High-resolution Molecular Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2)

• Published in: Chemistry : a European journal 2024-11, p.e202402534
• Main Authors: Delobelle, Quentin, Jaffrelot Inizan, Théo, Adjoua, Olivier, Lagardère, Louis, Célerse, Frederic, Maréchal, Vincent, Piquemal, Jean-Philip
• Format: Article
• Language: English
• Subjects: Biochemistry, Molecular Biology; Biophysics; Chemical Sciences; Life Sciences; or physical chemistry; Theoretical and
• ISSN: 1521-3765; 0947-6539; 1521-3765
• DOI: 10.1002/chem.202402534

Glucose metabolism plays a pivotal role in physiological processes and cancer growth. The final stage of glycolysis, converting phosphoenolpyruvate (PEP) into pyruvate, is catalyzed by the pyruvate kinase (PK) enzyme. Whereas PKM1 is mainly expressed in cells with high energy requirements, PKM2 is preferentially expressed in proliferating cells, including tumor cells. Structural analysis of PKM1 and PKM2 is essential to design new molecules with antitumoral activity. To understand their structural dynamics, we performed extensive high-resolution molecular dynamics (MD) simulations using adaptive sampling techniques coupled to the polarizable AMOEBA force field. Performing more than 6 µs of simulation, we considered all oligomerization states of PKM2 and propose structural insights for PKM1 to further study the PKM2-specific allostery. We focused on key sites including the active site and the natural substrate Fructose Bi-Phosphate (FBP) fixation pocket. Additionally, we present the first MD simulation of biologically active PKM1 and uncover important similarities with its PKM2 counterpart \textcolor{red}{bound} to FBP. We also analysed TEPP-46's fixation, a pharmacological activator binding a different pocket, on PKM2 and highlighted the structural differences and similarities compared to PKM2 bound to FBP. Finally, we determined potential new cryptic pockets specific to PKM2 for drug targeting.