Planejamento de inibidores da enzima 3-deoxy-D manooctulosonato 8-fosfato Sintase (KDO8PS): um novo alvo para tratamento de infecção bacteriana

Abstract

Bacteria can be distinguished in two groups through the Gram technique, where Gram positive and Gram-negative bacteria can be differentiated, the main differences between these organisms being the structure of the cell wall, its components and its functions. More evidence has emerged of bacteria resistant to antibiotics, the case of Gram-negative bacteria is more worrisome due to the emergence of strains resistant to various antibiotics. Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria responsible for toxic manifestations such as inflammation. 3-Deoxy-D-manno-octulosonate (KDO) is a site component of the inner core of LPS essential for its formation. The reaction for KDO production requires two substrates, phosphoenolpyruvate (PEP) and D-arabinose 5-phosphate (A5P), catalyzed by 8-phosphate synthase 3-Deoxy-D-mannoocobluconate (KDO8PS). This reaction is important because it plays a crucial role in the assembly of LPS. This enzyme is in two distinct forms as the dependence of the presence or absence of divalent metal ion in the active site. There are several inhibitors of KDO8P synthase, two were selected based on their inhibition constants (Ki), with BPH1, the most active among them with a value of 0.37 μM in KDO8P metal synthase independent in E. coli and BPH2 with value of 7.9 ± 1.6 μM for metal-independent KDO8P synthase in N. meningitidis, these K i values are approximately 2 to 3 times higher than the Km values for PEP that were also used in this work, in addition to a third hypothetical inhibitor that combines the main characteristics of the inhibitors already described in the literature. Molecular Dynamics, Molecular Dynamics and Free Energy of bonding with the methods MMGBA, MMPBSA, SIE and Energy decomposition by residue to analyze the coupling mode of these ligands and the PEP substrate were used. With the results obtained, we analyzed the main interactions of these ligands and the molecular behavior of both the ligands and the protein. Therefore, more favorable binding-free energy values were obtained for the complexes formed with the BPH1 linker with the three methods -96.07 Kcal / mol with MMGBSA, -107.09 Kcal / mol with MMPBSA and -13.53 with SIE and observed these complexes perform a greater number of effective interactions. Thus, it is suggested that the BPH1 linker has an excellent potential for inhibiting the catalytic activity of the enzyme KDO8P synthase responsible for the production of KDO, essential component of LPS for the formation of the outer membrane of Gram-negative bacteria.