Reconstruction of Ancient Enzyme Sequences to Understand Cancer: Evolvability and Drug Resistance of Abl1 Tyrosine kinase

Abstract

Kinase enzymes transfer phosphoryl groups to amino acids tyrosine, serine, and threonine situated on other proteins utilizing the ATP cofactor. Kinases are in some sense the true moderators that keep cells alive controlling important cellular process like cell division, metabolism, signaling, cell differentiation, etc. When a specific tyrosine kinase, Abl1 (Abelson kinase), escapes control and becomes highly active, a harmful condition emerges known as blood cancer. Abl1 inhibition is thus a promising avenue to treat blood cancers. However, drug resistance poses a great challenge during cancer treatment, and the main cause of this resistance is due to mutations in the Abl1 kinase domain. This selective pressure driving the resistance is not clearly apparent. Here we propose a way to achieve better understanding of the drug emergence investigated by the molecular evolution theory. Ancestral reconstruction of Abl1 will be predicted by phylogenetic reconstruction and their older-in-time sequences will be validated by rounds of optimization using Rosetta software suite. Especially structural features will come into focus in evaluation of the final models' sequence fitness. With today's modern biotechnological tools for expression and purification, ancient enzymes will be resurrected in vitro and their activity will be assayed by measuring kinetic parameters. This will provide valuable knowledge of the sequence space available for kinases and specifically for the aberrant and constantly active Abl1 involved in blood cancer. Predicting possible resistance mutations ahead of their emergence is an invaluable tool in our future fights against cancer. (AU)