A narrow thermodynamic design window governs selective membrane permeabilization and antiviral activity of amphipathic peptides

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Designing molecules that selectively target therapeutically relevant membranes, such as viral envelopes, while sparing host cells is challenging: these membranes closely resemble host bilayers, so selectivity must exploit subtle lipid composition and curvature differences and demands precise tuning of affinity and hydrophobicity, yet curated sequence–specificity data are scarce. Here we show that selective membrane permeabilization and membrane-selective activity of amphipathic peptides are governed by a narrow thermodynamic design window defined by membrane curvature affinity and molecular hydrophobicity. Using a physics-driven generative workflow combining evolutionary molecular dynamics and a transformer predictor (PMIpred), we systematically explored and thermodynamically mapped peptide sequence space de novo without reliance on natural templates or experimental training data. Across four design generations we synthesized and experimentally characterized 43 peptides. Mapping functional activity onto a low-dimensional free-energy landscape reveals a confined thermodynamic “sweet spot” separating weak membrane binding from excessive hydrophobic association and cytotoxicity. Peptides operating within this regime efficiently permeabilize model membranes while maintaining low cellular toxicity. Antiviral activity against Zika virus and HIV-1 emerges in the same region but depends sensitively on membrane lipid composition. Quantitative thermodynamic design rules emerge for membrane-active peptides, illustrating how low-dimensional free-energy landscapes can guide the engineering of selective interactions at soft-matter interfaces.

Authors 9

1. Niek van Hilten Aachen

   Leiden University · University of California, San Francisco

   Affiliation as printed

   Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States of America

   Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

2. Pascal von Maltitz

   Universität Ulm · University Hospital Ulm

   Affiliation as printed

   Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany

3. Dennis Aschmann Aachen

   Leiden University · University of Amsterdam

   Affiliation as printed

   Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

   Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands

4. Maria Hoernke

   University of Freiburg · Martin Luther University Halle-Wittenberg

   Affiliation as printed

   Pharmaceutical Technology and Biopharmacy, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany

   Physical Chemistry, Martin-Luther-University, Halle (S.), Germany

5. Maximilian Krebs

   TU Dortmund University

   Affiliation as printed

   Department of Physics, Technical University Dortmund, Dortmund, Germany

6. Jeroen Methorst Aachen

   Leiden University · TU Dortmund University

   Affiliation as printed

   Department of Physics, Technical University Dortmund, Dortmund, Germany

   Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

7. Alexander Kros Aachen

   Leiden University

   Affiliation as printed

   Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands

8. Jan Münch

   Universität Ulm · University Hospital Ulm

   Affiliation as printed

   Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany

9. Herre Jelger Risselada corresponding

   TU Dortmund University

   Affiliation as printed

   Department of Physics, Technical University Dortmund, Dortmund, Germany