Molecular Basis of the Selectivity of the Immunoproteasome Catalytic Subunit LMP2-Specific Inhibitor Revealed by Molecular Modeling and Dynamics Simulations

Abstract

Given that immunoproteasome inhibitors are currently being developed for a variety of potent therapeutic purposes, the unique specificity of an α′,β′-epoxyketone peptide (UK101) towards the LMP2 subunit of the immunoproteasome (analogous to β5 subunit of the constitutive proteasome) has been investigated in this study for the first time by employing homology modeling, molecular docking, molecular dynamics simulation, and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. Based on the simulated binding structures, the calculated binding free energies are in qualitative agreement with the corresponding experimental data and the selectivity of UK101 is explained reasonably. The observed selectivity of UK101 for the LMP2 subunit is rationalized by the requirement for both a linear hydrocarbon chain at the Nterminus and a bulky group at the C-terminus of the inhibitor, because that LMP2 subunit has a much more favorable hydrophobic pocket interacting with the linear hydrocarbon chain, and the bulky group at the C-terminus has a steric clash with the Tyr 169 in β5 subunit. Finally, our results help to clarify why UK101 is specific to the LMP2 subunit of immunoproteasome, and this investigation should be valuable for rational design of more potent LMP2-specific inhibitors.

Binding free energies for nicotine analogs inhibiting cytochrome P450 2A6 by a combined use of molecular dynamics simulations and QM/MM-PBSA calculations

“…27,28,31 In particular, the Amber ff03 force field 36 was used for all the amino acid residues of CYP2A6 and the general Amber force field (gaff) 37 was used for the heme group and inhibitors. Each of the CYP2A6-inhibitor complex structure was solvated in an orthorhombic box of TIP3P water molecules 38 with a minimum solvent-wall distance of 10 Å. Chloride counter ions (Cl - ) were added to neutralize the solvated system.…”

“…Among a series of methods of binding free energy calculations, molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) approach has been popularly used to determine the mode of ligand binding and to discover novel lead compounds in virtual screening. 26,27,28,29,30,31,32 However, the MM-PBSA calculations usually depend heavily on the conformation sampling by MD simulations and the type of force field parameters. 30 In our previous study, 33 a combined use of the hybrid quantum mechanical/molecular mechanical (QM/MM) geometry optimizations and the PBSA calculations ( i.e .…”

Structural features and binding free energies for non-covalent inhibitors interacting with immunoproteasome by molecular modeling and dynamics simulations

“…All of the 16 inhibitors were constructed in SYBYL 6.9 molecular modeling package [32]. Energy minimizations were performed using the Tripos force field with a distance-dependent dielectric and Powell method with a convergence criterion of 0.1 kcal/mol [33].…”

“…Thus, both of the two subunits were used in the subsequent docking and MD simulations. To facilitate the docking binding-site definition, the complex b5b6 binding with UK101 in our previous work [32] was aligned to b5ib6 and ligand UK101 was transferred into the active site of b5ib6. Before docking, the protein was prepared by adding hydrogen atoms, assigning protonation states, and carrying out energy minimization with a small number of steps to relax amino-acid residue side chains and UK101 to relative appropriate positions.…”

“…The general procedure for carrying out the MD simulations in water is similar to that used in our previously reported computational studies [32,[34][35][36][37][38][39]. Briefly, the MD simulations were performed using the Sander module of Amber (version 9) with Amber ff03 force field [40].…”