Peptidyl Fluoromethyl Ketones and Their Applications in Medicinal Chemistry

Abstract

Peptidyl fluoromethyl ketones occupy a pivotal role in the current scenario of synthetic chemistry, thanks to their numerous applications as inhibitors of hydrolytic enzymes. The insertion of one or more fluorine atoms adjacent to a C-terminal ketone moiety greatly modifies the physicochemical properties of the overall substrate, especially by increasing the reactivity of this functionalized carbonyl group toward nucleophiles. The main application of these peptidyl α-fluorinated ketones in medicinal chemistry relies in their ability to strongly and selectively inhibit serine and cysteine proteases. These compounds can be used as probes to study the proteolytic activity of the aforementioned proteases and to elucidate their role in the insurgence and progress on several diseases. Likewise, if the fluorinated methyl ketone moiety is suitably connected to a peptidic backbone, it may confer to the resulting structure an excellent substrate peculiarity and the possibility of being recognized by a specific subclass of human or pathogenic proteases. Therefore, peptidyl fluoromethyl ketones are also currently highly exploited for the target-based design of compounds for the treatment of topical diseases such as various types of cancer and viral infections.

SARS-CoV-2 Mpro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors

“…Peptidyl fluoromethyl ketones (pFMKs) have always been substrates capable of inhibiting viral and parasitic cysteine proteases [ 96 , 97 ], including the M pro of the coronavirus family. The presence of fluorine atoms in the C -terminal α position of a methyl ketone moiety enhances the susceptibility of carbonyl group to undergo a nucleophilic attack by the protease thiol group.…”

“…However, the therapeutic utility of MFMKs is compromised due to drawbacks related to their metabolism (formation of toxic fluoroacetate). Therefore, their use is essential limited to pharmacological tools as activity-based probes with selectivity toward cysteine proteases [ 96 ].…”

“…DFMKs and TFMKS instead appear to be much more promising with respect to MFMKs as therapeutics in view of their ability to target also serine proteases (increased electrophilicity of the carbonyl group) with no significant metabolic issues. Both fluorinated-type warheads may hit the target by a slow-binding competitive reversible mechanism or act as transition-state competitive analogues because they may stand in the hydrated form [ 96 ]. In this regard, the first notable outcome was obtained in 2008 by Shao Y.-M. and co-workers which developed a series of dipeptidyl TFMKs as good inhibitors of SARS-CoV M pro in vitro [ 99 ].…”

“…The cloning, expression, and purification procedures for SARS-CoV-2 M pro and SARS-CoV-2 PL pro and the synthesis of FRET-based peptide substrates were described in the literature [ 25 , 96 , 125 ]. The procedure, in the presence or not of the reducing agent, requires the incubation of the protease with various concentrations of inhibitors at 30 °C for 30 min in the assay buffer and the subsequent addition of the FRET-based substrate to initiate the reaction.…”

Pseudo-Dipeptide Bearing α,α-Difluoromethyl Ketone Moiety as Electrophilic Warhead with Activity against Coronaviruses

“…Part of our ongoing research is aimed at the discovery of small molecules endowed with an “electrophilic warhead” able to inactivate parasitic cysteine proteases by the formation of a reversible or irreversible covalent bond with the catalytic residue of the intended targets [ 9 , 10 , 11 , 12 ]. Peptide-based α-fluorinated ketones have long been considered compelling substrates in the drug discovery area to develop selective enzyme inhibitors and activity-based probes [ 13 ]. The α-fluorination of the methyl ketone functional group profoundly modifies the physicochemical properties of the related substrate and the reactivity of its carbonyl group [ 14 ].…”