Molecular dynamics simulation of d-Benzedrine transmitting through molecular channels within D₃R

Abstract

Dex-Benzedrine (known as d-Benzedrine or SAT) acts in dopamine receptors of central nerve cell system. In clinic, SAT is used to treat a variety of diseases; meanwhile, it has dependence and addiction. In order to investigate the pharmacology and addiction mechanisms of SAT as a medicine, in this paper, we have studied the structure of D₃R complex protein with SAT, and based on which, using potential mean force with umbrella samplings and the simulated phospholipid bilayer membrane (or POPC bilayer membrane), the molecular dynamics simulation was performed to obtain free energy changes upon the trajectories for SAT moving along the molecular channels within D₃R. The free energy change for SAT transmitting toward the outside of cell along the functional molecular channel within D₃R is 83.5 kJ mol⁻¹. The change of free energy for SAT to permeate into the POPC bilayer membrane along the protective molecular channel within D₃R is 87.7 kJ mol⁻¹. Our previous work gave that the free energy for Levo-Benzedrine (RAT) transmitting toward the outside of cell along the functional molecular channel within D₃R is 91.4 kJ mol⁻¹, while it is 117.7 kJ mol⁻¹ for RAT to permeate into the POPC bilayer membrane along the protective molecular channel within D₃R. The values of free energy suggest that SAT relatively prefers likely to pass through the functional molecular channel within D₃R for increasing the release of dopamine molecules resulting in a variety of functional effects for SAT. The obtained results show that the pharmacology and addiction mechanisms of SAT as a drug are closely related to the molecular dynamics and mechanism for SAT transmitting along molecular channels within D₃R.

Keywords:

• SAT
• D₃R
• POPC
• MD simulation
• free energy