Development of Novel Peptide-Based Michael Acceptors Targeting Rhodesain and Falcipain-2 for the Treatment of Neglected Tropical Diseases (NTDs)

Abstract

This paper describes the development of a class of peptide-based inhibitors as novel antitrypanosomal and antimalarial agents. The inhibitors are based on a characteristic peptide sequence for the inhibition of the cysteine proteases rhodesain of Trypanosoma brucei rhodesiense and falcipain-2 of Plasmodium falciparum. We exploited the reactivity of novel unsaturated electrophilic functions such as vinyl-sulfones, -ketones, -esters, and -nitriles. The Michael acceptors inhibited both rhodesain and falcipain-2, at nanomolar and micromolar levels, respectively. In particular, the vinyl ketone 3b has emerged as a potent rhodesain inhibitor (k = 67 × 10 M min), endowed with a picomolar binding affinity (K = 38 pM), coupled with a single-digit micromolar activity against Trypanosoma brucei brucei (EC = 2.97 μM), thus being considered as a novel lead compound for the discovery of novel effective antitrypanosomal agents.

Development of Novel Benzodiazepine‐Based Peptidomimetics as Inhibitors of Rhodesain from Trypanosoma brucei rhodesiense

“…In particular, superimposition between the binding pose achieved for 2 a and the one obtained for the potent peptidyl vinylketone RK‐52 (Cbz‐Phe‐hPhe‐VK‐Me) demonstrates that the two compounds occupy the same enzyme clefts. In particular, as shown in Figure a, the 2 a condensed benzodiazepine phenyl ring aligns with the Phe side chain of RK‐52 (S2 pocket) and 2a phenylethyl group aligns with the hPhe side chain of the same peptide (S1 pocket).…”

“… A) Superimposition of RK‐52 (green sticks) and 2 a (blue sticks) docked conformations in rhodesain (orange ribbons). B) Rhodesain/ 2 a complex.…”

“…In this case, as the newly devised ligands covalently bind to the enzyme, it was necessary to employ a specific docking protocol devised by Bianco et al., namely the “flexible side chain method”. The latter was also succesfully applied in our previous works on convalent Rhodesain inhibitors . This computational method requires the modification of the residue which takes part in the covalent bond and to attach it to the ligand; during the docking calculation, this modified residue is treated as flexible.…”

“…In this medicinal chemistry area, our research team has been involved in the last decade into the development of potent rhodesain inhibitors . In this paper, starting from the structure of the reversible rhodesain inhibitors 1 a – c , endowed with K i values in the low‐micromolar range (Scheme ), we designed a new series of peptidomimetics 2 a – g able to inactivate the target enzyme, considering that an irreversible inhibition is strongly desirable in the case of a parasitic target.…”

α‐Methylene‐β‐Lactone Scaffold for Developing Chemical Probes at the Two Ends of the Selectivity Spectrum

“…MeLac is small and rigid. It couples a moderately reactive acrylate type Michael acceptor [21,22] with a β‐lactone functionality [6,23,24] . Consequently, MeLac is prone to reactions with nucleophilic thiol (Cys), hydroxyl (Ser, Thr, and Tyr), and amino (Lys and the N terminus) groups on the protein.…”