Discrimination of ligands with different flexibilities resulting from the plasticity of the binding site in tubulin.
Tubulin, an α,β heterodimer, has four distinct ligand binding sites (for paclitaxel, peloruside/laulimalide, vinca, and colchicine). The site where colchicine binds is a promising drug target for arresting cell division and has been observed to accommodate compounds that are structurally diverse but possess comparable affinity. This investigation, using two such structurally different ligands as probes (one being colchicine itself and another, TN16), aims to provide insight into the origin of this diverse acceptability to provide a better perspective for the design of novel therapeutic molecules. Thermodynamic measurements reveal interesting interplay between entropy and enthalpy. Although both these parameters are  favourable for TN16 binding (ΔH < 0, ΔS > 0), but the magnitude of entropy has the determining role for colchicine binding as its enthalpic component is destabilizing (ΔH > 0, ΔS > 0). Molecular dynamics simulation provides atomistic insight into the mechanism, pointing to the inherent flexibility of the binding pocket that can drastically change its shape depending on the ligand that it accepts. Simulation shows that in the complexed states both the ligands have freedom to move within the binding pocket; colchicine can switch its interactions like a "flying trapeze", whereas TN16 rocks like a "swing cradle", both benefiting entropically, although in two different ways. Additionally, the experimental results with respect to the role of solvation entropy correlate well with the computed difference in the hydration: water molecules associated with the ligands are released upon complexation. The complementary role of van der Waals packing versus flexibility controls the entropy-enthalpy modulations. This analysis provides lessons for the design of new ligands that should balance between the "better fit" and "flexibility"', instead of focusing only on the receptor-ligand interactions.
Department of Biochemistry, Bose Institute, Kolkata 700054, India.
Soumyananda
S
Chakraborti
Devlina
D
Chakravarty
Suvroma
S
Gupta
Biswa Prasun
BP
Chatterji
Gopa
G
Dhar
Asim
A
Poddar
Dulal
D
Panda
Pinak
P
Chakrabarti
Shubhra
S
Ghosh Dastidar
Bhabatarak
B
Bhattacharyya
D000818:Animals; D001665:Binding Sites; D003078:Colchicine / Q000737:chemistry / Q000378:metabolism; D006041:Goats; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D013379:Substrate Specificity; D013816:Thermodynamics; D014404:Tubulin / Q000737:chemistry* / Q000378:metabolism*; D050257:Tubulin Modulators / Q000378:metabolism
D008024:Ligands; D014404:Tubulin; D050257:Tubulin Modulators; D003078:Colchicine