Molecular dynamics investigations of the bacterial cell envelope: Elucidating differential barriers for antimicrobials

Abstract

The bacterial cell envelopes possess a complex multilayered architecture exhibiting unique properties evolved to regulate interactions with the external environment and molecules with antimicrobial properties. A molecular understanding of the interactions of external molecules with the bacterial envelope will aid in the development of novel antibacterial formulations. Using detailed molecular models of the bacterial cell envelope, we have carried out molecular dynamics simulations and free energy computations to gain insights into the interactions of membrane targeting antibacterials and surfactants. We have elucidated the molecular basis for the interaction and transport of antibacterial therapeutics with both the Gram-negative inner membrane (IM) and outer membrane (OM) as well as the periplasmic peptidoglycan cell wall. Free-energy computations reveal the presence of a barrier in the core-saccharide region of the OM for the translocation of thymol a naturally occurring antibacterial while the external O-antigen region is easily traversed. In contrast, thymol spontaneously inserts into the IM and lipid diffusivities show a distinct increase in the presence of thymol. The all-atom simulations for these asymmetric bacterial membranes are challenging due to the large number of atoms involved in these models. Therefore, coarse-grained MARTINI models are preferred for these systems. We have compared the all-atom (CHARMM36) and coarse-grained (MARTINI) models of the IM, periplasmic peptidoglycan (PGN) and OM. The structural and barrier properties of the membrane were contrasted. Our results indicate that the MARTINI models accurately capture insertion free energies for small molecules and other structural properties with all-atom models of both the IM and PGN layer. We have also illustrated the lipid composition effects on the IM properties and affirmed the need to employ accurate all atom models for these membranes. Surfactants, with their ability to solubilize lipids, are another class of widely used antibacterial agents. We observe that the PGN layer does not offer a barrier to isolated surfactant molecules, however the passage of surfactant aggregates were restricted. We also observed greater changes to the IM structural and mechanical properties in the presence of laurate and rationalize differences in the efficacy of these surfactants with different aggregation properties, chain lengths, and electrostatic interaction with PGN. In the last part of the thesis, we have assessed the ability of ve coarse-grained MARTINI 1, 2-dipalmitoylsn- glycero-3-phosphocholine (DPPC) membranes to capture the ripple phase in membranes. Our study illustrates that the presence of the partly interdigitated ripple-like states are a strong function of system-size and occur as kinetically trapped structures in smaller lipid patches. The present MARTINI force elds will require additional re-parametrization to capture the ripple phase. Coupled with free energy computations our in silico study reveals lea etresolved insertion properties in bacterial membranes allowing one to assess the ability of naturally occurring small molecules such as thymol and surfactants to penetrate various membrane components. Molecular insights gained from our study can potentially be used in the design of novel antibacterial formulations to improve the efficacy of therapeutics and disinfectants to eventually combat the rise of resistant bacterial strains.