Parasitic cysteine protease inhibitors/ warhead design/ RNA-aptamer conjugation/ pharmacokinetic inhibitor monitoring

Natalie Fuchs, Mergim Meta, Collin Zimmer


Covalently binding drugs have proved to be successful therapeutic options for various indications, but largely owing to safety concerns, they began to be abandoned when initiating target-directed drug discovery projects in the past. These safety concerns include the potential of immunogenic and toxic reactions, arising from possible unspecific off-target protein modifications. Despite these concerns, covalent drugs were recognized to have several beneficial properties over their non-covalent counterparts, including better target-affinity, prolonged residence times, lower sensitivity against pharmacokinetic aspects, and high efficacy. Structure-based computational methods have rationalized the design of inhibitors that combine carefully tuned reactivity with specific non-covalent binding interactions to the target. Instead of irreversibly inhibiting the target structure, covalent reversible inhibition emerged as a strategy to avoid the potential risks of irreversible off-target modifications while maintaining some of the covalent benefits.

In our group, we investigate the influence of different electrophilic functional groups, localized at the P1-position of an inhibitor, the so-called `warhead`, with the aim of fine-tuning the reactivity versus the selectivity profile of parasitic (rhodesain) and other cysteine protease inhibitors involved in parasitic diseases like Human African Trypanosomiasis (HAT), cancer or viral infections (e. g. SARS-CoV 2).

A complementary approach to advance the selectivity profile of these highly active compounds is the design of a hybrid molecule, comprised of a covalent inhibitor against the trypanosomal protease rhodesain and an RNA-aptamer conferring specific targeting through mediated uptake and intracellular transport by the parasite.

Furthermore, we are interested in the pharmacokinetic characterization of our compounds using microsomal stability assays and in vivo distribution studies (in cooperation with the group of Prof. J. Klein, Goethe University Frankfurt).

Figure 1: Development of covalent (ir)reversible inhibitors.

Figure 2: Design of an Aptamer-Drug-Conjugate for selective targeting.

Figure 3: In vivo biodistribution studies (cooperation with AK Klein, Frankfurt).


Schirmeister, T., Kesselring, J., Jung, S., et al. Quantum Chemical-Based Protocol for the Rational Design of Covalent Inhibitors. J. Am. Chem. Soc. 2016, 138, 27, 8332–8335.