ChemMedChem

Nitrate esters of heteroaromatic compounds as novel Candida albicans CYP51 enzyme inhibitors ()
Four heteroaromatic compounds bearing nitrate esters were selected using a virtual screening procedure as putative sterol 14α-demethylase (CYP51) Candida albicans inhibitors. Compounds were examined for their inhibition on C. albicans growth and biofilm formation as well as for their toxicity. NMR studies, in silico docking and molecular dynamics simulations were used to further investigate selectivity of compounds to fungal CYP51. All compounds exhibited good antimicrobial properties, indicated with low minimal inhibitory concentrations and ability to inhibit formation of fungal biofilm. Moreover, all the compounds had the ability to inhibit growth of C. albicans cells. N-(2-nitooxyethyl)-1Η-indol-2-carboxamide was the only compound with selectivity on C. albicans CYP51 which did not exhibit cytotoxic effect on cells isolated from liver and should be further investigated for selective application in new leads for the treatment of candidiasis.
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Synthesis of α-branched acyclic nucleoside phosphonates as potential inhibitors of bacterial adenylate cyclases ()
Inhibition of Bordetella pertussis adenylate cyclase toxin (ACT) and Bacillus anthracis edema factor (EF), the key virulence factors with adenylate cyclase (AC) activity, represents a potential method how to treat or prevent toxemia related to whooping cough and anthrax, respectively. A novel series of α-branched acyclic nucleoside phosphonates (ANPs) having a hemiaminal ether moiety was synthesized as potential inhibitors of bacterial adenylate cyclases. ANPs prepared as bisamidates were not cytotoxic but did not exhibited any profound activity (IC50 > 10 µM) towards ACT in J774A.1 macrophage cells. The apparent lack of activity of the bisamidates was speculated to be due to the inefficient formation of the biologically active species (ANPpp) in the cells. On the other hand, two 5-haloanthraniloyl-substituted ANPs in the form of diphosphates (ANPpp) were shown to be potent ACT and EF inhibitors with IC50 values ranging from 55 to 360 nM.
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Discovery and Mechanistic Elucidation of a Class of PDI Inhibitors for the Treatment of Glioblastoma ()
Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein, we describe a novel, nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblastoma cell lines. We performed a medium throughput 20,000-compound screen of a diverse subset of 1,000,000 compounds to identify cytotoxic small molecules. Cytotoxic compounds were screened for PDI inhibition, and, from the screen, 35G8 emerged as the most cytotoxic inhibitor of PDI. Bromouridine-labeling and sequencing (Bru-seq) of nascent RNA revealed that 35G8 induced Nrf2 (nuclear factor-like 2) antioxidant response, endoplasmic reticulum stress response, and autophagy. Specifically, 35G8 upregulated heme oxygenase 1 and SLC7A11 (solute carrier family 7 member 11) transcription and protein expression and repressed PDI target genes such as TXNIP (thioredoxin-interacting protein 1) and EGR1 (early growth response 1). Interestingly, 35G8-induced cell death did not proceed via apoptosis or necrosis, but by a mixture of autophagy and ferroptosis. Cumulatively, our data demonstrate a mechanism for a novel PDI inhibitor as a chemical probe to validate PDI as a target for brain cancer.
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Achieving biocompatible SABRE: An in vitro cytotoxicity study ()
Production of a biocompatible hyperpolarized bolus by Signal Amplification By Reversible Exchange (SABRE) could open the door to simple clinical diagnosis via magnetic resonance imaging. Essential to successful progression to pre-clinical/clinical applications is the determination of the toxicology profile of the SABRE reaction mixture. Here we exemplify the cytotoxicity of the SABRE approach using in vitro cell assay. We conclude that the main cause of observed toxicity is due to the SABRE catalyst. Thus we develop two catalyst removal methods, one involving deactivation and ion-exchange chromatography and the second biphasic catalysis. These routes produce a bolus suitable for future in vivo study.
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[Carboxyl-11C]-Labeling of four high-affinity cPLA2a inhibitors and their evaluation as radioligands in mice with positron emission tomography ()
Cytosolic phospholipase A2α (cPLA2α) may play a critical role in neuropsychiatric and neurodegenerative disorders associated with oxidative stress and neuroinflammation. An effective PET radioligand for imaging cPLA2α in living brain might prove useful for biomedical research, especially on neuroinflammation. We selected four high-affinity (IC50 2.1 to 12 nM) indole-5-carboxylic acid-based inhibitors of cPLA2α (1-4), for labelling in carboxyl position with carbon-11 (t1/2 = 20.4 min) to provide candidate PET radioligands for imaging brain cPLA2α. [11C]1-4 were obtained for intravenous injection in adequate overall yields (1.1−5.5%) from cyclotron-produced [11C]carbon dioxide and with moderate molar activities (70−141 GBq/μmol) through the use of Pd(0)-mediated [11C]carbon monoxide insertion on iodo precursors. Measured logD7.4 values were within a narrow moderate range (1.9−2.4). After intravenous injection of [11C]1-4 in mice, radioactivity uptakes in brain peaked at low values (≤ 0.8 SUV) and decreased by about 90% over 15 min. Pre-treatments of the mice with high doses of the corresponding non-radioactive ligands did not alter brain time-activity curves. Brain uptakes of radioactivity after administration of [11C]1 to wild type and P-gp/BCRP dual knock-out mice were similar (peak 0.4 vs. 0.5 SUV), indicating that [11C]1 and others in this structural class, are not efflux transporters substrates.
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New Potent Inhibitors against Newcastle Disease Virus Haemagglutinin−Neuraminidase ()
Neuraminidase activity is essential for the infection and propagation of Paramyxoviruses, including human parainfluenza viruses (hPIVs) and the Newcastle Disease Virus (NDV). Thus, many inhibitors have been developed based on the 2-deoxy-2,3-didehydro-D-N-acetylneuraminic acid inhibitor (DANA) backbone. Along this line, we report here a series of neuraminidase inhibitors, having C-4 (ptoluensulfonamide and azido substituents) and C-5 (N-perfluorinated chains) modifications to the DANA backbone, that resulted 5- to 15-folds more potent than the current most active compound, the Ntrifluoroacetyl derivative of DANA (FANA), on the NDV haemagglutinin-neuraminidase (NDV-HN). Remarkably, these inhibitors resulted essentially inactive toward the human sialidase NEU3, which is present on the outer layer of the cell membrane and is highly affected by current NDV inhibitor FANA.
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Exploring structure-activity relationships with three-dimensional matched molecular pairs - A review ()
A Matched Molecular Pair consists of two small molecules which differ by a few atoms only. The minor structural difference between the molecules allows a detailed analysis of changes in property. Three dimensional matched molecular pairs extend the concept of chemical similarity by spatial similarity. Conformations have to be generated and superpositions have to be calculated. The additional complexity and uncertainty as well as the smaller amount of available experimental data substantially complicates derivation of models. Nonetheless, there are some benefits making the transition worthwhile. Detailed insights into mechanisms behind disrupted series of structure activity relations, extending the MMP concept with scaffold hopping or high confidence structure activity relationship transfer between series of analogs are just some examples the 3D concept provides access to. Several groups approached the problem from different directions. The models vary especially in three-dimensional similarity measure used and complexity of the applied descriptor selected or designed. Nonetheless, all approaches have increased the gain in information with incorporating three-dimensional structural information.
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Chemogenomic active learning's domain of applicability on small, sparse qHTS matrices: a study using CYP450 and nuclear hormone receptor families ()
Computational models for predicting the activity of small molecules against targets are now routinely developed and used in academia and industry, partially due to public bioactivity databases. While models based on bigger datasets are the trend, recent studies such as chemogenomic active learning have shown that only a fraction of data is needed for effective models in many cases. In this article, the chemogenomic active learning method is discussed and used to newly analyze public databases containing nuclear hormone receptor and cytochrome P450 receptor family bioactivity. In addition to existing results on kinases and G-protein coupled receptors, results here demonstrate the active learning methodology's effectiveness on extracting informative ligand-target pairs in sparse data scenarios. Experiments to assess the domain of the applicability demonstrate the influence of ligand profiles of similar targets within the family.
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A comprehensive structural overview of p38α MAPK in complex with ATP-site and non-ATP-site binders ()
We herein review all the currently available PDB ATP-site and non-ATP-site ligands bound to p38α MAPK. The co-crystallized inhibitors have been classified into different families according to their experimental binding mode and chemical structure, and the ligand-protein interactions discussed using the most representative compounds. This systematic structural analysis could provide take-home lessons for drug discovery programs aimed at the rational identification and optimization of new p38α MAPK inhibitors.
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Synthesis and Evaluation of N-Phenylpyrrolamides as DNA Gyrase B Inhibitors ()
ATP-competitive inhibitors of DNA gyrase and topoisomerase IV (topo IV) are among the most interesting classes of antibacterial drugs that do not have any representative in the antibacterial pipeline. We have developed thirty-two new N-phenylpyrrolamides and evaluated them against DNA gyrase and topoisomerase IV from Escherichia coli and Staphylococcus aureus. Antibacterial activities were studied against Gram-positive and Gram-negative bacterial strains. The most potent compound displayed an IC50 of 47 nM against E. coli DNA gyrase, and a minimum inhibitory concentration (MIC) of 12.5 µM against Gram-positive Enterococcus faecalis. Some compounds displayed good antibacterial activities against the efflux pump deficient E. coli strain (MICs = 6.25 µM) and against wild type E. coli in the presence of efflux pump inhibitor PAβN (MIC = 3.13 µM). We describe here new findings regarding structure-activity relationship of N-phenylpyrrolamide DNA gyrase B inhibitors and explore factors that are important for antibacterial activity of this class of compounds.
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Improving the Potency of Cancer Immunotherapy by Dual Targeting IDO1 and DNA ()
Here we report the first effort on exploration of the dual-targeting drug design strategy to improve the efficacy of small molecule cancer immunotherapy. New hybrids of IDO1 (indoleamine 2, 3-dioxygenase 1) inhibitors and DNA alkylating nitrogen mustards targeting respective IDO1 and DNA are rationally designed. As the first-in-class example of such molecules, they exhibited significantly enhanced anticancer activity in vitro and in vivo with low toxicity. The proof-of-concept by the studies has established a critical step toward developing novel and effective immunotherapy for the treatment of cancers.
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Synthetic Indolactam V Analogs as Inhibitors of PAR2 Induced Calcium Mobilization in Triple Negative Breast Cancer Cells ()
Human proteinase-activated receptor 2 (PAR2), a transmembrane G-Protein-coupled receptor (GPCR), represents an attractive target for a novel anti-cancer therapy as it plays a critical role in cell migration and invasion. Thus, selective PAR2 inhibitors possess a potential as anti-metastatic drugs. Knowing that the natural product teleocidin A2 is able to inhibit PAR2 in tumor cells, the goal of the present study was to elaborate structure-activity relationships and to identify potent PAR2 inhibitors with lower activity against the adverse target protein kinase C (PKC). For this purpose, an efficient gram scale total synthesis of indolactam V (i.e. the parent structure of all teleocidins) was developed and a library of derivatives was prepared. Some compounds indeed exhibited high potency as PAR2 inhibitors at low nanomolar concentrations with improved selectivity (as compared to teleocidin A2). The pseudopeptidic fragment bridging the C-3 and the C-4 positions of the indole core proved to be essential for target binding, while activity and target selectivity depends on the substituents at N-1 or C-7. The study revealed novel derivatives depicting high efficacy in PAR2 antagonism combined with increased selectivity.
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Consensus Predictive Model for the prediction of Human K562 Cell Growth Inhibition through Enalos Cloud Platform ()
Beta thalassemia is an inherited hematologic disorder caused by various mutations of the β-globin gene, thus resulting in a significant decrease of adult hemoglobin (HbA) production. Since no other specific treatment exists to date, apart from blood transfusion and chelation therapy, the increase of fetal hemoglobin (HbF) levels by drug molecules is considered of great potential in β-thalassemia treatment, being expected to counterbalance the impaired production of HbA. Within this context, we have worked towards the development of a predictive model that will allow the identification of new possible HbF inducers. To this end, we have selected the human erythroleukemia K562 cell line as a suitable target, since K562 cells are a well established system for validation of novel HbF inducers. Based on an available set of 129 experimentally tested biological inhibitors, we have developed and validated a computational QSAR model for the prediction of K562 functional inhibition, possibly associated with HbF induction. In an effort to facilitate future advancements in the field, we have incorporated our model into Enalos Cloud Platform that enabled online access to our computational scheme (http://enalos.insilicotox.com/K562) through a user-friendly interface. This online web service, dedicated to K562 biological inhibition assessment, is offered to the wider community in order to promote the in silico drug discovery through fast and reliable predictions.
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Monosaccharide derivatives with low nM lectin affinity and high selectivity based on combined fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond interactions ()
The design of small and high affinity lectin inhibitors remains a major challenge because lectin natural ligand binding sites often are shallow and have polar character. We report that derivatizing galactose with un-natural structural elements that form multiple non-natural lectin-ligand interactions (orthogonal multipolar fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond) can provide inhibitors with extraordinary affinity (low nM) for the model lectin, galectin-3, which is over 5 orders of magnitude higher than the parent galactose, and, moreover, is selective compared to other galectins.
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Harnessing the Maltodextrin Transport Mechanism for Targeted Bacterial Imaging: Structural Requirements for improved in vivo Stability in Tracer Design ()
Diagnosis and localization of bacterial infections remains a significant clinical challenge. Harnessing bacteria-specific metabolic pathways such as the maltodextrin transport mechanism may allow to specifically localize and image even small or hidden colonies. This requires that the intra-bacterial tracer accumulation provided by the transporter is matched by high serum stability of the tracer molecule. Herein we report radiolabeled maltodextrins of varying chain lengths and with free non-reducing/reducing ends and evaluate their behavior against the starch degrading enzymes in the blood that compromise their serum stability. We show successful SPECT/CT imaging in a footpad infection model in vivo using the newly developed model tracer [99mTc]MB1143, and compare the signal with [18F]FDG-PET as a non-bacterial specific marker for inflammation. Although the [99mTc]MB1143 imaging signal is highly specific it is low, most probably due to insufficient serum stability of the tracer. A series of stability tests with different 18F-labelled maltodextrins finally yielded clear structural guidelines regarding substitution patterns and chain lengths of maltodextrin-based tracers for nuclear imaging of bacterial infections.
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AquaMMapS: an alternative tool to monitor the role of water molecules during protein-ligand association. ()
Unquestionably water appears to be an active player in noncovalent protein-ligand association processes, as it can either bridge interactions between protein and ligand or can be replaced by the bound ligand. Accordingly, in the last decade, alternative computational methodologies have been sought, that guess the position and thermodynamic profile of water molecules (i.e., hydration sites) in the binding site using either the ligand-bound or ligand-free protein conformation. Herein, we present an alternative approach, named AquaMMapS, that provides a three-dimensional sampling of putative hydration sites. Interestingly, AquaMMapS can post-inspect molecular dynamics trajectories obtained from different molecular dynamics engines and using indifferently crystallographic or docking-driven structures as a starting point. Moreover, AquaMMapS is naturally integrated to supervised molecular dynamics (SuMD) simulations Finally, a penalty scoring method, named AquaMMapScoring,(AMS), has been developed to evaluate, during the binding event, the number and the nature of the water molecules displaced by a ligand approaching its binding site, guiding a medicinal chemist to explore the most suitable regions of a ligand that can be decorated either with or without interfering with the interaction networks mediated by water molecules with specific recognition regions of the protein.
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A Synthetic MUC1 Anticancer Vaccine Containing Mannose Ligands for Targeting Macrophages and Dendritic Cells ()
A MUC1 anticancer vaccine equipped with covalently linked divalent mannose ligands improved the antigen uptake and presentation by targeting mannose receptor-positive macrophages and dendritic cells. It induced much stronger specific IgG immune responses in mice than the non-mannosylated reference vaccine. Mannose coupling also led to increased numbers of macrophages, dendritic cells and CD4+ T cells in the local lymph organs. Comparison of di- and tetra-valent-mannose ligands revealed an increased binding of the tetra-valent version suggesting that higher valency improves the binding to the mannose receptor. The mannose-coupled vaccine and the non-mannosylated reference vaccine induced IgG antibodies that exhibited similar binding to human breast tumor cells.
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Anticancer Properties of Halogenated Pyrrolo[3,2-d]pyrimidines with Decreased Toxicity Via N5 Substitution ()
Abstract: Halogenated pyrrolo[3,2-d]pyrimidine analogues have shown anti-proliferative activity in recent studies, with cell accumulation occurring in the G2/M stage without apoptosis. However, the mechanism of action and pharmacokinetic (PK) profile of these compounds has yet to be determined. In order to investigate the PK profile of these compounds, a series of halogenated pyrrolo[3,2-d]pyrimidine compounds was synthesized and first tested for activity in various cancer cell lines, as well as in a mouse model. EC50 values ranged from 0.014 - 14.5 µM, and maximum tolerated doses (MTD) in mice were between 5-10 mg/kg. This indicates a wide variance in activity and toxicity that needed further study. To decrease toxicity, a second series of compounds were synthesized with N5 alkyl substitutions in an effort to slow the rate of metabolism, which was thought to be leading to the toxicity. The N-substituted compounds demonstrated comparable cell line activity (EC50 values between 0.83 - 7.3 µM) with significantly decreased toxicity (MTD = 40 mg/kg). Finally, the PK profile of the best compound shows an average plasma half-life of 32.7 minutes, and rapid conversion of the N-substituted compound into the parent unsubstituted analogue. Together, these data indicate that halogenated pyrrolo[3,2-d]pyrimidines present a promising lead into anti-proliferative agents with tunable activity and toxicity that have rapid metabolism but potent activity.
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Mapping of the Available Chemical Space versus the Chemical Universe of Lead-like Compounds ()
This is, to our knowledge, the to-date most comprehensive analysis based on Generative Topographic Mapping (GTM) of the fragment-like chemical space (40M molecules with no more than 17 heavy atoms, both from the theoretically enumerated GDB-17, and real-world PubChem/ChEMBL). The challenge was to prove that a robust map of fragment-like chemical space can actually be built, in spite of a limited (<<105) maximal number of compounds ("frame set") usable for fitting the GTM manifold. An evolutionary map building strategy has been updated with a "coverage check" step, discarding manifolds failing to accommodate compounds outside the frame set. The evolved map has a good propensity to separate actives from inactives for >20 external structure-activity sets. It was proven to properly accommodate the entire collection of 40M compounds. Next, it served as a library comparison tool, highlighting biases of real-world molecules (PubChem and ChEMBL) versus the Universe of all possible species represented by FDB-17, the 10M-large fragment-like subset of GDB-17. Specific patterns, proper to some library and absent from others (diversity holes) were highlighted.
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Micro- and Nanotechnology in Vaccine Development. Edited by Mariusz Skwarczynski and Istvan Toth ()
Elsevier, Amsterdam 2016. 460 pp., hardcover, £93.75—ISBN 978-0-323- 39981-4
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Preliminary Evaluation of Artemisinin–Cholesterol Conjugates as Potential Drugs for the Treatment of Intractable Forms of Malaria and Tuberculosis ()
To evaluate the feasibility of developing drugs that may be active against both malaria and tuberculosis (TB) by using in part putative cholesterol transporters in the causative pathogens and through enhancement of passive diffusion in granulomatous TB, artemisinin–cholesterol conjugates were synthesized by connecting the component molecules through various linkers. The compounds were screened in vitro against Plasmodium falciparum (Pf) and Mycobacterium tuberculosis (Mtb). Antimalarial activities (IC50) against Pf drug-sensitive NF54, and drug-resistant K1 and W2 strains ranged from 0.03–2.6, 0.03–1.9, and 0.02–1.7 μm. Although the compounds are less active than the precursor artemisinin derivatives, the cholesterol moiety renders the compounds relatively insoluble in the culture medium, and variation in solubilities among the different compounds may reflect in the range of efficacies observed. Activities against Mtb H37Rv were assessed using a standardized colony-forming unit (CFU) assay after 24 h pretreatment of cultures with each of the compounds. Percentage inhibition ranged from 3–38 % and 18–52 % at 10 and 80 μm, respectively. Thus, in contrast to the comparator drug artemether, the conjugates display enhanced activities. The immediate aims include the preparation of conjugates with enhanced aqueous solubilities, assays against malaria and TB in vivo, and for TB, assays using an infected macrophage model and assessment of granuloma influx. Teaming up: Because of the potential for initiating active transport of substrates containing a peroxide pharmacophore by way of a putative cholesterol transporter, a series of artemisinin–cholesterol conjugates were prepared. Although they are less active than the parent artemisinin against P. falciparum, they were found to be appreciably more active against M. tuberculosis in vitro. Poor solubility appears to limit activity of the conjugates.
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Inhibitors against Fungal Cell Wall Remodeling Enzymes ()
Fungal β-1,3-glucan glucanosyltransferases are glucan-remodeling enzymes that play important roles in cell wall integrity, and are essential for the viability of pathogenic fungi and yeasts. As such, they are considered possible drug targets, although inhibitors of this class of enzymes have not yet been reported. Herein we report a multidisciplinary approach based on a structure-guided design using a highly conserved transglycosylase from Sacharomyces cerevisiae, that leads to carbohydrate derivatives with high affinity for Aspergillus fumigatus Gel4. We demonstrate by X-ray crystallography that the compounds bind in the active site of Gas2/Gel4 and interact with the catalytic machinery. The topological analysis of noncovalent interactions demonstrates that the combination of a triazole with positively charged aromatic moieties are important for optimal interactions with Gas2/Gel4 through unusual pyridinium cation–π and face-to-face π–π interactions. The lead compound is capable of inhibiting AfGel4 with an IC50 value of 42 μm. Structure-guided design using a transglycosylase from Saccharomyces cerevisiae as a model led to a micromolar inhibitor of pathogenic Aspergillus fumigatus. X-ray crystallography studies show that the compounds in this series bind in the active site of Gas2/Gel4 transglycosylase and interact with the enzyme′s catalytic machinery.
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Synthesis and Biological Evaluation of Pyrrolo[2,1-f][1,2,4]triazine C-Nucleosides with a Ribose, 2′-Deoxyribose, and 2′,3′-Dideoxyribose Sugar Moiety ()
The synthesis of hitherto unknown pyrrolo[2,1-f][1,2,4]triazine C-nucleosides is described. Structural variations (chlorine, bromine, iodine, and cyano groups) were introduced at position 7 of 4-aza-7,9-dideazaadenine. In addition, pyrrolo[2,1-f][1,2,4]triazine C-nucleosides bearing a 2′-deoxy-, 2′,3′-dideoxy-, and 2′,3′-dehydrodideoxyribose moiety were also prepared. Among these analogues, the pyrrolo[2,1-f][1,2,4]triazine C-ribonucleosides with either a hydrogen atom or cyano group at position 7 of the nucleobase displayed potent cytotoxic activity in a panel of various cancer cell lines. A blue ribbon for position 7: The synthesis of pyrrolo[2,1-f][1,2,4]triazine C-nucleosides with structural variations of the 4-aza-7,9-dideazaadenine and the sugar moiety is described. Among these analogues, the pyrrolo[2,1-f][1,2,4]triazine C-ribonucleosides with either a hydrogen atom or cyano group at position 7 of the nucleobase were found to display potent cytotoxic activity in various cancer cell lines.
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Theranostic Hyaluronic Acid–Iron Micellar Nanoparticles for Magnetic-Field-Enhanced in vivo Cancer Chemotherapy ()
The delivery of therapeutic cancer agents using nanomaterials has recently attracted much attention. Although encouraging progress with chemotherapeutics has been made, tumor treatment response remains unsatisfactory. To address this concern, we constructed a new micellar nanocomplex by covalently conjugating hyaluronic acid (HA) with an iron oxide nanoparticle (IONP). When an external magnetic field was applied to the tumor area, HA–IONP specifically accumulated in the tumor, due to the strong IONP magnetism. In addition, HA was shown to bind to cluster determinant 44 (CD44), which is overexpressed on tumor cells. With combined magnetic, CD44, and enhanced permeability retention (EPR) targeting, the efficient delivery of HA–IONP to the tumor is expected to enhance cancer treatment efficiency. After encapsulation of the chemotherapy drug homocamptothecin (HCPT), the theranostic potency of HA–IONP/HCPT (HIH) was investigated both in vitro and in vivo. The improved tumor homing behavior of HIH was observed by magnetic resonance imaging (MRI) when an external magnetic field was used. Moreover, HIH showed remarkable tumor ablation efficiency, with magnetic targeting after 3 mg kg−1 intravenous administration (equivalent dose of free HCPT), and the tumors almost disappeared after treatment. No obvious systemic toxicity was detected. This excellent biocompatibility and tumor targetability suggests that HIH is a promising theranostic nanocomplex with great translational potency. Application of the HA–IONP platform could also be extended to delivery of other hydrophobic chemotherapy drugs or phototherapy agents. Small but mighty: A new micellar nanocomplex was prepared by covalently conjugating hyaluronic acid (HA) with an iron oxide nanoparticle (IONP) and encapsulating with the chemotherapeutic drug homocamptothecin (HCPT). The tumor ablation efficiency of the HA–IONP/HCPT complex improved significantly upon application of an external magnetic field to the tumor area. This HA–IONP platform could be extended to the targeted delivery of other hydrophobic chemotherapeutics or phototherapy agents.
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Activities of 11-Azaartemisinin and N-Sulfonyl Derivatives against Asexual and Transmissible Malaria Parasites ()
Dihydroartemisinin (DHA), either used in its own right or as the active drug generated in vivo from the other artemisinins in current clinical use—artemether and artesunate—induces quiescence in ring-stage parasites of Plasmodium falciparum (Pf). This induction of quiescence is linked to artemisinin resistance. Thus, we have turned to structurally disparate artemisinins that are incapable of providing DHA on metabolism. Accordingly, 11-azaartemisinin 5 and selected N-sulfonyl derivatives were screened against intraerythrocytic asexual stages of drug-sensitive Pf NF54 and drug-resistant K1 and W2 parasites. Most displayed appreciable activities against all three strains, with IC50 values <10.5 nm. The p-trifluoromethylbenzenesulfonyl-11-azaartemisinin derivative 11 [(4′-trifluoromethyl)benzenesulfonylazaartemisinin] was the most active, with IC50 values between 2 and 3 nm. The compounds were screened against Pf NF54 early and transmissible late intraerythrocytic-stage gametocytes using luciferase and parasite lactate dehydrogenase (pLDH) assays. The 2′-thienylsulfonyl derivative 16 (2′-thiophenesulfonylazaartemisinin) was notably active against late-stage (IV–V) gametocytes with an IC50 value of 8.7 nm. All compounds were relatively nontoxic to human fetal lung WI-38 fibroblasts, showing selectivity indices of >2000 toward asexual parasites. Overall, the readily accessible 11-azaartemisinin 5 and the sulfonyl derivatives 11 and 16 represent potential candidates for further development, in particular for transmission blocking of artemisinin-resistant parasites. Resistance fighters: New artemisinin antimalarial drugs that do not provide dihydroartemisinin upon hydrolysis or metabolism and that are active against transmissible blood stages of the malaria parasite are urgently required. We examined 11-azaartemisinin and sulfonyl derivatives, some of which possess low-nanomolar activities against the transmissible late-stage gametocytes of Plasmodium falciparum.
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LEGO-Inspired Drug Design: Unveiling a Class of Benzo[d]thiazoles Containing a 3,4-Dihydroxyphenyl Moiety as Plasma Membrane H+-ATPase Inhibitors ()
The fungal plasma membrane H+-ATPase (Pma1p) is a potential target for the discovery of new antifungal agents. Surprisingly, no structure–activity relationship studies for small molecules targeting Pma1p have been reported. Herein, we disclose a LEGO-inspired fragment assembly strategy for the design, synthesis, and discovery of benzo[d]thiazoles containing a 3,4-dihydroxyphenyl moiety as potential Pma1p inhibitors. A series of 2-(benzo[d]thiazol-2-ylthio)-1-(3,4-dihydroxyphenyl)ethanones was found to inhibit Pma1p, with the most potent IC50 value of 8 μm in an in vitro plasma membrane H+-ATPase assay. These compounds were also found to strongly inhibit the action of proton pumping when Pma1p was reconstituted into liposomes. 1-(3,4-Dihydroxyphenyl)-2-((6-(trifluoromethyl)benzo[d]thiazol-2-yl)thio)ethan-1-one (compound 38) showed inhibitory activities on the growth of Candida albicans and Saccharomyces cerevisiae, which could be correlated and substantiated with the ability to inhibit Pma1p in vitro. Toy story: A LEGO-inspired fragment assembly strategy for drug design, synthesis, and discovery is described. With this method, a series of benzo[d]thiazoles containing a 3,4-dihydroxyphenyl moiety was found to inhibit fungal plasma membrane H+-ATPase (Pma1p), with the most potent IC50 value of 8 μm (Ki=6 μm) in an in vitro assay. Structure–activity relationships were established. This LEGO design method will open new ways for the discovery of novel inhibitors for less studied targets.
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Novel Gold and Silver Carbene Complexes Exert Antitumor Effects Triggering the Reactive Oxygen Species Dependent Intrinsic Apoptotic Pathway ()
Cisplatin and other platinum-based drugs are well-known valid anticancer drugs. However, during chemotherapy, the presence of numerous side effects and the onset of frequent phenomena of resistance has pushed many research groups to devise new metal-based compounds holding improved anticancer properties and fewer undesired effects. Amongst the variety of synthesized compounds, significant antiproliferative effects have been obtained by employing organometallic compounds, particularly those based on silver and gold. With this in mind, we synthesized four compounds, two silver complexes and two gold complexes, with good inhibitory effects on the in vitro proliferation of breast and ovarian cancer-cell models. The antitumor activity of the most active compound, that is, AuL4, was found to be ninefold higher than that of cisplatin, and this compound induced dramatic morphological changes in HeLa cells. AuL4 induced PARP-1 cleavage, caspases 3/7 and 9 activation, mitochondria disruption, cytochrome c release in cancer-cell cytoplasm, and the intracellular production of reactive oxygen species. Thus, AuL4 treatment caused cancer-cell death by the intrinsic apoptotic pathway, whereas no cytotoxic effects were recorded upon treating non-tumor cell lines. The reported outcomes may be an important contribution to the expanding knowledge of medicinal bio-organometallic chemistry and enlarge the available anticancer toolbox, offering improved features, such as higher activity and/or selectivity, and opening the way to new discoveries and applications. Silver & gold: All the compounds synthesized in this study are light- and water-stable and possess antitumor properties, mostly against HeLa cells. AuL4 induces mitochondria disruption and cytochrome c release, which activates the intrinsic apoptotic pathway in a reactive oxygen species (ROS)-dependent fashion.
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Activities of 11-Azaartemisinin and N-Sulfonyl Derivatives against Neospora caninum and Comparative Cytotoxicities ()
Neosporosis caused by the apicomplexan parasite Neospora caninum is an economically important disease that induces abortion in dairy and beef cattle. There are no vaccines or drugs available on the market for control or treatment of the disease in bovines. The peroxide artemisinin and its derivatives used clinically for treatment of malaria are active against N. caninum and other apicomplexan parasites. We have now evaluated the activities of the readily accessible and chemically robust 11-azaartemisinin 5 and selected N-sulfonyl derivatives prepared as described in the accompanying paper against N. caninum tachyzoites grown in infected human foreskin fibroblasts. Azaartemisinin elicited an IC50 value of 150 nm, and the 2′,5′-dichloro-3′-thienylsulfonyl-11-azaartemisinin 17 was found to be the most active, with an IC50 value of 40 nm. Comparison with normal human fetal lung fibroblasts HFLF WI-38 revealed relatively benign cytotoxicity. The compounds were also screened in vitro against TK-10 (renal), UACC-62 (melanoma) and MCF-7 (breast) cancer cell lines; overall, in line with activities against HFLF cells, most compounds in the series were found to be inactive. A boost for bovines: 11-Azaartemisinin and its sulfonyl derivatives, noted for their thermal stability, are active in vitro against Neospora caninum, an important parasite of beef and dairy cattle. In contrast, the compounds displayed relatively low cytotoxicities toward normal human fetal lung fibroblasts, and with the exception of 17 with IC50 values of 14.5–16 μm, were not appreciably active toward proliferating cell lines.
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Synthetic Oligosaccharide Libraries and Microarray Technology: A Powerful Combination for the Success of Current Glycosaminoglycan Interactomics ()
Glycosaminoglycans (GAGs) are extracellular matrix and/or cell-surface sulfated glycans crucial to the regulation of various signaling proteins, the functions of which are essential in many pathophysiological systems. Because structural heterogeneity is high in GAG chains and purification is difficult, the use of structurally defined GAG oligosaccharides from natural sources as molecular models in both biophysical and pharmacological assays is limited. To overcome this obstacle, GAG-like oligosaccharides of well-defined structures are currently being synthesized by chemical and/or enzymatic means in many research groups around the world. These synthetic GAG oligosaccharides serve as useful molecular tools in studies of GAG–protein interactions. In this review, besides discussing the commonest routes used for the synthesis of GAG oligosaccharides, we also survey some libraries of these synthetic models currently available for research and discuss their activities in interaction studies with functional proteins, especially through the microarray approach. The combination of synthetic glycosaminoglycan (GAG) oligosaccharides and microarray technology has played a pivotal role in our understanding of GAG interactomics. Synthetic GAG libraries have been created by chemoenzymatic or de novo synthesis. Glycan microarrays based on these oligosaccharides have been used to assess GAG specificities and affinities of various GAG-binding proteins. This powerful combination has allowed significant progress in deciphering the intricacies of GAG–protein interactions.
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Design, Synthesis, and Evaluation of ω-(Isothiocyanato)alkylphosphinates and Phosphine Oxides as Antiproliferative Agents ()
A series of 21 novel, structurally diverse ω-(isothiocyanato)alkylphosphinates and phosphine oxides (ITCs) were designed and synthesized in moderate to good yields. The synthesized compounds were evaluated for in vitro antiproliferative activity using LoVo and LoVo/DX cancer cell lines. The biological activity of the synthesized compounds was higher than that of natural isothiocyanates such as benzyl isothiocyanate or sulforaphane. The antiproliferative activity of selected ITCs was also tested on selected cancer cell lines: A549, MESSA and MESSA/DX-5, HL60 and HL60MX2, BALB/3T3, and 4T1. These compounds were assessed for their mechanism of action as inducers of cell-cycle arrest and apoptosis. Ethyl (6-isothiocyanatohexyl)(phenyl)phosphinate (71) was tested in vivo on the 4T1 cell line and demonstrated moderate antitumor activity, similar to that benzyl isothiocyanate and cyclophosphamide. Phosphinate and phosphine oxide analogues of sulforaphane: New structurally diverse analogues of sulforaphane, in which the methylsulfinyl moiety was replaced with phosphinato or phosphine oxide groups with various alkyl chains were synthesized. Nearly all isothiocyanates obtained demonstrated better in vitro anticancer activity on colon cancer cell lines—LoVo and LoVo/DX—than sulforaphane.
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Phthalocyanine-Conjugated Upconversion NaYF4:Yb3+/Er3+@SiO2 Nanospheres for NIR-Triggered Photodynamic Therapy in a Tumor Mouse Model ()
Photodynamic therapy (PDT) has garnered immense attention as a minimally invasive clinical treatment modality for malignant cancers. However, its low penetration depth and photodamage of living tissues by UV and visible light, which activate a photosensitizer, limit the application of PDT. In this study, monodisperse NaYF4:Yb3+/Er3+ nanospheres 20 nm in diameter, that serve as near-infrared (NIR)-to-visible light converters and activators of a photosensitizer, were synthesized by high-temperature co-precipitation of lanthanide chlorides in a high-boiling organic solvent (octadec-1-ene). The nanoparticles were coated with a thin shell (≈3 nm) of homogenous silica via the hydrolysis and condensation of tetramethyl orthosilicate. The NaYF4:Yb3+/Er3+@SiO2 particles were further functionalized by methacrylate-terminated groups via 3-(trimethoxysilyl)propyl methacrylate. To introduce a large number of reactive amino groups on the particle surface, methacrylate-terminated NaYF4:Yb3+/Er3+@SiO2 nanospheres were modified with a branched polyethyleneimine (PEI) via Michael addition. Aluminum carboxyphthalocyanine (Al Pc-COOH) was then conjugated to NaYF4:Yb3+/Er3+@SiO2-PEI nanospheres via carbodiimide chemistry. The resulting NaYF4:Yb3+/Er3+@SiO2-PEI-Pc particles were finally modified with succinimidyl ester of poly(ethylene glycol) (PEG) in order to alleviate their future uptake by the reticuloendothelial system. Upon 980 nm irradiation, the intensive red emission of NaYF4:Yb3+/Er3+@SiO2-PEI-Pc-PEG nanoparticles completely vanished, indicating efficient energy transfer from the nanoparticles to Al Pc-COOH, which generates singlet oxygen (1O2). Last but not least, NaYF4:Yb3+/Er3+@SiO2-PEI-Pc-PEG nanospheres were intratumorally administered into mammary carcinoma MDA-MB-231 growing subcutaneously in athymic nude mice. Extensive necrosis developed at the tumor site of all mice 24–48 h after irradiation by laser at 980 nm wavelength. The results demonstrate that the NaYF4:Yb3+/Er3+@SiO2-PEI-Pc-PEG nanospheres have great potential as a novel NIR-triggered PDT nanoplatform for deep-tissue cancer therapy. Deep therapy: New monodisperse upconversion silica-coated NaYF4:Yb3+/Er3+ nanospheres with chemically bound aluminum carboxyphthalocyanine and coated with PEG were found to efficiently transfer energy, generating singlet oxygen. Intratumor administration of these nanospheres into a mouse model of mammary carcinoma causes extensive necrosis at the tumor site upon laser irradiation at 980 nm. The results demonstrate the potential of these nanospheres for NIR-triggered deep-tissue photodynamic cancer therapy.
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Design, Synthesis, Molecular Modeling, and Biological Evaluation of Novel Amine-based Histone Deacetylase Inhibitors ()
Histone deacetylases (HDACs) are promising drug targets for a variety of therapeutic applications. Herein we describe the design, synthesis, biological evaluation in cellular models of cancer, and preliminary drug metabolism and pharmacokinetic studies (DMPK) of a series of secondary and tertiary N-substituted 7-aminoheptanohydroxamic acid-based HDAC inhibitors. Introduction of an amino group with one or two surface binding groups (SBGs) yielded a successful strategy to develop novel and potent HDAC inhibitors. The secondary amines were found to be generally more potent than the corresponding tertiary amines. Docking studies suggested that the SBGs of tertiary amines cannot be favorably accommodated at the gorge region of the binding site. The secondary amines with naphthalen-2-ylmethyl, 5-phenylthiophen-2-ylmethyl, and 1H-indol-2-ylmethyl (2 j) substituents exhibited the highest potency against class I HDACs: HDAC1 IC50 39–61 nm, HDAC2 IC50 260–690 nm, HDAC3 IC50 25–68 nm, and HDAC8 IC50 320–620 nm. The cytotoxicity of a representative set of secondary and tertiary N-substituted 7-aminoheptanoic acid hydroxyamide-based inhibitors against HT-29, SH-SY5Y, and MCF-7 cancer cells correlated with their inhibition of HDAC1, 2, and 3 and was found to be similar to or better than that of suberoylanilide hydroxamic acid (SAHA). Compounds in this series increased the acetylation of histones H3 and H4 in a time-dependent manner. DMPK studies indicated that secondary amine 2 j is metabolically stable and has plasma and brain concentrations >23- and >1.6-fold higher than the IC50 value for class I HDACs, respectively. Overall, the secondary and tertiary N-substituted 7-aminoheptanoic acid hydroxyamide-based inhibitors exhibit excellent lead- and drug-like properties and therapeutic capacity for cancer applications. Say what you really amine: A novel series of secondary and tertiary N-substituted 7-aminoheptanohydroxamic acid based histone deacetylase inhibitors was designed, synthesized, and tested for anticancer activity. Systematic variation of the secondary and tertiary amine-based surface binding groups provided important insight into factors contributing to potency and selectivity. These studies resulted in N-(1H-indol-2-ylmethyl)-substituted secondary amine 2 j with excellent lead- and drug-like properties, superior in vitro anticancer activity, and a promising in vivo DMPK profile.
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A Molecular Hybrid for Mitochondria-Targeted NO Photodelivery ()
The design, synthesis, spectroscopic and photochemical properties, and biological evaluation of a novel molecular hybrid that is able to deliver nitric oxide (NO) into mitochondria are reported. This molecular conjugate unites a tailored o-CF3-p-nitroaniline chromophore, for photo-regulated NO release, and a rhodamine moiety, for mitochondria targeting, in the same molecular skeleton via an alkyl spacer. A combination of steady-state and time-resolved spectroscopic and photochemical experiments demonstrate that the two chromogenic units preserve their individual photophysical and photochemical properties in the conjugate quite well. Irradiation with violet light triggers NO release from the nitroaniline moiety and photoionization in the rhodamine center, which also retains considerable fluorescence efficiency. The molecular hybrid preferentially accumulates in the mitochondria of A549 lung adenocarcinoma cells where it induces toxicity at a concentration of 1 μm, exclusively upon irradiation. Comparative experiments, carried out with ad-hoc-synthesized model compounds, suggest that the phototoxicity observed at such a low concentration is probably not due to NO itself, but rather to the formation of the highly reactive peroxynitrite that is generated from the reaction of NO with the superoxide anion. Just say NO to cancer: A novel molecular hybrid effectively localizes in the mitochondria of A549 lung adenocarcinoma cells and releases NO therein under the control of visible light irradiation. A combination of steady-state and time-resolved spectroscopic and photochemical experiments demonstrate that the two chromogenic units preserve their individual photophysical and photochemical properties in the conjugate quite well.
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Structure–Activity Relationship of Propargylamine-Based HDAC Inhibitors ()
As histone deacetylases (HDACs) play an important role in the treatment of cancer, their selective inhibition has been the subject of various studies. These continuous investigations have given rise to a large collection of pan- and selective HDAC inhibitors, containing diverse US Food and Drug Administration (FDA)-approved representatives. In previous studies, a class of alkyne-based HDAC inhibitors was presented. We modified this scaffold in two previously neglected regions and compared their cytotoxicity and affinity toward HDAC1, HDAC6, and HDAC8. We were able to show that R-configured propargylamines contribute to increased selectivity for HDAC6. Docking studies on available HDAC crystal structures were carried out to rationalize the observed selectivity of the compounds. Substitution of the aromatic portion by a thiophene derivative results in high affinity and low cytotoxicity, indicating an improved drug tolerance. Chirality and angle matter: Histone deacetylases (HDACs) play an important role in cancer, and their selective inhibition has been the subject of many studies aimed at finding new anticancer drugs. R-configured propargyl amides and a thiophene linker inducing a slight kink in the linker moiety provide inhibitors of HDAC6 with significantly increased affinity, selectivity, and decreased cytotoxicity.
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Synthesis and Biological Evaluation of Stilbene Analogues as Hsp90 C-Terminal Inhibitors ()
The design, synthesis, and biological evaluation of stilbene-based novobiocin analogues is reported. Replacement of the biaryl amide side chain with a triazole side chain produced compounds that exhibited good antiproliferative activities. Heat shock protein 90 (Hsp90) inhibition was observed when N-methylpiperidine was replaced with acyclic tertiary amines on the stilbene analogues that also contain a triazole-derived side chain. These studies revealed that ≈24 Å is the optimal length for compounds that exhibit good antiproliferative activity as a result of Hsp90 inhibition. Optimized Hsp90 blockers: This work focused on the design and biological evaluation of stilbene-based novobiocin analogues. Initial efforts revealed the stilbene moiety as the optimal core. These studies revealed that replacement of the biaryl amide side chain with triazole-containing analogues and tertiary amines on the stilbene core produced more efficacious compounds as confirmed by IC50 values and western blot analyses.
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Activation of the Wnt Pathway by Small Peptides: Rational Design, Synthesis and Biological Evaluation ()
A computational analysis of the X-ray structure of the low-density lipoprotein receptor-related protein 6 (LRP6) with the Dickkopf-1 (DKK1) C-terminal fragment has allowed us to rationally design a small set of decapeptides. These compounds behave as agonists of the canonical Wnt pathway in the micromolar range when tested on a dual luciferase Wnt functional assay in glioblastoma cells. Two of the oligopeptides showed a lack of cytotoxicity in human primary osteoblasts isolated from sponge bone tissue (femoral heads or knees of elderly patients). According to the mechanism of action, the studies revealed a dose- and time-dependent increase in the viability of human osteoblasts. These results may indicate a potential therapeutic application of this class of compounds in the treatment of bone diseases related to aging, such as osteoporosis. A bone to pick with osteoporosis: By mimicking the DKK1 C-terminal domain, novel oligopeptides were developed as Wnt pathway agonists. The prototypic compounds 1 c and 1 d, devoid of cytotoxicity, were able to dose- and time-dependently increase cell viability in tests against human primary osteoblasts. These studies provide the starting point for the development of optimized potential therapeutics for the treatment of bone diseases related to aging, such as osteoporosis.
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Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin G Associated Kinase ()
4-Anilinoquinolines were identified as potent and narrow-spectrum inhibitors of the cyclin G associated kinase (GAK), an important regulator of viral and bacterial entry into host cells. Optimization of the 4-anilino group and the 6,7-quinoline substituents produced GAK inhibitors with nanomolar activity, over 50 000-fold selectivity relative to other members of the numb-associated kinase (NAK) subfamily, and a compound (6,7-dimethoxy-N-(3,4,5-trimethoxyphenyl)quinolin-4-amine; 49) with a narrow-spectrum kinome profile. These compounds may be useful tools to explore the therapeutic potential of GAK in prevention of a broad range of infectious and systemic diseases. Targeting GAK: The availability of chemical probes with improved selectivity for cyclin G associated kinase (GAK) or a different spectrum of off-targets would be useful in target validation studies. Herein we report the synthesis and characterization of 4-anilinoquinolines and 4-anilinoquinazolines as potent narrow-spectrum GAK inhibitors. Several of these compounds have the potential for development into high-quality chemical probes for the study of GAK biology.
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Comparative Molecular Dynamics Simulation of Aggregating and Non-Aggregating Inhibitor Solutions: Understanding the Molecular Basis of Promiscuity ()
The presence of false positives in enzyme inhibition assays is a common problem in early drug discovery, especially for compounds that form colloid aggregates in solution. The molecular basis of these aggregates could not be thoroughly explored because of their transient stability. In this study we conducted comparative molecular dynamics (MD) simulations of miconazole, a strong aggregator, and fluconazole, a known non-aggregator. Interestingly, miconazole displays full aggregation within only 50 ns, whilst fluconazole shows no aggregation over the 500 ns simulation. The simulations indicate that the center of the aggregate is densely packed by the hydrophobic groups of miconazole, whereas polar and nonpolar groups comprise the surface to form a micelle-like colloid. The amphiphilic moment and planar nature of the miconazole structure appear to promote its aggregating behavior. The simulations also predict rapid aggregate formation for a second known promiscuous inhibitor, nicardipine. Thus, MD appears to be a useful tool to characterize aggregate-prone inhibitors at molecular-level detail and has the potential to provide useful information for drug discovery and formulation design. Some truth behind false positives: Promiscuous inhibitors show up in enzyme assays as false positives, mainly because of aggregation. Molecular dynamics (MD) simulations were conducted for known aggregators and non-aggregators, revealing the forces and physicochemical properties behind the phenomenon of aggregation. This study also investigated the potential use of MD simulations as predictive tools in this regard.
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Effects of the Protonation State of Titratable Residues and the Presence of Water Molecules on Nocodazole Binding to β-Tubulin ()
Regulation of microtubule assembly by antimitotic agents is a potential therapeutic strategy for the treatment of cancer, parasite infections, and neurodegenerative diseases. One of these agents is nocodazole (NZ), which inhibits microtubule polymerization by binding to β-tubulin. NZ was recently co-crystallized in Gallus gallus tubulin, providing new information about the features of interaction for ligand recognition and stability. In this work, we used state-of-the-art computational approaches to evaluate the protonation effects of titratable residues and the presence of water molecules in the binding of NZ. Analysis of protonation states showed that residue E198 has the largest modification in its pKa value. The resulting E198 pKa value, calculated with pH-REMD methodology (pKa=6.21), was higher than the isolated E amino acid (pKa=4.25), thus being more likely to be found in its protonated state at the binding site. Moreover, we identified an interaction between a water molecule and C239 and G235 as essential for NZ binding. Our results suggest that the protonation state of E198 and the structural water molecules play key roles in the binding of NZ to β-tubulin. NZ–β-tubulin complex: Nocodazole (NZ) inhibits microtubule polymerization by binding to the β-tubulin subunit. In this study we evaluated the effect of the protonated states of titratable residues and structural water molecules in the binding mode of NZ, using different computational approaches. Our results suggest that the protonated state of E198 and the water molecule located between G235 and C239 are key structural features for the binding of NZ to β-tubulin.
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Comparison of Maximum Common Subgraph Isomorphism Algorithms for the Alignment of 2D Chemical Structures ()
The identification of the largest substructure in common when two (or more) molecules are overlaid is important for several applications in chemoinformatics, and can be implemented using a maximum common subgraph (MCS) algorithm. Many such algorithms have been reported, and it is important to know which are likely to be the useful in operation. A detailed comparison was hence conducted of the efficiency (in terms of CPU time) and the effectiveness (in terms of the size of the MCS identified) of eleven MCS algorithms, some of which were exact and some of which were approximate in character. The algorithms were used to identify both connected and disconnected MCSs on a range of pairs of molecules. The fastest exact algorithms for the connected and disconnected problems were found to be the fMCS and MaxCliqueSeq algorithms, respectively, while the ChemAxon_MCS algorithm was the fastest approximate algorithm for both types of problem. Finding the MCS (maximum common substructure) is a computationally difficult challenge, for which several attempts have been made to improve both the search speeds, and quality, of reported solutions. This article describes challenging benchmarks for a series of MCS algorithms, and reports the MCS type and algorithm combinations which generally yield the fastest and most sensible results in a chemoinformatic problem domain.
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In Silico Prediction of Compounds Binding to Human Plasma Proteins by QSAR Models ()
Plasma protein binding (PPB) is a significant pharmacokinetic property of compounds in drug discovery and design. Due to the high cost and time-consuming nature of experimental assays, in silico approaches have been developed to assess the binding profiles of chemicals. However, because of unambiguity and the lack of uniform experimental data, most available predictive models are far from satisfactory. In this study, an elaborately curated training set containing 967 diverse pharmaceuticals with plasma-protein-bound fractions (fb) was used to construct quantitative structure–activity relationship (QSAR) models by six machine learning algorithms with 26 molecular descriptors. Furthermore, we combined all of the individual learners to yield consensus prediction, marginally improving the accuracy of the consensus model. The model performance was estimated by tenfold cross validation and three external validation sets comprising 242 pharmaceutical, 397 industrial, and 231 newly designed chemicals, respectively. The models showed excellent performance for the entire test set, with mean absolute error (MAE) ranging from 0.126 to 0.178, demonstrating that our models could be used by a chemist when drawing a molecular structure from scratch. Meanwhile, structural descriptors contributing significantly to the predictive power of the models were related to the binding mechanisms, and the trend in terms of their effects on PPB can serve as guidance for the structural modification of chemicals. The applicability domain was also defined to distinguish favorable predictions from unfavorable predictions. In silico strategies: We used data curation, descriptor selection, machine learning algorithms, consensus modeling techniques, diverse validation strategies, and applicability domain analysis to develop quantitative structure–activity relationship (QSAR) models of compound plasma protein binding. Experimental data uncertainty was also assessed, helping us form reasonable expectations for potential models.
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Mitochondria-Targeting Polyamine–Protoporphyrin Conjugates for Photodynamic Therapy ()
Two polyamine derivatives of protoporphyrin IX (PPIX) were tested as photodynamic therapy (PDT) agents in HT29 colorectal cancer and HEP3B liver cancer cell lines. These compounds exhibit excellent singlet oxygen quantum yields and show strong in vitro PDT efficacy after 660 nm laser irradiation, whereas exogenous PPIX itself exhibits much weaker PDT effects. Confocal microscopy imaging studies reveal that a protoporphyrin derivative with eight amine moieties has excellent water solubility, and localizes mainly in the mitochondria of both HT29 and HEP3B cells, whereas the cellular distribution of a protoporphyrin derivative with four amine moieties is not as specific. This work demonstrates that polyamine moieties on macrocycles can enhance PDT efficacy by targeting mitochondria. Eight is great: Two polyamine derivatives of protoporphyrin IX exhibit excellent singlet oxygen quantum yields and show strong in vitro efficacy in photodynamic therapy (PDT) in HT29 colorectal cancer and HEP3B liver cancer cell lines after laser irradiation at 660 nm. The protoporphyrin IX derivative with eight amine moieties mainly permeates mitochondria, thereby enhancing PDT efficacy.
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IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein–Ligand Interactions ()
Structure-based ligand design requires an exact description of the topology of molecular entities under scrutiny. IChem is a software package that reflects the many contributions of our research group in this area over the last decade. It facilitates and automates many tasks (e.g., ligand/cofactor atom typing, identification of key water molecules) usually left to the modeler's choice. It therefore permits the detection of molecular interactions between two molecules in a very precise and flexible manner. Moreover, IChem enables the conversion of intricate three-dimensional (3D) molecular objects into simple representations (fingerprints, graphs) that facilitate knowledge acquisition at very high throughput. The toolkit is an ideal companion for setting up and performing many structure-based design computations. Taming complexity: IChem is a suite of software dedicated to the analysis and comparison of three-dimensional molecular objects. It converts an intricate three-dimensional information into much simpler fingerprints or graphs, thereby enabling high-throughput comparisons and fueling machine learning models for predicting important features like protein–protein interfaces, druggable cavities, interaction patterns, and binding poses.
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Rationalizing Promiscuity Cliffs ()
Compound promiscuity can be viewed in different ways. We distinguish “bad” promiscuity resulting from chemical liabilities, nonspecific binding, or assay artifacts, from “good” promiscuity representing true multitarget activities. Investigating multitarget activities of small molecules is scientifically stimulating and therapeutically relevant. To better understand the molecular basis of multitarget activities, structure-promiscuity relationships (SPRs) are explored. For this purpose, “promiscuity cliffs” (PCs) have been introduced, which can be rationalized as an extension of the activity cliff (AC) concept. A PC is defined as a pair of structural analogues that are active against different numbers of targets (given a difference threshold). As discussed herein PCs frequently capture surprising SPRs and encode many experimentally testable hypotheses. Promiscuity cliff: Shown is an exemplary promiscuity cliff comprising two structural analogues that were extensively tested in screening assays and displayed an unexpectedly large difference in the number of targets (PD) they were active against. The compound on the right was consistently inactive in all assays.
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Cross-Classified Multilevel Modelling of the Effectiveness of Similarity-Based Virtual Screening ()
The screening effectiveness of a chemical similarity search depends on a range of factors, including the bioactivity of interest, the types of similarity coefficient and fingerprint that comprise the similarity measure, and the nature of the reference structure that is being searched against a database. This study introduces the use of cross-classified multilevel modelling as a way to investigate the relative importance of these four factors when carrying out similarity searches on the ChEMBL database. Two principal conclusions can be drawn from the analyses: that the fingerprint plays a more important role than the similarity coefficient in determining the effectiveness of a similarity search, and that comparative studies of similarity measures should involve many more reference structures than has been the case in much previous work. We describe the use of cross-classified multilevel modelling to analyse the results of similarity-based virtual screening searches using 2D fingerprints. We show that the choice of fingerprint is more important than the choice of similarity coefficient, and that multiple reference structures need to be used in benchmark studies such as this.
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From Artemisia annua L. to Artemisinins: The Discovery and Development of Artemisinins and Antimalarial Agents. Edited by YouYou Tu ()
Academic Press, Cambridge 2017. 468 pp., hardcover, £100.30.—ISBN 978-0-12-811655-2
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DNA Microcapsule for Photo-Triggered Drug Release Systems ()
In this study we constructed spherical photo-responsive microcapsules composed of three photo-switchable DNA strands. These strands first formed a three-way junction (TWJ) motif that further self-assembled to form microspheres through hybridization of the sticky-end regions of each branch. To serve as the photo-switch, multiple unmodified azobenzene (Azo) or 2,6-dimethyl-4-(methylthio)azobenzene (SDM-Azo) were introduced into the sticky-end regions via a d-threoninol linker. The DNA capsule structure deformed upon trans-to-cis isomerization of Azo or SDM-Azo induced by specific light irradiation. In addition, photo-triggered release of encapsulated small molecules from the DNA microcapsule was successfully achieved. Moreover, we demonstrated that photo-triggered release of doxorubicin caused cytotoxicity to cultured cells. This biocompatible photo-responsive microcapsule has potential application as a photo-controlled drug-release system. Let there be light: We designed a photo-sensing DNA microcapsule. This DNA microcapsule was formed by assembly of the Y-shaped DNA-building blocks in which azobenzenes were located within the connecting regions. Upon irradiation with light, the microcapsules were found to rapidly collapse, thus releasing doped compounds through the cis isomerization of azobenzene units positioned at connecting regions between the building blocks.
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Biomedical Nanomaterials. Edited by Yuliang Zhao and Youqing Shen ()
Wiley-VCH, Weinheim 2016. 476 pp., hardcover, €159.00.—ISBN  978-3-527-33798-9
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Anti-aging Drugs: From Basic Research to Clinical Practice. Edited by Alexander M. Vaiserman ()
RSC, Cambridge 2017. 570 pp., hardcover, £199.00.—ISBN 978-1-78262-435-6
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Matched Molecular Pair Analysis on Large Melting Point Datasets: A Big Data Perspective ()
A matched molecular pair (MMP) analysis was used to examine the change in melting point (MP) between pairs of similar molecules in a set of ∼275k compounds. We found many cases in which the change in MP (ΔMP) of compounds correlates with changes in functional groups. In line with the results of a previous study, correlations between ΔMP and simple molecular descriptors, such as the number of hydrogen bond donors, were identified. In using a larger dataset, covering a wider chemical space and range of melting points, we observed that this method remains stable and scales well with larger datasets. This MMP-based method could find use as a simple privacy-preserving technique to analyze large proprietary databases and share findings between participating research groups. An MMP for MPs: A matched molecular pair analysis was used to examine the change in melting point (ΔMP) between molecules in a set of ∼275 000 compounds. We found many cases in which the ΔMP correlates with changes in functional groups and simple descriptors, such as number of hydrogen bond donors and acceptors. We observed that this method remains stable and scales well with larger datasets, indicating its utility as a simple privacy-preserving technique to analyze large proprietary databases and share findings.
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Kinome-Wide Profiling Prediction of Small Molecules ()
Extensive kinase profiling data, covering more than half of the human kinome, are available nowadays and allow the construction of activity prediction models of high practical utility. Proteochemometric (PCM) approaches use compound and protein descriptors, which enables the extrapolation of bioactivity values to thus far unexplored kinases. In this study, the potential of PCM to make large-scale predictions on the entire kinome is explored, considering the applicability on novel compounds and kinases, including clinically relevant mutants. A rigorous validation indicates high predictive power on left-out kinases and superiority over individual kinase QSAR models for new compounds. Furthermore, external validation on clinically relevant mutant kinases reveals an excellent predictive power for mutations spread across the ATP binding site. Kinome-wide prediction of kinase inhibitors: The capabilities of proteochemometric (PCM) models to make large-scale predictions on the entire kinome was explored. The combination of a compound fingerprint with a protein fingerprint 1) improves the activity prediction for each kinase relative to individually trained models and 2) enables prediction of the activity of compounds for the entire kinome, including cancer-related resistance mutations.
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Front Cover: A Dithiol Compound Binds to the Zinc Finger Protein TRAF6 and Suppresses Its Ubiquitination (ChemMedChem 23/2017) ()
The Front Cover shows that a dithiol compound named SN-1 binds to TRAF6 protein and suppresses its auto-ubiquitination and downstream NF-κB activation to express proteins related to cancer and inflammation. The TRAF6 has five zinc fingers C-terminal to the N-terminal RING finger domain with two zincs. SN-1 is considered to bind directly to a zinc of the first zinc finger, disrupting ubiquitin ligase activity of the neighboring RING finger. This study shows a platform for new small molecules targeting zinc finger proteins, coming after the conventional drugs targeting zinc enzymes. Cover illustration by Hiroe Kamasaki, Soft Sync Inc. More information can be found in the Full Paper by Masami Otsuka, Mikako Fujita et al. on page 1935 in Issue 23, 2017 (DOI: 10.1002/cmdc.201700399).
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Cover Feature: Methyl Fumarate-Derived Iron Carbonyl Complexes (FumET-CORMs) as Powerful Anti-inflammatory Agents (ChemMedChem 23/2017) ()
The Cover Feature shows the “championship” of anti-inflammatory agents for dendritic cells. The winners are FumET-CORMs which were developed by fusing a methyl fumarate and an enzyme-triggered carbon monoxide releasing molecule (ET-CORM). The intracellular activation of the FumET-CORMs by an esterase leads to the simultaneous release of CO and methyl fumarate. In contrast to the clinically used dimethyl fumarate or CO alone, the strong cellular response of dendritc cells towards FumET-CORMs reflects the synergetic action of the two agents as indicated by the suppression of secretion of inflammatory interleukins IL-12 and IL-23. More information can be found in the Communication by Thomas Wieder, Hans-Günther Schmalz et al. on page 1927 in Issue 23, 2017 (DOI: 10.1002/cmdc.201700488).
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Internal Targeting and External Control: Phototriggered Targeting in Nanomedicine ()
The photochemical control of structure and reactivity bears great potential for chemistry, biology, and life sciences. A key feature of photochemistry is the spatiotemporal control over secondary events. Well-established applications of photochemistry in medicine are photodynamic therapy (PDT) and photopharmacology (PP). However, although both are highly localizable through the application of light, they lack cell- and tissue-specificity. The combination of nanomaterial-based drug delivery and targeting has the potential to overcome limitations for many established therapy concepts. Even more privileged seems the merger of nanomedicine and cell-specific targeting (internal targeting) controlled by light (external control), as it can potentially be applied to many different areas of medicine and pharmaceutical research, including the aforementioned PDT and PP. In this review a survey of the interface of photochemistry, medicine and targeted drug delivery is given, especially focusing on phototriggered targeting in nanomedicine. Illuminating activation: The combination of drug delivery, targeting, and photochemistry is extremely powerful because it allows spatiotemporal control of targeting activity and drug liberation into specific cells. The development of new photochemical tools, as well as the use of novel cell-specific receptors, ligands, and properties will surely foster the true potential of phototriggered targeting.
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Largazole Analogues as Histone Deacetylase Inhibitors and Anticancer Agents: An Overview of Structure–Activity Relationships ()
Since the time of its identification, the natural compound largazole rapidly caught the attention of the medicinal chemistry community for its impressive potency as an inhibitor of histone deacetylases (HDACs) and its strong antiproliferative activity against a broad panel of cancer cell lines. The design of largazole analogues is an expanding field of study, due to their remarkable potential as novel anticancer therapeutics. At present, a large ensemble of largazole analogues has been reported, allowing the identification of important structure–activity relationships (SAR) that can guide the design of novel compounds with improved HDAC inhibitory profiles, anticancer activity, and pharmacokinetic properties. The aim of this review is to concisely summarize the information obtained by biological evaluations of the various largazole analogues reported to date, with particular attention given to the latest analogues, as well as to analyze the various SAR obtained from this data, with the purpose of providing useful guidelines for the development of novel potent and selective HDAC inhibitors to be used as anticancer agents. The power of depsipeptides: This review summarizes the various analogues obtained by structural modification of largazole, a natural depsipeptide characterized by impressive activity as a histone deacetylase inhibitor and anticancer agent. The main structure–activity relationships derived by biological evaluation of these compounds are analyzed and discussed, providing useful guidelines for the design of new anticancer agents.
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Methyl Fumarate-Derived Iron Carbonyl Complexes (FumET-CORMs) as Powerful Anti-inflammatory Agents ()
Autoimmune diseases are characterized by dendritic cell (DC)-driven activation of pro-inflammatory T cell responses. Therapeutic options for these severe diseases comprise small molecules such as dimethyl fumarate, or “gasotransmitters” such as CO. Herein we describe the synthesis of bifunctional enzyme-triggered CO-releasing molecules (ET-CORMs) that allow the simultaneous intracellular release of both CO and methyl fumarate. Using bone-marrow-derived DCs the impressive therapeutic potential of these methyl fumarate-derived compounds (FumET-CORMs) is demonstrated by strong inhibition of lipopolysaccharide-induced pro-inflammatory signaling pathways and blockade of downstream interleukin-12 or -23 production. The data also show that FumET-CORMs are able to transform DCs into an anti-inflammatory phenotype. Thus, these novel compounds have great clinical potential, for example, for the treatment of psoriasis or other inflammatory conditions of the skin. Safe CO delivery: Linked ET-CORM-(di)methyl fumarates (FumET-CORMs) were synthesized and investigated for their synergistic anti-inflammatory and immune-modulating properties. The results show a stronger HO-1 induction with simultaneous inhibition of STAT1 phosphorylation in primary murine DCs relative to dimethyl fumarate. In addition, inhibited secretion of the pro-inflammatory cytokines IL-12 and IL-23 could be detected.
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Hybrid BisQACs: Potent Biscationic Quaternary Ammonium Compounds Merging the Structures of Two Commercial Antiseptics ()
Benzalkonium chloride (BAC) and cetyl pyridinium chloride (CPC) are two of the most common household antiseptics, but show weaker efficacy against Gram-negative bacteria as well as against methicillin-resistant Staphylococcus aureus (MRSA) strains, relative to other S. aureus strains. We prepared 28 novel quaternary ammonium compounds (QACs) that represent a hybrid of these two structures, using 1- to 2-step synthetic sequences. The biscationic (bisQAC) species prepared show uniformly potent activity against six bacterial strains tested, with nine novel antiseptics displaying single-digit micromolar activity across the board. Effects of unequal chain lengths of two installed side chains had less impact than the overall number of side chain carbon atoms present, which was optimal at 22–25 carbons. This is further indication that simple refinements to multiQAC architectures can show improvement over current household antiseptics. Two heads are better than one: Biscationic quaternary ammonium compounds (bisQACs) are more potent antimicrobials than their monocationic counterparts, including commercially available benzalkonium chloride and cetyl pyridinium chloride. BisQACs that represent a hybrid of these two structures are efficiently produced and highly effective against Gram-positive and Gram-negative bacteria, including MRSA strains.
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A Dithiol Compound Binds to the Zinc Finger Protein TRAF6 and Suppresses Its Ubiquitination ()
Despite various inhibitors targeting the zinc center(s) of enzymes, drugs that target zinc fingers have not been examined in detail. We previously developed a dithiol compound named SN-1 that has an inhibitory effect on the function of zinc finger transcription factors, but its mechanism of action has not yet been elucidated. To establish a general principle for new drugs, the details of the action of SN-1 against a zinc finger protein were examined. As a zinc-finger-containing protein, we focused on TRAF6, which is related to cancer and inflammation. Binding of SN-1 to TRAF6 and its effect on TRAF6 ubiquitination were examined in vitro, and the binding mode was calculated by computational methodology. Furthermore, ubiquitination of TRAF6 and downstream signaling was examined by cell-based experiments. The results show that SN-1 binds to TRAF6, inhibiting its auto-ubiquitination and downstream NF-κB signaling. Docking studies indicate that SN-1 binds directly to the first zinc finger of TRAF6. This binding disrupts the neighboring structure, that is, the RING finger domain, to suppress the ubiquitin ligase activity of TRAF6. Taken together, this study provides a platform for developing new small molecules that target zinc finger proteins. A dithiol compound named SN-1 binds to TRAF6, inhibiting its auto-ubiquitination and downstream signaling. SN-1 is considered to bind directly to the first zinc finger of TRAF6, disrupting the neighboring RING finger domain, to suppress the ubiquitin ligase activity of TRAF6. This study provides a platform for developing new small molecules that target zinc finger proteins.
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Design, Synthesis, Biological Evaluation, and X-ray Studies of HIV-1 Protease Inhibitors with Modified P2′ Ligands of Darunavir ()
The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic HIV-1 protease inhibitors with rationally designed P2′ ligands are described. The inhibitors are designed to enhance backbone binding interactions, particularly at the S2′ subsite. Synthesis of inhibitors was carried out efficiently. The stereochemistry of alcohol functionalities of the P2′ ligands was set by asymmetric reduction of the corresponding ketone using (R,R)- or (S,S)-Noyori catalysts. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 3g and 3h showed enzyme Ki values of 27.9 and 49.7 pm and antiviral activity of 6.2 and 3.9 nm, respectively. These inhibitors also remained quite potent against darunavir-resistant HIV-1 variants. An X-ray structure of inhibitor 3g in complex with HIV-1 protease revealed key interactions in the S2′ subsite. Structured antivirals: We report the structure-based design, synthesis, biological evaluation, and X-ray structural studies of a series of highly potent HIV-1 protease inhibitors containing novel P2′ ligands to interact with protease active site residues. The inhibitors were designed to enhance backbone binding interactions, particularly at the S2′ subsite. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity and remained quite potent against darunavir-resistant HIV-1 variants. X-ray crystallographic work revealed key interactions in the S2′ subsite.
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Optimization of Substrate-Analogue Furin Inhibitors ()
The proprotein convertase furin is a potential target for drug design, especially for the inhibition of furin-dependent virus replication. All effective synthetic furin inhibitors identified thus far are multibasic compounds; the highest potency was found for our previously developed inhibitor 4-(guanidinomethyl)phenylacetyl-Arg-Tle-Arg-4-amidinobenzylamide (MI-1148). An initial study in mice revealed a narrow therapeutic range for this tetrabasic compound, while significantly reduced toxicity was observed for some tribasic analogues. This suggests that the toxicity depends at least to some extent on the overall multibasic character of this inhibitor. Therefore, in a first approach, the C-terminal benzamidine of MI-1148 was replaced by less basic P1 residues. Despite decreased potency, a few compounds still inhibit furin in the low nanomolar range, but display negligible efficacy in cells. In a second approach, the P2 arginine was replaced by lysine; compared to MI-1148, this furin inhibitor has slightly decreased potency, but exhibits similar antiviral activity against West Nile and Dengue virus in cell culture and decreased toxicity in mice. These results provide a promising starting point for the development of efficacious and well-tolerated furin inhibitors. Going (anti)viral: Given the limited tolerability of our benzamidine-derived furin inhibitor MI-1148, new analogues with less basic P1 groups were prepared. Some of them inhibit furin in the low nanomolar range, but are less active in cells. Secondly, only the P2 arginine has been replaced by lysine. This inhibitor possesses a similar inhibitory potency and activity in cell culture assays. Moreover, it exhibits decreased toxicity in mice.
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Biosynthetically Guided Structure–Activity Relationship Studies of Merochlorin A, an Antibiotic Marine Natural Product ()
The onset of new multidrug-resistant strains of bacteria demands continuous development of antibacterial agents with new chemical scaffolds and mechanisms of action. We present the first structure–activity relationship (SAR) study of 16 derivatives of a structurally novel antibiotic merochlorin A that were designed using a biosynthetic blueprint. Our lead compounds are active against several Gram-positive bacteria such as Staphylococcus aureus (SA), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE) and Bacillus subtilis, inhibit intracellular growth of Mycobacterium bovis, and are relatively nontoxic to human cell lines. Furthermore, derivative 12 c {(±)-(3aR,4S,5R,10bS)-5-bromo-7,9-dimethoxy-4-methyl-4-(4-methylpent-3-en-1-yl)-2-(propan-2-ylidene)-1,2,3,3a,4,5-hexahydro-6H-5,10b-methanobenzo[e]azulene-6,11-dione} was found to inhibit the growth of Bacillus Calmette–Guérin (BCG)-infected cells at concentrations similar to rifampicin. These results outperform the natural product, underscoring the potential of merochlorin analogues as a new class of antibiotics. Antibiotic architecture: SAR studies of 16 derivatives of the structurally novel antibiotic merochlorin A, designed using a biosynthetic blueprint, were conducted. Our lead compounds are active against several Gram-positive bacteria, and are relatively nontoxic to human cell lines.
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Structure–Activity Studies of N-Butyl-1-deoxynojirimycin (NB-DNJ) Analogues: Discovery of Potent and Selective Aminocyclopentitol Inhibitors of GBA1 and GBA2 ()
Analogues of N-butyl-1-deoxynojirimycin (NB-DNJ) were prepared and assayed for inhibition of ceramide-specific glucosyltransferase (CGT), non-lysosomal β-glucosidase 2 (GBA2) and the lysosomal β-glucosidase 1 (GBA1). Compounds 5 a–6 f, which carry sterically demanding nitrogen substituents, and compound 13, devoid of the C3 and C5 hydroxy groups present in DNJ/NB-DGJ (N-butyldeoxygalactojirimycin) showed no inhibitory activity for CGT or GBA2. Inversion of stereochemistry at C4 of N-(n-butyl)- and N-(n-nonyl)-DGJ (compounds 24) also led to a loss of activity in these assays. The aminocyclopentitols N-(n-butyl)- (35 a), N-(n-nonyl)-4-amino-5-(hydroxymethyl)cyclopentane- (35 b), and N-(1-(pentyloxy)methyl)adamantan-1-yl)-1,2,3-triol (35 f), were found to be selective inhibitors of GBA1 and GBA2 that did not inhibit CGT (>1 mm), with the exception of 35 f, which inhibited CGT with an IC50 value of 1 mm. The N-butyl analogue 35 a was 100-fold selective for inhibiting GBA1 over GBA2 (Ki values of 32 nm and 3.3 μm for GBA1 and GBA2, respectively). The N-nonyl analogue 35 b displayed a Ki value of ≪14 nm for GBA1 inhibition and a Ki of 43 nm for GBA2. The N-(1-(pentyloxy)methyl)adamantan-1-yl) derivative 35 f had Ki values of ≈16 and 14 nm for GBA1 and GBA2, respectively. The related N-bis-substituted aminocyclopentitols were found to be significantly less potent inhibitors than their mono-substituted analogues. The aminocyclopentitol scaffold should hold promise for further inhibitor development. β-Glucosidase-selective inhibitors: Aminocyclopentitols were prepared and assayed for inhibition of carbohydrate-processing enzymes, including CGT, GBA1, and GBA2. N-Butylaminocyclopentitol was found to be a potent and selective inhibitor of GBA1. The N-nonyl and N-1-((pentyloxy)methyl)adamantan-1-yl analogues potently inhibited both GBA1 (Ki≪14 nm, and Ki≤16, respectively) and GBA2 (Ki≪43 nm, and Ki=14 nm, respectively). The butyl and nonyl analogues did not inhibit CGT at 1 mm, and the Ki value for the adamantyl analogue was 1 mm. The N-alkylaminocyclopentitols hold promise for future inhibitor development.
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Head-to-Tail Cyclic Peptide Inhibitors of the Interaction between Human von Willebrand Factor and Collagen ()
The development of peptide-based therapeutics is on the rise, with macrocyclic compounds providing the added stability and drug-like characteristics sought after. Currently, therapies and preventatives for pathogenic thrombosis target platelet interactions at the site of the clot and have many complications. Herein we describe novel cyclic peptides as moderate inhibitors of the protein–protein interaction between von Willebrand factor (vWF) and collagen that initiates blood clot formation. We based our designs on two known disulfide-containing, peptide-based inhibitors of the vWF–collagen interaction. Replacing the disulfide with a head-to-tail cyclization strategy confers remarkable stability to the peptides when treated with a panel of proteases. Our peptides also showed moderate activity in our developed fluorescently linked immunosorbent assay (FLISA), similar to the most active disulfide-containing peptide. These peptides provide a springboard for future advances in exceptionally stable, active cyclic peptides as drugs. Small but mighty: Small head-to-tail cyclized peptides were developed that are moderately active inhibitors of the protein–protein interaction between von Willebrand Factor and collagen that initiates thrombosis. The peptides showed exceptional stability in the cellular environment relative to similar existing cyclic peptides that use a disulfide bond.
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Optimization and Evaluation of Antiparasitic Benzamidobenzoic Acids as Inhibitors of Kinetoplastid Hexokinase 1 ()
Kinetoplastid-based infections are neglected diseases that represent a significant human health issue. Chemotherapeutic options are limited due to toxicity, parasite susceptibility, and poor patient compliance. In response, we studied a molecular-target-directed approach involving intervention of hexokinase activity—a pivotal enzyme in parasite metabolism. A benzamidobenzoic acid hit with modest biochemical inhibition of Trypanosoma brucei hexokinase 1 (TbHK1, IC50=9.1 μm), low mammalian cytotoxicity (IMR90 cells, EC50>25 μm), and no appreciable activity on whole bloodstream-form (BSF) parasites was optimized to afford a probe with improved TbHK1 potency and, significantly, efficacy against whole BSF parasites (TbHK1, IC50=0.28 μm; BSF, ED50=1.9 μm). Compounds in this series also inhibited the hexokinase enzyme from Leishmania major (LmHK1), albeit with less potency than toward TbHK1, suggesting that inhibition of the glycolytic pathway may be a promising opportunity to target multiple disease-causing trypanosomatid protozoa. Power play: The discovery of novel target-based, antiparasitic agents is necessary to address the dearth of therapeutic options for neglected diseases such as sleeping sickness and leishmaniasis. Inhibitors of hexokinase 1, a key metabolic enzyme in these parasites, have been identified and explored as a means to interrupting glucose metabolism on which these parasites rely. Low micromolar efficacy has been observed in whole bloodstream-form trypanosomes, suggesting that this strategy may be useful in targeting glucose-dependent parasites.
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Live Cell Labeling with Terpyridine Derivative Proligands to Measure Cytotoxicity Mediated by Immune Cells ()
Immunotherapy using immune checkpoint inhibitors and CAR-T cells has revolutionized treatment for patients with malignant tumors. However, measuring tumor cell cytotoxicity mediated by immune effector cells in clinical laboratories has been difficult due to the requirement for radioactive substances. In this study, a series of novel terpyridine derivative proligands were synthesized, and a non-radioactive cellular cytotoxicity assay using the newly synthesized compounds was developed for use in preclinical and clinical studies for cancer immunotherapy. Once internalized into target cells, the compounds are hydrolyzed by esterases, resulting in the intracellular accumulation of the negatively charged terpyridine derivatives. When the labeled target cells are recognized and killed by immune effector cells, the integrity of the cell membrane is disrupted, and the terpyridine derivatives are released. Upon combining the culture supernatant with europium (Eu3+), the cytotoxicity of immune effector cells for the target cells can be quantitatively determined by measuring the intensity of the Eu3+/ligand-derived time-resolved fluorescence. Thus, the assay developed in this study would facilitate the development of novel cancer immunotherapies. Gauging the effectors: Immune checkpoint inhibitors have revolutionized the treatment of cancer patients. Although many clinical trials have been conducted to develop novel immunotherapies, measuring cellular cytotoxicity has been difficult. In this study, a series of chelate-forming proligands were synthesized to improve non-radioactive cytotoxicity assays. This assay is ideal for measuring the effector functions of immune cells in clinical laboratories.
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