Understanding the Mechanism of Direct Activation of AMP-Kinase: Toward a Fine Allosteric Tuning of the Kinase Activity

Abstract

Mammalian AMP-activated protein kinase (AMPK) is a Ser/Thr protein kinase with a key role as a sensor in cellular energy homeostasis. It has a major role in numerous metabolic disorders, such as type 2 diabetes, obesity, and cancer, and hence it has gained progressive interest as a potential therapeutic target. AMPK is a heterotrimeric enzyme composed by an α-catalytic subunit and two regulatory subunits, β and γ. It is regulated by several mechanisms, including indirect activators such as metformin and direct activators such as compound A-769662. The crystal structure of AMPK bound to A-769662 has been recently reported, suggesting a hypothetical allosteric mechanism of AMPK activation assisted by phosphorylated Ser108 at the β-subunit. Here, we have studied the direct activation mechanism of A-769662 by means of molecular dynamics simulations, suggesting that the activator may act as a glue, coupling the dynamical motion of the βsubunit and the N-terminal domain of the α-subunit, and assisting the preorganization of the ATP-binding site. This is achieved through the formation of an allosteric network that connects the activator and ATP-binding sites, particularly through key interactions formed between αAsp88 and βArg83 and between βpSer108 and αLys29. Overall, these studies shed light into key mechanistic determinants of the allosteric regulation of this cellular energy sensor, and pave the way for the fine-tuning of the rational design of direct activators of this cellular energy sensor.

Structural basis of the selective activation of enzyme isoforms: Allosteric response to activators of β1- and β2-containing AMPK complexes

“…On the other hand, the system related to the complex of α2β2γ1 bound to SC4 (PDB entry 6B2E) [29] was also used as a template to model the complexes with A-769662. Following our previous studies [32] , the γ-subunit was not considered in MD simulations due to several reasons. First, the ADaM site is shaped only by α- and β-isoforms.…”

“…In particular, was determined by fitting the asymptotic behaviour of the curve according to the expression , where is an adjustable parameter by curve fitting. In order to enable a direct comparison between the conformational entropies of the different α2β1 and α2β2 systems, only the set of atoms of the protein backbone were considered in entropy calculations, thus avoiding a bias originated from the residue substitutions between β1- and β2-isoforms in the calculated entropies (note that a different choice of atoms, including both backbone and side chains, was used in the comparison of the conformational entropies reported for α2β1 bound to A-769662 in a previous study [32] ).…”

Main Mechanisms of Action of Policosanol in Animal and Plant Cells

“…AMPK is a Ser/Thr protein kinase and consists of a heterotrimeric complex of three subunits: the catalytic αsubunit, which can be phosphorylated at Thr172; the Thr258 and Ser485 sites; and the regulatory β and γ subunits [26,27]. AMPK is involved in the regulation of ATP synthesis and consumption; the activation of AMPK comprises its phosphorylation by several kinases and compounds.…”

Mechanistic insights into dimethyl cardamonin-mediated pharmacological effects: A double control of the AMPK-HMGB1 signaling axis

“…There are numerous natural products known to activate AMPK but they generally function in an indirect manner and therefore they may cause off-target effects [ 72 ]. Only a few compounds are known to interact directly with AMPK, such as the drug salicylate, the synthetic allosteric activator A-769662 and a few others [ [73] , [74] , [75] ].…”