pH-Dependent Molecular Dynamics of BACE1 Inhibitors

Continuous constant pH molecular dynamics (CpHMD) simulations ^{23 (link),24 (link)} with a hybrid-solvent scheme and pH replica-exchange protocol ^{26 (link)} were performed on BACE1 in complex with inhibitors 1 and 2 starting from the respective crystal structures (PDB ID 4FRS ^{7 (link)} and 4YBI ^{8 (link)}) using CHARMM (version C37b). ^{29 (link)} The CHARMM22/CMAP all-atom force field ^{30 (link),31 (link)} was used to represent BACE1, while the force field parameters for the inhibitors were obtained in house following the protocol of CHARMM General Force Field (CGenFF) ^{32 (link)}. Each system was simulated using 20 pH replicas in the pH range 1.3–8. Each BACE1 complex was simulated for 26 ns per replica under NPT conditions, resulting in a total simulation time of 520 ns. The last 18 ns per replica (360 ns in total) were used for analysis. Other simulation parameters and setting were identical to those in our previous work ^{5 (link)}. The titratable sites include all Asp, Glu and His residues on the protein and the amine group on the pyridine/pyrimidine ring of the inhibitor (see Table S1 for all calculated pK_a’s). The model pK_a’s for Asp, Glu and His are 4.0, 4.4, and 6.5, respectively, ^{26 (link)} while those for inhibitor 1 and 2 are 2.9 and 3.7, respectively. The latter pK_a’s were estimated using the program MoKa. ^{33 (link)} The pK_a measurements for the inhibitors were conducted using capillary electrophoresis experiment following the protocol from ref. ^{34 (link)}