CpHMD Simulations. The simulations described in this work utilized a scalable CpHMD method implemented by the Groenhof and Hess groups in a custom fork of GROMACS 2021. Due to the environment and conformation-dependent pKa values of all the weakly ionizable functional groups in the peptide and the SNACs, the enhanced accuracy of a CpHMD model is crucial to meaningfully predict the charges and interactions between semagtlutide, SNAC, and the membrane. Specifically, we found that the charges of the permeation enhancers and the peptides (which are directly controlled by the protonation states) are highly environment-dependent, which significantly affects the free energy change associated with membrane insertion of SNAC (Fig. ). In this work, the CpHMD model enabled the simulation of all the titratable sites in the peptide and ~400 permeation enhancers under constant pH conditions at ~80% of the efficiency of standard MD simulations. The 400:1 molar ratio of SNAC:semaglutide in the simulations was chosen based on the current formulations in Rybelsus, which contains ~1 mmol of SNAC per tablet in a ~300:1 to ~1300:1 SNAC:semaglutide molar ratio).