The Discovery of Novel BCR-ABL Tyrosine Kinase Inhibitors Using a Pharmacophore Modeling and Virtual Screening Approach.

Ting-Ting Huang,Zhen-Nan Zhao,Zhuo-Xun Wu,Shao-Jia Qiang,Charles R Ashby,Jia-Zhong Li,Xin Wang,Zhe-Sheng Chen

doi:10.3389/fcell.2021.649434

Abstract

Chronic myelogenous leukemia (CML) typically results from a reciprocal translocation between chromosomes 9 and 22 to produce the bcr-abl oncogene that when translated, yields the p210 BCR-ABL protein in more than 90% of all CML patients. This protein has constitutive tyrosine kinase activity that activates numerous downstream pathways that ultimately produces uncontrolled myeloid proliferation. Although the use of the BCR-ABL tyrosine kinase inhibitors (TKIs), such as imatinib, nilotinib, dasatinib, bosutinib, and ponatinib have increased the overall survival of CML patients, their use is limited by drug resistance and severe adverse effects. Therefore, there is the need to develop novel compounds that can overcome these problems that limit the use of these drugs. Therefore, in this study, we sought to find novel compounds using Hypogen and Hiphip pharmacophore models based on the structures of clinically approved BCR-ABL TKIs. We also used optimal pharmacophore models such as three-dimensional queries to screen the ZINC database to search for potential BCR-ABL inhibitors. The hit compounds were further screened using Lipinski’s rule of five, ADMET and molecular docking, and the efficacy of the hit compounds was evaluated. Our in vitro results indicated that compound ZINC21710815 significantly inhibited the proliferation of K562, BaF3/WT, and BaF3/T315I leukemia cells by inducing cell cycle arrest. The compound ZINC21710815 decreased the expression of p-BCR-ABL, STAT5, and Crkl and produced apoptosis and autophagy. Our results suggest that ZINC21710815 may be a potential BCR-ABL inhibitor that should undergo in vivo evaluation.

Highlights

Chronic myelogenous leukemia (CML) is a hematopoietic neoplastic disease that primarily results from the reciprocal translocation between chromosomes 9 and 22 (t9;22) (q34; q11) in a hematopoietic stem cell (HSC), resulting in the formation of the bcr-abl oncogene (Deininger et al, 2005; Ren, 2005; Kimura, 2006)
The chemicals used to construct the Hypogen pharmacophore models are shown in Supplementary Figure 1
The selectivity indexes (SI) were 1, 168.71, 174.97, and 101.80, respectively, for the CCC-DEL-1, K562, BaF3/WT, and BaF3/T315I cells. These results suggest that ZINC21710815 was not cytotoxic in normal CCC-HEL-1 cells and it significantly inhibited the proliferation of wild-type BCR-ABL and T315I mutated BCR-ABL leukemia cells

Summary

Introduction

Chronic myelogenous leukemia (CML) is a hematopoietic neoplastic disease that primarily results from the reciprocal translocation between chromosomes 9 and 22 (t9;22) (q34; q11) in a hematopoietic stem cell (HSC), resulting in the formation of the bcr-abl oncogene (Deininger et al, 2005; Ren, 2005; Kimura, 2006). The most common BCR-ABL proteins produced in CML patients, based on the loci of the chromosomal breaks, are p210, p190, and p230 (Winter et al, 1999; Discover Novel BCR-ABL TKIs. Arana-Trejo et al, 2002). The p210 protein is a constitutively active, non-receptor tyrosine kinase that phosphorylates its Tyr177 residue, which subsequently activates a number of downstream signaling pathways that causes HSC cells undergo significant abnormal proliferation and differentiation compared to normal cells, producing the pathogenic changes reported in CML patients (Deininger et al, 2000; Gora-Tybor and Robak, 2008; Cao et al, 2015; Wang et al, 2016). Imatinib (Gleevec), which selectively targets the ATP binding site of the BCR-ABL protein, is a first generation BCR-ABL tyrosine kinase inhibitor (TKI) that was approved in 2001 by the FDA for treating CML (Gontarewicz et al, 2008; Wu et al, 2014). Subsequent clinical trials indicated that patients with advancedstage CML experience relapse due to development of resistance caused by point mutations within the BCR-ABL domain (notably T315I), amplification of the BCR-ABL protein, overexpression of BCR-ABL protein or the ABC transporter, P-glycoprotein (Coutre et al, 2000; von Bubnoff et al, 2002; Apperley, 2007; Tanaka and Kimura, 2008)

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Results

Conclusion