Probing Structure–Function Relationships of Serine Hydrolases and Proteases with Carbamate and Thiocarbamate Inhibitors

An Irreversible Inhibitor to Probe the Role of Streptococcus pyogenes Cysteine Protease SpeB in Evasion of Host Complement Defenses

Members of the CA class of cysteine proteases have multifaceted roles in physiology and virulence for many bacteria. Streptococcal pyrogenic exotoxin B (SpeB) is secreted by Streptococcus pyogenes and implicated in the pathogenesis of the bacterium through degradation of key human immune effector proteins. Here, we developed and characterized a clickable inhibitor, 2S-alkyne, based on X-ray crystallographic analysis and structure-activity relationships. Our SpeB probe showed irreversible enzyme inhibition in biochemical assays and labeled endogenous SpeB in cultured S. pyogenes supernatants. Importantly, application of 2S-alkyne decreased S. pyogenes survival in the presence of human neutrophils and supports the role of SpeB-mediated proteolysis as a mechanism to limit complement-mediated host defense. We posit that our SpeB inhibitor will be a useful chemical tool to regulate, label, and quantitate secreted cysteine proteases with SpeB-like activity in complex biological samples and a lead candidate for new therapeutics designed to sensitize S. pyogenes to host immune clearance.

5,6-Benzoflavones as cholesterol esterase inhibitors: synthesis, biological evaluation and docking studies

In a continued effort to develop potent cholesterol esterase (CEase) inhibitors, a series of 5,6-benzoflavone derivatives was rationally designed and synthesized by changing the position of the benzene ring attached to the flavone skeleton in previously reported 7,8-benzoflavones. All the synthesized compounds were checked for their inhibitory potential against cholesterol esterase (CEase) using a spectrophotometric assay. Among the series of forty compounds, seven derivatives (B-10 to B-16) exhibited above 90 percent inhibition against CEase in an in vitro enzymatic assay. Compound B-16 showed the most promising activity with an IC50 value of 0.73 nM against cholesterol esterase. To determine the type of inhibition, enzyme kinetic studies were carried out for B-16, which revealed its mixed-type inhibition approach. Moreover, to figure out the key binding interactions of B-16 with the amino acid residues of the enzyme's active site, molecular protein-ligand docking studies were also performed. B-16 completely blocks the catalytic assembly of CEase and prevents it from participating in the ester hydrolysis mechanism. The favorable binding conformation of B-16 suggests its prevailing role as a CEase inhibitor. Overall, the study showed that the cis-orientation of ring A with respect to the carbonyl group of ring C is responsible for the potent CEase inhibitory activity of the newly synthesized compounds.

Crystal structure of phenyl N-(3,5-di-methyl-phenyl)carbamate

The asymmetric unit of the title carbamate, contains two independent mol­ecules (A and B) with similar conformations. In the crystal, they are arranged alternately, forming –A–B–A–B– chains linked by N—H⋯O(carbon­yl) hydrogen bonds, which extend along the a-axis direction.

The asymmetric unit of the title compound, C₁₅H₁₅NO₂, contains two independent mol­ecules (A and B). The di­methyl­phenyl ring, the phenyl ring and the central carbamate N—C(=O)—O group are not coplanar. In mol­ecule A, the di­methyl­phenyl and phenyl rings are inclined to the carbamate group mean plane by 27.71 (13) and 71.70 (4)°, respectively, and to one another by 84.53 (13)°. The corresponding dihedral angles in mol­ecule B are 34.33 (11), 66.32 (13) and 85.48 (12)°, respectively. In the crystal, the A and B mol­ecules are arranged alternately linked through N—H⋯O(carbon­yl) hydrogen bonds, forming –A–B–A–B– chains, which extend along [100]. Within the chains and linking neighbouring chains there are C—H⋯π inter­actions present, forming columns along the a-axis direction. The columns are linked by offset π–π stacking inter­actions, forming a three-dimensional network [shortest centroid–centroid distance = 3.606 (1) Å].

Benzoflavones as cholesterol esterase inhibitors: Synthesis, biological evaluation and docking studies

A library of forty 7,8-benzoflavone derivatives was synthesized and evaluated for their inhibitory potential against cholesterol esterase (CEase). Among all the synthesized compounds seven benzoflavone derivatives (A-7, A-8, A-10, A-11, A-12, A-13, A-15) exhibited significant inhibition against CEase in in vitro enzymatic assay. Compound A-12 showed the most promising activity with IC₅₀ value of 0.78nM against cholesterol esterase. Enzyme kinetic studies carried out for A-12, revealed its mixed-type inhibition approach. Molecular protein-ligand docking studies were also performed to figure out the key binding interactions of A-12 with the amino acid residues of the enzyme's active site. The A-12 fits well at the catalytic site and is stabilized by hydrophobic interactions. It completely blocks the catalytic assembly of CEase and prevents it to participate in ester hydrolysis mechanism. The favorable binding conformation of A-12 suggests its prevailing role as CEase inhibitor.

Crystal structures of 4-chloro-phenyl N-(3,5-di-nitro-phen-yl)carbamate and phenyl N-(3,5-di-nitro-phen-yl)carbamate

The title compounds, C13H8ClN3O6, (I), and C13H9N3O6, (II), differ in the orientation of the two aromatic rings. In (I), they are essentially coplanar, making a dihedral angle of 8.2 (1)°, while in (II), they are inclined to one another by 76.2 (1)°. The two nitro groups are essentially coplanar with the attached benzene rings, as indicated by the dihedral angles of 1.4 (2) and 2.3 (2)° in (I), and 4.96 (18) and 5.4 (2)° in (II). The carbamate group is twisted slightly from the attached benzene ring, with a C-N-C-O torsion angle of -170.17 (15)° for (I) and 168.91 (13)° for (II). In the crystals of of both compounds, mol-ecules are linked via N-H⋯O hydrogen bonds, forming chains propagating along [010]. In (I), C-H⋯O hydrogen bonds also link mol-ecules within the chains. The crystal packing in (I) also features a very weak π-π inter-action [centroid-centroid distance = 3.7519 (9) Å].

Synthesis and biological evaluation of phosphorylated flavonoids as potent and selective inhibitors of cholesterol esterase

A series of phosphorylated flavonoids were synthesized and investigated in vitro as inhibitors of pancreatic cholesterol esterase (CEase) and acetylcholinesterase (AChE). The results showed that most of the synthesized compounds exhibited nanomolar potency against CEase, much better than the parent flavonoids. Furthermore, these phosphorylated flavonoids demonstrated good to high selectivity for CEase over AChE, which only showed micromolar potency inhibition of AChE. The most selective and potent inhibitor of CEase (3e) had IC₅₀ value of 0.72 nM and 11800-fold selectivity for CEase over AChE. The structure-activity relationships revealed that the free hydroxyl group at position 5 and phosphate group at position 7 of the phosphorylated flavonoids are favorable to the inhibition of CEase. The inhibition mechanism and kinetic characterization studies indicated that they are irreversible competitive inhibitors of CEase.

Structure-property relationships of a class of carbamate-based fatty acid amide hydrolase (FAAH) inhibitors: chemical and biological stability

Cyclohexylcarbamic acid aryl esters are a class of fatty acid amide hydrolase (FAAH) inhibitors, which includes the reference compound URB597. The reactivity of their carbamate fragment is involved in pharmacological activity and may affect their pharmacokinetic and toxicological properties. We conducted in vitro stability experiments in chemical and biological environments to investigate the structure-stability relationships in this class of compounds. The results show that electrophilicity of the carbamate influences chemical stability, as suggested by the relation between the rate constant of alkaline hydrolysis (log k(pH9)) and the energy of the lowest unoccupied molecular orbital (LUMO). Introduction of small electron-donor substituents at conjugated positions of the O-aryl moiety increased the overall hydrolytic stability of the carbamate group without affecting FAAH inhibitory potency, whereas peripheral non-conjugated hydrophilic groups, which favor FAAH recognition, helped decrease oxidative metabolism in the liver.