Discovery of enzyme inhibitors through combinatorial chemistry

Summary This review serves to highlight the recent examples of combinatoric methodology as applied to the discovery and optimization of enzyme inhibitors. Early research efforts focused on the identification of polypeptides from libraries as inhibitors of proteases. As solution- and solid-phase chemistries gain in sophistication, libraries containing less peptidic structural motifs have been created. A recurring design stratagem relies on the synthesis of libraries incorporating pharmacophores with known affinity for the target enzyme. Screening of these structure-based libraries has led to the discovery of small-molecule inhibitors of both proteolytic and non-proteolytic enzymes alike. Two tables are provided listing the enzyme targeted libraries through 1996. A name, generic structure and size is given for each library citation, accompanied by the enzyme screen and the structure and potency of the most active library member.     

Thermodynamic study of CN~- ion inhibition of Jack bean urease using the extended solvation theory

Cyanide ion was studied as an inhibitor of Jack bean urease at 300 K in 30 mmol/L tris buffer,pH 7.The inhibition was investigated by isothermal titration calorimetry(ITC).The extended solvation model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the solvation model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a non-cooperative inhibitor of urease,and there is a set of 12±0.12 identical and in...     

Systematic Profiling and Evaluation of Structure-based Kinase–Inhibitor Interactome in Cervical Cancer by Integrating In Silico Analyses and In Vitro Assays at Molecular and Cellular Levels

Various protein kinases are implicated in the pathogenesis of human cervical cancer and many kinase inhibitors have been used to regulate the activity of protein kinases involved in the disease signaling networks. In the present study, a systematic kinase–inhibitor interactome is created for various small-molecule inhibitors across diverse cervical cancer-related kinases by using ontology enrichment, molecular docking, dynamics simulation and energetics analysis. The interactome profile is examined in detail with heatmap analysis and heuristic clustering to derive promising inhibitors that are highly potential to target the kinome of human cervical cancer in a multi-target manner. A number of hit and unhit inhibitors are selected and their cell-suppressing effects are tested against human cervical carcinoma HeLa, from which several inhibitor compounds with high cytotoxicity are successfully identified. A further kinase assay confirms that these inhibitors can generally target their noncognate kinases HER3 and BRaf in cervical cancer with a high or moderate activity; the activity profile are comparable with or even better than that of cognate kinases inhibitors, with IC₅₀ values ranging between 4.8 and 340.6 nM for HER3 and between 37.2 and 638.2 nM for BRaf. This work would help to identify those unexpected kinase–inhibitor interactions in human cervical cancer and to develop new and efficient therapeutic strategy combating the disease.     

Macrocyclic peptides as regulators of protein-protein interactions

Protein-protein interactions are attractive but challenging targets for drug discovery. Recent technological progress and examples using macrocyclic peptides as protein interaction modulators are reviewed.     

N-bromosuccinimide mediated decarboxylative sulfonylation of β-keto acids with sodium sulfinates toward β-keto sulfones: Evaluation of human carboxylesterase 1 activity

A N-bromosuccinimide (NBS) mediated decarboxylative sulfonylation of β-keto acids with sodium sulfinates is developed. The transformation exhibits a broad substrate scope and good functional group tolerance. Preliminary mechanistic studies showed that this reaction is likely to proceed through a nucleophilic substitution of β-keto acid with sulfonyl bromide pathway. All synthesized β-keto sulfones were evaluated the inhibitory effect against human carboxylesterase 1 (CES1). This investigation offers an expedient strategy for efficient synthesis of β-keto sulfones that are widely present in biologically active natural products and pharmaceutical agents.     

Enantioselective synthesis of phomallenic acid C, an inhibitor of FAS II pathway

Enantioselective synthesis of phomallenic acid C, an inhibitor of bacterial FAS II pathway, was successful. Allenyldiyne structure was constructed by a direct anti-S_N2′ coupling of propargyl mesylate with diynylindium in the presence of palladium catalyst. Enantiomeric purity was determined by Ohrui-Akasaka method to be 83%ee.     

A Versatile Strategy for Screening Custom-Designed Warhead-Armed Cyclic Peptide Inhibitors

Demand for peptide-based pharmaceuticals has been steadily increasing, but only limited success has been achieved to date. To expedite peptide-based drug discovery, we developed a general scheme for cell-based screening of cyclic peptide inhibitors armed with a user-designed warhead. We combined unnatural amino acid incorporation and split intein-mediated peptide cyclization techniques and integrated a yeast-based colorimetric screening assay to generate a new scheme that we call the custom-designed warhead-armed cyclic peptide screening platform (CWCPS). This strategy successfully discovered a potent inhibitor, CY5-6Q, that targets human histone deacetylase 8 (HDAC8) with a K_D value of 15 nM. This approach can be a versatile and general platform for discovering cyclic peptide inhibitors.     

Structure-based design of Aurora A & B inhibitors

The Aurora family of serine/threonine kinases are mitotic regulators involved in centrosome duplication, formation of the bipolar mitotic spindle and the alignment of the chromosomes along the spindle. These proteins are frequently overexpressed in tumor cells as compared to normal cells and are therefore potential therapeutic oncology targets. An Aurora A high throughput screen revealed a promising sub-micromolar indazole-benzimidazole lead. Modification of the benzimidazole portion of the lead to a C2 linker with a phenyl ring was proposed to achieve novelty. Docking revealed that a conjugated linker was optimal and the resulting compounds were equipotent with the lead. Further structure-guided optimization of substituents on the 5 & 6 position of the indazole led to single digit nanomolar potency. The homology between the Aurora A & Aurora B kinase domains is 71% but their binding sites only differ at residues 212 & 217 (Aurora A numbering). However interactions with only the latter residue may be used for obtaining selectivity. An analysis of published Aurora A and Aurora B X-ray structures reveals subtle differences in the shape of the binding sites. This was exploited by introduction of appropriately sized substituents in the 4 & 6 position of the indazole leading to Aurora B selective inhibitors. Finally we calculate the conformational energy penalty of the putative bioactive conformation of our inhibitors and show that this property correlates well with the Aurora A binding affinity.     

聚天冬氨酸与钨酸钠复配对白铜B10的缓蚀作用

应用光电化学的方法研究了两种环境友好型缓蚀剂聚冬天氨酸(PASP)和钨酸钠(Na2WO4)的单一配方及其复配对白铜B10在硼砂-硼酸缓冲溶液中的缓蚀作用援研究表明, 在光电流循环伏安测试中, 单一的PASP与Na2WO4均能够使B10表面Cu2O膜引起的p型光电流响应增大, 这说明缓蚀剂增大了Cu2O膜的厚度, 使B10的腐蚀速率减小. 单一的PASP与Na2WO4的最佳添加浓度分别为3和5 mg·L-1, 单一的Na2WO4比单一的PASP使p型光电流响应增大趋势更大. 若以总浓度为5 mg·L-1时对两者进行复配, 当PASP与Na2WO4的质量浓度比为1:1和1:3时, 两者复配比单一使用时的p型电流光响应都更大, B10的腐蚀更小, 即缓蚀剂的效果更好. 交流阻抗测试结果与光电化学测试相一致.     

A novel photoelectrochemical biosensor for protein kinase activity assay based on phosphorylated graphite-like carbon nitride

Protein kinases are general and significant regulators in the cell signaling pathway, and it is still greatly desired to achieve simple and quick kinase detection. Herein, we develop a simple and sensitive photoelectrochemical strategy for the detection of protein kinase activity based on the bond between phosphorylated peptide and phosphorylated graphite-like carbon nitride (P-g-C₃N₄) conjugates triggered by Zr⁴⁺ ion coordination. Under optimal conditions, the increased photocurrent is proportional to the protein kinase A (PKA) concentration ranging from 0.05 to 50 U/mL with a detection limit of 0.077 U/mL. Moreover, this photoelectrochemical assay can be also applied to quantitative analysis of kinase inhibition. The results indicated that the IC₅₀ value (inhibitor concentration producing 50% inhibitor) for ellagic acid was 9.1 μM. Moreover, the developed method is further applied to detect PKA activity in real samples, which contains serum from healthy person and gastric cancer patients and breast tissue from healthy person and breast cancer patients. Therefore, the established protocol provides a new and simple tool for assay of kinase activity and its inhibitors with low cost and high sensitivity.