Abstract
Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes αβII, αβIII and αβIV show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. Here, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human αβII, αβIII and αβIV isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. The sequence analysis study shows that the residue compositions are different in the colchicine binding pocket of αβII and αβIII, whereas no such difference is present in αβIV tubulin isotypes. Further, the molecular docking and molecular dynamics simulations results show that residue differences present at the colchicine binding pocket weaken the bonding interactions and the correct binding of DAMA-colchicine at the interface of αβII and αβIII tubulin isotypes. Post molecular dynamics simulation analysis suggests that these residue variations affect the structure and dynamics of αβII and αβIII tubulin isotypes, which in turn affect the binding of DAMA-colchicine. Further, the binding free-energy calculation shows that αβIV tubulin isotype has the highest binding free-energy and αβIII has the lowest binding free-energy for DAMA-colchicine. The order of binding free-energy for DAMA-colchicine is αβIV ≃ αβII >> αβIII. Thus, our computational approaches provide an insight into the effect of residue variations on differential binding of αβII, αβIII and αβIV tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes.
Highlights
Microtubules (MTs) play crucial roles in various important cellular functions such as cell division, cell motility, transport of vesicles, cell signaling, cell shaping and sensory transduction [1]
We performed homology modeling of these tubulin isotypes, followed by docking of DAMA-colchicine, molecular dynamics simulations and binding energy calculations, to understand the effect of change of residue composition observed in different isotypes on the binding of DAMA-colchicine
We investigated the differential binding affinity of human tubulin isotypes αβII, αβIII and αβIV towards DAMA-colchicine using molecular docking, molecular dynamics simulation and binding free energy calculations
Summary
Microtubules (MTs) play crucial roles in various important cellular functions such as cell division, cell motility, transport of vesicles, cell signaling, cell shaping and sensory transduction [1]. They are polymers of a heterodimeric protein, tubulin (Fig 1A). ΒI tubulin isotype is the most abundant type and is constitutively expressed, whereas βIII expression is restricted to neuronal tissues and testis. Cancerous cells deregulate tissue-specific expression of different isotypes; the overexpression of βIII has been associated with aggressive drug resistant cancer cells [12,13,14]. Mutations in tubulin have been associated with certain diseases e.g. Polymicrogyria (PMG), Malformation of Cortical Development (MCD) and Congenital Fibrosis of Extraocular Muscle type 3 (CFEOM3) [15,16,17]
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