Tubulin-colchicine complex

The above theory can be extended to deal with other more complex cases. For example, the two ends of a biopolymer need not behave identically, and microtubules, as noted earlier, are helical polymers of asymmetric protomer units. Thus, two sets of on- and off-constants might be necessary. In other cases, such as in the polymerization of tubulin in the presence of tubulin—colchicine complex (Sternlicht and Ringel, 1979 Sternlicht et al., 1980), there may be the need to consider copolymerization possibilities. 

All ligand-based molecular modeling studies focusing on agents able to bind the colchicine site were performed before the determination of the X-ray structure of the tubulin-colchicine complex (see below). Computational tools in this field were mainly used to derive three-dimensional QS ARs (through comparative molecular field analysis (CoMFA) and other original approaches), but CSI also constituted useful... 

Colchicine and compounds that bind in the vicinity of the colchicine-binding domain of tubulin comprise another class of dmgs with potential for treatment of cancer. Colchicine binds to tubulin at a P dimer interface, and acts by being incorporated with low stoichiometry at the ends of the microtubules as a tubulin-colchicine complex (39). Although colchicine has... 

Panda D, Daijo JE, Jordan MA, Wilson L. Kinetic stabilization of microtubule dynamics at steady state in vitro by substoichio-metric concentrations of tubulin-colchicine complex. Biochemistry 1995 34 9921-9929. 

Sternlicht H, Ringel I, Szasz J. 1983. Theory for modeling the copolymerization of tubulin and tubulin-colchicine complex. Biophys J 42 255 - 267. 

Several groups of drugs that bind to tubulin at different sites interfere with its polymerization into microtubules. These drugs are of experimental and clinical importance (Bershadsky and Vasiliev, 1988). For example, colchicine, an alkaloid derived from the meadow saffron plant Colchicum autumnale or Colchicum speciosum), is the oldest and most widely studied of these drugs. It forms a molecular complex with tubulin in the cytosol pool and prevents its polymerization into microtubules. Other substances such as colcemid, podophyllotoxin, and noco-dazole bind to the tubulin molecule at the same site as colchicine and produce a similar effect, albeit with some kinetic differences. Mature ciliary microtubules are resistant to colchicine, whereas those of the mitotic spindle are very sensitive. Colchicine and colcemid block cell division in metaphase and are widely used in cytogenetic studies of cultured cells to enhance the yield of metaphase plate chromosomes. 

Ravelli, R. B., Gigant, B., Curmi, P. A. et al. Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature 428 198-202, 2004. 

Ultraviolet irradiation of the tritiated colchicine-tubulin complex led to direct photolabeling with low but, still, practical efficiency. The bulk of the labeling occurred on the /3 subunit of tubulin. Glycerol increased the /3la distribution. The possibility that the drugs bind at the interface between a and f subunits, and span this interface, and that both subunits may contribute to the binding site was suggested (137). 

Fig. 4 Diagram of the crystal structure of the T2R complex showing the binding sites of MT-destabilizing drugs (PDB entry 1Z2B) [13]. Protein subunits are represented as ribbons. RB3-SLD is colored orange, a-tubulin is purple, and p-tubulin is green. Small-molecule ligands are represented as spheres (vinblastine orange, colchicine red, GTP yellow, and GDP magenta). Colchicine binds to the p-subunit at the intradimer interface. Vinblastine binds at the interdimer interface...

Since the discovery of the therapeutic potential of tubulin targeting drugs, there has been a demand for structural information at the molecular level about the binding pose of the small-molecule ligands, very much needed by the medicinal chemists for the rational design of novel derivatives. Even nowadays, near-atomic resolution structures are available only for a few tubulin binders, namely, the EC-derived structures of the MT-stabilizers PTX [11] and EpoA [26], and the X-ray structures of complexes of tubulin/RB3-SLD with the MT-destabilizers colchicine [12] and vinblastine [13]. 

Interestingly, the initial tubulin coordinates used in the study of HTI-286 are those of straight tubulin in 2D sheets (PDB entry 1JFF) [83], The X-ray structure of the T2R complex with vinblastine showed that the unpolymerized tubulin heterodimer is bent and that there are local conformational changes at the interdimer interface in comparison with straight tubulin [13], The discrepancy between the experimental [12] and computationally predicted [31] binding modes of colchicine has been attributed to the fact that the computational model was derived from... 

Tc)2R complex of tubulin with colchicine and with the stathmin-like domain of... 

As for colchicine [40, 41], numerous compounds have been reported to inhibit the binding of vinblastine to tubulin. But whereas the colchicine site ligands share the property of being relatively simple molecules easily amenable to chemical diversification, those targeting the tubulin vinca site are far more complex [41, 42]. 

Fig. 6 The colchicine and vinblastine sites, a Ribbon representation of RB3-SLD and of the two tubulin a 3 heterodimers. The nucleotides (GTP on a, GDP on P), colchicine (Col, yellow) and vinblastine (Vlb, cyan) are shown as ball-and-stick models. The dashed line shows the location of the RB3-SLD linker between the N-terminal cap and the C-terminal helix, which is the least ordered part of RB3-SLD. The sulfur atom of Cys 12 of the P subunit contacting vinblastine is highlighted as a yellow sphere. b,c Illustration of the interfacial interference of destabilizing molecules with MT assembly schematic representation of the (Tc)2R-vinblastine complex (b) and of a straight protofilament (c). Longitudinal MT-specific contacts (black rectangles in c) cannot be established between vinblastine- or colchicine-bound monomers...

The exact binding site of vinca alkaloids remained unknown until 2005, when the crystal structure of vinblastine bound to tubulin complexed with colchicine and with the stathmin-like domain of RB3 was determined (PDB entry 1Z2B) [3], The structure revealed that vinblastine binds to curved tubulin at the interface between two a/p-tubulin heterodimers (interdimer interface, Fig. 4), introducing a wedge that interferes with tubulin assembly. The vinblastine binding site is defined by loop T7, helix H10 and strand S9 in the a subunit of the first heterodimer, and by helix H6 and loops T5 and H6-H7 in the p subunit of the second heterodimer. In microtubules, this region is located toward the inner lumen and is... 

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