Inhibitors of rhomboid proteases

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.

Rapid synthesis of internal peptidyl α-ketoamides by on resin oxidation for the construction of rhomboid protease inhibitors

Rhomboid proteases are intramembrane serine proteases, which are involved in a wide variety of biological processes and have been implied in various human diseases. Recently, peptidyl α-ketoamides have been reported as rhomboid inhibitors with high potency and selectivity – owing to their interaction with both the primed and non-primed site of the target protease. However, their synthesis has been performed by solution phase chemistry. Here, we report a solid phase strategy towards ketoamides as rhomboid protease inhibitors, allowing rapid synthesis and optimization. We found that the primed site binding part of inhibitors is crucial for potency.

Rhomboid intramembrane serine proteases are involved in various biological processes. A solid phase synthesis of internal α-ketoamides reported here shows that primed site elements are crucial for rhomboid protease inhibition.

Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria

Rhomboid intramembrane proteases regulate pathophysiological processes, but their targeting in a disease context has never been achieved. We decoded the atypical substrate specificity of malaria rhomboid PfROM4, but found, unexpectedly, that it results from "steric exclusion": PfROM4 and canonical rhomboid proteases cannot cleave each other's substrates due to reciprocal juxtamembrane steric clashes. Instead, we engineered an optimal sequence that enhanced proteolysis >10-fold, and solved high-resolution structures to discover that boronates enhance inhibition >100-fold. A peptide boronate modeled on our "super-substrate" carrying one "steric-excluding" residue inhibited PfROM4 but not human rhomboid proteolysis. We further screened a library to discover an orthogonal alpha-ketoamide that potently inhibited PfROM4 but not human rhomboid proteolysis. Despite the membrane-immersed target and rapid invasion, ultrastructural analysis revealed that single-dosing blood-stage malaria cultures blocked host-cell invasion and cleared parasitemia. These observations establish a strategy for designing parasite-selective rhomboid inhibitors and expose a druggable dependence on rhomboid proteolysis in non-motile parasites.

Exploring the antioxidant effects of peptides from almond proteins using PAni-Ag-GONC conjugated trypsin by improving enzyme stability & applications

Functionalized graphene oxide nano-sheets (PAni-Ag-GONC) were prepared and employed as carrier for covalent immobilization of trypsin. This low cost setting, which involves loading of high amount of enzyme on the matrix, displayed significantly enhanced thermo-stability and pH resistance. The nano-composite (NC) bound trypsin preserved 90% of activity whereas native trypsin retained only 44% of activity after 60 days of storage at a temperature of 4°C. Immobilized trypsin conserved 80.5% of activity even after its ten repeated uses. Almond protein hydrolysates prepared by native and conjugated enzyme was investigated for antioxidant activities and found that peptides resulted from NC bound trypsin displayed increase in radical scavenging activity (i.e. around 30% and 37% scavenging activity observed, respectively by native and NC bound trypsin from same concentration of peptides). This strategy provides a new approach for production of potential biopeptides which may be incorporated in drugs and functional food industries applying PAni-Ag-GONC based biocatalysis. CHEMICAL COMPOUNDS: Trichloroacetic acid (PubChem CID: 6421); Tris (hydroxymethyl)aminomethane (PubChem CID: 6503); Glycine (PubChem CID: 750); and 2,2'-diphenyl-1-picrylhydrazyl (PubChem CID: 74358); Nα- Benzoyl-DL-arginine 4-nitroanilide hydrochloride (PubChem CID: 2724371); Ammonium sulphate (PubChem CID: 6097028).

Isolation of intramembrane proteases in membrane-like environments

Intramembrane proteases (IMPs) are proteolytic enzymes embedded in the lipid bilayer, where they cleave transmembrane substrates. The importance of IMPs relies on their role in a wide variety of cellular processes and diseases. In order to study the activity and function of IMPs, their purified form is often desired. The production of pure and active IMPs has proven to be a challenging task. This process unavoidably requires the use of solubilizing agents that will, to some extent, alter the native environment of these proteases. In this review we present the current solubilization and reconstitution techniques that have been applied to IMPs. In addition, we describe how these techniques had an influence on the activity and structural studies of IMPs, focusing on rhomboid proteases and γ-secretase.

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.

Tailored Ahp-cyclodepsipeptides as Potent Non-covalent Serine Protease Inhibitors

The S1 serine protease family is one of the largest and most biologically important protease families. Despite their biomedical significance, generic approaches to generate potent, class-specific, bioactive non-covalent inhibitors for these enzymes are still limited. In this work, we demonstrate that Ahp-cyclodepsipeptides represent a suitable scaffold for generating target-tailored inhibitors of serine proteases. For efficient synthetic access, we developed a practical mixed solid- and solution-phase synthesis that we validated through performing the first chemical synthesis of the two natural products Tasipeptin A and B. The suitability of the Ahp-cyclodepsipeptide scaffold for tailored inhibitor synthesis is showcased by the generation of the most potent human HTRA protease inhibitors to date. We anticipate that our approach may also be applied to other serine proteases, thus opening new avenues for a systematic discovery of serine protease inhibitors.

A guide to the rhomboid protein superfamily in development and disease

Rhomboid proteins are considered to be the most widespread membrane proteins across all forms of life. This superfamily comprises both active intramembrane serine proteases that catalyze the release of factors from the membrane, and a eukaryotic subset of non-catalytic members in which rhomboid architecture supports deviating functions. Although rhomboid was discovered in genetic studies of insect development, rhomboid research has broadened dramatically over the past 15 years; rhomboid enzymes are now the best biophysically understood of all intramembrane proteases, and are considered promising therapeutic targets for diseases ranging from parasitic infections to Parkinsonian neurodegeneration. Perhaps the most rapid progress has come with the catalytically inert rhomboid proteins, some of which regulate protein trafficking and/or function, and their prominence is underscored by clinical mutations. Such a diverse collection of advances mark an excellent point to review the state of this vibrant area of research, not because central questions have been answered, but instead because a firm grip in key areas has been established, and the field is now poised for breakthroughs.

Chemical Tools for the Study of Intramembrane Proteases

Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.