Identification,SAR Studies,and X‐ray Co‐crystallographic Analysis of a Novel Furanopyrimidine Aurora Kinase A Inhibitor

Herein we reveal a simple method for the identification of novel Aurora kinase A inhibitors through substructure searching of an in‐house compound library to select compounds for testing. A hydrazone fragment conferring Aurora kinase activity and heterocyclic rings most frequently reported in kinase inhibitors were used as substructure queries to filter the in‐house compound library collection prior to testing. Five new series of Aurora kinase inhibitors were identified through this strategy, with IC₅₀ values ranging from ～300 nM to ～15 μM , by testing only 133 compounds from a database of ～125 000 compounds. Structure–activity relationship studies and X‐ray co‐crystallographic analysis of the most potent compound, a furanopyrimidine derivative with an IC₅₀ value of 309 nM toward Aurora kinase A, were carried out. The knowledge gained through these studies could help in the future design of potent Aurora kinase inhibitors.     

Discovery of 7‐Aryl‐Substituted (1,5‐Naphthyridin‐4‐yl)ureas as Aurora Kinase Inhibitors

As part of our research projects to identify new chemical entities of biological interest, we developed a synthetic approach and the biological evaluation of (7‐aryl‐1,5‐naphthyridin‐4‐yl)ureas as a novel class of Aurora kinase inhibitors for the treatment of malignant diseases based on pathological cell proliferation. 1,5‐Naphthyridine derivatives showed excellent inhibitory activities toward Aurora kinases A and B, and the most active compound, 1‐cyclopropyl‐3‐[7‐(1‐methyl‐1H‐pyrazol‐4‐yl)‐1,5‐naphthyridin‐4‐yl]urea ( 49 ), displayed IC₅₀ values of 13 and 107 nM against Aurora kinases A and B, respectively. In addition, the selectivity toward a panel of seven cancer‐related protein kinases was highlighted. In vitro ADME properties were also determined in order to rationalize the difficulties in correlating antiproliferative activity with Aurora kinase inhibition. Finally, the good safety profile of these compounds imparts promising potential for their further development as anticancer agents.     

3D-QSAR and Molecular Docking Studies on Derivatives of MK-0457, GSK1070916 and SNS-314 as Inhibitors against Aurora B Kinase

Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q(2) = 0.605, r(2) (pred) = 0.826), (q(2) = 0.52, r(2) (pred) = 0.798) and (q(2) = 0.582, r(2) (pred) = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors.     

Combined 3D-QSAR Modeling and Molecular Docking Studies on Pyrrole-Indolin-2-ones as Aurora A Kinase Inhibitors

Aurora kinases have emerged as attractive targets for the design of anticancer drugs. 3D-QSAR (comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)) and Surflex-docking studies were performed on a series of pyrrole-indoline-2-ones as Aurora A inhibitors. The CoMFA and CoMSIA models using 25 inhibitors in the training set gave r(2) (cv) values of 0.726 and 0.566, and r(2) values of 0.972 and 0.984, respectively. The adapted alignment method with the suitable parameters resulted in reliable models. The contour maps produced by the CoMFA and CoMSIA models were employed to rationalize the key structural requirements responsible for the activity. Surflex-docking studies revealed that the sulfo group, secondary amine group on indolin-2-one, and carbonyl of 6,7-dihydro-1H-indol-4(5H)-one groups were significant for binding to the receptor, and some essential features were also identified. Based on the 3D-QSAR and docking results, a set of new molecules with high predicted activities were designed.     

Kinesin Spindle Protein (KSP) Inhibitors in Combination with Chemotherapeutic Agents for Cancer Therapy

A diverse group of proteins, the activities of which are precisely orchestrated during mitosis, have emerged as targets for cancer therapeutics; these include the Aurora kinases (AKs), Polo‐like kinases (PLKs), and the kinesin spindle protein (KSP). KSP is essential for the proper separation of spindle poles during mitosis. Agents that target KSP selectively act on cells undergoing cell division, which means that KSP inhibitors are mitosis‐specific drugs, and have demonstrated remarkable activities in vitro. However, a significant obstacle to the success of KSP inhibitors is that these compounds, with tremendous efficacy in vitro, have demonstrated little or even no antitumor activity in vivo. Accumulated data suggest that a combination of KSP inhibitors with various cytostatic drugs will result in a more powerful tumor‐killing effect than monotherapy. Combination therapies might predominate and represent the next frontier in the discovery research of KSP inhibitors as potential anticancer drugs. Few published studies have reviewed combination therapy using KSP inhibitors. Herein we provide a comprehensive review of the literature on KSP inhibitor monotherapy and therapeutic combinations. The current state and problems are also discussed.     

Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies

Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC₅₀ = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91).     

Long Residence Times Revealed by Aurora A Kinase‐Targeting Fluorescent Probes Derived from Inhibitors MLN8237 and VX‐689

We report the development of three fluorescent probes for protein kinase Aurora A that are derived from the well‐known inhibitors MLN8237 and VX‐689 (MK‐5108). Two of these probes target the ATP site of Aurora A, and one targets simultaneously the ATP and substrate sites of the kinase. The probes were tested in an assay with fluorescence polarisation/anisotropy readout, and we demonstrated slow association kinetics and long residence time of the probes (k_on 10⁵–10⁷ M ^?1 s^?1, k_off 10^?3–10^?4 s^?1; residence time 500–3000 s). The presence of the Aurora A activator TPX2 caused a significant reduction in the on‐rate and increase in the off‐rate of fluorescent probes targeting ATP site. These observations were supported by Aurora A inhibition assays with MLN8237 and VX‐689. Overall, our results emphasise the importance of rational design of experiments with these compounds and correct interpretation of the obtained data.     

4-Sulfamoylphenylalkylamides as Inhibitors of Carbonic Anhydrases Expressed in Vibrio cholerae

A current issue of antimicrobial therapy is the resistance to treatment with worldwide consequences. Thus, the identification of innovative targets is an intriguing challenge in the drug and development process aimed at newer antimicrobial agents. The state-of-art of anticholera therapy might comprise the reduction of the expression of cholera toxin, which could be reached through the inhibition of carbonic anhydrases expressed in Vibrio cholerae (VchCAα, VchCAβ, and VchCAγ). Therefore, we focused our interest on the exploitation of sulfonamides as VchCA inhibitors. We planned to design and synthesize new benzenesulfonamides based on our knowledge of the VchCA catalytic site. The synthesized compounds were tested thus collecting useful SAR information. From our investigation, we identified new potent VchCA inhibitors, some of them displayed high affinity toward VchCAγ class, for which few inhibitors are currently reported in literature. The best interesting VchCAγ inhibitor (S)-N-(1-oxo-1-((4-sulfamoylbenzyl)amino)propan-2-yl)furan-2-carboxamide ( 40 ) resulted more active and selective inhibitor when compared with acetazolamide (AAZ) as well as previously reported VchCA inhibitors.     

USP48 Governs Cell Cycle Progression by Regulating the Protein Level of Aurora B

Deubiquitinating enzymes play key roles in the precise modulation of Aurora B—an essential cell cycle regulator. The expression of Aurora B increases before the onset of mitosis and decreases during mitotic exit; an imbalance in these levels has a severe impact on the fate of the cell cycle. Dysregulation of Aurora B can lead to aberrant chromosomal segregation and accumulation of errors during mitosis, eventually resulting in cytokinesis failure. Thus, it is essential to identify the precise regulatory mechanisms that modulate Aurora B levels during the cell division cycle. Using a deubiquitinase knockout strategy, we identified USP48 as an important candidate that can regulate Aurora B protein levels during the normal cell cycle. Here, we report that USP48 interacts with and stabilizes the Aurora B protein. Furthermore, we showed that the deubiquitinating activity of USP48 helps to maintain the steady-state levels of Aurora B protein by regulating its half-life. Finally, USP48 knockout resulted in delayed progression of cell cycle due to accumulation of mitotic defects and ultimately cytokinesis failure, suggesting the role of USP48 in cell cycle regulation.     

Effect of Human Flavin-Containing Monooxygenase 3 Polymorphism on the Metabolism of Aurora Kinase Inhibitors

Aurora kinases were recently identified as a potential target in anticancer therapy and, amongst their available inhibitors, Tozasertib (VX-680) and Danusertib (PHA-739358) have been indicated as possible substrates of human flavin-containing monooxygenase 3 (hFMO3). Here we report the in vitro rate of oxidation of these drugs by wild-type hFMO3 and its polymorphic variant V257M. The conversion of Tozasertib and Danusertib to their corresponding metabolites, identified by LC-MS, by the purified wild-type and V257M hFMO3 show significant differences. In the case of Tozasertib, the V257M variant shows a catalytic efficiency, expressed as k_cat/K_m, similar to the wild-type: 0.39 ± 0.06 min⁻¹μM⁻¹ for V257M compared to 0.33 ± 0.04 min⁻¹μM⁻¹ for the wild type. On the other hand, in the case of Danusertib, V257M shows a 3.4× decrease in catalytic efficiency with k_cat/K_m values of 0.05 ± 0.01 min⁻¹μM⁻¹ for V257M and 0.17 ± 0.03 min⁻¹μM⁻¹ for the wild type. These data reveal how a simple V257M substitution ascribed to a single nucleotide polymorphism affects the N-oxidation of relevant anticancer drugs, with important outcome in their therapeutic effects. These findings demonstrate that codon 257 is important for activity of the hFMO3 gene and the codon change V to M has an effect on the catalytic efficiency of this enzyme.     

Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα

In this study, we utilized human DNA topoisomerase IIα as a model target to outline a dynophore-based approach to catalytic inhibitor design. Based on MD simulations of a known catalytic inhibitor and the native ATP ligand analog, AMP-PNP, we derived a joint dynophore model that supplements the static structure-based-pharmacophore information with a dynamic component. Subsequently, derived pharmacophore models were employed in a virtual screening campaign of a library of natural compounds. Experimental evaluation identified flavonoid compounds with promising topoisomerase IIα catalytic inhibition and binding studies confirmed interaction with the ATPase domain. We constructed a binding model through docking and extensively investigated it with molecular dynamics MD simulations, essential dynamics, and MM-GBSA free energy calculations, thus reconnecting the new results to the initial dynophore-based screening model. We not only demonstrate a new design strategy that incorporates a dynamic component of molecular recognition, but also highlight new derivates in the established flavonoid class of topoisomerase II inhibitors.     

Enzyme isoselective inhibitors: a tool for binding-trend analysis

A transition-state analogue inhibitor that covalently reversibly binds to an enzyme formally consists of two parts: the chemical site, CS and the recognition site, RS. We have experimentally and theoretically demonstrated that the trend of binding affinity in a series of isoselective inhibitors (with identical RS and different CS fragments) depends mainly on their CS fragments. Isoselective inhibitors have the same affinity trend toward different enzymes of the same family with a common catalytic mechanism. Thus, very good correlation between experimentally determined and theoretically calculated Ki values was demonstrated. A practical outcome is the application of the described method as a tool for an expert analysis in virtual screening of inhibitor libraries and in the design of new enzyme inhibitors.     

Characterization of irreversible kinase inhibitors by directly detecting covalent bond formation: a tool for dissecting kinase drug resistance

Targeting protein kinases in cancer therapy with irreversible small-molecule inhibitors is moving to the forefront of kinase-inhibitor research and is thought to be an effective means of overcoming mutation-associated drug resistance in epidermal growth factor receptor kinase (EGFR). We generated a detection technique that allows direct measurements of covalent bond formation without relying on kinase activity, thereby allowing the straightforward investigation of the influence of steric clashes on covalent inhibitors in different resistant kinase mutants. The obtained results are discussed together with structural biology and biochemical studies of catalytic activity in both wild-type and gatekeeper mutated kinase variants to draw conclusions about the impact of steric hindrance and increased catalytic activity in drug-resistant kinase variants.     

Effectiveness of UV Advanced Oxidation for Destruction of Micro-Pollutants

UV light has become increasingly well-established as an effective primary disinfectant for Giardia and Cryptosporidium. Many utilities are now focusing attention on control of emerging contaminants, and looking at the effectiveness of UV advanced oxidation as part of a multiple-barrier treatment train for improving water quality. In research and a small number of full-scale applications, a UV advanced oxidation process (AOP) has been shown to be effective as part of a multiple-barrier water purification train. For the City of Aurora, Colorado, the Aurora Reservoir Water Purification Facility will include UV AOP as part of a multiple barrier approach to provide disinfection, nitrosamine destruction, and micro-pollutant removal. Bench-scale testing was performed to evaluate the effectiveness of UV AOP for the control of nitrosamines and other micro-pollutants. Compounds tested included N-nitrosodimethylamine (NDMA) and 8 other nitrosamines. The test results showed predictable and repeatable destruction of NDMA, and destruction of other tested nitrosamines exceeded NDMA destruction at the same collimated beam UV doses.     

Protease Substrate-Independent Universal Assay for Monitoring Digestion of Native Unmodified Proteins

Proteases are a group of enzymes with a catalytic function to hydrolyze peptide bonds of proteins. Proteases regulate the activity, signaling mechanism, fate, and localization of many proteins, and their dysregulation is associated with various pathological conditions. Proteases have been identified as biomarkers and potential therapeutic targets for multiple diseases, such as acquired immunodeficiency syndrome, cardiovascular diseases, osteoporosis, type 2 diabetes, and cancer, where they are essential to disease progression. Thus, protease inhibitors and inhibitor-like molecules are interesting drug candidates. To study proteases and their substrates and inhibitors, simple, rapid, and sensitive protease activity assays are needed. Existing fluorescence-based assays enable protease monitoring in a high-throughput compatible microtiter plate format, but the methods often rely on either molecular labeling or synthetic protease targets that only mimic the hydrolysis site of the true target proteins. Here, we present a homogenous, label-free, and time-resolved luminescence utilizing the protein-probe method to assay proteases with native and denatured substrates at nanomolar sensitivity. The developed protein-probe method is not restricted to any single protein or protein target class, enabling digestion and substrate fragmentation studies with the natural unmodified substrate proteins. The versatility of the assay for studying protease targets was shown by monitoring the digestion of a substrate panel with different proteases. These results indicate that the protein-probe method not only monitors the protease activity and inhibition, but also studies the substrate specificity of individual proteases.     

Thiooligosaccharides as tools for structural biology

Oligosaccharides in which at least one glycosidic oxygen atom is replaced with a sulfur atom can be routinely synthesized and act as competitive inhibitors of various glycoside hydrolases. Recent studies using both X-ray crystallography and other biophysical techniques provide structural insight into binding, recognition, and the catalytic mechanism of action of these enzymes.     

Comparative study of CHA- and AEI-type zeolytic catalysts for the conversion of chloromethane into light olefins

Three pairs of CHA- and AEI-type zeolytic materials with similar crystallite size but with different framework atoms, i.e., silicoaluminophosphate SAPO-34 and SAPO-18, aluminosilicate SSZ-13 and SSZ-39, and titaniumin-corporated TiAPSO-34 and TiAPO-18, were prepared and their catalytic activities of chloromethane into light olefins were compared according to the structure types, as well as acidic properties. The AEI-type catalysts were found to have lower ethene/propene ratios, indicating relatively higher propene selectivity, because their aei-cage was larger compared to the cha-cage. However, all the CHA-type catalysts exhibited better activity and higher selectivity to light olefins. Both H-SAPO-34 and H-TiAPSO-34 showed good catalytic stability over all the reaction times studied here. When compared to H-SAPO-34, however, H-TiAPSO-34 exhibited ca. 20mol% higher selectivity to ethene and propene, despite a similar total density of acid site. This performance may be due to the higher strength of medium acid sites.     

Synthetic applications of nonmetal catalysts for homogeneous oxidations

Nonmetal oxidation catalysts have gained much attention in recent years. The reason for this surge in activity is 2-fold: On one hand, a number of such catalysts has become readily accessible; on the other hand, such catalysts are quite resistant toward self-oxidation and compatible under aerobic and aqueous reaction conditions. In this review, we have focused on five nonmetal catalytic systems which have attained prominence in the oxidation field in view of their efficacy and their potential for future development; stoichiometric cases have been mentioned to provide overview and scope. Such nonmetal oxidation catalysts include the alpha-halo carbonyl compounds 1, ketones 2, imines 3, iminium salts 4, and nitroxyl radicals 5. In combination with a suitable oxygen source (H2O2, KHSO5, NaOCl), these catalysts serve as precursors to the corresponding oxidants, namely, the perhydrates I, dioxiranes II, oxaziridines III, oxaziridinium ions IV, and finally oxoammonium ions V. A few of the salient features about these nonmetal, catalytic systems shall be reiterated in this summary. The first class entails the alpha-halo ketones, which catalyze the oxidation of a variety of organic substrates [figure: see text] by hydrogen peroxide as the oxygen source. The perhydrates I, formed in situ by the addition of hydrogen peroxide to the alpha-halo ketones, are quite strong electrophilic oxidants and expectedly transfer an oxygen atom to diverse nucleophilic acceptors. Thus, alpha-halo ketones have been successfully employed for catalytic epoxidation, heteroatom (S, N) oxidation, and arene oxidation. Although high diastereoselectivities have been achieved by these nonmetal catalysts, no enantioselective epoxidation and sulfoxidation have so far been reported. Consequently, it is anticipated that catalytic oxidations by perhydrates hold promise for further development, especially, and should ways be found to transfer the oxygen atom enantioselectively. The second class, namely, the dioxiranes, has been extensively used during the last two decades as a convenient oxidant in organic synthesis. These powerful and versatile oxidizing agents are readily available from the appropriate ketones by their treatment [figure: see text] with potassium monoperoxysulfate. The oxidations may be performed either under stoichiometric or catalytic conditions; the latter mode of operation is featured in this review. In this case, a variety of structurally diverse ketones have been shown to catalyze the dioxirane-mediated epoxidation of alkenes by monoperoxysulfate as the oxygen source. By employing chiral ketones, highly enantioselective (up to 99% ee) epoxidations have been developed, of which the sugar-based ketones are so far the most effective. Reports on catalytic oxidations by dioxiranes other than epoxidations are scarce; nevertheless, fructose-derived ketones have been successfully employed as catalysts for the enantioselective CH oxidation in vic diols to afford the corresponding optically active alpha-hydroxy ketones. To date, no catalytic asymmetric sulfoxidations by dioxiranes appear to have been documented in the literature, an area of catalytic dioxirane chemistry that merits attention. A third class is the imines; their reaction with hydrogen peroxide or monoperoxysulfate affords oxaziridines. These relatively weak electrophilic oxidants only manage to oxidize electron-rich substrates such as enolates, silyl enol ethers, sulfides, selenides, and amines; however, the epoxidation of alkenes has been achieved with activated oxaziridines produced from perfluorinated imines. Most of the oxidations by in-situ-generated oxaziridines have been performed stoichiometrically, with the exception of sulfoxidations. When chiral imines are used as catalysts, optically active sulfoxides are obtained in good ee values, a catalytic asymmetric oxidation by oxaziridines that merits further exploration. The fourth class is made up by the iminium ions, which with monoperoxysulfate lead to the corresponding oxaziridinium ions, structurally similar to the above oxaziridine oxidants except they possess a much more strongly electrophilic oxygen atom due to the positively charged ammonium functionality. Thus, oxaziridinium ions effectively execute besides sulfoxidation and amine oxidation the epoxidation of alkenes under catalytic conditions. As expected, chiral iminium salts catalyze asymmetric epoxidations; however, only moderate enantioselectivities have been obtained so far. Although asymmetric sulfoxidation has been achieved by using stoichiometric amounts of isolated optically active oxaziridinium salts, iminium-ion-catalyzed asymmetric sulf-oxidations have not been reported to date, which offers attractive opportunities for further work. The fifth and final class of nonmetal catalysts concerns the stable nitroxyl-radical derivatives such as TEMPO, which react with the common oxidizing agents (sodium hypochlorite, monoperoxysulfate, peracids) to generate oxoammonium ions. The latter are strong oxidants that chemoselectively and efficiently perform the CH oxidation in alcohols to produce carbonyl compounds rather than engage in the transfer of their oxygen atom to the substrate. Consequently, oxoammonium ions behave quite distinctly compared to the previous four classes of oxidants in that their catalytic activity entails formally a dehydrogenation, one of the few effective nonmetal-based catalytic transformations of alcohols to carbonyl products. Since less than 1 mol% of nitroxyl radical is required to catalyze the alcohol oxidation by the inexpensive sodium hypochlorite as primary oxidant under mild reaction conditions, this catalytic process holds much promise for future practical applications.     

Combination Treatment of OSI-906 with Aurora B Inhibitor Reduces Cell Viability via Cyclin B1 Degradation-Induced Mitotic Slippage

Insulin-like growth factor 1 receptor (IGF1R), a receptor-type tyrosine kinase, transduces signals related to cell proliferation, survival, and differentiation. We recently reported that OSI-906, an IGF1R inhibitor, in combination with the Aurora B inhibitor ZM447439 suppresses cell proliferation. However, the mechanism underlying this suppressive effect is yet to be elucidated. In this study, we examined the effects of combination treatment with OSI-906 and ZM447439 on cell division, so as to understand how cell proliferation was suppressed. Morphological analysis showed that the combination treatment generated enlarged cells with aberrant nuclei, whereas neither OSI-906 nor ZM447439 treatment alone caused this morphological change. Flow cytometry analysis indicated that over-replicated cells were generated by the combination treatment, but not by the lone treatment with either inhibitors. Time-lapse imaging showed mitotic slippage following a severe delay in chromosome alignment and cytokinesis failure with furrow regression. Furthermore, in S-trityl-l-cysteine–treated cells, cyclin B1 was precociously degraded. These results suggest that the combination treatment caused severe defect in the chromosome alignment and spindle assembly checkpoint, which resulted in the generation of over-replicated cells. The generation of over-replicated cells with massive aneuploidy may be the cause of reduction of cell viability and cell death. This study provides new possibilities of cancer chemotherapy.