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Key Event Title
|Level of Biological Organization|
Key Event Components
Key Event Overview
AOPs Including This Key Event
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Key Event Description
The site of action is the tubulin in the cytoplasm. Tubulins represent a large superfamily, and several isotypes are described for both α and β tubulin in mammalian cells [Luduena 2013]. At least six different isotypes of the α subunit are known, while eight isotypes are known for the β subunit. These subunits share a high degree of homology (90% similarity). In addition to α- and β-tubulin, other tubulin homologues have been identified (γ, δ and ε), but their roles in the life cycle of the cell are uncertain [Bhattacharya and Cabral 2009]. All available isotypes are incorporated within microtubules, although with different tissue distributions in normal cells [Berrieman et al. 2004]. The currently known microtubule-disrupting agents bind to all isotypes, having only a slight preference for one over another [Miller et al. 2010].
Binding sites on the α/β-tubulin heterodimer: Conventionally, microtubule-interfering agents are categorized into two main groups: (1) microtubule destabilizers, including colchicine and a variety of vinca alkaloids; and (2) microtubule stabilizers, including taxanes and epothilones. Most agents interact with known binding pockets of α/β-tubulin; however, there are compounds that bind to tubulin on undefined sites. Three distinct sites are well characterized in the literature [Marchetti et al., submitted; Botta et al., 2009]: (1) the colchicine-binding domain at the interface between the α- and β-tubulin dimers; (2) the vinca domain surrounding the GTP binding site on β- and α-tubulin; and, (3) the taxane domain located on β-tubulin [Botta et al. 2009].
Colchicine binding domain on tubulin: The colchicine binding domain is a deep pocket located at the α/β interface of tubulin heterodimers. Crystal structures for tubulin and different ligands are available, although their resolution is not high [Lu et al. 2012; Massarotti et al. 2012]. Notwithstanding its deep location, significant conformational changes in the protein are necessary for accommodating the inhibitors. Both the A and C rings of colchicine are necessary for high affinity binding, while the B ring may only function as a linker between the other two. Three methoxy residues are present in the A ring and all of them are involved in the high affinity binding to tubulin. The C ring of colchicine interacts through van der Waals contacts with Valα181, Serα178, and Valβ315. The carbonyl group behaves as a hydrogen bond acceptor, interacting with Val181a. The A ring is buried in a hydrophobic pocket delimited by Lysβ352, Asnβ350, Leuβ378, Alaβ316, Leuβ255, Lysβ254, Alaβ250, and Leuβ242, and the methoxy group at position 3 is involved in a hydrogen bond interaction within the thiol group of Cysβ241 [Marchetti et al., submitted]. Different ligands may compete with colchicine for the same binding site, even in the absence of high structural correspondence [Lu et al. 2012].
How It Is Measured or Detected
Binding properties to tubulin are generally evaluated in vitro, typically on tubulin extracts derived from brain tissues [Miller and Wilson 2010]. To determine whether a compound can bind to tubulin, a competitive [3H]colchicine tubulin-binding assay is conducted in vitro to measure whether the binding of colchicine is inhibited by the presence of the test agent [Verdier-Pinard et al. 1998]. A reaction mixture containing tubulin, [3H]colchicine and a potential inhibitor is incubated and after the addition of the scintillation fluid, the radioactivity of [3H]colchicine-bound tubulin is measured using a scintillation counter. The reduction of [3H]colchicine-bound tubulin value is inversely proportional to the test agent binding affinity [Hamel and Lin 1981]. A reaction mixture with only tubulin and [3H]colchicine is generally used as an experimental control standard. The inhibition constant (Ki) of colchicine is 5.75 μM [Zavala et al. 1980] and the ability of new chemicals to interfere with colchicine binding to tubulin is benchmarked against this value.
Domain of Applicability
Chemical binding to tubulin has been measured in somatic and germ cells in a variety of species, from rodents in vivo to human cells in culture. Theoretically, chemical binding to tubulin can occur in any cell type in any organism.
Evidence for Perturbation by Stressor
Overview for Molecular Initiating Event
Colchicine is a prototypical spindle poison that has been extensively used to investigate binding to tubulin. The kinetics of colchicine binding are well established [Lambeir and Engelborghs, 1981; Engelborghs, 1998] and can be measured experimentally with high precision [Hamel and Lin, 1981]. Colchicine binds non-polymerized α/β dimeric tubulin by a two-step process. The first step is rapid but weak, resulting in the formation of an initial pre-equilibrium complex, which involves a low affinity binding of colchicine that is reversible. This is followed by slow conformational changes in tubulin, which finally lead to the formation of an irreversible final state tubulin–colchicine complex that has high activation energy [Garland 1978]. The conformational change in tubulin heterodimers, followed by the addition of the complex at the ends of microtubules, is responsible for the suppressed polymerization at microtubule ends leading to their depolymerization [Ravelli et al., 2004]. The binding kinetics have been studied at different temperatures. The standard enthalpy change of the first step (ΔH°1 = -33±8 kJ · mol–1) and the activation energy of the second step (ΔH°2 = 100±5 kJ · mol–1) were determined based on the temperature dependence [Lambeir and Engelborghs, 1981]. Using eight different analogues to study the binding mechanisms of colchicine, it was demonstrated that the C-ring of colchicine is responsible for the first step of the binding mechanism, while the second step involves the rearrangement of the initial complex to interact with the A-ring [Engelborghs, 1998].
Other chemicals are also known to bind to tubulin [Marchetti et al., 2016]. These chemicals can be grouped in two general classes: colchicine domain binders and vinca domain binders.
Known colchicine domain binders:
1. Podophyllotoxin ((5R,5aR,8aR,9R)-5-hydroxy-9-(3,4,5-trimethoxyphenyl)-5a,6,8a,9-tetrahydro-5H-benzofuro[5,6-f][1,3]benzodioxol-8-one, POD) has a trimethoxybenzoic chemical structure similar to colchicine. It inhibits colchicine binding to the colchicine-binding domain of tubulin. However, although colchicine and podophyllotoxin bind in the same pocket on β-tubulin, their binding sites are not completely overlapping [Desbene and Giorgi-Renault 2002].
2. 2-methoxyestradiol ((8R,9S,13S,14S,17S)-2-methoxy-13-methyl-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthrene-3,17-diol, 2ME) binds to the colchicine domain of tubulin [D'Amato et al. 1994].
3. Nocodazole (methyl (5-[2-thienylcarbonyl]-1H-benzimidazol-2-yl, NOC) belongs to the group of benzimidazole derivatives that were patented, as a class, for the treatment of cancer in conjunction with other pharmaceuticals. Nocodazole has been shown to bind in the colchicine domain [Xu et al. 2002].
4. Benomyl (methyl N-[1-(butylcarbamoyl)benzimidazol-2-yl]carbamate, BEN), another benzimidazole derivative, is the active compound in several agricultural fungicides. The benomyl-binding site is located in the core of β-tubulin at a site distinct from the colchicine domain [Clement et al. 2008].
5. Carbendazim (methyl N-(1H-benzimidazol-2-yl)carbamate, MBC) is a fungicide commonly used in agriculture for the control of a wide range of fungal diseases. Carbendazim is the methylbenzimidazolcarbamate product of the spontaneous hydrolyzation process incurred by benomyl in aqueous solution (it is the major metabolite). Therefore, it is at least partially responsible for the benomyl effects observed in vivo. The affinity of carbendazim for mammalian tubulin is less than that of benomyl, most probably because it lacks the position 1 side chain of benomyl. Like benomyl, carbendazim does not compete with colchicine for binding to tubulin [Yenjerla et al., 2008].
6. Thiabendazole (4-(1H-benzimidazol-2-yl)-1,3-thiazole, TBZ) is a benzimidazole-derived anthelmintic and an agricultural fungicide, structurally related to NOC, benomyl and MBC. TBZ competitively inhibits MBC binding to fungal tubulin [Davidse and Flach, 1978].
7. ABT-751 (N-(2-((4-hydroxyphenyl)amino)pyridin-3-yl)-4-methoxybenzenesulfonamide) has a scaffold based on a benzsulfamide group. It was identified as a potent antiproliferative agent and was subsequently found to be an antitubulin agent by targeting the colchicine binding site [Yoshimatsu et al., 1997].
8. A compound base on m-ethoxyaniline group (2-(6-ethoxy-3-(3-ethoxyphenylamino)-1-methyl-1,4-dihydroindeno[1,2-c]pyrazol-7-yloxy)acetamide) showed noteworthy low nanomolar potency against cancer cell lines. In mechanistic studies, it inhibited tubulin polymerization and disorganized microtubule by binding to tubulin colchicine binding site [Liu et al., 2016].
Vinca domain binders:
The vinca alkaloids, a class of antimitotic compounds derived from the periwinkle plant, Catharanthus roseus [Cutts et al., 1960], bind near the GTP-binding site on the β-subunit of tubulin at a site distinct from the colchicine-binding one [Rai and Wolff 1996]. Vinblastine and vincristine are ﬁrst-generation vinca alkaloids [Kingston, 2009]. At low concentrations, vincas bind to the plus ends of microtubules producing a conformational change of dimers from a straight ‘‘growing’’ vector to a curved ‘‘peeling’’ vector [Toso et al., 1993]. At higher concentrations, the vinca alkaloids have afﬁnity for free tubulin heterodimers, again potentially forming an altered, curved geometry of the dimeric biological vector [Warfield and Bouck, 1974]. Although vincas do not share structural similarity with colchicine and bind to a different site on tubulin, they similarly act by destabilizing microtubules [Stanton et al., 2011].
Vinca domain binders include:
1. Vinblastine (dimethyl (2β,3β,4β,5α,12β,19α)-15-[(5S,9S)-5-ethyl-5-hydroxy-9-(methoxycarbonyl)-1,4,5,6,7,8,9,10-octahydro-2H-3,7-methanoazacycloundecino[5,4b]indol-9-yl]-3-hydroxy-16-methoxy-1-methyl-6,7-didehydroaspidospermidine-3,4-dicarboxylate, VBL) is an anticancer drug that is used extensively. The crystal structure of vinblastine bound to tubulin has been determined [Gigant et al., 2005]. In contrast with the binding site for colchicine, which is mostly embedded in β-tubulin subunit, the vinblastine binding site is shared equally between α/β-heterodimer [Marchetti et al., 2016]. In the β-subunit, vinblastine interacts through van der Waals contacts with residues Serβ174-Aspβ179, Asnβ206-Aspβ211, Pheβ214 and Tyrβ224; while in the α-subunit, Pheα351, Lysα352, Valα353 and Ileα355 delimit the pocket occupied by VBL. Amino acids Proβ222 and Asnα329 are also involved in hydrogen bond interactions with VBL [Marchetti et al., 2016]. Following a mechanism similar to colchicine, VBL binds to tubulin in two consecutive steps: formation of a rapid equilibrium complex followed by a slower rearrangement linked to changes in the structure of the heterodimer. A major effect of VBL is the formation of spiral-like tubulin aggregates [Weisenberg and Timasheff, 1970; Himes, 1991]. VBL binds to microtubule ends [Wilson et al., 1982] and at low concentrations suppresses the dynamic instability of plus ends [Toso et al., 1993]. When used at much higher concentrations, VBL depolymerizes microtubules, giving rise in particular to protofilament spirals and curls.
2. Vincristine (methyl (3aR,3a1R,4R,5S,5aR,10bR)-4-acetoxy-3a-ethyl-9-((5S,7S,9S)-5-ethyl-5-hydroxy-9-(methoxycarbonyl)1,4,5,6,7,8,9,10-octahydro-2H-3,7-methanoazacycloundecino[5,4-b]indol-9-yl)-6-formyl-5-hydroxy-8-methoxy-3a,3a1,4,5,5a,6,11,12-octahydro-1H-indolizino[8,1-cd]carbasole-5-carboxylate, VCR) is an anticancer drug that binds to tubulin in the vinca binding domain [Kingston, 2009].
3. Vinflunine (methyl (3aR,3a1R,4R,5S,5aR,10bR)-4-acetoxy-9-((4R,6R,8S)-4-(1,1-difluoroethyl)-8-(methoxycarbonyl)-1,3,4,5,6,7,8,9-octahydro-2,6-methanoazecino[4,3-b]indol-8-yl)-3a-ethyl-5-hydroxy-8-methoxy-6-methyl-3a,3a1,4,5,5a,6,11,12-octahydro-1H-indolizino[8,1-cd]carbazole-5-carboxylate) is a florinated Vinca alkaloid, like vinblastine and vincristine, and appears to interact at the Vinca binding domain [Kruczynski et al., 1998].
4. Vintafolide ((2R,5S,8S,11S,14S,19S)-19-(4-(((2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl)amino)benzamido)-5,8,14-tris(carboxymethyl)-2-(((2-((2-((3aR,3a1R,4R,5S,5aR,10bR)-3a-ethyl-9-((5S,7R,9S)-5-ethyl-5-hydroxy-9-(methoxycarbonyl)-1,4,5,6,7,8,9,10-octahydro-2H-3,7-methanoazacycloundecino[5,4-b]indol-9-yl)-4,5-dihydroxy-8-methoxy-6-methyl-3a,3a1,4,5,5a,6,11,12-octahydro-1H-indolizino[8,1-cd]carbazole-5-carbonyl)hydrazine-1-carbonyl)oxy)ethyl)disulfanyl)methyl)-11-(3-guanidinopropyl)-4,7,10,13,16-pentaoxo-3,6,9,12,15-pentaazaicosanedioic acid) is a drug conjugate consisting of a small molecule targeting the folate receptor and vinblastine. Vintafolide is designed to deliver vinblastine selectively to cells over-expressing the folate receptor such as ovarian cancer cells [Vergote and Leamon, 2015].
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