2026-10-14T10:41:41Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33619702 2026-09-21T11:00:13Z category_25258 category_24862 category_25252 item_type_3 month_year_09_2026

Concentration-dependent effects from the permeation enhancers capric acid and SNAC on peptide permeability: coarse-grained MD topologies, input files, and analysis code Shakhawath Hossain (23670990) Per Larsson (21986786) Maria Karlgren (1286226) Rosita Kneiszl (11845078) Moamin Alkakaei (24798453) King Bwaila (24798467) Computational chemistry Pharmaceutical sciences Physical chemistry not elsewhere classified Salcaprozate sodium (SNAC) Capric acid (C10) Permeation enhancers Peptide permeability Molecular dynamics simulations Umbrella sampling (US) simulations <blockquote><p dir="ltr">This dataset supports the study "Concentration-dependent effects from the permeation enhancers capric acid and SNAC on peptide permeability." Using coarse-grained (Martini 2.2) molecular dynamics simulations in GROMACS, we investigated how two medium-chain-fatty-acid-based permeation enhancers — capric acid (C10) and salcaprozate sodium (SNAC) — partition into POPC and POPC–cholesterol (70:30) bilayers, how they alter membrane structural and dynamic properties, and how they modulate the membrane permeability of three model peptide drugs (octreotide, desmopressin, and triptorelin). Effective permeabilities were obtained from umbrella-sampling potentials of mean force via the inhomogeneous solubility–diffusion model.</p><p dir="ltr">The archive provides everything needed to reproduce the simulations and analyses:<br>• <b>topologies/</b> — Martini 2.2 coarse-grained topologies for the force field, POPC and cholesterol, the neutral forms of capric acid and SNAC, and the three peptides.<br>• <b>mdp_files/</b> — GROMACS parameter files for the full free-energy workflow (energy minimization, equilibration, steered pulling to generate umbrella windows, and umbrella-sampling production).<br>• <b>example_system/</b> — a complete, ready-to-run built system (octreotide in a POPC–cholesterol bilayer with water and ions) with its topology and included parameter files.<br>• <b>analysis_code/</b> — Python and Bash scripts to compute effective permeabilities (D(z), R(z), Peff from WHAM PMFs and integrated autocorrelation times), assess PMF convergence, and quantify membrane properties (area per lipid, thickness, lipid-tail order parameters, flip-flop rates, enhancer incorporation, and fractional interaction matrices).<br>• <b>figure_source_data/</b> — Excel workbooks containing the numerical source data behind each main figure, including per-replicate PMF profiles and effective permeabilities with standard deviations.</p><p dir="ltr">All simulations were performed at 310.15 K with semi-isotropic pressure coupling. Permeation-enhancer concentrations are reported as actual membrane mole fractions (34% and 50% for capric acid; 28% and 43% for SNAC). Effective permeabilities are geometric means over three independent replicates, with uncertainties reported as the standard deviation of log₁₀(Peff).</p><p><br></p></blockquote><p></p> 2026-09-21T11:00:13Z Dataset Dataset 10.6084/m9.figshare.33619702.v1 https://figshare.com/articles/dataset/Concentration-dependent_effects_from_the_permeation_enhancers_capric_acid_and_SNAC_on_peptide_permeability_coarse-grained_MD_topologies_input_files_and_analysis_code/33619702 CC BY 4.0