Crosstalk of\nNucleic Acid Mimics with Lipid Membranes:\nA Multifaceted Computational and Experimental Study

Nucleic acid mimics (NAMs) have demonstrated high potential\nas\nantibacterial drugs. However, very few studies have assessed their\npossible diffusion across the bacterial envelope. In this work, we\nstudied NAMs’ diffusion in lipid bilayer systems that mimic\nthe bacterial outer membrane using molecular dynamics (MD) simulations.\nAdditionally, we examined the interactions of a NAM sequence with\nlipid membranes and ascertained the partition constants (<i>K</i><sub>p</sub>) through MD and spectroscopic investigations. The NAM\nsequences were composed of locked nucleic acid (LNA) and 2′-O-methyl\n(2′-OMe) residues, whereas the membrane models were composed\nof 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) or 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phospho-(1′-rac-glycerol) (POPG) phospholipids.\nThe parametrization protocol followed was validated against literature\ndata and demonstrated the reliability of our approach for simulating\nNAM sequences. Investigation into the interaction of the sequences\nwith zwitterionic and anionic membranes revealed a preference for\nhydrogen bond formation with the anionic model over the zwitterionic\none. Additionally, potential of mean force (PMF) calculations unveiled\na lower free energy barrier for translocation across the zwitterionic\nbilayer model. Contrarily, the partition constants derived suggested\na slightly higher partitioning within the anionic membrane, emphasizing\na nuanced interplay of factors. Finally, spectroscopic partition measurements\nwith liposomes presented challenges in quantifying the partition of\nNAMs due to minimal signal variations. However, a tendency for quenching\nin anionic vesicles suggested a potential, albeit small, partitioning\neffect that warrants further investigation. In summary, our study\nrevealed that NAMs will not, in principle, be able to cross an intact\nbacterial outer membrane by passive diffusion.