Aplicação de métodos de dinâmica molecular e QM/MM no estudo reacional da enzima lisina metiltransferase G9a

Abstract

Epigenetics is the area of knowledge responsible for examining the behavior of genes and how they react to numerous factors that are present throughout the individual's life. One way to perform this kind of study is through the molecular dynamics (MD) method, which is widely used in systems with biological characteristics, allowing computationally replicated systems to resemble the real biological situation. In this work we investigated the reaction mechanisms and activity of the enzyme lysine methyltransferase (MT) G9a by means of molecular dynamics simulations. The mutations that histone 3 lysine 9 (H3K9) can suffer due to epigenetic mechanisms were analyzed, and the free energy values for each one of these mutations were calculated. The average distance of H3K9 and its mutations in complex with the MT G9a and the reaction behavior of the mutant systems were also verified. For the development of the work, structures obtained from the Protein Data Bank were used to utilize the structures used throughout the research where these structures/systems were treated with the CHARMM32 force field and simulated in AMBER software. Five systems were constructed: H3K9 native and mutants: H3K9M, H3K9A, H3K9I and H3K9Nle. Different analyses were performed in order to verify which of these mutants would stand out when in complex with the G9a enzyme and consequently the inhibition of the methyltransferase process related to the neoplasm process. The first 150ns molecular dynamics results show that the H3K9M and H3K9I mutants showed more stable complexes, free energy calculations using MM/PBSA and MM/GBSA again pointed out the H3K9M and H3K9I mutations as the most energetically favorable. These results are in agreement with experimental observations available in the literature. Thus lysine 9 with the methionine and isoleucine mutation can act as efficient inhibitors of the G9a enzyme, subsequently leading to problems such as cancer.