Molecular imaging of isolated peptidoglycans as novel platform for antibiotic development
Molecular imaging of a native isolated Escherichia coli peptidoglycan sacculus. Note the nanoscale resolution of single glycan chains, allowing the interpretation of murein network morphology on a molecular scale. (white arrow = single glycan strand, blue arrow = single transpeptide bridge)
Molecular imaging of ampicillin-treated isolated Escherichia coli peptidoglycan sacculus. Note the nanoscale resolution of single structurally impaired glycan chains, allowing the depiction of reduced cross linking and the interpretation of the mechanism of action exerted by ampcillin treatment. (white arrow = impaired cross linking evoked by ampicillin treatment)
Natural products´ mechanisms of action
Although modern medicinal chemistry has achieved striking advances in the past, the plethora of new anti-infective and anti-cancer agents are still initially identified in a plant, animal or microorganism.
The subsequent elucidation of the mechanisms of action of such bioactive natural products (NPs) is yet still an essential but tedious process, hindered by a number of shortcomings.
In order to identify a target structure in an alternative way, our group is using ultrastructural morphological assessments of cells, tissues and whole organisms as a shortcut to pinpoint potential mechanisms of action of a bioactive NP. This information can subsequently allow the more detailed description of a possible mechanism of action as well as of protein targets affected by the investigated NP.
(Ultra)-structural elucidation by microscopic techniques
The assessment of relevant structural alterations in our group is performed by a variety of microscopic techniques. On the one hand, classical light microscopic approaches (brightfield, darkground, phase contrast, polarization, fluorescence as well as DIC) are represented in our lab, allowing the examination of biological material on the lower micrometer scale (lateral resolution down to 0.2 µm).
On the other hand, innovative investigations on a nanometer scale are also possible by four atomic force microscopes (AFMs) in our lab, allowing lateral resolutions down to a fraction of an ångström (typically down to roughly 5 nm in biological material and under ambient conditions).
As a topographical technique, gaining insight into internal features of biological material by atomic force microscopy is still a challenging process. We therefore established an ultra-microtomic protocol, allowing insight into internal features of virtually any cell, tissue and organism by AFM for the first time. This technique was used in the recent years to describe the mechanism of action of different bioactive natural products.
Developed workflow for the facile ultrastructural elucidation of internal features of organisms, tissues or single cells by Atomic Force Microscopy (Herrmann et al., J. Struc. Biol. 2019)
AFM-elucidated ultrastructure of C. elegans L4 hermaphrodite´s spermathecal tissues after treatment with the quassinoid ailanthone (C, 50 µM) and compared to untreated morphology (A). S = single spermatocyte, Sp = single spermatid. (Adapted from Knetzger et al., Doi:10.3390/molecules26237354)
Additionally, our group is also focused on enzymatic as well as in silico techniques. After the identification and structural elucidation of a target protein, in silico techniques can be applied to screen large substance databases for compounds potentially interacting with the protein of interest (virtual screening). Furthermore, molecular docking analyses subsequently allow the estimation of the possible interaction of a set of given compounds with a protein, enabling us to identify the most promising hits for in vitro testing.
Spectroscopy-based in vitro inhibition experiments employing the recombinantly produced target protein are afterwards applied in order to verify the in silico predictions as well as to gain further insight into the mechanism of action of an enzyme inhibitor.
Current research projects
Supervised PhD theses