Investigating the Impact of Covalent and Non-covalent Binding Modes of
Inhibitors on Bruton’s Tyrosine Kinase in the Treatment of B Cell
Malignancies - Computational Insights

Abdul   Rashid   Issahaku; Mahmoud   E.S.   Soliman

doi:10.2174/1389201023666220617151552

Abstract

Background: Bruton tyrosine kinase plays a key role in the survival, proliferation, activation, and differentiation of B-lineage cells and the signaling of other receptors. It is overexpressed and constitutively active in the pathogenesis of B cell malignancies and has therefore become a target for therapeutic intervention. Some success has been achieved in the discovery of small molecules, especially in the development of irreversible inhibitors. However, these inhibitors are punctuated by off target effects and have also become less effective in patients with mutations at Cys481. This motivated the search for inhibitors with improved efficacy and different binding modes.

Methods: In this study, we employed two new second generation inhibitors with different binding modes, Zanubrutinib and AS-1763, which are at various levels of clinical trials, to highlight the molecular determinants in the therapeutic inhibition of BTK through computational studies.

Results: This study revealed that Zanubrutinib and AS-1763 exhibited free total binding energies of -98.76 ± 4.63 kcal/mol and -51.81 ± 9.94 kcal/mol, respectively, with Zanubrutinib engaging in peculiar hydrogen bond interactions with the hinge residues Glu475 and Met477 including Asn484 and Tyr485 while AS-1763 engaged Lys430, Asp539, and Arg525. These residues contributed the most towards the free total binding energy with energies above -1.0 kcal/mol. The compounds further interacted differentially with other binding site residues through pi-alkyl, pi-cation, pianion, pi-pi-T-shaped, pi-sigma, pi-sulfur and pi-donor hydrogen bonds, and Van der Waals interactions. These interactions resulted in differential fluctuations of the residues with the consequential unfolding of the protein.

Conclusion: Insights herein would be useful in guiding the discovery of more selective and potent small molecules.

Keywords: Bruton’s Tyrosine Kinase, Zanubrutinib, AS-1763, B cell malignancies, Molecular Dynamics Simulation, covalent inhibitor

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Investigating the Impact of Covalent and Non-covalent Binding Modes of Inhibitors on Bruton’s Tyrosine Kinase in the Treatment of B Cell Malignancies - Computational Insights

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