Binding conformations and QSAR of CA-4 analogs as tubulin inhibitors

Molecular modeling study, synthesis and biological evaluation of combretastatin A-4 analogues as anticancer agents and tubulin inhibitors

As the major structural component of microtubules, tubulin is an interesting target for the development of anticancer agents. In this study, 64 tubulin polymerization inhibitors of five-membered heterocycle-based combretastatin A-4 analogues were studied by a combination of molecular modeling techniques including 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation. The CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) models were established with desirable statistical parameters and excellent predictive ability. 20 ns MD simulations were successfully performed to confirm the detailed binding mode and validate the rationality of docking results. Combining the binding free energy calculations and 3D-QSAR results, some new heterocycle-based combretastatin A-4 analogues were designed. Three of them were synthesized and biologically evaluated. Compound 13a displayed potent antiproliferative activity (IC₅₀ value of 1.31 μM against HepG2 cells, IC₅₀ value of 1.37 μM against A549 cells) and inhibition of tubulin polymerization activity (IC₅₀ value of 0.86 μM). Compound 13b also presented good activity against HepG2 cells (IC₅₀ value of 4.75 μM). The experimental results demonstrated that the built models were effective for the development of novel anticancer agents and tubulin inhibitors.

Identification of potential tubulin polymerization inhibitors by 3D-QSAR, molecular docking and molecular dynamics

View of the correlation between experimental and predicted pIC₅₀c values, and the compound 22c docked into the binding site of 3UT5.

Docking and molecular dynamics studies of the binding between Peloruside A and tubulin

The molecular docking, MD simulation and binding free energy calculation were performed to explore the probable binding modes between PLA and tubulin. Through docking study, three possible binding sites for PLA were speculated as follows: the taxane site, the alternative site and a new site in α-tubulin. Then, 12.0 ns MD simulations show that these binding modes predicted by docking have been changed more or less, whereas the MD simulations offer more reliable binding details. The MM-PBSA binding free-energy calculations reasonably identify that the taxane site is the most favorable binding site of PLA and the alternative site is the secondary one, which can be used to explain some experimental facts. These studies theoretically resolve the priority of binding sites for PLA and offer the reliable binding modes between PLA and tubulin, and thus help to understanding the action mechanism for this kind of inhibitor.

3D-QSAR Study of Combretastatin A-4 Analogs Based on Molecular Docking

Combretastatin A-4 (CA-4), its analogues and their excellent antitumoral and antivascular activities, have attracted considerable interest of medicinal chemists. In this article, a docking simulation was used to identify molecules having the same binding mode as the lead compound, and 3D-QSAR models had been built by using CoMFA based on docking. As a result, these studies indicated that the QSAR models were statistically significant with high predictabilities (CoMFA model, q² = 0.786, r² = 0.988). Our models may offer help to better comprehend the structure-activity relationships for this class of compounds and also facilitate the design of novel inhibitors with good chemical diversity.