TY  - JOUR
A1  - Klein, Philipp
A1  - Barthels, Fabian
A1  - Johe, Patrick
A1  - Wagner, Annika
A1  - Tenzer, Stefan
A1  - Distler, Ute
A1  - Le, Thien Anh
A1  - Schmid, Paul
A1  - Engel, Volker
A1  - Engels, Bernd
A1  - Hellmich, Ute A.
A1  - Opatz, Till
A1  - Schirmeister, Tanja
T1  - Naphthoquinones as covalent reversible inhibitors of cysteine proteases — studies on inhibition mechanism and kinetics
JF  - Molecules
N2  - The facile synthesis and detailed investigation of a class of highly potent protease inhibitors based on 1,4-naphthoquinones with a dipeptidic recognition motif (HN-l-Phe-l-Leu-OR) in the 2-position and an electron-withdrawing group (EWG) in the 3-position is presented. One of the compound representatives, namely the acid with EWG = CN and with R = H proved to be a highly potent rhodesain inhibitor with nanomolar affinity. The respective benzyl ester (R = Bn) was found to be hydrolyzed by the target enzyme itself yielding the free acid. Detailed kinetic and mass spectrometry studies revealed a reversible covalent binding mode. Theoretical calculations with different density functionals (DFT) as well as wavefunction-based approaches were performed to elucidate the mode of action.
KW  - protease
KW  - rhodesain
KW  - covalent reversible inhibition
KW  - 1,4-naphthoquinone
KW  - nucleophilic addition
KW  - prodrug
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203791
SN  - 1420-3049
VL  - 25
IS  - 9
ER  - 
TY  - JOUR
A1  - Klein, Philipp
A1  - Johe, Patrick
A1  - Wagner, Annika
A1  - Jung, Sascha
A1  - Kühlborn, Jonas
A1  - Barthels, Fabian
A1  - Tenzer, Stefan
A1  - Distler, Ute
A1  - Waigel, Waldemar
A1  - Engels, Bernd
A1  - Hellmich, Ute A.
A1  - Opatz, Till
A1  - Schirmeister, Tanja
T1  - New cysteine protease inhibitors: electrophilic (het)arenes and unexpected prodrug identification for the Trypanosoma protease rhodesain
JF  - Molecules
N2  - Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the S\(_N\)Ar addition/elimination reactions. Such building blocks have only rarely been employed for the design of enzyme inhibitors. Herein, we demonstrate the combination of a peptidic recognition sequence with such electrophilic (het)arenes to generate highly active inhibitors of disease-relevant proteases. We further elucidate an unexpected mode of action for the trypanosomal protease rhodesain using NMR spectroscopy and mass spectrometry, enzyme kinetics and various types of simulations. After hydrolysis of an ester function in the recognition sequence of a weakly active prodrug inhibitor, the liberated carboxylic acid represents a highly potent inhibitor of rhodesain (K\(_i\) = 4.0 nM). The simulations indicate that, after the cleavage of the ester, the carboxylic acid leaves the active site and re-binds to the enzyme in an orientation that allows the formation of a very stable π-complex between the catalytic dyad (Cys-25/His-162) of rhodesain and the electrophilic aromatic moiety. The reversible inhibition mode results because the S\(_N\)Ar reaction, which is found in an alkaline solvent containing a low molecular weight thiol, is hindered within the enzyme due to the presence of the positively charged imidazolium ring of His-162. Comparisons between measured and calculated NMR shifts support this interpretation
KW  - cysteine protease
KW  - rhodesain
KW  - electrophilic (het)arene
KW  - nucleophilic aromatic substitution
KW  - Meisenheimer complex
KW  - π-complex
KW  - prodrug
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203380
SN  - 1420-3049
VL  - 25
IS  - 6
ER  - 
TY  - JOUR
A1  - Dietschreit, Johannes C. B.
A1  - Wagner, Annika
A1  - Le, T. Anh
A1  - Klein, Philipp
A1  - Schindelin, Hermann
A1  - Opatz, Till
A1  - Engels, Bernd
A1  - Hellmich, Ute A.
A1  - Ochsenfeld, Christian
T1  - Predicting \(^{19}\)F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex
JF  - Angewandte Chemie International Edition
N2  - The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable \(^{19}\)F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the \(^{19}\)F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of \(^{19}\)F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.
KW  - African sleeping sickness
KW  - covalent inhibitors
KW  - NMR spectroscopy
KW  - quantum chemistry
KW  - structural biology
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-214879
VL  - 59
IS  - 31
SP  - 12669
EP  - 12673
ER  -