Structure-based design of non-peptide, carbohydrazide-based cathepsin K inhibitors

Investigation of Masked N-Acyl-N-isocyanates: Support for Oxadiazolones as Blocked N-Isocyanate Precursors

In contrast to carbon-substituted isocyanates that are common building blocks, N-substituted isocyanates remain underdeveloped and reports on their N-acyl derivatives (i. e. amido-isocyanates) are exceedingly rare. Herein, amido-isocyanates were investigated in the context of syntheses of aza-tripeptide and hydantoins subunits starting from simple bench-stable precursors. A key finding is that the amido-isocyanate formed in situ cyclized to yield an oxadiazolone, and that under suitable reaction conditions this heterocycle is a traceless blocked (masked) N-isocyanate. Using organic bases as catalysts and upon heating, oxadiazolone formation is observed, and various nucleophiles to provide the desired aza-dipeptides or hydantoins in moderate to high yields. Further support for an amido-isocyanate intermediate was obtained using carboxylic acids as nucleophiles, affording N-acylhydrazide products.

Discovery of novel triazolophthalazine derivatives as DNA intercalators and topoisomerase II inhibitors

A new series of triazolophthalazine derivatives was designed and synthesized as topoisomerase II (Topo II) inhibitors and DNA intercalators. The synthesized derivatives were evaluated in vitro for their cytotoxic activities against three human cancer cell lines: HepG2, MCF-7, and HCT-116 cells. Compound IX_b was the most potent counterpart with IC₅₀ values of 5.39 ± 0.4, 3.81 ± 0.2, and 4.38 ± 0.3 µM, as it was about 1.47, 1.77, and 1.19 times more active than doxorubicin (IC₅₀  = 7.94 ± 0.6, 6.75 ± 0.4, and 5.23 ± 0.3 µM) against HepG2, MCF-7, and HCT-116 cells, respectively. Additionally, the binding affinity of the synthesized compounds toward the DNA molecule was assessed using the DNA/methyl green assay. Compound IX_b showed an excellent DNA binding affinity with an IC₅₀ value of 27.16 ± 1.2 µM, which was better than that of the reference drug doxorubicin (IC₅₀  = 31.02 ± 1.80 µM). Moreover, compound IX_b was the most potent member among the tested compounds when investigated for their Topo II inhibitory activity. Furthermore, compound IX_b induced apoptosis in HepG2 cells and arrested the cell cycle at the G2/M phase. Additionally, compound IX_b showed Topo II poisoning effects at 2.5 μM and Topo II catalytic inhibitory effects at 5 and 10 μM. Finally, molecular docking studies were carried out against the DNA-Topo II complex and DNA, to investigate the binding patterns of the designed compounds.

One-pot preparation of trifluoromethylated homoallylic N-acylhydrazines or α-methylene-γ-lactams from acylhydrazines, trifluoroacetaldehyde methyl hemiacetal, allyl bromide and tin

Tin promoted one-pot preparation of trifluoromethylated homoallylic N-acylhydrazines or α-methylene-γ-lactams has been developed instead of using toxic stannanes.

Phenyliodonium diacetate mediated carbotrifluoromethylation of N-acylhydrazones

A concise, efficient and direct trifluoromethylation method of aldehyde-derived N-acylhydrazones has been firstly developed by using the combination of inexpensive, stable and commercially available TMSCF₃ and PhI(OAc)₂ as the CF₃ source under mild reaction conditions.

Residue-specific annotation of disorder-to-order transition and cathepsin inhibition of a propeptide-like crammer from D. melanogaster

Drosophila melanogaster crammer is a novel cathepsin inhibitor involved in long-term memory formation. A molten globule-to-ordered structure transition is required for cathepsin inhibition. This study reports the use of alanine scanning to probe the critical residues in the two hydrophobic cores and the salt bridges of crammer in the context of disorder-to-order transition and cathepsin inhibition. Alanine substitution of the aromatic residues W9, Y12, F16, Y20, Y32, and W53 within the hydrophobic cores, and charged residues E8, R28, R29, and E67 in the salt bridges considerably decrease the ability of crammer to inhibit Drosophila cathepsin B (CTSB). Far-UV circular dichroism (CD), intrinsic fluorescence, and nuclear magnetic resonance (NMR) spectroscopies show that removing most of the aromatic and charged side-chains substantially reduces thermostability, alters pH-dependent helix formation, and disrupts the molten globule-to-ordered structure transition. Molecular modeling indicates that W53 in the hydrophobic Core 2 is essential for the interaction between crammer and the prosegment binding loop (PBL) of CTSB; the salt bridge between R28 and E67 is critical for the appropriate alignment of the α-helix 4 toward the CTSB active cleft. The results of this study show detailed residue-specific dissection of folding transition and functional contributions of the hydrophobic cores and salt bridges in crammer, which have hitherto not been characterized for cathepsin inhibition by propeptide-like cysteine protease inhibitors. Because of the involvements of cathepsin inhibitors in neurodegenerative diseases, these structural insights can serve as a template for further development of therapeutic inhibitors against human cathepsins.

Lysosomotropism of Basic Cathepsin K Inhibitors Contributes to Increased Cellular Potencies against Off-Target Cathepsins and Reduced Functional Selectivity

The lysosomal cysteine protease cathepsin K is a target for osteoporosis therapy. The aryl-piperazine-containing cathepsin K inhibitor CRA-013783/L-006235 (1) displays greater than 4000-fold selectivity against the lysosomal/endosomal antitargets cathepsin B, L, and S. However, 1 and other aryl-piperazine-containing analogues, including balicatib (10), are approximately 10-100-fold more potent in cell-based enzyme occupancy assays than against each purified enzyme. This phenomenon arises from their basic, lipophilic nature, which results in lysosomal trapping. Consistent with its lysosomotropic nature, 1 accumulates in cells and in rat tissues of high lysosome content. In contrast, nonbasic aryl-morpholino-containing analogues do not exhibit lysosomotropic properties. Increased off-target activities of basic cathepsin K inhibitors were observed in a cell-based cathepsin S antigen presentation assay. No potency increases of basic inhibitors in a functional cathepsin K bone resorption whole cell assay were detected. Therefore, basic cathepsin K inhibitors, such as 1, suffer from reduced functional selectivities compared to those predicted using purified enzyme assays.

The crystal structure of human cathepsin F and its implications for the development of novel immunomodulators

Cathepsin F is a lysosomal cysteine protease of the papain family, and likely plays a regulatory role in processing the invariant chain that is associated with the major histocompatibility complex (MHC) class II. Evidence suggests that inhibiting cathepsin F activity will block MHC class II processing in macrophages. Consequently, inhibitors of this enzyme may be useful in treating certain diseases that involve an inappropriate or excessive immune response. We have determined the 1.7A structure of the mature domain of human cathepsin F associated with an irreversible vinyl sulfone inhibitor. This structure provides a basis for understanding cathepsin F's substrate specificity, and suggests ways of identifying potent and selective inhibitors of this enzyme.

Solid-phase synthesis of cyclic alkoxyketones, inhibitors of the cysteine protease cathepsin K

Using solid-phase synthesis, a library of novel cyclic alkoxyketones has been constructed which show strong inhibitory activity against the cysteine protease, cathepsin K (EC 3.4.22.38).

QSAR based on biological microcalorimetry

In this paper we describe a QSAR based on biological microcalorimetry for a set of antimicrobial hydrazides acting against Saccharomyces cerivisiae and Escherichia coli. Results show that an extrathermodynamic relationship exists based upon partitioning (log P(TA)) and microcalorimetrically measured biopotencies using the same cell systems. Moreover, the extrathermodynamic relationship between drug potencies for these two cell systems shows that both cellular systems appear to behave in the same way with respect to the importance of partitioning. This means that the same set of congeneric compounds experience a similar environment in the two systems. This represents a lateral validation of the method and discloses the validity of the QSAR model.