Theoretical study of myriocin‐binding mechanism targeting serine palmitoyltransferase

Abstract

Sphingolipids (SLs) are vital for cells as forming membrane and transducing signals. The first step for de novo biosynthesis of SLs is catalyzed by the pyridoxal-5′phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT), which has been proven to be a promising drug target for treating various diseases. However, there are few SPT-specific inhibitors have been identified so far. Myriocin, a natural fungal product, is confirmed as the most potent inhibitor of SPT and has been widely used, but studies of its molecular mechanism are still underway. Besides, there is no intact co-crystal structure of SPT-binding myriocin until now. Aiming to uncover the interaction mechanism between SPT-and PLP-binding myriocin at the molecular level, a systematic computational strategy was performed in this present study. Firstly, covalent docking was implemented to preliminarily predict the binding pose SPT/PLP-myriocin aldimine and its structurally similar intermediate SPT/PLP-βketoacid aldimine. Secondly, two binding complexes were treated as initial structures to perform molecular dynamics simulations and binding free energy calculations. The calculated docking scores and predicted binding energies were consistent with the reported bioactivities. Finally, the binding mechanism of myriocin binding with SPT was meticulously described, and the key residues making favorable contributions were highlighted. Taken together, the current study could provide some important information and valuable guidance for further rational screening, design, and modification of potent specific SPT inhibitors.

1,3-Proton Transfer of Pyridoxal 5′-Phosphate Schiff Base in the Branched-Chain Aminotransferase: Concerted or Stepwise Mechanism?

“…Arg101, which contributes the highest favorable energetic contribution among the active site residues by forming an ionic bond and a hydrogen bond with the phosphate O atom of PLP, other residues such as Ile271, Thr272, and Thr314 also play significant roles in binding PLP-Glu through strong hydrogen bond interactions. The phosphate group of PLP also makes multiple contacts with residues in the highly conserved phosphate-binding pocket of serine palmitoyltransferase (SPT), which further highlights its importance in the catalytic process . The binding free energies of SPT/PLP-myriocin aldimine and SPT/PLP-β-ketoacid aldimine were calculated to be −77.85 and −71.41 kcal mol –1 , respectively, using the MM-GBSA method.…”

“…The phosphate group of PLP also makes multiple contacts with residues in the highly conserved phosphate-binding pocket of serine palmitoyltransferase (SPT), which further highlights its importance in the catalytic process. 51 The binding free energies of SPT/PLP-myriocin aldimine and SPT/PLP-β-ketoacid aldimine were calculated to be −77.85 and −71.41 kcal mol −1 , respectively, using the MM-GBSA method. In PLPdependent enzymes, the phosphate group is known to significantly contribute to the binding energy.…”

Mysterious sphingolipids: metabolic interrelationships at the center of pathophysiology

“…By inhibiting SPT, myriocin disrupts sphingolipid generation leading to varied sphingolipid profiles within cells. Myriocin, thus, has been used to investigate the impact of altered sphingolipid levels on cellular processes, including cellular signaling, immune cell function, apoptosis, autophagy, and membrane dynamics, to name a few ( Scarlatti et al, 2003 ; Johnson et al, 2004 ; Rentz et al, 2005 ; Ordoñez et al, 2015 ; Guo et al, 2020 ; Yu et al, 2022 ). It has also been instrumental in understanding the roles of sphingolipids in various diseases, such as cancer, cardiovascular diseases, and neurodegenerative disorders ( Park et al, 2008 ; Adachi et al, 2018 ; Mingione et al, 2021 ; Weiss et al, 2021 ).…”