Predicting Binding Affinity of Some Imatinib Derivatives as BCR-ABL Tyrosine Kinase Inhibitors Based on Monte Carlo Optimization

Lotfi , Shahram; Ahmadi , Shahin; Vardast Baghmisheh , Sharare; Almasirad , Ali

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Volume 32, Issue 4 (9-2024)

Journal of Ilam University of Medical Sciences 2024, 32(4): 66-86

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Predicting Binding Affinity of Some Imatinib Derivatives as BCR-ABL Tyrosine Kinase Inhibitors Based on Monte Carlo Optimization

Shahram Lotfi¹

, Shahin Ahmadi ^*

², Sharare Vardast Baghmisheh³

, Ali Almasirad⁴

1- Dept of Chemistry, Payame Noor University (PNU), Tehran, Iran
2- Dept of Pure and Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran medical sciences, Islamic Azad University, Tehran, Iran , ahmadi.chemometrics@gmail.com
3- Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
4- Dept of Pure and Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Tehran medical sciences, Islamic Azad University, Tehran, Iran

Abstract: (156 Views)

Introduction: The Imatinib drug is used to treat blood cancer by inhibiting the BCR-ABL tyrosine kinase enzyme, which prevents the proliferation of cancer cells.
Materials & Methods: In order to predict the binding affinity of 555 compounds of imatinib derivatives as ABL-BCR tyrosine kinase inhibitors, quantitative structure-activity relationship (QSAR) modeling was performed using the Monte Carlo method. The data were randomly divided into four series, including training, invisible training, calibration, and validation sets, as well as they were randomly repeated three times.
Results: The results of three random divisions indicated reliable models for predicting the set of external tests with correlation coefficient (R2) and cross-validation correlation coefficient (Q2) in the range of 0.8575-0.8775 and 0.7620-0.7793. Consequently, the obtained models help identify hybrid descriptors for increasing or decreasing binding affinity (Ki) as BCR-ABL tyrosine kinase inhibitors. The mechanical interpretation of the model is given in the form of a report of descriptors that decrease and increase pKi, as well as examples of these descriptors.
Conclusion: The results reveal that the designed models can be considerably effective in estimating the biological effect of imatinib derivatives proposed by researchers and medicinal chemists. Therefore, it is possible to predict its possible biological effects by spending less time and money before conducting in vitro or in vivo experiments.

Keywords: Quantitative structure-activity relationship (QSAR), Chronic myeloid leukemia, Imatinib derivatives, Tyrosine kinase inhibitor, Binding affinity

Full-Text [PDF 2180 kb] (101 Downloads)

Type of Study: Research | Subject: ststistrcs and mathematics
Received: 2023/12/28 | Accepted: 2024/05/19 | Published: 2024/09/22

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Lotfi S, Ahmadi S, Vardast Baghmisheh S, Almasirad A. Predicting Binding Affinity of Some Imatinib Derivatives as BCR-ABL Tyrosine Kinase Inhibitors Based on Monte Carlo Optimization. J. Ilam Uni. Med. Sci. 2024; 32 (4) :66-86
URL: http://sjimu.medilam.ac.ir/article-1-8190-en.html

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