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{"family": "Welborn", "given": "Valerie Vaissier", "initials": "VV"}, {"family": "Wetmore", "given": "Stacey D", "initials": "SD", "orcid": "0000-0002-5801-3942", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/156e1f23f71d4511a8c5274d2cdf7a79.json"}}, {"family": "Wheeler", "given": "Travis J", "initials": "TJ"}, {"family": "Wong", "given": "Chung F", "initials": "CF"}, {"family": "Yang", "given": "Lee-Wei", "initials": "LW", "orcid": "0000-0002-3971-6386", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/242ed7f7cf9148cbad08da4d80284c6f.json"}}, {"family": "Zacharias", "given": "Martin", "initials": "M", "orcid": "0000-0001-5163-2663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69971c7616b54a81aa4869f7e398874f.json"}}, {"family": "Orozco", "given": "Modesto", "initials": "M", "orcid": "0000-0002-8608-3278", "researcher": {"href": 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Methods", "issn": "1548-7105", "volume": "22", "issue": "4", "pages": "641-645", "issn-l": "1548-7091"}, "abstract": "In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.", "doi": "10.1038/s41592-025-02635-0", "pmid": "40175561", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2081560"}, {"db": "pmc", "key": "PMC12950262"}, {"db": "pii", "key": "10.1038/s41592-025-02635-0"}], "notes": [], "created": "2026-08-20T09:03:25.648Z", "modified": "2026-08-20T09:03:27.707Z"}, {"entity": "publication", "iuid": "e442230f6db64c3e8e8a81d3a19ef3eb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e442230f6db64c3e8e8a81d3a19ef3eb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e442230f6db64c3e8e8a81d3a19ef3eb"}}, "title": "Simulating the Skin Permeation Process of Ionizable Molecules.", "authors": [{"family": "Lundborg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0873-7854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1b1b7c73fd44b9b880106feaa56feb.json"}}, {"family": "Wennberg", "given": "Christian", "initials": "C", "orcid": "0000-0003-4012-1678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a7c95013dd467591e4e9603cc7bfad.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Norl\u00e9n", "given": "Lars", "initials": "L", "orcid": "0000-0002-8049-2556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1a3490a42364d7b9925fcfae614d33f.json"}}], "type": "journal article", "published": "2024-07-08", "journal": {"title": "J Chem Inf Model", "issn": "1549-960X", "volume": "64", "issue": "13", "pages": "5295-5302", "issn-l": "1549-9596"}, "abstract": "It is commonly assumed that ionizable molecules, such as drugs, permeate through the skin barrier in their neutral form. By using molecular dynamics simulations of the charged and neutral states separately, we can study the dynamic protonation behavior during the permeation process. We have studied three weak acids and three weak bases and conclude that the acids are ionized to a larger extent than the bases, when passing through the headgroup region of the lipid barrier structure, at pH values close to their pKa. It can also be observed that even if these dynamic protonation simulations are informative, in the cases studied herein they are not necessary for the calculation of permeability coefficients. It is sufficient to base the calculations only on the neutral form, as is commonly done.", "doi": "10.1021/acs.jcim.4c00722", "pmid": "38917349", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11234375"}], "notes": [], "created": "2026-08-20T08:10:30.487Z", "modified": "2026-08-20T08:10:30.583Z"}, {"entity": "publication", "iuid": "5e745725d48c4b14b3fd095607998d4f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e745725d48c4b14b3fd095607998d4f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e745725d48c4b14b3fd095607998d4f"}}, "title": "Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations.", "authors": [{"family": "Wennberg", "given": "Christian", "initials": "C", "orcid": "0000-0003-4012-1678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a7c95013dd467591e4e9603cc7bfad.json"}}, {"family": "Lundborg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0873-7854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1b1b7c73fd44b9b880106feaa56feb.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E"}, {"family": "Norl\u00e9n", "given": "Lars", "initials": "L", "orcid": "0000-0002-8049-2556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1a3490a42364d7b9925fcfae614d33f.json"}}], "type": "journal article", "published": "2023-08-14", "journal": {"title": "J Chem Inf Model", "issn": "1549-960X", "volume": "63", "issue": "15", "pages": "4900-4911", "issn-l": "1549-9596"}, "abstract": "Our skin constitutes an effective permeability barrier that protects the body from exogenous substances but concomitantly severely limits the number of pharmaceutical drugs that can be delivered transdermally. In topical formulation design, chemical permeation enhancers (PEs) are used to increase drug skin permeability. In vitro skin permeability experiments can measure net effects of PEs on transdermal drug transport, but they cannot explain the molecular mechanisms of interactions between drugs, permeation enhancers, and skin structure, which limits the possibility to rationally design better new drug formulations. Here we investigate the effect of the PEs water, lauric acid, geraniol, stearic acid, thymol, ethanol, oleic acid, and eucalyptol on the transdermal transport of metronidazole, caffeine, and naproxen. We use atomistic molecular dynamics (MD) simulations in combination with developed molecular models to calculate the free energy difference between 11 PE-containing formulations and the skin's barrier structure. We then utilize the results to calculate the final concentration of PEs in skin. We obtain an RMSE of 0.58 log units for calculated partition coefficients from water into the barrier structure. We then use the modified PE-containing barrier structure to calculate the PEs' permeability enhancement ratios (ERs) on transdermal metronidazole, caffeine, and naproxen transport and compare with the results obtained from in vitro experiments. We show that MD simulations are able to reproduce rankings based on ERs. However, strict quantitative correlation with experimental data needs further refinement, which is complicated by significant deviations between different measurements. Finally, we propose a model for how to use calculations of the potential of mean force of drugs across the skin's barrier structure in a topical formulation design.", "doi": "10.1021/acs.jcim.3c00625", "pmid": "37462219", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10428223"}], "notes": [], "created": "2026-08-20T08:10:23.956Z", "modified": "2026-08-20T08:10:24.127Z"}, {"entity": "publication", "iuid": "00fb33b0ffc2407fa8e012742cc82da6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/00fb33b0ffc2407fa8e012742cc82da6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/00fb33b0ffc2407fa8e012742cc82da6"}}, "title": "Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates", "authors": [{"family": "Lundborg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0873-7854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab1b1b7c73fd44b9b880106feaa56feb.json"}}, {"family": "Wennberg", "given": "Christian", "initials": "C", "orcid": "0000-0003-4012-1678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4a7c95013dd467591e4e9603cc7bfad.json"}}, {"family": "Lidmar", "given": "Jack", "initials": "J", "orcid": "0000-0002-9881-7857", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4965270ce074cb6ace42b3ddb931768.json"}}, {"family": "Hess", "given": "Berk", "initials": "B", "orcid": "0000-0002-7498-7763", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f8bd0772d1341ddbcd9bba2f66b042d.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}, {"family": "Norl\u00e9n", "given": "Lars", "initials": "L", "orcid": "0000-0002-8049-2556", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1a3490a42364d7b9925fcfae614d33f.json"}}], "type": "posted-content", "published": "2022-02-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.10.479880", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:32.716Z", "modified": "2026-08-20T10:09:32.806Z"}]}