With a combination of molecular dynamics simulations and experimental methods, we have, for the first time, observed how a polar peptide like semaglutide can spontaneously sink into a membrane in the presence of a permeation enhancer (SNAC), to get delivered across the intestinal barrier. Dynamic protonation of weakly ionizable sites is crucial for this process, which we were able to observe with a CpHMD model that can accurately represent the environment-and aggregation-/conformation-dependent charges in this system. While dynamic protonation of ionizable sites is well-known to influence biological processes and membrane permeability for small molecules (see Fig. for a seminal example), this work has now advanced the application of CpHMD models to permeation-enhancer facilitated peptide permeation by treating all the permeation enhancers and all ionizable sites on a peptide drug (>400 ionizable groups in total) with a CpHMD model. Furthermore, while both SNAC and semaglutide are known to form aggregates by themselves in Colston, Faivre, and Schneebeli* ______________________________________________________________________________ 13 buffered aqueous solutions based on DLS and DOSY NMR, our CpHMD simulations have now clearly demonstrated co-association of the peptide with the permeation enhancer in the aqueous phase. We hypothesize that this observed co-aggregation is primarily responsible for the previously reported monomerization of the peptide drug in an aqueous buffer in the presence of SNAC, a mechanism that was previously unknown. In addition, since we found a clear affinity of SNAC toward itself and semaglutide in both aqueous and hydrophobic environments, the coaggregation of SNAC with semaglutide might also play an important role in helping to recruit the SNAC-bound semaglutide from the aqueous layer to the membrane (with the SNAC around the semaglutide fusing with membrane-bound SNAC). Based on our combined computational and experimental results, we propose the overall mechanism shown in Figure for peptide permeation with SNAC. Key steps include: (3) Solution-based semaglutide-SNAC aggregates fuse with dynamic, membrane-bound SNAC-filled membrane defects, adsorbing semaglutide onto the membrane surface.