Conformational flexibility and binding energy profile of c-Abl tyrosine kinase complexed with Imatinib: an insight from MD study

Abstract

Structural biology of kinase and in particular of tyrosine kinase has given detailed insights into the intrinsic flexibility of the catalytic domain and has provided a rational basis for obtaining selective inhibitors. In this paper, we have studied the conformational flexibility of c-Abl tyrosine kinase complexed with Imatinib (STI), in the presence of TIP3P water in physiological conditions at neutral pH. The conformational studies suggest that the flexibility of activation loop is responsible to facilitate the nucleotide binding and release. Owing to the conformational adaptability, adenosine triphosphate (ATP) binds at a particular site in the loop region of the tyrosine kinase. The molecular mechanics Poisson–Boltzmann surface area methods are analysed, as is a free-energy pathways method, which shows the stable binding with free energy − 6.04 kcal/mol for STI. The binding energy calculated by the Sietraj method is approximately the same as the experimental binding energy of STI with c-Abl kinase. It is suggested that the conserved glutamic acid and lysine residues are necessary for the stability and optimum activity of inhibitor. This study may be helpful in rational drug designing of new kinase inhibitors.

Keywords:

• MM-PBSA method
• salt bridges
• protein hydration

Acknowledgements

A part of the computational work was supported by the DST, FIST scheme of the department. The other part of the computational work was carried out at C-DAC, PUNE, India, for which their support is gratefully acknowledged. KDD acknowledges CSIR for the award of SRF.

Notes

1. Email: [email protected]

Additional information

Notes on contributors

Kshatresh D. Dubey

1