristine to tubulin was studied. The results showed that the reaction of tubulin dimer with vincristine formed an electrochemically active complex to be 1:2. Its stability constant is 2.5 ± 10¹⁴. The reduction process of the complex is irreversible with adsorptive characteristics.     

Separation of tubulin subunits by reversed-phase high-performance liquid chromatography

When properly solubilized with trifluoroacetic acid (TFA), alpha- and beta-tubulin subunits from a variety of sources may be resolved at high yield by reversed-phase high-performance liquid chromatography (HPLC), using a Waters muBondapak C18 column and simple linear aqueous acetonitrile gradients containing TFA. The tubulin subunits are typically the most non-polar proteins present, with the beta-tubulin subunit eluting before the alpha. Column temperature above ambient improve both the resolution and the yield; less polar solvent systems do not. Tubulins not freely soluble in aqueous TFA may be solubilized in 6 M guanidine-hydrochloric acid with no change in retention time. Other columns with shorter carbon chain lengths and larger pore size produce a single, unresolved tubulin peak. Reversed-phase HPLC analysis provides an independent comparative evaluation of organelle-specific tubulins, with characteristic retention time differences observed between homologous ciliary and flagellar outer doublet tubulin subunits and also between them and their cytoplasmic counterparts.     

Anticancer activity of chamaejasmine: effect on tubulin protein

In this work, the anticancer activity of chamaejasmine was studied by evaluating its in vitro cytotoxicity against several human cancer cell lines (MCF-7, A549, SGC-7901, HCT-8, HO-4980, Hela, HepG2, PC-3, LNCap, Vero and MDCK) using the MTT assay. Results indicated chamaejasmine showed more notable anticancer activity than taxol against PC-3 cells, with IC?? values of 2.28 and 3.98 μM, respectively. Furthermore, Western blot analysis showed that chamaejasmine was able to increase the expression of β-tubulin, but not α-tubulin. In silico simulations indicated that chamaejasmine specifically interacts with the active site which is located at the top of β-tubulin, thanks to the presence of strong hydrophobic effects between the core templates and the hydrophobic surface of the TB active site. The binding energy (E(inter)) was calculated to be -164.77 kcal·mol?1. Results presented here suggest that chamaejasmine possesses anti-cancer properties relating to β-tubulin depolymerization inhibition, and therefore is a potential source of anticancer leads for the pharmaceutical industry.     

Stereoselective synthesis of 3,3-diarylacrylonitriles as tubulin polymerization inhibitors

A series of 3,3-diarylacrylonitriles were synthesized stereoselectively as tubulin polymerization inhibitors for potential use in cancer chemotherapy. This synthetic route features stannylcupration and palladium-catalyzed Stille cross-coupling chemistry, allowing both E and Z isomers of 3,3-diarylacrylonitriles to be prepared in a very short sequence of reactions.     

Isolation of mammalian brain tubulin by amino-activated gel chromatography

In the present study, we report the isolation of the acidic structural protein tubulin using a number of amino-activated gels. Crude 100,000 g supernatant derived from sheep brain was applied to gels activated with either aminohexyl, aminoethyl, argininyl, diethylaminoethyl, lysinyl and polylysinyl residues and eluted with three distinct sequential buffer changes (pH 6.5): (i) 0.025-0.4 M morpholinoethanesulphonic acid; (ii) 0.076 and 0.379 M ammonium sulphate in 0.025 M morpholinoethanesulphonic acid; and (iii) 0.8 M sodium chloride in 0.025 M morpholinoethanesulphonic acid. Tubulin was recovered from all columns in an enriched form. However, the elution profile and purity, as judged by [3H]colchicine binding and electrophoresis, varied with the ligand. Hydrophobic gels, such as diethylaminoethyl and aminohexyl, required elution with high-ionic-strength buffers (0.8 M sodium chloride) and significant inhibition of [3H]colchicine activity resulted. This problem was avoided with the hydrophilic ligands such as arginine, polylysine and aminoethyl. Manipulation of elution conditions enabled complete elution of tubulin from arginine-activated gels in 2.5% ammonium sulphate without detectable losses of [3H]colchicine binding activity and with purity comparable to that achieved using diethylaminoethyl Sephacel.     

The action of cytochalasin A on the in vitro polymerization of brain tubulin and muscle G-actin.

The presence of cytochalasin A inhibits the self-assembly of beef brain tubulin and rabbit muscle G-actin in vitro and also decreases the colchicine binding of tubulin. Prior reaction of cytochalasin A with 2-mercaptoethanol destroys its inhibitory effects. It is shown that cytochalasin A exerts its actions by reacting with sulfhydryl groups, possibly causing irreversible structural changes in the proteins. Cytochalasin B does not affect the tubulin assembly reaction.     

Vinblastine perturbation of tubulin protofilament structure: a computational insight

Tubulin is a heterodimeric protein whose self assembly leads to the formation of protofilaments and of more complex structures called microtubules, key components of the cytoskeleton which have a fundamental role in the cell division process. Due to its biological function, tubulin is the target of many antitumoral molecules that exert their action on proliferating tumoral cells. Among these drugs, vinblastine has been widely used in therapy for a long time, albeit its mechanism of interaction with tubulin has remained elusive until recently. Vinblastine acts as a microtubule destabilizing agent and induces the formation of curved or ring-shaped tubulin polymers instead of linear protofilaments in vitro. In this paper we compare, using molecular dynamics simulations and free energy calculations, the network of interactions that allow the assembly of model linear protofilaments with those present in curved tubulin polymers complexed with vinblastine. It is shown that vinblastine, wedging between tubulin heterodimers, actually mediates part of the interactions between them and acts by crosslinking the two proteins, leading to the observed curved polymers rather than to their disassembly.     

Bicyclic isothioureas for conjugation with tubulin targeted anticancer agents

Two bicyclic annulated isothiourea derivatives were synthesized using as a key stage either the reaction of isothiocyanate halide with sodium sulfide or cyclization of unsaturated thiourea in the presence of bromine. X-ray molecular structure of N-[(3aSR,7aRS,Z)-hexahydro-1,3-benzothiazol-2(3H)-ylidene]glycine was determined. The conjugate of colchicine with [(3aR,5S,6aS)-2-(tert-butylamino)-3a,5,6,6a-tetrahydro-4H-cyclopenta[d]thiazol-5-yl]methanol obtained demonstrated pronounced cytotoxic effect on cancer cells.     

Use of the tubulin bound paclitaxel conformation for structure-based rational drug design

A new computational docking protocol has been developed and used in combination with conformational information inferred from REDOR-NMR experiments on microtubule bound 2-(p-fluorobenzoyl)paclitaxel to delineate a unique tubulin binding structure of paclitaxel. A conformationally constrained macrocyclic taxoid bearing a linker between the C-14 and C-3'N positions has been designed and synthesized to enforce this "REDOR-taxol" conformation. The novel taxoid SB-T-2053 inhibits the growth of MCF-7 and LCC-6 human breast cancer cells (wild-type and drug resistant) on the same order of magnitude as paclitaxel. Moreover, SB-T-2053 induces in vitro tubulin polymerization at least as well as paclitaxel, which directly validates our drug design process. These results open a new avenue for drug design of next generation taxoids and other microtubule-stabilizing agents based on the refined structural information of drug-tubulin complexes, in accordance with typical enzyme-inhibitor medicinal chemistry precepts.     

Synthesis and click reaction of tubulin polymerization inhibitor 9-azido-α-noscapine

Research on Chemical Intermediates - An efficient protocol for the synthesis of tubulin polymerization inhibitor, 9-azido-α-noscapine 2h from 9-amino-α-noscapine 2g is developed using...     

Probing the interaction of HTI-286 with tubulin using a stilbene analogue

HTI-286 is a synthetic analogue of the natural product hemiasterlin. HTI-286 is a potent antitumor agent that induces tubulin oligomerization. To investigate the binding stoichiometry and the binding site during this ligand-induced tubulin association, we synthesized an analogue of HTI-286 containing the chromophore stilbene. Using the distinct absorbance of the stilbene analogue, we determined the amounts of inhibitors bound to different tubulin oligomers by analytical ultracentrifugation. Herein we describe our findings based on these experiments. At the ratio of inhibitor to protein equal to or greater than 1, the stilbene analogue induces oligomerization of tubulin to a ring structure. The binding stoichiometry in the ring is one inhibitor per tubulin monomer (defined as an alpha/beta-heterodimer). At the ratio of inhibitor to protein less than 1, tubulin forms multiple intermediates, with the binding stoichiometry less than one inhibitor per tubulin monomer for all intermediates. The stable complex between the inhibitor and tubulin monomer was not detected under our experimental conditions. The binding site of the stilbene analogue does not overlap with the classic tubulin-binding agent, colchicine.     

Dimethylarsinic acid targets tubulin in mitotic cells to induce abnormal spindles

Dimethylarsinic acid (DMA) is the most effective inducer of cell‐cycle disruption among the arsenic compounds and their metabolites. The present study was conducted to gain further insight into cell‐cycle disruption induced by DMA. The inhibition of cell proliferation and the mitotic arrest induced by DMA were significant and dose‐dependent in Chinese hamster V79 cells and the two seemed to be closely related. At less than 140 µM the DMA did not inhibit the proliferation of cells, but it significantly induced mitotic arrest. An indirect immunofluorescence assay using anti‐α‐tubulin antibodies revealed that DMA induced the formation of abnormal spindles in the metaphase cells even at 350 µM with 5 h of treatment. At 1.4 mM DMA no metaphase cells could form a definite spindle structure. The spindle figures were similar to those induced by colchicine (125 nM ) or vinblastine (110 nM ), major antimitotic agents. In DMA‐treated interphase cells, the microtubule networks were indistinguishable from those of normal cells. With the tubulin‐assembly assay estimated by turbidity, DMA at less than 200 µM suppressed tubulin assembly in a dose‐dependent manner, whereas at more than 700 µM it enhanced tubulin polymerization remarkably with or without addition of excess guanosine‐5′‐triphosphate. According to the above findings, we discussed the possibility that DMA, a primary metabolite of inorganic arsenic in mammals, is related to arsenic carcinogenicity. Copyright © 2001 John Wiley & Sons, Ltd.     

Competitive mass spectrometry binding assay for characterization of three binding sites of tubulin

Tubulin is an attractive and established target for anticancer therapy. To date, the only method to determine the binding of inhibitor to tubulin has been competitive radioligand binding assays. We developed a non‐radioactive mass spectrometry (MS) binding assay to study the tubulin binding of colchicine, vinblastine and paclitaxel and to identify which of these three binding sites that a novel inhibitor binds. The method involves a very simple step of separating the unbound ligand from macromolecules using ultrafiltration. The unbound ligand in the filtrate can be accurately determined using highly sensitive and specific liquid chromatography tandem mass spectrometry (LC‐MS/MS) method using multiple reaction monitoring (MRM) mode. The assay was validated using podophyllotoxin, vincristine and docetaxel, drugs that compete to the colchicine‐, vinblastine‐ and paclitaxel‐binding sites in tubulin, respectively. This competitive binding assay allowed the reliable detection of interactions of these drugs with three binding sites on tubulin. This method was subsequently applied to determine the tubulin‐binding site of 4‐substituted methoxylbenzoyl‐aryl‐thiazoles (SMART‐H), a potent antitubulin agent developed in our laboratory. The results indicated that SMART‐H specifically and reversibly bound only to the colchicine‐binding site, but not to vinblastine‐ or paclitaxel sites. This new non‐radioligand binding method to determine the binding site on tubulin will function as a useful tool to study the binding sites of tubulin inhibitors. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis and biological evaluation of fluorescently labeled epothilone analogs for tubulin binding studies

The two fluorescently labeled epothilones 14 and 15 have been synthesized using a modification of Nicolaou's macrolactonization and Stille coupling strategy. The cytotoxicities of the compounds were 6.1 and 2.7 μg/mL, respectively, against the A2870 ovarian cancer cell line, and 0.5 and 1.0 μg/mL, respectively, against the PC-3 prostate cancer cell line. The critical concentration of tubulin was 0.5 and 1.0 μM in the presence of 14 and 15, respectively, compared with 0.3 μM for paclitaxel. The fluorescent properties of the two molecules in solution and bound to microtubules are described.