Rhomboid proteases form one of the most widespread intramembrane protease families. They have been implicated in variety of human diseases. The currently reported rhomboid inhibitors display some selectivity, but their construction involves multistep synthesis protocols. Here, we report benzoxazin-4-ones as novel inhibitors of rhomboid proteases with a covalent, but slow reversible inhibition mechanism. Benzoxazin-4-ones can be synthesized from anthranilic acid derivatives in a one-step synthesis, making them easily accessible. We demonstrate that an alkoxy substituent at the 2-position is crucial for potency and results in low micromolar inhibitors of rhomboid proteases. Hence, we expect that these compounds will allow rapid synthesis and optimization of inhibitors of rhomboids from different organisms.

• MeSH
• Bacillus subtilis enzymologie   MeSH
• benzoxaziny chemická syntéza   chemie   farmakologie   MeSH
• chymotrypsin antagonisté a inhibitory   MeSH
• DNA vazebné proteiny antagonisté a inhibitory   MeSH
• endopeptidasy MeSH
• enzymatické testy MeSH
• Escherichia coli enzymologie   MeSH
• inhibitory serinových proteinas chemická syntéza   chemie   farmakologie   MeSH
• inhibitory trypsinu chemická syntéza   chemie   farmakologie   MeSH
• membránové proteiny antagonisté a inhibitory   MeSH
• molekulární struktura MeSH
• ortoaminobenzoáty chemie   MeSH
• proteiny z Escherichia coli antagonisté a inhibitory   MeSH
• skot MeSH
• trypsin chemie   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• zvířata MeSH
• Check Tag
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Rhomboids are intramembrane serine proteases with diverse physiological functions in organisms ranging from archaea to humans. Crystal structure analysis has provided a detailed understanding of the catalytic mechanism, and rhomboids have been implicated in various disease contexts. Unfortunately, the design of specific rhomboid inhibitors has lagged behind, and previously described small molecule inhibitors displayed insufficient potency and/or selectivity. Using a computer-aided approach, we focused on the discovery of novel scaffolds with reduced liabilities and the possibility for broad structural variations. Docking studies with the E. coli rhomboid GlpG indicated that 2-styryl substituted benzoxazinones might comprise novel rhomboid inhibitors. Protease in vitro assays confirmed activity of 2-styryl substituted benzoxazinones against GlpG but not against the soluble serine protease α-chymotrypsin. Furthermore, mass spectrometry analysis demonstrated covalent modification of the catalytic residue Ser201, corroborating the predicted mechanism of inhibition and the formation of an acyl enzyme intermediate. In conclusion, 2-styryl substituted benzoxazinones are a novel rhomboid inhibitor scaffold with ample opportunity for optimization.

• MeSH
• benzoxaziny chemická syntéza   chemie   MeSH
• chymotrypsin chemie   MeSH
• DNA vazebné proteiny antagonisté a inhibitory   chemie   genetika   MeSH
• Drosophila chemie   MeSH
• endopeptidasy chemie   genetika   MeSH
• enzymatické testy MeSH
• Escherichia coli enzymologie   MeSH
• inhibitory serinových proteinas chemická syntéza   chemie   MeSH
• katalytická doména MeSH
• lidé MeSH
• membránové proteiny antagonisté a inhibitory   chemie   genetika   MeSH
• mutace MeSH
• objevování léků MeSH
• proteiny Drosophily metabolismus   MeSH
• proteiny z Escherichia coli antagonisté a inhibitory   chemie   genetika   MeSH
• serin chemie   MeSH
• simulace molekulového dockingu MeSH
• skot MeSH
• styreny chemická syntéza   chemie   MeSH
• transformující růstový faktor alfa metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• skot MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl-chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. We show that peptidyl-CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate-like manner, and their co-crystal structures with GlpG reveal the S1 to S4 subsites of the protease. The S1 subsite is prominent and merges into the 'water retention site', suggesting intimate interplay between substrate binding, specificity and catalysis. Unexpectedly, the S4 subsite is plastically formed by residues of the L1 loop, an important but hitherto enigmatic feature of the rhomboid fold. We propose that the homologous region of members of the wider rhomboid-like protein superfamily may have similar substrate or client-protein binding function. Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG.

• MeSH
• chloromethylketony aminokyselin chemická syntéza   farmakologie   MeSH
• DNA vazebné proteiny antagonisté a inhibitory   chemie   genetika   metabolismus   MeSH
• endopeptidasy chemie   genetika   metabolismus   MeSH
• Escherichia coli chemie   enzymologie   genetika   MeSH
• katalytická doména MeSH
• krystalografie rentgenová MeSH
• membránové proteiny antagonisté a inhibitory   chemie   genetika   metabolismus   MeSH
• molekulární modely * MeSH
• mutace MeSH
• proteiny z Escherichia coli antagonisté a inhibitory   chemie   genetika   metabolismus   MeSH
• Providencia chemie   MeSH
• rekombinantní proteiny MeSH
• simulace molekulární dynamiky * MeSH
• substrátová specifita MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A series of N (alpha)-acyl (alkyl)- and N (alpha)-alkoxycarbonyl-derivatives of L- and D-ornithine were prepared, characterized, and analyzed for their potency toward the bacterial enzyme N (alpha)-acetyl-L-ornithine deacetylase (ArgE). ArgE catalyzes the conversion of N (alpha)-acetyl-L-ornithine to L-ornithine in the fifth step of the biosynthetic pathway for arginine, a necessary step for bacterial growth. Most of the compounds tested provided IC(50) values in the muM range toward ArgE, indicating that they are moderately strong inhibitors. N (alpha)-chloroacetyl-L-ornithine (1g) was the best inhibitor tested toward ArgE providing an IC(50) value of 85 microM while N (alpha)-trifluoroacetyl-L-ornithine (1f), N (alpha)-ethoxycarbonyl-L-ornithine (2b), and N (alpha)-acetyl-D-ornithine (1a) weakly inhibited ArgE activity providing IC(50) values between 200 and 410 microM. Weak inhibitory potency toward Bacillus subtilis-168 for N (alpha)-acetyl-D-ornithine (1a) and N (alpha)-fluoro- (1f), N (alpha)-chloro- (1g), N (alpha)-dichloro- (1h), and N (alpha)-trichloroacetyl-ornithine (1i) was also observed. These data correlate well with the IC(50) values determined for ArgE, suggesting that these compounds might be capable of getting across the cell membrane and that ArgE is likely the bacterial enzymatic target.

• MeSH
• amidohydrolasy antagonisté a inhibitory   MeSH
• antibakteriální látky chemická syntéza   chemie   farmakologie   MeSH
• Bacillus subtilis účinky léků   MeSH
• fosgen analogy a deriváty   chemie   MeSH
• hmotnostní spektrometrie s elektrosprejovou ionizací MeSH
• inhibitory enzymů chemická syntéza   chemie   farmakologie   MeSH
• kinetika MeSH
• magnetická rezonanční spektroskopie MeSH
• mikrobiální testy citlivosti MeSH
• molekulární struktura MeSH
• molekulová hmotnost MeSH
• ornithin analogy a deriváty   chemická syntéza   chemie   farmakologie   MeSH
• polystyreny chemie   MeSH
• proteiny z Escherichia coli antagonisté a inhibitory   MeSH
• racionální návrh léčiv MeSH
• vysokoúčinná kapalinová chromatografie MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH