Biomolecular conformational changes and transient druggable binding sites through full-length AMPK molecular dynamics simulations

Abstract

AMPK (AMP-activated protein kinase) is a crucial signaling protein found in essentially all eukaryotic organisms and acts as an energy sensor. When activated by metabolic stress, AMPK phosphorylates a variety of molecular targets, altering enzyme activity and gene expression to regulate cellular responses. In general, in response to low intracellular ATP levels (high ADP:ATP ratio), AMPK triggers the activation of energy-producing pathways while simultaneously inhibiting energy-consuming processes. Recent studies have established a connection between molecular pathways involved in sensing energy and potential for extending longevity. AMPK indirect activator compounds have shown a potential strategy to obtain an anti-aging biological activity. This study explores the conformational changes and transient druggable binding pockets over the 1 μs trajectory of molecular dynamics simulations to comprehend the behavior of main domains and allosteric drug and metabolite (ADaM) site. The described conformations of the apo-ADaM site suggest an important influence of specific residues on the cavity volume variations. A clustering set of representative AMPK conformations allowed to identify the more favorable binding site volume and shape at the protein apo form, including the carbohydrate-binding module (CBM) region which exhibited a stable movement near the ADaM site of the alpha-subunit. The identification of gamma-subunit transient druggable binding pocket CBS3 during the microscale time trajectory simulations also offers valuable insights into structure-based AMP-mimetic drug design for AMPK activation.