The Herrmann AFM Group
Elucidating the mechanisms of action of bioactive natural products by AFM

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 site of action in an alternative way, our group is using ultrastructural morphological assessments of cells, tissues and whole organisms as a shortcut to pinpoint histological changes evoked by a bioactive NP and therefore allowing the identification of a possible mechanism of action. 

(Ultra)-structural elucidation by microscopy

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, investigations on a nanometer scale are also possible by three atomic force microscopes (AFMs) in our lab, allowing lateral resolutions down to a fraction of an ångström (typically down to roughly 1 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.

In silico and enzymatic techniques

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

  • Development of ultramicrotomy-based techniques allowing the ultrastructural characterization of cells, tissues and organisms by AFM and light microscopy

  • AFM-based analysis of isolated peptidoglycan sacculi to establish a screening assay for novel cell wall inhibiting antibiotics

  • Ultrastructural evaluation of the antibacterial effects of galectins 3 and 4

  • Ultrastructural evaluation of the mechanism of action of different quassinoids and proanthocyanidins against Caenorhabditis elegans