Presentations

Abstract

Introduction: Tubulin is a protein complex that makes up microtubules, which are essential for critical cellular functions, including mitosis, cell signaling, intracellular trafficking, and angiogenesis. When cancerous cells form, they undergo rapid cell division in which microtubules play an essential role by aiding mitosis and cell signaling. Inserting an inhibitor into a specific tubulin binding site can prevent microtubule polymerization. If the rate of monomer formation can be altered, this could be an effective strategy for anti-cancer research. There are multiple known binding sites for the tubulin protein complex, including the taxane binding site, the vinca binding site and the colchicine binding site. This research focuses specifically on the colchicine binding site. The colchicine binding site is found at the junction between the alpha and beta tubulin subunits, specifically within the beta subunit of tubulin. The colchicine binding site has a distinct advantage over other tubulin binding sites in that it is less susceptible to multidrug resistance. Finding new binding agents is essential to anticancer research as it gives scientists critical information on protein-ligand interactions and the resulting protein-ligand complex's effect on cancer cells.

Methods: The X-ray crystal structure of tubulin complexed with colchicine (PDB 4O2B) (Prota ref I emailed to Erin) was used in molecular modeling studies. Briefly, chain B of the tubulin-colchicine complex (less the solvent and the inhibitor) was used as the receptor model in docking studies. The inhibitors were energy-minimized using the MM2 module, and subsequently converted to .pdb files, using Chem3D Pro 14.0 (CambridgeSoft). Docking studies were performed using AutoDock Vina (Trott, O., Olson, A.J. (2010) AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization and Multithreading. J. Comput. Chem. 31, 455-461.) and analyzed in the PyMOL Molecular Graphics System, Version 2.5.0 (Schrödinger, LLC). As a control, colchicine was also modeled and compared to the known crystal structure.

Results: PY-407-C was chosen for modeling given its demonstrated anti-tubulin activity.4 The most favorable predicted binding of PY-407-C is shown in Figure 2. Like colchicine (Figure 3), PY-407-C binds into the pocket of the beta subunit. Determination of specific binding interactions is still in progress, but previous studies indicated that PY-407-C made many of the same interactions as colchicine. The predicted free energy of binding of PY-407-C is lower than that of the colchicine control, suggesting that it is a more potent inhibitor

Conclusion: Modeling of ligand PY-407-C showed that models 1 and 2 had the lowest predicted free energies of binding. Models 1 and 2 were bound directly in the pocket. The low energy implies that there is a higher chance of the ligand binding to the colchicine site. These results will help to inform the in silico design and subsequent synthesis of more potent analogues. Finding new binding agents is essential to anticancer research because it gives scientists more information on protein ligand interactions. Each ligand and each binding site has unique benefits and risks so by learning as much as possible about these benefits and risks, scientists can evaluate which ligand is safest and most effective. Additionally, the information discovered can be used to influence future research by proving promising theoretical ligand structure.