Pedro Martínez defends his Bachelor’s Degree Final Project

Exploring 14S-HpDHA binding modes and its negative allosteric modulation in hALOX12-catalyzed MaR1 biosynthesis

Pedro Martínez Zaragoza

The inflammatory response is present in many diseases as the body’s defense against injuries and infections. Generally, it consists of two phases. In the first phase, the biosynthesis of substances such as leukotrienes and prostaglandins takes place. Subsequently, the resolution phase of inflammation occurs, characterized by the biosynthesis of specialized pro-resolving mediators (SPMs) such as resolvins, lipoxins, and maresins. In many cases, this second stage is not effective, and inflammation can become chronic. Therefore, it is necessary to enhance the biosynthesis of SPMs.

Lipoxygenases are a wide family of enzymes that actively participate in both phases of inflammatory processes. They catalyze the hydroperoxidation of polyunsaturated fatty acids in a highly regio- and stereoselective manner. Recently, the biosynthesis of a potent SPM involving human platelet 12-lipoxygenase, called maresin 1, has gained great interest. It begins with the hydroperoxidation of docosahexaenoic acid, followed by an epoxidation and an enzymatic hydrolysis. Experimental studies have shown that the epoxidation step competes with a second allosterically regulated hydroperoxidation.

In this research, we explored this competitive pathway using computational methods such as molecular docking and molecular dynamics (MD) based on two different conformations of the protein: open and closed structures. The starting point was to investigate the differences between these two structures and how they affect the ligand binding mode. Ligand orientation is a key factor, as it is postulated that the competitive pathway must occur when the ligand enters the catalytic cavity with the carboxylate end. As a result, four complexes were generated from the docking calculations.

The evolution of these systems was studied through molecular dynamics simulations. In the trajectory analysis, special emphasis was placed on parameters directly related to reactivity, such as ligand orientation relative to the enzyme cofactor and the distance between them. These results, together with the analysis of oxygen access tunnels, indicate that the competitive pathway is favored in the open structure with the ligand’s carboxylate group oriented head-first.