Design, In Silico Evaluation, and Determination of Antitumor Activity of Potential Inhibitors Against Protein Kinases: Application to Bcr-Abl Tyrosine Kinase

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Abstract

Despite significant progress made over the past two decades in the treatment of chronic myeloid leukemia (CML), there is currently still an unmet need for effective and safe drugs to treat patients with resistance and intolerance to clinically used drugs. In this work, 2-arylaminopyrimidine amides of isoxazole-3-carboxylic acid were designed followed by in silico assessment of the inhibitory potential of these compounds against Bcr-Abl tyrosine kinase and determination of their antitumor activity on cell models of the K562 (chronic myeloid leukemia), HL-60 (acute promyelocytic leukemia), and HeLa (cervical cancer) lines. As a result of the joint analysis of computational and experimental data, three compounds exhibiting antitumor activity against cells of the K562 and HL-60 lines were identified. A lead compound demonstrating effective inhibition of the growth of these cells was found, as evidenced by the low values of IC50 equal to 2.8 ± 0.8 μM (K562) and 3.5 ± 0.2 μM (HL-60). The results obtained indicate that the identified compounds form good scaffolds for the design of novel, effective and safe anticancer drugs able to inhibit the catalytic activity of Bcr-Abl kinase by blocking the ATP-binding site of the enzyme.

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About the authors

E. V. Koroleva

Institute of Chemistry of New Materials of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

A. L. Ermolinskaya

Institute of Chemistry of New Materials of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

Zh. V. Ignatovich

Institute of Chemistry of New Materials of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

Yu. V. Kornoushenko

Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

O. V. Panibrat

Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

V. I. Potkin

Institute of Physical-Organic Chemistry of the National Academy of Sciences of Belarus

Email: alexande.andriano@yandex.ru
Belarus, Minsk

A. M. Andrianov

Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus

Author for correspondence.
Email: alexande.andriano@yandex.ru
Belarus, Minsk

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Supplementary files

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2. Fig. 1. Chemical structures of the designed compounds

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3. Fig. 2. Time dependences of RMSD values (Å) calculated between the dynamic and starting structures of complexes of compounds I-V with tyrosine kinase Bcr-Abl (blue line) and Bcr-AblT315I (blue line). In the upper right corner, the mean RMSD values and standard deviations for the native enzyme and in the lower right corner for its mutant form are indicated. The corresponding data for the control compounds and the enzyme in the free state are also given

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4. Fig. 3. RMSD heat maps obtained for complexes of tyrosine kinase Bcr-Abl (a) and its mutant form T315I (b) with compounds I-V, control inhibitors and the enzyme in the free state at different times of CBM modelling. RMSD values were calculated for tyrosine kinase main chain atoms. Time is measured on the abscissa and ordinate axes. The RMSD value between the structures of the complexes at times t1 and t2 is at the intersection of the values of t1 on the abscissa axis and t2 on the ordinate axis

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5. Fig. 4. Time dependences of binding free energy for complexes of compounds I-V with tyrosine kinase Bcr-Abl (blue line) and Bcr-AblT315I (blue line). The orange and yellow lines show a simple moving average with a window size of 20 ns. The mean binding free energy and their corresponding standard deviations calculated for native and mutant Bcr-Abl tyrosine kinase, respectively, are shown above and below. The corresponding data for the control compounds are also given

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6. Fig. 5. Dependences of cell viability (% of control) on the concentration of tested compounds (log concentration [mol/litre]). III* - Salt form of compound III in the form of methanesulfonate

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7. Fig. 6. Complexes of compounds I-III with native and mutant tyrosine kinase Bcr-Abl constructed by molecular docking. The compounds are represented by the ball-and-stick-ball model. Residues of the enzyme that form interatomic contacts with ligands are marked. Residues involved in hydrogen bonding are labelled with the stick model. Hydrogen bonds are shown as red dashed lines. The wire model is used to denote the residues of tyrosine kinase Bcr-Abl forming van der Waals contacts

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