Investigation of Inhibitory Potency of BHQ Derivatives as SERCA Inhibitors to use as Potential Drugs as well as Tools to Study the SERCA Function: Binding Free Energy Computation using FEP/MD Simulations

Abstract

Sarco/endoplasmic reticulum calcium-ATPase (SERCA) is an integral membrane C2+ ion pump that play a vital role in skeletal muscle contraction/relaxation and signal transduction by pumping Ca2+ ions into intracellular storage compartments while transporting protons in the opposite direction. Most SERCA inhibitors bind to its E2 conformation, thereby blocking the conformational change to the E1 form, which is a step necessary for the catalytic cycle. We investigate the interactions between SERCA and its highly potent allosteric inhibitor: di-tert butylhydroquinone (BHQ) and its derivatives with diverse chemical and structural groups, using molecular dynamics (MD) simulations. We effectively simulate the ligand bound active spherical region with explicit molecular dynamics while the rest of the system is treated with implicit solvent model known as generalized boundary solvent potential (GSBP). Our goal is to compute the absolute binding free energy of BHQ derivatives by using the all-atom free energy perturbation molecular dynamics (FEP/MD) simulations. This FEP/MD method involve a sequence of intermediate alchemical steps that restrain the translation, orientation, and conformation of the ligand as well as sequential steps during which the ligand-surrounding interactions are turned “on” and “off”. These features are implemented to improve the accuracy and enhance the convergence of the free energy calculations. The force field for the BHQ derivatives are automatically generated by the CHARMM additive CGenFF force field and later optimized by using quantum computations to obtain a good compatibility with the CHARMM force field, which simulates biopolymers effectively. BHQ ligand structure files are obtained from PDB without modification. Information gained from these simulations will guide the future synthesis of novel compounds with improved properties for SERCA inhibition.