New Cysteine Protease Inhibitors: Electrophilic (Het)arenes and Unexpected Prodrug Identification for the Trypanosoma Protease Rhodesain.

Electrophilic (het)arenes can undergo reactions with nucleophiles yielding π- or Meisenheimer (σ-) complexes or the products of the SNAr 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 (Ki = 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 SNAr 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.

Library of Azabenz-Annulated Core-Extended Perylene Derivatives with Diverse Substitution Patterns and Tunable Electronic and Optical Properties.

Here, we present a collection of different azabenz-annulated perylene derivatives. By developing new synthetic strategies and improving existing protocols, we have expanded the structural diversity of these dye molecules to a multifunctional class of ligating chromophores. The Pictet-Spengler (PS) reaction of 1-amino-perylenes with different aldehydes is used to modify the terminal substitution pattern. PS transformations of 1,6- and/or 1,7-diamino perylenes result in 2-fold annulated nitrogen-containing coronene-type molecules like anti-(ab)2-PBI 15, syn-(ab)2-PBI 16, and syn-(ab)2-PTE 18. In addition, azabenz-annulated perylene bisanhydrides (ab-PBA 6 and syn-(ab)2-PBA 19) were explored as universal starting materials providing access to any desired imide functionality. Furthermore, a newly developed regioselective nitration procedure for perylene monoimide diesters (PMIDE) enables the synthesis of 1-nitro-PMIDE 10 and thus of azabenz-annulated perylene derivatives with unsymmetric peri-substitution patterns (ab-PMIDE 12 and ab-PMIMA 13). According to our spectroscopic and theoretical investigations, the optical and electrochemical properties of these multifunctional chromophores can easily be modified and adjusted to many desirable applications following the synthetic strategies presented in this work.

Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies.

Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on molecular modeling approaches. 2d, the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymatic dilution assays and MS experiments indicate that 2d is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated 2d-(H) shows favorable metabolism and biodistribution by accumulation in mice brain tissue after intraperitoneal and oral administration. The highest antitrypanosomal activity was observed for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 (2e/4e) with nanomolar EC50 values (0.14/0.80 µM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calculations and MD simulations.