Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases

Extensive targeting of chemical space at the prime side of ketoamide inhibitors of rhomboid proteases by branched substituents empowers their selectivity and potency

Rhomboid intramembrane serine proteases have been implicated in several pathologies, and emerge as attractive pharmacological target candidates. The most potent and selective rhomboid inhibitors available to date are peptidyl α-ketoamides, but their selectivity for diverse rhomboid proteases and strategies to modulate it in relevant contexts are poorly understood. This gap, together with the lack of suitable in vitro models, hinders ketoamide development for relevant eukaryotic rhomboid enzymes. Here we explore the structure-activity relationship principles of rhomboid inhibiting ketoamides by medicinal chemistry and enzymatic in vitro and in-cell assays with recombinant rhomboid proteases GlpG, human mitochondrial rhomboid PARL and human RHBDL2. We use X-ray crystallography in lipidic cubic phase to understand the binding mode of one of the best ketoamide inhibitors synthesized here containing a branched terminal substituent bound to GlpG. In addition, to extend the interpretation of the co-crystal structure, we use quantum mechanical calculations and quantify the relative importance of interactions along the inhibitor molecule. These combined experimental analyses implicates that more extensive exploration of chemical space at the prime side is unexpectedly powerful for the selectivity of rhomboid inhibiting ketoamides. Together with variations in the peptide sequence at the non-prime side, or its non-peptidic alternatives, this strategy enables targeted tailoring of potent and selective ketoamides towards diverse rhomboid proteases including disease-relevant ones such as PARL and RHBDL2.

Activity-Based Protein Profiling of RHBDL4 Reveals Proteolysis of the Enzyme and a Distinct Inhibitor Profile

Rhomboid proteases have fascinated scientists by virtue of their membrane-embedded active sites and proposed involvement in physiological and disease pathways. The human rhomboid protease RHBDL4 has generated particular interest due to its role in endoplasmic reticulum-associated protein degradation and upregulation in several cancers; however, chemical tools for studying this enzyme are currently lacking. Here, we describe the development of an activity-based protein profiling (ABPP) assay for RHBDL4. We have employed this assay to determine that human RHBDL4 undergoes proteolytic processing in cells to produce multiple active proteoforms with truncated C-termini. We have also used this assay to identify chemical scaffolds capable of inhibiting RHBDL4 activity and have observed distinct inhibitor preferences between RHBDL4 and a second human rhomboid protease PARL. Our work demonstrates the power of ABPP technology to characterize active forms of enzymes that might otherwise elude detection and the potential to achieve selective inhibition among the human rhomboid proteases.

4-Oxo-β-Lactams as Novel Inhibitors for Rhomboid Proteases

Intramembrane serine proteases (rhomboid proteases) are involved in a variety of biological processes and are implicated in several diseases. Here, we report 4-oxo-β-lactams as a novel scaffold for inhibition of rhomboids. We show that they covalently react with the active site and that the covalent bond is sufficiently stable for detection of the covalent rhomboid-lactam complex. 4-Oxo-β-lactams may therefore find future use as both inhibitors and activity-based probes for rhomboid proteases.

N-Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction

With a resurgence of covalent drugs, there is an urgent need for the identification of new moieties capable of cysteine bond formation. Herein, we report on the N-acylamino saccharin moieties capable of novel covalent reactions with cysteine. Their utility as alternative electrophilic warheads was demonstrated through the covalent modification of fructose-1,6-bisphosphatase (FBPase), a promising target associated with cancer and type 2 diabetes. The cocrystal structure of title compound W8 bound with FBPase unexpectedly revealed that the N-acylamino saccharin moiety worked as an electrophile warhead that covalently modified the noncatalytic C128 site in FBPase while releasing saccharin, suggesting a previously undiscovered covalent reaction mechanism of saccharin derivatives with cysteine. Treatment of title compound W8 displayed potent inhibition of glucose production in vitro and in vivo. This newly discovered reactive warhead supplements the current repertoire of cysteine covalent modifiers while avoiding some of the limitations generally associated with established moieties.

A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor

Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions.

Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.

Development of succinimide-based inhibitors for the mitochondrial rhomboid protease PARL

While the biochemistry of rhomboid proteases has been extensively studied since their discovery two decades ago, efforts to define the physiological roles of these enzymes are ongoing and would benefit from chemical probes that can be used to manipulate the functions of these proteins in their native settings. Here, we describe the use of activity-based protein profiling (ABPP) technology to conduct a targeted screen for small-molecule inhibitors of the mitochondrial rhomboid protease PARL, which plays a critical role in regulating mitophagy and cell death. We synthesized a series of succinimide-containing sulfonyl esters and sulfonamides and discovered that these compounds serve as inhibitors of PARL with the most potent sulfonamides having submicromolar affinity for the enzyme. A counterscreen against the bacterial rhomboid protease GlpG demonstrates that several of these compounds display selectivity for PARL over GlpG by as much as two orders of magnitude. Both the sulfonyl ester and sulfonamide scaffolds exhibit reversible binding and are able to engage PARL in mammalian cells. Collectively, our findings provide encouraging precedent for the development of PARL-selective inhibitors and establish N-[(arylsulfonyl)oxy]succinimides and N-arylsulfonylsuccinimides as new molecular scaffolds for inhibiting members of the rhomboid protease family.

Assessment of anti-inflammatory-like, antioxidant activities and molecular docking of three alkynyl-substituted 3-ylidene-dihydrobenzo[d]isothiazole 1,1-dioxide derivatives

The presence of enyne and benzoisothiazole functions in the molecular architecture of compounds 1, 2 and 3 were expected to provide biochemical activities. In the present work, we first examined the molecular surface contact of three alkynyl-substituted 3-ylidenedihydrobenzo[d] isothiazole 1,1-dioxides. The analysis of the Hirshfeld surfaces reveals that only compound 3 exhibited a well-defined red spots, indicating intermolecular interactions identified as S-O⋯H, C-H⋯O and C-O⋯H contacts. Comparative fingerprint histograms of the three compounds show that close pair interactions are dominated by C-H⋯H-C contact. By UV-visible analysis, compound 1 showed the most intense absorbances at 407 and 441 nm, respectively. The radical scavenging activity explored in the DPPH test, shows that only 1 exhibited low anti-radical activity. Furthermore, cellular antioxidant capacity of benzoisothiazoles 1-3 was investigated with PMA-activated HL-60 cells using chemiluminescence and fluorescence techniques in the presence of L-012 and Amplex Red probe, respectively. Results highlight that compound 1 exhibited moderate anti-ROS capacity while compounds 2 and 3 enhanced ROS production. The cytotoxicity test performed on HL-60 cells, using the MTS assay, confirmed the lack of toxicity of the tested benzoisothiazole 1 compared to 2 and 3 which show low cytotoxicity (≤30%). Anti-catalytic activity was evaluated by following the inhibitory potential of the benzoisothiazoles on MPO activity and depicted benzoisothiazoles-MPO interactions by docking. Both SIEFED and docking studies demonstrated an anti-catalytic activity of the tested benzoisothiazoles towards MPO with the best activity for compound 2.

Stable and Functional Rhomboid Proteases in Lipid Nanodiscs by Using Diisobutylene/Maleic Acid Copolymers

Rhomboid proteases form a paradigm for intramembrane proteolysis and have been implicated in several human diseases. However, their study is hampered by difficulties in solubilization and purification. We here report on the use of polymers composed of maleic acid and either diisobutylene or styrene for solubilization of rhomboid proteases in lipid nanodiscs, which proceeds with up to 48% efficiency. We show that the activity of rhomboids in lipid nanodiscs is closer to that in the native membrane than rhomboids in detergent. Moreover, a rhomboid that was proteolytically unstable in detergent turned out to be stable in lipid nanodiscs, underlining the benefit of using these polymer-stabilized nanodiscs. The systems are also compatible with the use of activity-based probes and can be used for small molecule inhibitor screening, allowing several downstream applications.