The in silico investigation of the perplexity of synergistic duality: inter-molecular mechanisms of communication in Bcr–Abl.

Abstract

Due to their important role in normal cellular physiology, protein kinase activity is tightly regulated and their aberrant activation can lead to cancer. Chronic myeloid leukaemia (CML) is a blood cancer described by unregulated growth of myeloid cells caused by a fusion protein, Bcr-Abl, a constitutively active form of the Abelson tyrosine kinase (Abl). Drug targeting of either the ATP binding pocket or allosteric pocket has led to durable therapeutic response, however the development of drug resistance still poses a major clinical challenge. Recent studies exploring synergistic inhibition as an effective approach, by dual targeting of Bcr-Abl using both catalytic and allosteric binding inhibitors. This thesis implements the use of advanced computational tools to unravel molecular insights to aid in the suppression of the emergence of resistance to Bcr-Abl when Nilotinib and ABL001 are co-administered to target both the catalytic and allosteric binding site of Bcr-Abl protein, respectively. Our studies revealed co-binding induced a stable Bcr-Abl protein structure, increased the degree of compactness of binding site residues around Nilotinib and subsequently improved the binding affinity of Nilotinib. Findings in this thesis further provide an atomistic perspective underlying the developed resistance of Nilotinib by point mutation at the catalytic active site only and both catalytic and activation loop sites. We also recognized and rationalized the structural interplay of this single and double mutation upon co-binding of Nilotinib with the novel inhibitor, ABL001. Our findings report the distortion of the overall conformational landscape of Bcr-Abl fusion oncoprotein caused by the mutation, resulting in a reduction of binding affinity of Nilotinib upon single binding. Interesting, co-administration with ABL001 impacted by the mutation results in a more compact and stable protein conformation. Findings reveal a structural mechanism by which the novel inhibitor ABL001 stabilizes Bcr-Abl fusion oncoprotein upon co-binding with Nilotinib, thus suppressing Nilotinib resistance. We also provide vital conformational dynamics and structural mechanisms of the mutant enzyme at the catalytic site-ligand interaction and mutant enzyme at both catalytic and activation loop ligand interactions which could potentially shift the current therapeutic protocol in chronic myeloid leukemia treatment, thus aiding in the design of novel inhibitors with improved therapeutic features against the mutant proteins.