In-silico development of a method for the selection of optimal enzymes using L-asparaginase II against Acute Lymphoblastic Leukemia as an example

ABSTRACT

L-Asparaginase II (asnB), a periplasmic protein, commercially extracted from E. coli and Erwinia, is often used to treat Acute Lymphoblastic Leukemia. L-Asparaginase is an enzyme that converts L-asparagine to aspartic acid and ammonia. Cancer cells are dependent on asparagine from other sources for growth and when these cells are deprived of asparagine by the action of the enzyme the cancer cells selectively die. Questions remain as to whether asnB from E. coli and Erwinia is the best asparaginase as they have many side-effects. asnB with the lowest Michaelis constant (Km) (most potent), and with the lowest immunogenicity is considered the most optimal enzyme. In this paper asnB sequence of E. coli was used to search for homologous proteins in different bacterial and archaeal phyla and a maximum likelihood phylogenetic tree was constructed. The sequences that are most distant from E. coli and Erwinia were considered best candidates in terms of immunogenicity and were chosen for further processing. The structures of these proteins were built by homology modeling and asparagine was docked with these proteins to calculate the binding energy. asnBs from Streptomyces griseus, Streptomyces venezuelae and Streptomyces collinus were found to have the highest binding energy i.e. −5.3 kcal/mol, −5.2 kcal/mol, and −5.3 kcal/mol respectively (Higher than the E.coli and Erwinia asnBs) and were predicted to have the lowest Kms as we found that there is an inverse relationship between binding energy and Km. Besides predicting the most optimal asparaginase, this technique can also be used to predict the most optimal enzymes where the substrate is known and the structure of one of the homologs is solved.