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The absolute performance of any all-atom molecular dynamics simulation is typically limited by the length of the individual timesteps taken when integrating the equations of motion. In the GROMACS simulation software, it has for a long time been possible to use so-called virtual sites to increase the length of the timestep, resulting in a large gain of simulation efficiency. Up until now, support for this approach has in practice been limited to the standard 20 amino acids however, shrinking the applicability domain of virtual sites. MkVsites is a set of python tools which provides a convenient way to obtain all parameters necessary to use virtual sites for virtually any molecules in a simulation. Required as input to MkVsites is the molecular topology of the molecule(s) in question, along with a specification of where to find the parent force field. As such, MkVsites can be a very valuable tool suite for anyone who is routinely using GROMACS for the simulation of molecular systems.

Medium-chain fatty acid-based permeation enhancers (PEs) have gained significant attention due to their potential application in various industries, including within the pharmaceutics sector as absorption enhancers for, e.g., peptide drugs. In this study, we performed computational experiments to investigate the impact of two different PEs, capric acid and Salcaprozate sodium (SNAC), at three different concentrations (0%, 30%, 50%), on the structural properties of a bilayer consisting of 70% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 30% cholesterol. We employed coarse-grained molecular dynamics simulations first to explore the interactions of the PEs with lipid bilayers at the molecular level and then to examine the consequences of these interactions for the permeability of three different peptides (octreotide, desmopressin, and triptorelin). We employed umbrella sampling simulations to obtain the permeability rates of the PEs at several concentrations and of the peptides in the absence and presence of the two PEs, also at different concentrations. We observed that the impact on the membrane structural properties changed with increasing PE concentration. We also found that the effective permeability values increased with increasing PE concentration. However, the permeability values were significantly higher (6-7 orders of magnitude) for capric acid than for SNAC, which we argue is mainly because capric acid has more pronounced effects on the structural properties of the membrane. Peptide permeability also increased with increasing PE concentration. The Peff values followed the trend: octreotide > triptorelin > desmopressin across all systems. For each peptide, the lowest Peff values were observed in the no-PE systems, while the highest values were observed in the systems with 50% capric acid. Capric acid exhibited an increasing trend in Peff values with higher concentrations within the membrane. In contrast, the peptide Peff values in the SNAC systems were similar between the 30% and 50% concentrations, aligning with the trends observed in free energy profiles and the membrane structural characteristics. Thus, for SNAC, there seems to be a concentration where the permeability-enhancing effect plateaus. With these results, we hope to pave the way for more knowledge-based design of pharmaceutical dosage forms that involve PEs for increasing transcellular peptide permeability, considering the differences in compatibility between PEs and peptides, and the apparent synergistic effect of combining PEs.

Oral administration of drugs is generally considered convenient and patient-friendly. However, oral administration of biological drugs exhibits low oral bioavailability (BA) due to enzymatic degradation and low intestinal absorption. A possible approach to circumvent the low BA of oral peptide drugs is to coformulate the drugs with permeation enhancers (PEs). PEs have been studied since the 1960s and are molecules that enhance the absorption of hydrophilic molecules with low permeability over the gastrointestinal epithelium. In this study, we investigated the impact of six PEs on the structural properties of a model membrane using molecular dynamics (MD) simulations. The PEs included were the sodium salts of the medium chain fatty acids laurate, caprate, and caprylate and the caprylate derivative SNAC─all with a negative charge─and neutral caprate and neutral sucrose monolaurate. Our results indicated that the PEs, once incorporated into the membrane, could induce membrane leakiness in a concentration-dependent manner. Our simulations suggest that a PE concentration of at least 70–100 mM is needed to strongly affect transcellular permeability. The increased aggregation propensity seen for neutral PEs might provide a molecular-level mechanism for the membrane disruptions seen at higher concentrations in vivo. The ability for neutral PEs to flip-flop across the lipid bilayer is also suggestive of possible intracellular modes of action other than increasing membrane fluidity. Taken together, our results indicate that MD simulations are useful for gaining insights relevant to the design of oral dosage forms based around permeability enhancer molecules.

Permeability enhancer-based formulations offer a promising approach to enhance the oral bioavailability of peptides. We used all-atom molecular dynamics simulations to investigate the interaction between two permeability enhancers (sodium caprate, and SNAC), and four different peptides (octreotide, hexarelin, degarelix, and insulin), in the presence of taurocholate, an intestinal bile salt. The permeability enhancers exhibited distinct effects on peptide release based on their properties, promoting hydrophobic peptide release while inhibiting water-soluble peptide release. Lowering peptide concentrations in the simulations reduced peptide-peptide interactions but increased their interactions with the enhancers and taurocholates. Introducing peptides randomly with enhancer and taurocholate molecules yielded dynamic molecular aggregation, and reduced peptide-peptide interactions and hydrogen bond formation compared to peptide-only systems. The simulations provided insights into molecular-level interactions, highlighting the specific contacts between peptide residues responsible for aggregation, and the interactions between peptide residues and permeability enhancers/taurocholates that are crucial within the mixed colloids. Therefore, our results can provide insights into how modifications of these critical contacts can be made to alter drug release profiles from peptide-only or mixed peptide-PE-taurocholate aggregates. To further probe the molecular nature of permeability enhancers and peptide interactions, we also analyzed insulin secondary structures using Fourier transform infrared spectroscopy. The presence of SNAC led to an increase in beta-sheet formation in insulin. In contrast, both in the absence and presence of caprate, alpha-helices, and random structures dominated. These molecular-level insights can guide the design of improved permeability enhancer-based dosage forms, allowing for precise control of peptide release profiles near the intended absorption site. Molecular-level insights can guide the design of improved permeability enhancer-based dosage forms, allowing for precise control of peptide release profiles near the intended absorption site.