ChemMedChem

Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations ()
Abstract Computational methods, namely molecular dynamics (MD) simulations in combination with inhomogeneous fluid solvation theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein–ligand interaction energy, ligand solvation free energies, and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein–ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Nevertheless, MD simulations can provide insight regarding which water molecules can be targeted for displacement.
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Expanding the SAR of Nontoxic Antiplasmodial Indolyl‐3‐ethanone Ethers and Thioethers ()
Abstract Despite major strides in reducing Plasmodium falciparum infections, this parasite still accounts for roughly half a million annual deaths. This problem is compounded by the decreased efficacy of artemisinin combination therapies. Therefore, the development and optimisation of novel antimalarial chemotypes is critical. In this study, we describe our strategic approach to optimise a class of previously reported antimalarials, resulting in the discovery of 1‐(5‐chloro‐1H‐indol‐3‐yl)‐2‐[(4‐cyanophenyl)thio]ethanone (13) and 1‐(5‐chloro‐1H‐indol‐3‐yl)‐2‐[(4‐nitrophenyl)thio]ethanone (14), whose activity was equipotent to that of chloroquine against the P. falciparum 3D7 strain. Furthermore, these compounds were found to be nontoxic to HeLa cells as well as being non‐haemolytic to uninfected red blood cells. Intriguingly, several of our most promising compounds were found to be less active against the isogenic NF54 strain, highlighting possible issues with long‐term dependability of malarial strains. Finally compound 14 displayed similar activity against both the NF54 and K1 strains, suggesting that it inhibits a pathway that is uncompromised by K1 resistance.
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Design, Synthesis, and Biological Evaluation of Tetrahydro‐β‐carboline Derivatives as Selective Sub‐Nanomolar Gelatinase Inhibitors ()
Abstract Targeting matrix metalloproteinases (MMPs) is a pursued strategy for treating several pathological conditions, such as multiple sclerosis and cancer. Herein, a series of novel tetrahydro‐β‐carboline derivatives with outstanding inhibitory activity toward MMPs are present. In particular, compounds 9 f, 9 g, 9 h and 9 i show sub‐nanomolar IC50 values. Interestingly, compounds 9 g and 9 i also provide remarkable selectivity toward gelatinases; IC50=0.15 nm for both toward MMP‐2 and IC50=0.63 and 0.58 nm, respectively, toward MMP‐9. Molecular docking simulations, performed by employing quantum mechanics based partial charges, shed light on the rationale behind binding involving specific interactions with key residues of S1′ and S3′ domains. Taken together, these studies indicate that tetrahydro‐β‐carboline represents a promising scaffold for the design of novel inhibitors able to target MMPs and selectively bias gelatinases, over the desirable range of the pharmacokinetics spectrum.
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Identification of Potentially Potent Heme Oxygenase 1 Inhibitors through 3D‐QSAR Coupled to Scaffold‐Hopping Analysis ()
Abstract A 3D quantitative structure–activity relationship (3D‐QSAR) model for predicting the activity of heme oxygenase 1 (HO‐1) inhibitors was constructed with the aim of providing a useful tool for the identification, design, and optimization of novel HO‐1 inhibitors. The model was built using a set of 222 HO‐1 inhibitors recovered from the Heme Oxygenase Database (HemeOxDB) and developed with the software Forge. The present model showed high statistical quality, as confirmed by its robust predictive potential and satisfactory descriptive capability. The drawn‐up 3D map enables prompt visual comprehension of the electrostatic, hydrophobic, and shaping features underlying the interactions with HO‐1 inhibitors. A theoretical approach for the generation of new lead compounds was performed by means of scaffold‐hopping analysis. For the first time, a 3D‐QSAR model is reported for this target, and was built with a number of chemically diverse HO‐1 inhibitors; the model also accounts well for individual ligand affinities. The new model contains all of the inhibitors published to date with high potency toward the selected target and contains a complete pharmacophore description of the binding cavity of HO‐1. These features will ensure application in accelerating the identification of new potent and selective HO‐1 inhibitors.
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Chiral Cliffs: Investigating the Influence of Chirality on Binding Affinity ()
Abstract Chirality is understood by many as a binary concept: a molecule is either chiral or it is not. In terms of the action of a structure on polarized light, this is indeed true. When examined through the prism of molecular recognition, the answer becomes more nuanced. In this work, we investigated chiral behavior on protein–ligand binding: when does chirality make a difference in binding activity? Chirality is a property of the 3D structure, so recognition also requires an appreciation of the conformation. In many situations, the bioactive conformation is undefined. We set out to address this by defining and using several novel 2D descriptors to capture general characteristic features of the chiral center. Using machine‐learning methods, we built different predictive models to estimate if a chiral pair (a set of two enantiomers) might exhibit a chiral cliff in a binding assay. A set of about 3800 chiral pairs extracted from the ChEMBL23 database was used to train and test our models. By achieving an accuracy of up to 75 %, our models provide good performance in discriminating chiral cliffs from non‐cliffs. More importantly, we were able to derive some simple guidelines for when one can reasonably use a racemate and when an enantiopure compound is needed in an assay. We critically discuss our results and show detailed examples of using our guidelines. Along with this publication we provide our dataset, our novel descriptors, and the Python code to rebuild the predictive models.
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Design, Synthesis, and in vitro Biological Evaluation of 3,5‐Dimethylisoxazole Derivatives as BRD4 Inhibitors ()
Abstract BRD4 has been identified as a potential target for blocking proliferation in a variety of cancer cell lines. In this study, 3,5‐dimethylisoxazole derivatives were designed and synthesized with excellent stability in liver microsomes as potent BRD4 inhibitors, and were evaluated for their BRD4 inhibitory activities in vitro. Gratifyingly, compound 11 h [3‐((1‐(2,4‐difluorophenyl)‐1H‐1,2,3‐triazol‐4‐yl)methyl)‐6‐(3,5‐dimethylisoxazol‐4‐yl)‐4‐phenyl‐3,4‐dihydroquinazolin‐2(1H)‐one] exhibited robust potency for BRD4(1) and BRD4(2) inhibition with IC50 values of 27.0 and 180 nm, respectively. Docking studies were performed to illustrate the strategy of modification and analyze the conformation in detail. Furthermore, compound 11 h was found to potently inhibit cell proliferation in the BRD4‐sensitive cell lines HL‐60 and MV4‐11, with IC50 values of 0.120 and 0.09 μm, respectively. Compound 11 h was further demonstrated to downregulate c‐Myc levels in HL‐60 cells. In summary, these results suggest that compound 11 h is most likely a potential BRD4 inhibitor and is a lead compound for further investigations.
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Front Cover: Designing Anticancer Peptides by Constructive Machine Learning (ChemMedChem 13/2018) ()
ChemMedChem, Volume 13, Issue 13, Page 1260-1260, July 6, 2018.
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Cover Feature: A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition (ChemMedChem 13/2018) ()
ChemMedChem, Volume 13, Issue 13, Page 1261-1261, July 6, 2018.
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Benzofuran and Indole: Promising Scaffolds for Drug Development in Alzheimer's Disease ()
Abstract Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The Food and Drug Administration has approved drugs (e.g., rivastigmine, donepezil, galantamine, and memantine) that at best provide marginal benefits, thus emphasizing the urgent need to explore other molecular entities as future drug candidates for AD. Looking at the wide pharmaceutical applications of heterocyclic compounds and particularly those containing benzofuran and indole ring systems, these molecular frameworks have drawn special attention from medicinal chemists for further evaluation in numerous diseases. This article focuses on the history and recent advances of benzofuran‐ and indole‐based compounds as inhibitors of butyrylcholinesterase, acetylcholinesterase, γ‐secretase, β‐secretase, tau misfolding, and β‐amyloid aggregation.
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Oxoisoaporphine Alkaloids: Prospective Anti‐Alzheimer's Disease, Anticancer, and Antidepressant Agents ()
Abstract Oxoisoaporphine alkaloids are a family of oxoisoquinoline‐derived alkaloids that were first isolated from the rhizome of Menispermum dauricum DC. (Menispermaceae). It has been demonstrated that oxoisoaporphine alkaloids possess various biological properties, such as cholinesterase and β‐amyloid inhibition, acting as a topoisomerase intercalator, monoamine oxidase A inhibition, and are expected to become anti‐Alzheimer's disease, anticancer, and antidepressant drugs. This review provides an overview of natural sources, synthetic routes, bioactivities, structure–function relationship, and modification investigations into oxoisoaporphine alkaloids, with the aim of providing references to the structure–activity relationships for the design and development of oxoisoaporphine derivatives with higher efficacy and therapeutic potential.
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Modeling the Accumulation of Degradable Polymer Drug Carriers in the Brain ()
Abstract The blood–brain barrier (BBB) limits the access of drugs to the brain. Intensive research is being conducted on the development of nanoparticulate drug carriers that mediate transfer across the BBB. A question that has been neglected so far is the potential accumulation of the carrier in the brain upon long‐term exposure. Here, we address this question by implementing a kinetic model to relate drug loading, required concentration of drug in the brain, and drug clearance to the degradation half‐life of the carrier. As a test case with clinical relevance we chose poly‐lactic‐co‐glycolic‐acid (PLGA) as a carrier material and a chemotherapeutic for which the required parameters could be recovered from the literature. For methotrexate with a drug load of 8.5 %, a required concentration of free drug of 1 μm, a release from PLGA of 6 hours, a drug clearance from the brain of 3 hours and a half‐life of polymer degradation of 28 days, a steady‐state accumulation of 1.3 g polymer would be reached in the brain (1.5 L) after seven months. While this number is surprisingly small, further physiological research is warranted to assess to which degree this will be in a tolerable range.
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Designing Anticancer Peptides by Constructive Machine Learning ()
Abstract Constructive (generative) machine learning enables the automated generation of novel chemical structures without the need for explicit molecular design rules. This study presents the experimental application of such a deep machine learning model to design membranolytic anticancer peptides (ACPs) de novo. A recurrent neural network with long short‐term memory cells was trained on α‐helical cationic amphipathic peptide sequences and then fine‐tuned with 26 known ACPs by transfer learning. This optimized model was used to generate unique and novel amino acid sequences. Twelve of the peptides were synthesized and tested for their activity on MCF7 human breast adenocarcinoma cells and selectivity against human erythrocytes. Ten of these peptides were active against cancer cells. Six of the active peptides killed MCF7 cancer cells without affecting human erythrocytes with at least threefold selectivity. These results advocate constructive machine learning for the automated design of peptides with desired biological activities.
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A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition ()
Abstract A DNA‐encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5‐bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a Kd value of 6 nm, while compounds with the same substituents on an equidistant but flexible l‐lysine scaffold showed 140‐fold lower affinity. A 18 nm tankyrase‐1 binder featured l‐lysine as linking moiety, while molecules based on d‐Lysine or (2S,4S)‐amino‐l‐proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.
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Targeted Delivery of DNA‐Au Nanoparticles across the Blood–Brain Barrier Using Focused Ultrasound ()
Abstract Nanoparticles have been widely studied as versatile platforms for in vivo imaging and therapy. However, their use to image and/or treat the brain is limited, as they are often unable to cross the blood–brain barrier (BBB). To overcome this problem, herein we report the use of focused ultrasound in vivo to successfully deliver DNA‐coated gold nanoparticles to specific locations in the brains of mice.
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PET Imaging of T Cells: Target Identification and Feasibility Assessment ()
Abstract Imaging T cells using positron emission tomography (PET) would be highly useful for diagnosis and monitoring in immunology and oncology patients. There are, however, no obvious targets that can be used to develop imaging agents for this purpose. We evaluated several potential target proteins with selective expression in T cells, and for which lead molecules were available: protein kinase C isozyme θ (PKC θ), lymphocyte‐specific protein tyrosine kinase (Lck), zeta‐chain‐associated protein kinase 70 (ZAP70), and interleukin‐2‐inducible T‐cell kinase (Itk). Ultimately, we focused on Itk and identified a tool molecule with properties suitable for in vivo imaging of T cells: (5aR)‐5,5‐difluoro‐5a‐methyl‐N‐(1‐((S)‐3‐(methylsulfonyl)phenyl)(tetrahydro‐2H‐pyran‐4‐yl)methyl)‐1H‐pyrazol‐4‐yl)‐1,4,4a,5,5a,6‐hexahydrocyclopropa[f]indazole‐3‐carboxamide (23). Although it does not have the optimal profile for clinical use, this molecule indicates that it might be possible to develop Itk‐selective PET ligands for imaging the distribution of T cells in patients.
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Synthesis and Pharmacological Evaluation of Enantiomerically Pure GluN2B Selective NMDA Receptor Antagonists ()
Abstract To determine the eutomers of potent GluN2B‐selective N‐methyl‐d‐aspartate (NMDA) receptor antagonists with a 3‐benzazepine scaffold, 7‐benzyloxy‐3‐(4‐phenylbutyl)‐2,3,4,5‐tetrahydro‐1H‐3‐benzazepin‐1‐ols (S)‐2 and (R)‐2 were separated by chiral HPLC. Hydrogenolysis and subsequent methylation of the enantiomerically pure benzyl ethers of (S)‐2 and (R)‐2 provided the enantiomeric phenols (S)‐3 and (R)‐3 [3‐(4‐phenylbutyl)‐2,3,4,5‐tetrahydro‐1H‐3‐benzazepine‐1,7‐diol] and methyl ethers (S)‐4 and (R)‐4. All enantiomers were obtained with high enantiomeric purity (≥99.7 % ee). The absolute configurations were determined by CD spectroscopy. R‐configured enantiomers turned out to be the eutomers in receptor binding studies and two‐electrode voltage clamp experiments. The most promising ligand of this compound series is the R‐configured phenol (R)‐3, displaying high GluN2B affinity (Ki=30 nm), high inhibition of ion flux (IC50=61 nm), and high cytoprotective activity (IC50=93 nm). Whereas the eudismic ratio in the receptor binding assay is 25, the eudismic ratio in the electrophysiological experiment is 3.
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Effect of Acylation on the Antimicrobial Activity of Temporin B Analogues ()
Abstract New peptides derived from the natural antimicrobial temporin B were obtained. The design, antimicrobial activity, and characterization of the secondary structure of peptides in the presence of bacterial cells is described herein. TB_KKG6K (KKLLPIVKNLLKSLL) has been identified as the most active analogue against Gram‐positive and ‐negative bacteria, compared with natural temporin B (LLPIVGNLLKSLL) and TB_KKG6A (KKLLPIVANLLKSLL). Acylation with hydrophobic moieties generally led to reduced activity; however, acylation at the 6‐position of TB_KKG6K led to retained sub‐micromolar activity against Staphylococcus epidermidis.
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Fragment‐Based Phenotypic Lead Discovery: Cell‐Based Assay to Target Leishmaniasis ()
Abstract A rapid and practical approach for the discovery of new chemical matter for targeting pathogens and diseases is described. Fragment‐based phenotypic lead discovery (FPLD) combines aspects of traditional fragment‐based lead discovery (FBLD), which involves the screening of small‐molecule fragment libraries to target specific proteins, with phenotypic lead discovery (PLD), which typically involves the screening of drug‐like compounds in cell‐based assays. To enable FPLD, a diverse library of fragments was first designed, assembled, and curated. This library of soluble, low‐molecular‐weight compounds was then pooled to expedite screening. Axenic cultures of Leishmania promastigotes were screened, and single hits were then tested for leishmanicidal activity against intracellular amastigote forms in infected murine bone‐marrow‐derived macrophages without evidence of toxicity toward mammalian cells. These studies demonstrate that FPLD can be a rapid and effective means to discover hits that can serve as leads for further medicinal chemistry purposes or as tool compounds for identifying known or novel targets.
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Targeting of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Protein with a Technetium‐99m Imaging Probe ()
Abstract Cystic fibrosis (CF) is caused by mutations in the gene that encodes the CF transmembrane conductance regulator (CFTR) protein. The most common mutation, F508del, leads to almost total absence of CFTR at the plasma membrane, a defect potentially corrected via drug‐based therapies. Herein, we report the first proof‐of‐principle study of a noninvasive imaging probe able to detect CFTR at the plasma membrane. We radiolabeled the CFTR inhibitor, CFTRinh‐172a, with technetium‐99m via a pyrazolyl‐diamine chelating unit, yielding a novel 99mTc(CO)3 complex. A non‐radioactive surrogate showed that the structural modifications introduced in the inhibitor did not affect its activity. The radioactive complex was able to detect plasma membrane CFTR, shown by its significantly higher uptake in wild‐type versus mutated cells. Furthermore, assessment of F508del CFTR pharmacological correction in human cells using the radioactive complex revealed differences in corrector versus control uptake, recapitulating the biochemical correction observed for the protein.
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Dual‐Responsive Carbon Dot for pH/Redox‐Triggered Fluorescence Imaging with Controllable Photothermal Ablation Therapy of Cancer ()
Abstract Herein we describe fluorescence resonance energy transfer (FRET) for a pH/redox‐activatable fluorescent carbon dot (FNP) to realize “off–on” switched imaging‐guided controllable photothermal therapy (PTT). The FNP is a carbonized self‐crosslinked polymer that allows IR825 loading (FNP[IR825]) via hydrophobic interactions for cancer therapy. Fluorescence bioimaging was achieved by the internalization of FNP(IR825) into tumor cells, wherein glutathione (GSH) disulfide bonds are reduced, and benzoic imine groups are cleaved under acidic conditions. The release of IR825 from the FNP core in this system may be used to efficiently control PTT‐mediated cancer therapy via its photothermal conversion after near‐infrared (NIR) irradiation. In vitro and in vivo cellular uptake studies revealed efficient uptake of FNP(IR825) by tumor cells to treat the disease site. In this way we demonstrated in mice that our smart nanocarrier can effectively kill tumor cells under exposure to a NIR laser, and that the particles are biocompatible with various organs. This platform responds sensitively to the exogenous environment inside the cancer cells and may selectively induce the release of PTT‐mediated cytotoxicity. Furthermore, this platform may be useful for monitoring the elimination of cancer cells through the fluorescence on/off switch, which can be used for various applications in the field of cancer cell therapy and diagnosis.
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Bis‐Cyclic Guanidines as a Novel Class of Compounds Potent against Clostridium difficile ()
Abstract Clostridium difficile infection (CDI) symptoms range from diarrhea to severe toxic megacolon and even death. Due to its rapid acquisition of resistance, C. difficile is listed as an urgent antibiotic‐resistant threat, and has surpassed methicillin‐resistant Staphylococcus aureus (MRSA) as the most common hospital‐acquired infection in the USA. To combat this pathogen, a new structural class of pseudo‐peptides that exhibit antimicrobial activities could play an important role. Herein we report a set of bis‐cyclic guanidine compounds that show potent antibacterial activity against C. difficile with decent selectivity. Eight compounds showed high in vitro potency against C. difficile UK6 with MIC values of 1.0 μg mL−1, and cytotoxic selectivity index (SI) values up to 37. Moreover, the most selective compound is also effective in the treatment of C. difficile‐induced disease in a mouse model of CDI, and appears to be a very promising new candidate for the treatment of CDI.
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Synthesis and Evaluation of a Series of Bis(pentylpyridinium) Compounds as Antifungal Agents ()
Abstract A series of bis(4‐pentylpyridinium) compounds with a variety of spacers between the pyridinium headgroups was synthesised, and the antifungal activity of these compounds was investigated. Lengthening the alkyl spacer between the pentylpyridinium headgroups from 12 to 16 methylene units resulted in increased antifungal activity against C. neoformans and C. albicans, but also resulted in increased hemolytic activity and cytotoxicity against mammalian cells. However, inclusion of an ortho‐substituted benzene ring in the centre of the alkyl spacer resulted in decreased cytotoxicity and hemolytic activity, while maintaining antifungal potency. Replacement of the alkyl and aromatic‐containing spacers by more hydrophilic ethylene glycol groups resulted in a loss of antifungal activity. Some of the compounds inhibited fungal PLB1 activity, but the low correlation of this inhibition with antifungal potency indicates PLB1 inhibition is unlikely to be the predominant mode of antifungal action of this class of compounds, with preliminary studies suggesting they may act via disruption of fungal mitochondrial function.
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Synthesis and Evaluation of the Anticancer and Trypanocidal Activities of Boronic Tyrphostins ()
Abstract Molecules containing an (cyanovinyl)arene moiety are known as tyrphostins because of their ability to inhibit proteins from the tyrosine kinase family, an interesting target for the development of anticancer and trypanocidal drugs. In the present work, (E)‐(cyanovinyl)benzeneboronic acids were synthesized by Knoevenagel condensations without the use of any catalysts in water through a simple protocol that completely avoided the use of organic solvents in the synthesis and workup process. The in vitro anticancer and trypanocidal activities of the synthesized boronic acids were also evaluated, and it was discovered that the introduction of the boronic acid functionality improved the activity of the boronic tyrphostins. In silico target fishing with the use of a chemogenomic approach suggested that tyrosine‐phosphorylation‐regulated kinase 1a (DYRK1A) was a potential target for some of the designed compounds.
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Atomic‐Resolution Structure of a Class C β‐Lactamase and Its Complex with Avibactam ()
Abstract β‐Lactamases (BLs) are important antibiotic‐resistance determinants that significantly compromise the efficacy of valuable β‐lactam antibacterial drugs. Thus, combinations with BL inhibitor were developed. Avibactam is the first non‐β‐lactam BL inhibitor introduced into clinical practice. Ceftazidime–avibactam represents one of the few last‐resort antibiotics available for the treatment of infections caused by near‐pandrug‐resistant bacteria. TRU‐1 is a chromosomally encoded AmpC‐type BL of Aeromonas enteropelogenes, related to the FOX‐type BLs and constitutes a good model for class C BLs. TRU‐1 crystals provided ultrahigh‐resolution diffraction data for the native enzyme and for its complex with avibactam. A comparison of the native and avibactam‐bound structures revealed new details in the conformations of residues relevant for substrate and/or inhibitor binding. Furthermore, a comparison of the TRU‐1 and Pseudomonas aeruginosa AmpC avibactam‐bound structures revealed two inhibitor conformations that were likely to correspond to two different states occurring during inhibitor carbamylation/recyclization.
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Synthesis, Biological Activity, and Mechanism of Action of 2‐Pyrazyl and Pyridylhydrazone Derivatives, New Classes of Antileishmanial Agents ()
Abstract In this work, we report the antileishmanial activity of 23 compounds based on 2‐pyrazyl and 2‐pyridylhydrazone derivatives. The compounds were tested against the promastigotes of Leishmania amazonensis and L. braziliensis, murine macrophages, and intracellular L. amazonensis amastigotes. The most potent antileishmanial compound was selected for investigation into its mechanism of action. Among the evaluated compounds, five derivatives [(E)‐3‐((2‐(pyridin‐2‐yl)hydrazono)methyl)benzene‐1,2‐diol (2 b), (E)‐4‐((2‐(pyridin‐2‐yl)hydrazono)methyl)benzene‐1,3‐diol (2 c), (E)‐4‐nitro‐2‐((2‐(pyrazin‐2‐yl)hydrazono)methyl)phenol (2 s), (E)‐2‐(2‐(pyridin‐2‐ylmethylene)hydrazinyl)pyrazine (2 u), and (E)‐2‐(2‐((5‐nitrofuran‐2‐yl)methylene)hydrazinyl)pyrazine (2 v)] exhibited significant activity against L. amazonensis amastigote forms, with IC50 values below 20 μm. The majority of the compounds did not show any toxic effect on murine macrophages. Preliminary studies on the mode of action of members of this hydrazine‐derived series indicate that the accumulation of reactive oxygen species (ROS) and disruption of parasite mitochondrial function are important for the pharmacological effect on L. amazonensis promastigotes.
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Structural Analysis of Small‐Molecule Binding to the BAZ2A and BAZ2B Bromodomains ()
Abstract The bromodomain‐containing protein BAZ2A is a validated target in prostate cancer research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a similar binding site for their natural ligand, the acetylated lysine side chain. Here, we present an analysis of the binding modes of eight compounds belonging to three distinct chemical classes. For all compounds, the moiety mimicking the natural ligand engages in essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent‐exposed and adopts different orientations with different interactions in the two bromodomains. Some of these differences could be exploited for designing inhibitors with selectivity within the BAZ2 bromodomain subfamily.
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Structure–Activity Relationship Studies on (R)‐PFI‐2 Analogues as Inhibitors of Histone Lysine Methyltransferase SETD7 ()
Abstract SETD7 is a histone H3K4 lysine methyltransferase involved in human gene regulation. Aberrant expression of SETD7 has been associated with various diseases, including cancer. Therefore, SETD7 is considered a good target for the development of new epigenetic drugs. To date, few selective small‐molecule inhibitors have been reported that target SETD7, the most potent being (R)‐PFI‐2. Herein we report structure–activity relationship studies on (R)‐PFI‐2 and its analogues. A library of 29 structural analogues of (R)‐PFI‐2 was synthesized and evaluated for inhibition of recombinantly expressed human SETD7. The key interactions were found to be a salt bridge and a hydrogen bond formed between (R)‐PFI‐2′s NH2+ group and SETD7′s Asp256 and His252 residue, respectively.
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Dichlorophenylacrylonitriles as AhR Ligands That Display Selective Breast Cancer Cytotoxicity in vitro ()
Abstract Knoevenagel condensation of 3,4‐dichloro‐ and 2,6‐dichlorophenylacetonitriles gave a library of dichlorophenylacrylonitriles. Our leads (Z)‐2‐(3,4‐dichlorophenyl)‐3‐(1H‐pyrrol‐2‐yl)acrylonitrile (5) and (Z)‐2‐(3,4‐dichlorophenyl)‐3‐(4‐nitrophenyl)acrylonitrile (6) displayed 0.56±0.03 and 0.127±0.04 μm growth inhibition (GI50) and 260‐fold selectivity for the MCF‐7 breast cancer cell line. A 2,6‐dichlorophenyl moiety saw a 10‐fold decrease in potency; additional nitrogen moieties (‐NO2) enhanced activity (Z)‐2‐(2,6‐dichloro‐3‐nitrophenyl)‐3‐(2‐nitrophenyl)acrylonitrile (26) and (Z)‐2‐(2,6‐dichloro‐3‐nitrophenyl)‐3‐(3‐nitrophenyl)acrylonitrile (27), with the corresponding ‐NH2 analogues (Z)‐2‐(3‐amino‐2,6‐dichlorophenyl)‐3‐(2‐aminophenyl)acrylonitrile (29) and (Z)‐2‐(3‐amino‐2,6‐dichlorophenyl)‐3‐(3‐aminophenyl)acrylonitrile (30) being more potent. Despite this, both 29 (2.8±0.03 μm) and 30 (2.8±0.03 μm) were found to be 10‐fold less cytotoxic than 6. A bromine moiety effected a 3‐fold enhancement in solubility with (Z)‐3‐(5‐bromo‐1H‐pyrrol‐2‐yl)‐2‐(3,4‐dichlorophenyl)acrylonitrile 18 relative to 5 at 211 μg mL−1. Modeling‐guided synthesis saw the introduction of 4‐aminophenyl substituents (Z)‐3‐(4‐aminophenyl)‐2‐(3,4‐dichlorophenyl)acrylonitrile (35) and (Z)‐N‐(4‐(2‐cyano‐2‐(3,4‐dichlorophenyl)vinyl)phenyl)acetamide (38), with respective GI50 values of 0.030±0.014 and 0.034±0.01 μm. Other analogues such as 35 and 36 were found to have sub‐micromolar potency against our panel of cancer cell lines (HT29, colon; U87 and SJ‐G2, glioblastoma; A2780, ovarian; H460, lung; A431, skin; Du145, prostate; BE2‐C, neuroblastoma; MIA, pancreas; and SMA, murine glioblastoma), except compound 38 against the U87 cell line. A more extensive evaluation of 38 ((Z)‐N‐(4‐(2‐cyano‐2‐(3,4‐dichlorophenyl)vinyl)phenyl)acetamide) in a panel of drug‐resistant breast carcinoma cell lines showed 10–206 nm potency against MDAMB468, T47D, ZR‐75‐1, SKBR3, and BT474. Molecular Operating Environment docking scores showed a good correlation between predicted binding efficiencies and observed MCF‐7 cytotoxicity. This supports the use of this model in the development of breast‐cancer‐specific drugs.
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Deciphering Specificity Determinants for FR900359‐Derived Gqα Inhibitors Based on Computational and Structure–Activity Studies ()
Abstract Direct targeting of intracellular Gα subunits of G protein‐coupled receptors by chemical tools is a challenging task in current pharmacological studies and in the development of novel therapeutic approaches. In this study we analyzed novel FR900359‐based analogs from natural sources, synthetic cyclic peptides, as well as all so‐far known Gqα inhibitors in a comprehensive study to devise a strategy for the elucidation of characteristics that determine interactions with and inhibition of Gq in the specific FR/YM‐binding pocket. Using 2D NMR spectroscopy and molecular docking we identified unique features in the macrocyclic structures responsible for binding to the target protein correlating with inhibitory activity. While all novel compounds were devoid of effects on Gi and Gs proteins, no inhibitor surpassed the biological activity of FR. This raises the question of whether depsipeptides such as FR already represent valuable chemical tools for specific inhibition of Gq and, at the same time, are suitable natural lead structures for the development of novel compounds to target Gα subunits other than Gq.
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Synthesis, Crystallization Studies, and in vitro Characterization of Cinnamic Acid Derivatives as SmHDAC8 Inhibitors for the Treatment of Schistosomiasis ()
Abstract Schistosomiasis is a neglected parasitic disease that affects more than 265 million people worldwide and for which the control strategy relies on mass treatment with only one drug: praziquantel. Based on the 3‐chlorobenzothiophene‐2‐hydroxamic acid J1075, a series of hydroxamic acids with different scaffolds were prepared as potential inhibitors of Schistosoma mansoni histone deacetylase 8 (SmHDAC8). The crystal structures of SmHDAC8 with four inhibitors provided insight into the binding mode and orientation of molecules in the binding pocket as well as the orientation of its flexible amino acid residues. The compounds were evaluated in screens for inhibitory activity against schistosome and human HDACs. The most promising compounds were further investigated for their activity toward the major human HDAC isotypes. The most potent inhibitors were additionally screened for lethality against the schistosome larval stage using a fluorescence‐based assay. Two of the compounds showed significant, dose‐dependent killing of the schistosome larvae and markedly impaired egg laying of adult worm pairs maintained in culture.
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Design, Synthesis, Biological Activity, and Structural Analysis of Lactam‐Constrained PTPRJ Agonist Peptides ()
Abstract PTPRJ is a receptor‐like protein tyrosine phosphatase mainly known for its antiproliferative and tumor‐suppressive functions. PTPRJ dephosphorylates several growth factors and their receptors, negatively regulating cell proliferation and migration. We recently identified a disulfide‐bridged nonapeptide, named PTPRJ‐19 (H‐[Cys‐His‐His‐Asn‐Leu‐Thr‐His‐Ala‐Cys]‐OH), which activates PTPRJ, thereby causing cell growth inhibition and apoptosis of both cancer and endothelial cells. With the aim of replacing the disulfide bridge by a chemically more stable moiety, we have synthesized and tested a series of lactam analogues of PTPRJ‐19. This replacement led to analogues with higher activity and greater stability than the parent peptide.
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Structure‐Based Design of a Eukaryote‐Selective Antiprotozoal Fluorinated Aminoglycoside ()
Abstract Aminoglycosides (AG) are antibiotics that lower the accuracy of protein synthesis by targeting a highly conserved RNA helix of the ribosomal A‐site. The discovery of AGs that selectively target the eukaryotic ribosome, but lack activity in prokaryotes, are promising as antiprotozoals for the treatment of neglected tropical diseases, and as therapies to read‐through point‐mutation genetic diseases. However, a single nucleobase change A1408G in the eukaryotic A‐site leads to negligible affinity for most AGs. Herein we report the synthesis of 6′‐fluorosisomicin, the first 6′‐fluorinated aminoglycoside, which specifically interacts with the protozoal cytoplasmic rRNA A‐site, but not the bacterial A‐site, as evidenced by X‐ray co‐crystal structures. The respective dispositions of 6′‐fluorosisomicin within the bacterial and protozoal A‐sites reveal that the fluorine atom acts only as a hydrogen‐bond acceptor to favorably interact with G1408 of the protozoal A‐site. Unlike aminoglycosides containing a 6′‐ammonium group, 6′‐fluorosisomicin cannot participate in the hydrogen‐bonding pattern that characterizes stable pseudo‐base‐pairs with A1408 of the bacterial A‐sites. Based on these structural observations it may be possible to shift the biological activity of aminoglycosides to act preferentially as antiprotozoal agents. These findings expand the repertoire of small molecules targeting the eukaryotic ribosome and demonstrate the usefulness of fluorine as a design element.
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A New Class of 1‐Aryl‐5,6‐dihydropyrrolo[2,1‐a]isoquinoline Derivatives as Reversers of P‐Glycoprotein‐Mediated Multidrug Resistance in Tumor Cells ()
Abstract A number of aza‐heterocyclic compounds, which share the 5,6‐dihydropyrrolo[2,1‐a]isoquinoline (DHPIQ) scaffold with members of the lamellarin alkaloid family, were synthesized and evaluated for their ability to reverse in vitro multidrug resistance in cancer cells through inhibition of P‐glycoprotein (P‐gp) and/or multidrug‐resistance‐associated protein 1. Most of the investigated DHPIQ compounds proved to be selective P‐gp modulators, and the most potent modulator, 8,9‐diethoxy‐1‐(3,4‐diethoxyphenyl)‐3‐(furan‐2‐yl)‐5,6‐dihydropyrrolo[2,1‐a]isoquinoline‐2‐carbaldehyde, attained sub‐micromolar inhibitory potency (IC50: 0.19 μm). Schiff bases prepared by the condensation of some 1‐aryl‐DHPIQ aldehydes with p‐aminophenol also proved to be of some interest, and one of them, 4‐((1‐(4‐fluorophenyl)‐5,6‐dihydro‐8,9‐dimethoxypyrrolo[2,1‐a]isoquinolin‐2‐yl)methyleneamino)phenol, had an IC50 value of 1.01 μm. In drug combination assays in multidrug‐resistant cells, some DHPIQ compounds, at nontoxic concentrations, significantly increased the cytotoxicity of doxorubicin in a concentration‐dependent manner. Studies of structure–activity relationships and investigation of the chemical stability of Schiff bases provided physicochemical information useful for molecular optimization of lamellarin‐like cytotoxic drugs active toward chemoresistant tumors as well as nontoxic reversers of P‐gp‐mediated multidrug resistance in tumor cells.
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Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV‐1 Integrase ()
Abstract The p75 splice variant of lens epithelium‐derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre‐integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X‐ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV‐1 integrase core domain. Although the X‐ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low‐energy solution and bound conformations.
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Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine ()
Abstract The histone methyltransferase SET7/9 methylates not only histone but also non‐histone proteins as substrates, and therefore, SET7/9 inhibitors are considered candidates for the treatment of diseases. Previously, our group identified cyproheptadine, used clinically as a serotonin receptor antagonist and histamine receptor (H1) antagonist, as a novel scaffold of the SET7/9 inhibitor. In this work, we focused on dibenzosuberene as a substructure of cyproheptadine and synthesized derivatives with various functional groups. Among them, the compound bearing a 2‐hydroxy group showed the most potent activity. On the other hand, a 3‐hydroxy group or another hydrophilic functional group such as acetamide decreased the activity. Structural analysis clarified a rationale for the improved potency only by tightly restricted location and type of the hydrophilic group. In addition, a SET7/9 loop, which was only partially visible in the complex with cyproheptadine, became more clearly visible in the complex with 2‐hydroxycyproheptadine. These results are expected to be helpful for further structure‐based development of SET7/9 inhibitors.
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Targeting Serotonin 2A and Adrenergic α1 Receptors for Ocular Antihypertensive Agents: Discovery of 3,4‐Dihydropyrazino[1,2‐b]indazol‐1(2H)‐one Derivatives ()
Abstract Glaucoma affects millions of people worldwide and causes optic nerve damage and blindness. The elevation of the intraocular pressure (IOP) is the main risk factor associated with this pathology, and decreasing IOP is the key therapeutic target of current pharmacological treatments. As potential ocular hypotensive agents, we studied compounds that act on two receptors (serotonin 2A and adrenergic α1) linked to the regulation of aqueous humour dynamics. Herein we describe the design, synthesis, and pharmacological profiling of a series of novel bicyclic and tricyclic N2‐alkyl‐indazole‐amide derivatives. This study identified a 3,4‐dihydropyrazino[1,2‐b]indazol‐1(2H)‐one derivative with potent serotonin 2A receptor antagonism, >100‐fold selectivity over other serotonin subtype receptors, and high affinity for the α1 receptor. Moreover, upon local administration, this compound showed superior ocular hypotensive action in vivo relative to the clinically used reference compound timolol.
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Understanding the Rate‐Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase ()
Abstract Liver glycogen phosphorylase (GP) is a key enzyme for human health, as its increased activity is associated with type 2 diabetes. The GP catalytic mechanism has been explored by quantum mechanics/molecular mechanics (QM/MM) methods. Herein, we propose a mechanism that proceeds by three steps: 1) it begins with transfer of a hydrogen atom from the phosphate group of the pyridoxal 5′‐phosphate (HPO42−‐PLP) cofactor to the phosphate substrate; 2) the glycosidic linkage is then cleaved through protonation of the glycosidic oxygen atom by a hydroxy group of the inorganic phosphate group; and 3) an oxygen atom of the phosphate performs a nucleophilic attack on the anomeric carbon atom of glucose, concomitant with the return of a proton from phosphate to PO43−‐PLP, which finally leads to formation of the glucose‐1‐phosphate product and recovers the initial state of the PLP cofactor. The glycosidic bond cleavage and nucleophilic attack from the phosphate group to the glycosyl molecule have the highest activation free energies. The structural properties of the hereby characterized transition states could be very useful in structure‐based drug design studies against liver GP.
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Structure‐Based Design of a Monosaccharide Ligand Targeting Galectin‐8 ()
Abstract Galectin‐8 is a β‐galactoside‐recognising protein that has a role in the regulation of bone remodelling and is an emerging new target for tackling diseases with associated bone loss. We have designed and synthesised methyl 3‐O‐[1‐carboxyethyl]‐β‐d‐galactopyranoside (compound 6) as a ligand to target the N‐terminal domain of galectin‐8 (galectin‐8N). Our design involved molecular dynamics (MD) simulations that predicted 6 to mimic the interactions made by the galactose ring as well as the carboxylic acid group of 3′‐O‐sialylated lactose (3′‐SiaLac), with galectin‐8N. Isothermal titration calorimetry (ITC) determined that the binding affinity of galectin‐8N for 6 was 32.8 μm, whereas no significant affinity was detected for the C‐terminal domain of galectin‐8 (galectin‐8C). The crystal structure of the galectin‐8N–6 complex validated the predicted binding conformation and revealed the exact protein–ligand interactions that involve evolutionarily conserved amino acids of galectin and also those unique to galectin‐8N for recognition. Overall, we have initiated and demonstrated a rational ligand design campaign to develop a monosaccharide‐based scaffold as a binder of galectin‐8.
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Development of Potent Pyrazolopyrimidinone‐Based WEE1 Inhibitors with Limited Single‐Agent Cytotoxicity for Cancer Therapy ()
Abstract WEE1 kinase regulates the G2/M cell‐cycle checkpoint, a critical mechanism for DNA repair in cancer cells that can confer resistance to DNA‐damaging agents. We previously reported a series of pyrazolopyrimidinones based on AZD1775, a known WEE1 inhibitor, as an initial investigation into the structural requirements for WEE1 inhibition. Our lead inhibitor demonstrated WEE1 inhibition in the same nanomolar range as AZD1775, and potentiated the effects of cisplatin in medulloblastoma cells, but had reduced single‐agent cytotoxicity. These results prompted the development of a more comprehensive series of WEE1 inhibitors. Herein we report a series of pyrazolopyrimidinones and identify a more potent WEE1 inhibitor than AZD1775 and additional compounds that demonstrate that WEE1 inhibition can be achieved with reduced single‐agent cytotoxicity. These studies support that WEE1 inhibition can be uncoupled from the potent cytotoxic effects observed with AZD1775, and this may have important ramifications in the clinical setting where WEE1 inhibitors are used as chemosensitizers for DNA‐targeted chemotherapy.
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Antibiotic Drug Discovery: New Targets and Molecular Entities. Edited by Steven M. Firestine and Troy Lister ()
ChemMedChem, EarlyView.
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Drug Discovery for Leishmaniasis. Edited by Luis Rivas and Carmen Gil ()
ChemMedChem, EarlyView.
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Recent Advances in the Development of Indazole‐based Anticancer Agents ()
Abstract Cancer is one of the leading causes of human mortality globally; therefore, intensive efforts have been made to seek new active drugs with improved anticancer efficacy. Indazole‐containing derivatives are endowed with a broad range of biological properties, including anti‐inflammatory, antimicrobial, anti‐HIV, antihypertensive, and anticancer activities. In recent years, the development of anticancer drugs has given rise to a wide range of indazole derivatives, some of which exhibit outstanding activity against various tumor types. The aim of this review is to outline recent developments concerning the anticancer activity of indazole derivatives, as well as to summarize the design strategies and structure–activity relationships of these compounds.
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Identification of Broad‐Spectrum Dengue/Zika Virus Replication Inhibitors by Functionalization of Quinoline and 2,6‐Diaminopurine Scaffolds ()
Abstract Social and demographic changes across the world over the past 50 years have resulted in significant outbreaks of arboviruses such as dengue virus (DENV) and Zika virus (ZIKV). Despite the increased threat of infection, no approved drugs or fully protective vaccines are available to counteract the spread of DENV and ZIKV. The development of “broad‐spectrum” antivirals (BSAs) that target common components of multiple viruses can be a more effective strategy to limit the rapid emergence of viral pathogens than the classic “one‐bug/one‐drug” approach. Starting from previously identified multitarget DENV inhibitors, herein we report the identification of novel 2,6‐diaminopurine derivatives that are able to block the replication of both Zika virus and all serotypes of dengue virus (DENV 1–4) in infected cells.
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1,2,3‐Triazolium‐Based Cationic Amphipathic Peptoid Oligomers Mimicking Antimicrobial Helical Peptides ()
Abstract Amphipathic cationic peptoids (N‐substituted glycine oligomers) represent a promising class of antimicrobial peptide mimics. The aim of this study is to explore the potential of the triazolium group as a cationic moiety and helix inducer to develop potent antimicrobial helical peptoids. Herein we report the first solid‐phase synthesis of peptoid oligomers incorporating 1,2,3‐triazolium‐type side chains and their evaluation against Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus. Several triazolium‐based oligomers, even of short length, selectively kill bacteria over mammalian cells. SEM visualization of S. aureus cells treated with a dodecamer and a hexamer reveals severe cell membrane damage and suggests that the longer oligomer acts by pore formation.
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Efficient Synthesis of Immunomodulatory Drug Analogues Enables Exploration of Structure–Degradation Relationships ()
Abstract The immunomodulatory drugs (IMiDs) thalidomide, pomalidomide, and lenalidomide have been approved for the treatment of multiple myeloma for many years. Recently, their use as E3 ligase recruiting elements for small‐molecule‐induced protein degradation has led to a resurgence in interest in IMiD synthesis and functionalization. Traditional IMiD synthesis follows a stepwise route with multiple purification steps. Herein we describe a novel one‐pot synthesis without purification that provides rapid access to a multitude of IMiD analogues. Binding studies with the IMiD target protein cereblon (CRBN) reveals a narrow structure–activity relationship with only a few compounds showing sub‐micromolar binding affinity in the range of pomalidomide and lenalidomide. However, anti‐proliferative activity as well as Aiolos degradation could be identified for two IMiD analogues. This study provides useful insight into the structure–degradation relationships for molecules of this type as well as a rapid and robust method for IMiD synthesis.
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What has come out from phytomedicines and herbal edibles for the treatment of cancer? ()
Several modern treatment strategies have been adopted to combat cancer with the aim of minimizing toxicity. Medicinal plant‐based compounds with the potential to treat cancer have been widely studied in preclinical research and have elicited many innovative ways of leading‐edge clinical research. In parallel, researchers have eagerly tried to reduce the toxicity of current chemotherapeutic agents either by combining them with herbals or in using herbals alone. The focus of this article is to present an update of medicinal plants and their bioactive compounds, or mere changes in the bioactive compounds, and herbal edibles, which display efficacy against diverse cancer cells and in anticancer therapy. It describes the basic mechanism(s) of action of phytochemicals used either alone or in combo therapy with other phytochemicals/herbal edibles. Additionally, it also highlights the remarkable synergistic effects arising between some herbals and chemotherapeutic agents used in oncology. The anticancer phytochemicals used in clinical research are also described and further, we stated our own experience related to semi synthetic derivatives, which are developed based on the phytochemicals. Overall, this compilation aims at facilitating research and development projects on phytopharmaceuticals for successful anticancer drug discovery.
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Nucleobase modified adefovir (PMEA) analogues as potent and selective inhibitors of adenylate cyclases from Bordetella pertussis and Bacillus anthracis ()
A series of 13 acyclic nucleoside phosphonates (ANPs) as bisamidate prodrugs was prepared. Five compounds were found to be non‐cytotoxic and selective inhibitors of Bordetella pertussis adenylate cyclase toxin (ACT) in J774A.1 macrophage cell‐based assays. The 8‐aza‐7‐deazapurine derivative of adefovir (PMEA) was the most potent ACT inhibitor in the series (IC50 = 16 nM) with substantial selectivity over mammalian adenylate cyclases (mACs). AC inhibitory properties of the most potent analogues were confirmed by direct evaluation of the corresponding phosphonodiphosphates in cell‐free assays and were found to be potent inhibitors of both ACT and edema factor (EF) from Bacillus anthracis (IC50 values ranging from 0.5 to 21 nM). Moreover, 7‐halo‐7‐deazapurine analogues of PMEA were discovered to be potent and selective mammalian AC1 inhibitors (no inhibition of AC2 and AC5) with IC50 values ranging from 4.1‐5.6 µM in HEK293 cell‐based assays.
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Brain‐penetrant, triazolopyrimidine and phenylpyrimidine microtubule‐stabilizers as potential leads to treat human African trypanosomiasis ()
In vitro whole‐organism screens of T. brucei with representative examples of brain‐penetrant microtubule (MT)‐stabilizing agents identified lethal triazolopyrimidines and phenylpyrimidines with sub‐µM potency. In mammalian cells, these anti‐proliferative compounds disrupt MT‐integrity and reduce total tubulin levels. Their parasiticidal potency, combined with their generally favorable pharmacokinetic properties, which include oral bioavailability and brain‐penetration, suggest that these compounds are potential leads against African trypanosomiasis.
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Cholesterol: A Key in the Pathogenesis of Alzheimer's Disease ()
Cholesterol has been identified as a key component for catalyzed aggregation of Aβ42, which leads to the Alzheimer's disease. This Highlight discusses this work and its enormous potentials in understanding and addressing the inhibition of such processes.
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Design and synthesis of pyrophosphate‐targeting vancomycin derivatives for combating vancomycin‐resistant Enterococci ()
Vancomycin, as the last resort for intractable Gram‐positive bacterial infections, is losing the efficacy with the emergence of vancomycin‐resistant bacteria especially vancomycin‐resistant Enterococci (VRE). To combat this threat, we rationally designed and synthesized 39 novel vancomycin derivatives, via respective or combined modifications with metal‐chelating, lipophilic, and galactose‐attached strategies, for extensive SAR analysis. In a proposed mechanism, the conjugation of dipicolylamine (DPA) on 7th amino acid resorcinol position or C‐terminus endued the vancomycin backbone with the binding activity to pyrophosphate moiety in lipid II while keeping the intrinsic binding affinity to the dipeptide terminus of the bacterial cell wall peptidoglycan precursor. The in vitro antibacterial activities were evaluated and the optimal compounds indicated 16‐1024 fold higher activity against VRE compared with vancomycin. It was also found compound 11b showed the synergistic effect combining two peripheral modification and mechanism especially towards VRE.
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A Compact and Synthetically Accessible Fluorine‐18 Labelled Cyclooctyne Prosthetic Group for Labelling of Biomolecules by Copper‐free Click Chemistry ()
A new fluorine‐containing azadibenzocyclooctyne (ADIBO‐F) has been designed using a synthetically accessible pathway. The fluorine‐18 prosthetic group was prepared from its tosylate precursor and isolated in 21‐35% radiochemical yield in 30 minutes. The ADIBO‐F has been incorporated into azide‐functionalized, cancer‐targeting peptides through a strain‐promoted alkyne‐azide cycloaddition with high radiochemical yields and purities. The final products are novel peptide‐based PET imaging agents possessing high affinities to their targets of GHSR‐1a and GRPR with IC50 values of 9.7 and 0.50 nM, respectively. This exhibits a new, rapid labelling option for the incorporation of fluorine‐18 into biomolecules for PET imaging.
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Methinylogation approach in chiral pharmacophore design: from alkynyl‐ to allenyl‐carbinol warheads against tumor cells ()
Extension of a structure‐activity relationship study of the antitumor cytotoxicity of lipidic dialkynylcarbinols (DACs) is envisaged by formal methinylogation of one of the ethyndiyl moieties of the DAC warhead into the corresponding allenylalkynylcarbinol (AllAC) counterpart. External AllACs were directly obtained by methynylation of the parent DACs with formaldehyde in either the racemic or scalemic series. Isomers containing external progargyl and propynyl motifs were also prepared. Internal AllACs were obtained as racemic statistical mixtures of stereoisomers in two steps from the key C5‐DAC rac‐TIPS‐C≡C‐CH(OH)‐C≡CH and aldehydes. Kinetic resolution of the (S)‐C5‐DAC in 97% ee and (R)‐C5‐DAC in 99% ee, was achieved by sequential lipase‐mediated acetylation/hydrolysis using the Candida antartica lipase (Novozym 435). The four internal AllAC stereoisomers were prepared by Ma's asymmetric methinylation with (R)‐ or (S)‐diphenylprolinol as chiral auxiliary. Cytotoxicity assays on HCT116 cancer cells showed that the most active (eutomeric) external or internal AllAC exhibits a S configuration, a fatty chain length n = 12, and a 50 % inhibitory concentration IC50 ≈ 1.0 µM.
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Differentiating antiproliferative and chemopreventive modes of activity for electron‐deficient aryl isothiocyanates against human MCF‐7 cells ()
Consumption of Brassica vegetables provides beneficial effects due to organic isothiocyanates (ITCs), a resultant product of the enzymatic hydrolysis of glucosinolate secondary metabolites. The ITC L‐sulforaphane (L‐SFN) is the principle agent in broccoli that demonstrates several modes of anticancer action. While the anticancer properties of ITCs like L‐SFN have been extensively studied and L‐SFN has been the subject of multiple human clinical trials, the scope of this work has largely been limited to those derivatives found in nature. Previous studies have demonstrated that structural changes in an ITC can lead to marked differences in a compound's potency to (1) inhibit growth of cancer cells, and (2) alter cellular transcriptional profiles. This study describes the preparation of a library of non‐natural aryl ITCs and the development of a bifurcated screening approach to evaluate the dose‐ and time‐dependence on antiproliferative and chemopreventive properties against human MCF‐7 breast cancer cells. Antiproliferative effects were evaluated using a commercial MTS cell viability assay. Chemopreventive properties were evaluated using an antioxidant response element (ARE)‐promoted luciferase reporter assay. The results of this study have led to the identification of (1) several key structure‐activity relationships and (2) lead ITCs for continued development.
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Tertiary amine based inhibitors of the astacin protease meprin alpha ()
Metalloproteinases of the astacin family are more and more drawing attention as potential drug targets. However, the knowledge about inhibitors thereof is limited in most cases. Crucial for the development of metalloprotease inhibitors is a high selectivity to avoid side effects through the inhibition of off‐target proteases and the interference with physiological pathways. Here we aimed at the design of novel selective inhibitors for the astacin proteinase meprin α. Based on a recently identified tertiary amine scaffold, a series of compounds was synthesized and evaluated. The compounds exhibit reasonable inhibitory activity with high selectivity over other metalloproteases. Also the isoenzyme meprin β is only slightly inhibited. Hence, the present study revealed a novel class of selective meprin α inhibitors with improved selectivity compared to known compounds.
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NVP‐BHG712: Effects of regioisomers on the affinity and selectivity towards the EPHrin family ()
Abstract: EPH receptors are transmembrane receptor tyrosine kinases. Their extracellular domains bind specifically to ephrin A/B ligands, and this binding modulates the intracellular kinase activity. EPHs are key players in bidirectional intercellular signaling, controlling cell morphology, adhesion and migration. They are increasingly recognized as cancer drug targets. We analyzed the binding of the Novartis inhibitor NVP‐BHG712 (NVP) to EPHA2 and EPHB4. Unexpectedly, all tested commercially available NVP samples turned out to be a regioisomer (NVPiso) of the inhibitor, initially described in a Novartis patent application. They only differ by the localization of a single methylation on either one of two adjacent nitrogen atoms. The two compounds of identical mass revealed different binding modes. Further, both in vitro and in vivo experiments showed that the isomers differ in their kinase affinity and selectivity.
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A minimalist approach to the design of complexity‐enriched bioactive small molecules: discovery of phenanthrenoid mimics as antiproliferative agents. ()
Over the last decades, much effort has been devoted to the design of the "ideal" library for screening, the most promising strategies being those which draw inspiration from biogenic compounds, as they seek to add biological relevance to such libraries. On the other hand, there is a growing understanding of the role that molecular complexity plays in the discovery of new bioactive small molecules. Nevertheless, the introduction of molecular complexity must be balanced with synthetic accessibility. In this work, we show that both concepts can be efficiently merged ‐in a minimalist way‐ by using very simple guidelines during the design process along with the application of multicomponent reactions as key steps in the synthetic process. Natural phenanthrenoids, a class of plant aromatic metabolites, served as inspiration for the synthesis of a library where complexity‐enhancing features were introduced in few steps using multicomponent reactions. These resulting chemical entities were not only more complex than the parent natural products, but also interrogated an alternative region of the chemical space, which led to an outstanding hit rate in an antiproliferative assay: four out of twenty‐six compounds showed in vitro activity, one of them being more potent than the clinically useful drug 5‐fluorouracil.
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Towards novel angiogenesis inhibitors based on the conjugation of organometallic platinum(II) complexes to RGD peptides ()
A novel conjugate between a cyclometalated platinum(II) complex with dual anti‐angiogenic and antitumor activity and a cyclic peptide containing the RGD sequence (‐Arg‐Gly‐Asp‐) has been synthesized by combining solid‐ and solution‐phase methodologies. Although peptide conjugation rendered a non‐cytotoxic compound in all tested tumor cell lines (+/‐ αVβ3 and αVβ5 integrin receptors), the anti‐angiogenic activity of the Pt‐c(RGDfK) conjugate in HUVEC cells at sub‐cytotoxic concentrations opens the way to the design of a novel class of angiogenesis inhibitors through conjugation of metallodrugs with high anti‐angiogenic activity to cyclic RGD‐containing peptides or peptidomimetic analogues.
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Synthesis and Antiviral Evaluation of TriPPPro‐AbacavirTP, TriPPPro‐CarbovirTP and their 1',2'‐cis‐disubstituted Analogues ()
Herein we describe the synthesis of lipophilic triphosphate prodrugs of Abacavir, Carbovir and their 1',2'‐cis‐substituted carbocyclic analogues. The 1',2'‐cis‐carbocyclic nucleosides were prepared starting from enantiomerically pure (1R,2S)‐2‐((benzyloxy)methyl)cyclopent‐3‐en‐1‐ol by a microwave assisted Mitsunobu‐type reaction with 2‐amino‐6‐chloropurine. All four nucleoside analogues were prepared from their 2‐amino‐6‐chloropurine precursors. The nucleosides were converted into their corresponding nucleoside triphosphate prodrugs (TriPPPro‐approach) by application of the H‐phosphonate route.
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Quinone‐fused pyrazoles through regio‐selective 1,3‐dipolar cycloadditions: synthesis of tricyclic scaffolds and in vitro cytotoxic activity evaluation on glioblastoma cancer cells ()
A novel and straightforward synthesis of highly substituted isoquinoline‐5,8‐dione fused tricyclic pyrazoles is reported. The key step of the synthetic sequence is a regioselective, Ag2CO3 promoted, 1,3‐dipolar cycloaddition of C‐heteroaryl‐N‐aryl nitrilimines and substituted isoquinoline‐5,8‐diones. The broad functional group tolerability and the mild reaction conditions were suitable for the preparation of a small library of compounds. These scaffolds were designed to interact with multiple biological residues and two of them, after brief synthetic elaborations, were analysed by molecular docking studies in silico as potential anti‐cancer drugs. In vitro studies confirmed the potent anti‐cancer capability, showing interesting IC50 values down to 2.5 μM on three different glioblastoma cell lines. Their cytotoxic activity was finally positively correlated to their ability of inhibiting PI3K/mTOR kinases, which are responsible for the regulation of diverse cellular processes in human cancer cells.
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Hydroxypyridonecarboxylic acids as inhibitors of human cytomegalovirus pUL89 endonuclease ()
Human cytomegalovirus (HCMV) infection poses a major health threat for immuno‐compromised individuals. Until very recently treatment of HCMV infection has relied solely on polymerase inhibitors which suffer from safety and resistance issues. pUL89 provides the enzymatic functions for HCMV terminase complex in viral DNA packaging and represents an attractive target for developing a new class of HCMV drugs. However, inhibitors of the endonuclease activity of the C terminus of pUL89 (pUL89‐C) were unknown prior to our recently characterized hydroxypyridonecarboxylic acid (HPCA) hit 7r (numbered as 10k in the original publication; Wang et al.; J Virol., 2017). We report herein the structure‐activity relationship (SAR) of the HPCA chemotype concerning mainly the N‐1 site through the synthesis of 35 analogues. These SAR studies, along with molecular modeling, revealed a possible pharmacophore model consisting of minimally a chelating triad and a hydrophobic phenyl or biphenyl methyl substituent at N‐1. In the end, our best compounds consistently inhibited pUL89‐C in low µM range in biochemical assays, and exhibited strong antiviral activity without cytotoxicity, laying a solid medicinal chemistry foundation for further HCMV drug discovery efforts targeting pUL89‐C.
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Synthesis of a Novel Series of Structurally Different MB327 Derivatives and Their Affinity Characterization at the Nicotinic Acetylcholine Receptor ()
A novel series of 30 symmetric bispyridinium and related N‐heteroaromatic bisquaternary salts with a propane‐1,3‐diyl linker was synthesized and characterized for their binding affinity at the MB327 binding site of nAChR (nicotinic acetylcholine receptor) from Torpedo californica. Compounds targeting this binding site are of particular interest for the research into new antidotes against organophosphate poisoning, as therapeutically active 4‐tert‐butyl substituted bispyridinium salt MB327 was previously identified as nAChR resensitizer. Efficient access to the target compounds was provided by newly developed methods enabling N‐alkylation of sterically hindered or electronically deactivated heterocycles exhibiting a wide variety of functional groups. Determination of binding affinities towards the MB327 binding site at the nAChR, using a recently developed mass spectrometry (MS) based Binding Assay, revealed that several compounds reached affinities similar to that of MB327 (pKi = 4.73 ± 0.03). Notably, newly prepared lipophilic 4‐tert‐butyl‐3‐phenyl substituted bispyridinium salt PTM0022 (3h), was found to have a significantly higher binding affinity with a pKi value of 5.16 ± 0.07, thus representing a considerable progress towards the development of more potent nAChR resensitizers.
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The Impact of Adrenomedullin Thr22 on Selectivity within the Calcitonin Receptor‐like Receptor/ Receptor Activity‐Modifying Protein System ()
Adrenomedullin (ADM) is a peptide hormone of the calcitonin gene‐related peptide (CGRP) family. It is involved in the regulation of cardiovascular processes such as angiogenesis, vasodilation and the reduction of oxidative stress. ADM mediates its effects by activation of the ADM 1 and 2 receptors (AM1R/AM2R), but also activates the CGRP receptor (CGRPR) with reduced potency. It binds to the extracellular domains of the receptors with its C‐terminal binding motif (residues 41‐52). The activation motif, consisting of a disulfide‐bonded ring structure (residues 16‐21) and an adjacent helix (residues 22‐30), binds to the transmembrane region and stabilizes the receptor conformation in the active state. While it was shown that the binding motif of ADM guides AM1R selectivity, there is little information on the activation motif itself. Here, we demonstrate that Thr22 of ADM contributes to the selectivity. By using solid phase peptide synthesis and cAMP‐based signal transduction, we studied the effects of analogues in the activation motif of ADM on AM1R and CGRPR activity. Our results indicate that Thr22 terminates the α‐helix and orientates the ring segment by H‐bonding. Using olefin stapling, we showed that the α‐helical arrangement of the ring segment leads to reduced AM1R activity, but does not affect the CGRPR activation. These results demonstrate that the conformation of the ring segment of ADM has a strong impact on the selectivity within the receptor system.
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X‐ray structures and feasibility assessment of CLK2 inhibitors for Phelan McDermid syndrome ()
CLK2 inhibition has been proposed as a potential mechanism to improve autism and neuronal functions in Phelan‐McDermid syndrome (PMDS). Herein, we report the discovery of a very potent indazole CLK inhibitor series, and the CLK2 X‐ray structure of its most potent analog. This new indazole series was identified via a biochemical CLK2 Caliper assay screen with 30k compounds that were selected by an in silico approach. Novel high resolution X‐ray structures of all CLKs, including the first CLK4 X‐ray structure, bound to known CLK2 inhibitor tool compounds (e.g. TG003, CX‐4945), are also shown and yield insights into inhibitor selectivity in the CLK family. Efficacy of our new CLK2 inhibitors from the indazole series was demonstrated in the mouse brain slice assay, and potential safety concerns were investigated. We show genotoxicity findings in the human lymphocyte MNT assay using two structurally different CLK inhibitors, which reveals a major concern for pan‐CLK inhibition in PMDS.
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