Modeling the Antileukemia Activity of Ellipticine-Related Compounds: QSAR and Molecular Docking Study

Abstract

The antileukemia cancer activity of organic compounds analogous to ellipticine representes a critical endpoint in the understanding of this dramatic disease. A molecular modeling simulation on a dataset of 23 compounds, all of which comply with Lipinski's rules and have a structure analogous to ellipticine, was performed using the quantitative structure activity relationship (QSAR) technique, followed by a detailed docking study on three different proteins significantly involved in this disease (PDB IDs: SYK, PI3K and BTK). As a result, a model with only four descriptors (HOMO, softness, AC1RABAMBID, and TS1KFABMID) was found to be robust enough for prediction of the antileukemia activity of the compounds studied in this work, with an R² of 0.899 and Q² of 0.730. A favorable interaction between the compounds and their target proteins was found in all cases; in particular, compounds 9 and 22 showed high activity and binding free energy values of around -10 kcal/mol. Theses compounds were evaluated in detail based on their molecular structure, and some modifications are suggested herein to enhance their biological activity. In particular, compounds 22_1, 22_2, 9_1, and 9_2 are indicated as possible new, potent ellipticine derivatives to be synthesized and biologically tested.

Keywords: QSAR; cancer; leukemia; molecular descriptors; molecular modeling.

Figure 1

Chemical structures of ellipticine-analogous compounds studied in this work.

Figure 2

Experimental pIC₅₀ vs. pIC₅₀ predicted using Equation (3).

Figure 3

On the left, the 3D representation is shown, and on the right, the 2D interactions of compound 9 (a), fostamitinib (b), and compound 22 (c) at the active site of spleen tyrosine kinase (SYK).

Figure 3

On the left, the 3D representation is shown, and on the right, the 2D interactions of compound 9 (a), fostamitinib (b), and compound 22 (c) at the active site of spleen tyrosine kinase (SYK).

Figure 4

On the left, the 3D representation is shown, and on the right the 2D interactions of compounds 9 and 22 at the active site of PI3K.

Figure 5

Structures, pIC₅₀, and scoring values against SYK protein for new proposed compounds based on QSAR results.

Figure 6

On the left, the 3D representation is shown, and on the right, the 2D interactions of the proposed compound at the spleen tyrosine kinase (SYK) active site.

Figure 7

Possible synthetic schema for proposed anticancer compounds. (1) Compounds 9_1 and 9_2. (2) Compounds 22_1 and 22_2.