ChemMedChem

Discovery of novel wtRET and V804MRET inhibitors: from hit to lead ()
Oncogenic activation of the RET kinase has been found in several neoplastic diseases, like medullary thyroid carcinoma, multiple endocrine neoplasia, papillary thyroid carcinoma and non-small cells lung cancer. Currently approved RET inhibitors were not originally designed to be RET inhibitors and their potency against RET kinase has not been optimized. Hence, novel compounds able to inhibit both wtRET and its mutants (e.g. V804MRET) are needed. Herein we present the development and the preliminary evaluation of a new sub-micromolar wtRET/V804MRET inhibitor (69) endowed with 4-anilinopyridine structure, starting from our previously identified 4-anilinopyrimidine hit compound. Profiling against a panel of kinases indicated 69 as a multi cKIT/wtRET/ V804MRET inhibitor.
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New multifunctional radiotheranostic agent for dual targeting of breast cancer cells ()
A straightforward synthetic route for a new multifunctional DOTA derivative is described. To prove the versatility of this prochelator to prepare radiolabelled hybrid compounds containing two different biological targeting moieties, an antitumoral agent (e.g. DNA intercalating agent) and an Estrogen Receptor ligand (e.g. LXXLL based peptide) were regiospecifically conjugated to the DOTA derivative. The bifunctional probe was radiolabelled with the Auger electron emitter Indium-111 and the radioconjugate demonstrated to induce DNA damage in vitro which along with the nuclear internalization exhibited in breast cancer cells might enhance its therapeutic activity. This favourable in vitro performance suggests that this hybrid compounds could be attractive probes for theranostic applications.
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Acyclic nucleoside phosphonates containing 9-deazahypoxanthine and a 5-membered heterocycle as selective inhibitors of plasmodial 6-oxopurine phosphoribosyltransferases ()
Acyclic nucleoside phosphonates (ANPs) are an important class of therapeutic drugs that act as antiviral agents by inhibiting viral DNA polymerases and reverse transcriptases. ANPs containing a 6-oxopurine instead of 6-aminopurine or pyrimidine bases are inhibitors of the purine salvage enzyme, hypoxanthine-guanine-[xanthine]-phosphoribosyltransferase (HG[X]PRT). Such compounds, and their prodrugs, are able to arrest the growth of Plasmodium falciparum (Pf) in cell culture. A new series of ANPs has been synthesized and tested as inhibitors of human HGPRT, PfHGXPRT and Plasmodium vivax (Pv) HGPRT. The novelty of these compounds is that they contain a 5-membered heterocycle (imidazoline, imidazole or triazole) inserted between the acyclic linker(s) and the nucleobase, namely 9-deazahypoxanthine. Five of the compounds were found to be micromolar inhibitors of PfHGXPRT and PvHGPRT but no inhibition of human HGPRT was observed under the same assay conditions. This demonstrates selectivity of this type of compounds for the two parasitic enzymes compared to the human counterpart and confirms the importance of the chemical nature of the acyclic moiety in conferring affinity/selectivity for these three enzymes.
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Amphiphilic Cargo-loaded Nanocarrier Enhances Antibiotic Uptake and Perturbs Efflux: Effective Synergy for Mitigation of Methicillin-resistant Staphylococcus aureus ()
A pyridinium amphiphile-loaded Poly(lactic-co-glycolic acid) (PLGA) nanocarrier (C1-PNC) was developed as an adjuvant in order to break the resistance and restore susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) cells to therapeutic antibiotics. Notably, against a clinical MRSA strain, C1-PNC could render 8 × and 6 × reduction of the minimum biofilm eradication concentration (MBEC90) of gentamicin and ciprofloxacin, respectively. Mechanistic studies on MRSA planktonic cells revealed that in case of gentamicin, C1-PNC promoted enhanced cellular uptake of the antibiotic, while the propensity of C1-PNC to inhibit efflux pump activity could be leveraged to enhance cellular accumulation of ciprofloxacin leading to effective killing of MRSA cells. Interestingly, the combinatorial dosing regimen of C1-PNC and the antibiotics was non-toxic to cultured HEK 293 cells. It is conceived that the non-toxic amphiphile-loaded nanomaterial holds considerable prospect as an adjuvant for antibiotic-mediated alleviation of MRSA biofilm.
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Critical Evaluation of Native Electrospray Ionization Mass Spectrometry for Fragment-Based Screening ()
Fragment-based screening presents a promising alternative to high-throughput screening and has gained great attention over the last years. So far, only a few studies discuss mass spectrometry as a screening technology for fragments. Here, we applied native electrospray ionization mass spectrometry (ESI-MS) for screening defined sets of fragments against four different target proteins. Fragments were selected from a primary screen conducted by thermal shift assay (TSA) and represent different binding categories. Our data show that beside specific complex formation, many fragments show extensive multiple binding as well as charge-state shifts. Both of these factors complicate automated data analysis and lower the attractiveness of native MS as a primary screening tool for fragments. A comparison of hits identified by native MS and TSA shows good agreement for two proteins. Furthermore, we discuss general obstacles including the determination of an optimal fragment concentration and the question of how to rank fragment hits according to their affinity. In conclusion, we consider native MS a highly valuable tool for the validation and deeper investigation of promising fragment hits rather than a method for primary screening.
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High Affinity "Click" RGD Peptidomimetics as Radiolabeled Probes for Imaging αvβ3 Integrin ()
Non-peptidic RGD-mimic ligands were designed and synthesized by click chemistry between an arginine-azide mimic and an aspartic acid-alkyne mimic. Some of these molecules combine excellent in vitro properties (high αvβ3 affinity, selectivity, drug-like logD, high metabolic stability) with a variety of radiolabeling options (e.g. tritium and [18F]fluorine, plus compatibility with radio-iodination), not requiring the use of chelators or prosthetic groups. The binding mode of the resulting triazole RGD-mimics to αvβ3 or αIIbβ3 receptors was investigated by molecular modeling simulations. Compound 12 was successfully radiofluorinated and used for in vivo PET/CT studies in U87-tumour models, which showed only modest tumour uptake and retention, owing to rapid excretion. These results demonstrate that the novel click-RGD mimics are excellent radiolabeled probes for in vitro and cell-based studies on αvβ3 integrin, whereas further optimization of their pharmaco-kinetic and dynamic profile would be necessary for a successful use in in vivo imaging.
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Synthesis and Biological Evaluation of Glycyrrhetic Acid Derivatives as Potential VEGFR2 Inhibitors ()
Vascular endothelial growth factor receptor 2 (VEGFR2) has been proven to play a major role in the regulation of tumor angiogenesis. A series of novel glycyrrhetic acid derivatives have been synthesized and evaluated for their VEGFR2 inhibitory activity as well as their antiproliferative properties against four cancer cell lines (MCF-7, Hela, HepG2 and A549). In vitro biological evaluation against four human tumor cell lines indicated that most of the prepared compounds showed antiproliferative activities, and compound 3a exhibited the best inhibitory activity against MCF-7 with the IC50 value of 1.08 μM. Also, compound 3a showed the most potent inhibitory activities against VEGFR2 tyrosine kinase with the IC50 value of 0.35 μM. A docking simulation study was performed with the aim of discovering the binding mode of compound 3a, and the result showed that compound 3a could bind well at the VEGFR2 active site.
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Searching for Novel Inhibitors of the S. aureus NorA Efflux Pump: Synthesis and Biological Evaluation of the 3-Phenyl-1,4-benzothiazine Analogues ()
Bacterial resistance to antimicrobial agents has become an increasingly serious health problem in recent years. Among the strategies by which resistance can be achieved, overexpression of efflux pumps such as NorA of S. aureus leads to a sub-lethal concentration of the antibacterial at the active site that in turn may predispose the organism to the development of high-level target-based resistance. With the aim to improve both the chemical stability and the potency of our previously reported 3-phenyl-1,4-benzothiazine NorA inhibitors, we replaced the benzothiazine core with different nuclei. None of the new synthesized compounds showed any appreciable intrinsic antibacterial activity and, in particular, the 2-phenylquinoline 6c was able to reduce, in a concentration-dependent manner, the ciprofloxacin MIC against the norA-overexpressing strains S. aureus SA-K2378 (norA++) and SA-1199B (norA+/ A116E GrlA).
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Repurposing of human kinase inhibitors in neglected protozoan diseases ()
Human African trypanosomiasis (HAT), Chagas disease and leishmaniasis, belong to a group of infectious diseases defined as neglected tropical diseases, induced by infection with protozoan parasites named trypanosomatids. Current drugs present several issues and the development of new candidates appears to be needed. The majority of the current therapeutic trypanosomatid targets are represented by enzymes or cell surface receptors. Among these, eukaryotic protein kinases represent a major group of protein targets whose modulation may be beneficial for the treatment of neglected tropical protozoan diseases. This review summarizes over the finding of new hit compounds for neglected tropical protozoan diseases, by repurposing known human kinase inhibitors on trypanosomatids. Kinase inhibitors were grouped by human kinase family and discussed according to the screenings (target-based or phenotypic) reported for these drugs on trypanosomatids. This collection aims to provide an insight into repurposed human kinase inhibitors and their importance in the development of new chemical entities with potential beneficial effects on trypanosomatids diseases.
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2,6-Difluorobenzamide inhibitors of the bacterial cell division protein FtsZ: design, synthesis and Structure Activity Relationship study ()
A wide variety of drug-resistant microorganism are continuously emerging, restricting the therapy of common bacterial infections. Originally potent antimicrobial agents are now no longer helpful, due to their weak or null activity towards these antibiotic-resistant bacteria. In addition, none of the recently approved antibiotics affects innovative targets, resulting in a requirement of novel drugs, with innovative antibacterial mechanisms of action. The essential cell division protein FtsZ (Filamentous temperature sensitive Z) emerged as a possible target, thanks to its ubiquitous expression and its homology to eukaryotic -tubulin. In the latest years, several compounds proved to interact with this prokaryotic protein and to selectively inhibit bacterial cell division. Recently, our research group developed interesting derivatives displaying good antibacterial activities against methicillin-resistant Staphylococcus aureus, as well as vancomycin-resistant Enterococcus faecalis and Mycobacterium tuberculosis. The aim of the present work is to summarize the Structure Activity Relationship of differently substituted heterocycles, linked by a methylenoxy-bridge to the 2,6-difluoro-benzamide, and to validate FtsZ as the real target of this class of antimicrobicals.
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Discovery of Potent Dual Binding Site Acetylcholinesterase Inhibitors via Homo- and Heterodimerization of Coumarin-based Moieties ()
Acetylcholinesterase (AChE) inhibitors are still the majority of the marketed drugs for Alzheimer's disease (AD). The structural arrangement of the enzyme, featuring a narrow gorge that separates the catalytic from a peripheral anionic subsite (CAS and PAS, respectively), inspired the development of bivalent ligands able to bind and block the catalytic activity of CAS as well as the role of PAS in beta amyloid (Aβ) fibrillogenesis. Aiming at discovering novel AChE dual binders with improved druglikeness, homo- and heterodimers containing 2H-chromen-2-one building blocks were developed. By exploring diverse linkage of neutral and protonatable amino moieties through aliphatic spacers of different length, a nanomolar bivalent AChE inhibitor was identified (6d, IC50 = 59 nM) starting from original weakly active fragments. To assess its potential against AD, disease-related biological properties of 6d were investigated. It performed a mixed-type AChE enzyme kinetics (Ki = 68 nM) and inhibited Aβ self-aggregation. Moreover, it displayed an outstanding ability to protect SH-SY5Y cells from Aβ₁-₄₂ damage.
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Structure-Activity Relationship Studies on 6,7-Dimethoxy-2-phenethyl-1,2,3,4-tetrahydroisoquinoline Derivatives as Multidrug Resistance (MDR) reversers ()
A series of derivatives were synthesized and studied with the aim to investigate the structure-activity relationships of the two P-glycoprotein (P-gp) modulators elacridar and tariquidar. Then different aryl substituted amides were inserted and to explore the effects of varying the amide function, the corresponding isosteric ester derivatives and some alkylamine analogues were synthesized. The new compounds were studied to evaluate their P-gp interaction profile and selectivity towards the two other ABC transporters, Multidrug-Resistance-associated Protein-1 (MRP-1) and Breast Cancer Resistance Protein (BCRP). The investigation on the chemical stability of amide and ester derivatives towards spontaneous or enzymatic hydrolysis, showed that these compounds resulted stable in phosphate buffer solution and human plasma. This study allowed us to evaluate the selectivity of the three series on the three efflux pumps and to propose the structural requirements that define the P-gp interaction profile. We identified two P-gp substrates and a P-gp inhibitor and three ester derivatives active on BCRP that opens a new scenario in the development of ligands active towards this pump.
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Kinome-Wide Profiling Prediction of Small Molecules ()
Extensive kinase profiling data, covering more than half of the human kinome, are nowadays available and allow construction of activity prediction models of high practical use. Proteochemometric (PCM) approaches utilize compound and protein descriptors, which enables the extrapolation of bioactivity values also to so 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 prediction 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 prediction power for mutations spread across the ATP binding site.
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Comparison of the Human A2A Adenosine Receptor Recognition by Adenosine and Inosine: New Insights from Supervised Molecular Dynamics Simulations. ()
Adenosine deaminase converts adenosine to inosine. Differently by adenosine, modest attention has been dedicated to the physiological roles of inosine. Nevertheless, recent studies demonstrate that inosine has neuroprotective, cardioprotective immunomodulatory, and antidepressive effects. It has been recently reported by Welihinda and collaborators that inosine is a less potent agonist than adenosine at the A2A AR. To better depict the differences in receptor recognition mechanism of both adenosine and inosine, in this work supervised molecular dynamics (SuMD) simulations have been performed and analyzed.
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Residence Time, a New parameter to Predict Neurosteroidogenic Efficacy of Translocator Protein (TSPO) Ligands: the Case Study of N,N-Dialkyl-2-arylindol-3-ylglyoxylamides ()
Targeting the biosynthetic pathway of neuroactive steroids with specific 18 kDa translocator protein (TSPO) ligands may be a viable therapeutic approach for a variety of neurodegenerative and neuropsychiatric diseases. However, the lack of correlation between binding affinity and in vitro steroidogenic efficacy has limited the identification of lead compounds by traditional affinity-based drug discovery strategies. Our recent research indicates that the key factor for robust steroidogenic TSPO ligand efficacy is not the binding affinity per se, but rather the time the compound spends in the target, namely its residence time (RT). The assessment of this kinetic parameter during the in vitro characterization of compounds appears mandatory in order to obtain structure–efficacy relationships suitable for the future development of novel molecules with promising pharmacological properties. How long can you stay? The neurosteroidogenic efficacy of translocator protein (TSPO) ligands can be predicted by evaluating the amount of time—the residence time—that a given ligand spends in the target rather than the binding affinity. This aids in the development of novel compounds with promising pharmacological properties and therapeutic potential.
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Thiazole-Based σ1 Receptor Ligands: Diversity by Late-Stage C−H Arylation of Thiazoles, Structure–Affinity and Selectivity Relationships, and Molecular Interactions ()
Spirocyclic thiophene derivatives represent promising σ1 ligands with high σ1 affinity and selectivity over the σ2 subtype. To increase ligand efficiency, the thiophene ring was replaced bioisosterically by a thiazole ring, and the pyran ring was opened. Late-stage diversification by regioselective C−H arylation of thiazoles 9 a–c resulted in a set of 53 compounds with high diversity. This set of compounds was analyzed with respect to σ1 affinity, σ1/σ2 selectivity, lipophilicity (logD7.4), lipophilicity-corrected ligand efficiency (LELP), and molecular target interactions. The most promising candidates were pyridyl-substituted thiazole derivatives 33 c (2-(1-benzyl-4-ethoxypiperidin-4-yl)-5-(pyridin-3-yl)thiazole) and 34 c (2-(1-benzyl-4-ethoxypiperidin-4-yl)-5-(pyridin-4-yl)thiazole), possessing low-nanomolar σ1 affinity (Ki=1.3 and 1.9 nm), high σ1/σ2 selectivity (>1500-fold), low lipophilicity (logD7.4=1.8) and very good ligand efficiency (LELP=5.5), indicating promising pharmacodynamics and pharmacokinetics. Molecular simulation studies, including docking and deconvolution of the free binding energy into its major components, led to decreased hydrophobic stabilization of pyridyl derivatives 33 c and 34 c, which was compensated by lower desolvation energy. Bioisosteric benefits: To increase σ1 receptor ligand efficiency of spirocylic thiophenes, the thiophene ring was replaced with a thiazole, and the pyran ring was opened to afford 53 derivatives. Among these, two pyridyl-substituted thiazole derivatives were most promising, with low-nanomolar σ1 affinity, high σ1/σ2 selectivity, low lipophilicity, and very good ligand efficiency, indicating promising pharmacodynamics and pharmacokinetics.
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CarbORev-5901: The First Carborane-Based Inhibitor of the 5-Lipoxygenase Pathway ()
The progression of cancer is accelerated by increased proliferation, angiogenesis, and inflammation. These processes are mediated by leukotrienes. Several cancer cell lines overexpress 5-lipoxygenase, an enzyme that converts arachidonic acid into leukotrienes. An early inhibitor of the 5-lipoxygenase pathway is Rev-5901, which, however, lacks in in vivo efficacy, as it is rapidly metabolized. We investigated the introduction of carboranes as highly hydrophobic and metabolically stable pharmacophores into lipoxygenase inhibitors. Carboranes are icosahedral boron clusters that are remarkably stable and used to increase the metabolic stability of unstable pharmaceutics without changing their biological activity. By introduction of meta-carborane into Rev-5901, the first carborane-based inhibitor of the 5-lipoxygenase pathway was obtained. We report the synthesis and inhibitory and cytotoxic behavior of these compounds toward several melanoma and colon cancer cell lines and their related anticancer mechanisms. High activity against LO: The progression of cancer is accelerated by processes that are mediated by leukotrienes. Several cancer cell lines overexpress 5-lipoxygenase (5-LO), which converts arachidonic acid into leukotrienes. The introduction of carboranes as highly hydrophobic and metabolically stable pharmacophores in Rev-5901 has generated the first carborane-based inhibitor of the 5-LO pathway.
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Structural States of RORγt: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds ()
The T-cell-specific retinoic acid receptor (RAR)-related orphan receptor-γ (RORγt) is a key transcription factor for the production of pro-inflammatory Th17 cytokines, which are implicated in the pathogenesis of autoimmune diseases. Over the years, several structurally diverse RORγt inverse agonists have been reported, but combining high potency and good physicochemical properties has remained a challenging task. We recently reported a new series of inverse agonists based on an imidazopyridine core with good physicochemical properties and excellent selectivity. Herein we report eight new X-ray crystal structures for different classes of natural and synthetic compounds, including examples selected from the patent literature. Analysis of their respective binding modes revealed insight into the molecular mechanisms that lead to agonism, antagonism, or inverse agonism. We report new molecular mechanisms for RORγt agonism and propose a separation of the inverse agonists into two classes: those that act via steric clash and those that act via other mechanisms (for the latter, co-crystallization with a co-activator peptide and helix 12 in the agonist position is still possible). For the non-steric clash inverse agonists, we propose a new mechanism (“water trapping”) which can be combined with other mechanisms (e.g., close contacts with H479). In addition, we compare the interactions made for selected compounds in the “back pocket” near S404 and in the “sulfate pocket” near R364 and R367. Taken together, these new mechanistic insights should prove useful for the design and optimization of further RORγt modulators. We disclose eight new X-ray crystal structures for different classes of natural and synthetic RORγt modulators, including a putative clinical candidate from the patent literature. We performed structural analyses to elucidate their molecular mechanisms that lead to agonism, antagonism, or inverse agonism. We compared the interactions made for selected compounds in the “back pocket” near S404 and in the “sulfate pocket” near R364 and R367. Altogether, these findings should prove useful in the design and optimization of further RORγt modulators.
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Small Molecule Medicinal Chemistry: Strategies and Technologies. Edited by Werngard Czechtizky and Peter Hamley ()
Wiley, Hoboken 2015. 528 pp., hardcover, $150.00.—ISBN 978-1-118-77160-0
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Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery. Edited by Sylke Müller, Rachel Cerdan and Ovidiu Radulescu; Series Editor: Paul M. Selzer ()
Wiley-VCH, Weinheim 2016. 576 pp., hardcover, €179.00.—ISBN 978-3-527-33904-4
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Synthetic Methods in Drug Discovery, Volumes 1+2. Edited by David C. Blakemore, Paul M. Doyle and Yvette M. Fobian ()
RSC, Cambridge 2016. Vol. 1: 455 pp., hardcover, £179.00.—ISBN 978-1-849-73803-3. Vol. 2: 517 pp., hardcover, £179.00.—ISBN 978-1-782-62786-9.
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Identification of Breast Cancer Inhibitors Specific for G Protein-Coupled Estrogen Receptor (GPER)-Expressing Cells ()
Together with estrogen receptors ERα and ERβ, the G protein-coupled estrogen receptor (GPER) mediates important pathophysiological signaling pathways induced by estrogens and is currently regarded as a promising target for ER-negative (ER−) and triple-negative (TN) breast cancer. Only a few selective GPER modulators have been reported to date, and their use in cancer cell lines has often led to contradictory results. Herein we report the application of virtual screening and cell-based studies for the identification of new chemical scaffolds with a specific antiproliferative effect against GPER-expressing breast cancer cell lines. Out of the four different scaffolds identified, 8-chloro-4-(4-chlorophenyl)pyrrolo[1,2-a]quinoxaline 14 c was found to be the most promising compound able to induce: 1) antiproliferative activity in GPER-expressing cell lines (MCF7 and SKBR3), similarly to G15; 2) no effect on cells that do not express GPER (HEK293); 3) a decrease in cyclin D1 expression; and 4) a sustained induction of cell-cycle negative regulators p53 and p21. Positive news for ER-negative: We show how the combination of virtual screening on a GPER model and cell-based assays quickly leads to the identification of new chemical entities that induce a specific antiproliferative effect on GPER-expressing cells (MCF7 and SKBR3), but that have no effect on cells that do not express GPER. Further in vitro studies allowed identification of pyrrolo[1,2-a]quinoxaline 14 c as the most interesting compound for hit-to-lead optimization aimed at developing new drugs to treat breast cancer.
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Synthesis, ADMET Properties, and Biological Evaluation of Benzothiazole Compounds Targeting Chemokine Receptor 2 (CXCR2) ()
Herein we describe the synthesis and biological evaluation of a series of novel benzothiazoles based on a diaryl urea scaffold previously reported in some allosteric chemokine receptor 2 (CXCR2) inhibitors. From a library of 41 new compounds, 17 showed significant inhibition of CXCR2, with IC50 values less than 10 μm and selectivity over CXCR4. Our ADMET simulations suggest favorable drug-like properties for the active compounds. Importantly, we developed a predictive model that can distinguish active from inactive compounds; this will serve as a valuable tool to guide the design of optimized compounds to be evaluated in preclinical models. Discriminating taste in receptors: We combined benzothiazoles and diaryl urea scaffolds to design new CXCR2 inhibitors that display selectivity over CXCR4. Our molecular modeling studies support a robust approach to further optimize these inhibitors for selecting highly potent compounds for in vivo studies.
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Identification of α7 Nicotinic Acetylcholine Receptor Silent Agonists Based on the Spirocyclic Quinuclidine-Δ2-Isoxazoline Scaffold: Synthesis and Electrophysiological Evaluation ()
Compound 11 (3-(benzyloxy)-1′-methyl-1′-azonia-4H-1′-azaspiro[isoxazole-5,3′-bicyclo[2.2.2]octane] iodide) was selected from a previous set of nicotinic ligands as a suitable model compound for the design of new silent agonists of α7 nicotinic acetylcholine receptors (nAChRs). Silent agonists evoke little or no channel activation but can induce the α7 desensitized Ds state, which is sensitive to a type II positive allosteric modulator, such as PNU-120596. Introduction of meta substituents into the benzyloxy moiety of 11 led to two sets of tertiary amines and quaternary ammonium salts based on the spirocyclic quinuclidinyl-Δ2-isoxazoline scaffold. Electrophysiological assays performed on Xenopus laevis oocytes expressing human α7 nAChRs highlighted four compounds that are endowed with a significant silent-agonism profile. Structure–activity relationships of this group of analogues provided evidence of the crucial role of the positive charge at the quaternary quinuclidine nitrogen atom. Moreover, the present study indicates that meta substituents, in particular halogens, on the benzyloxy substructure direct specific interactions that stabilize a desensitized conformational state of the receptor and induce silent activity. Shh, it's a “silent” activation: Designed quinuclidine spirocyclic derivatives were characterized as silent agonists of α7 nicotinic acetylcholine receptors (nAChRs) with electrophysiological assays. The 3-halo-substituted tertiary amine 17 a and quaternary ammonium salt 18 b exhibited the best silent activity in the set of analogues. Thus, both a protonatable and a permanently charged nitrogen atom may promote the silent activation of α7 nAChRs.
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Design, Synthesis, and Structure–Activity Relationship Analysis of Thiazolo[3,2-a]pyrimidine Derivatives with Anti-inflammatory Activity in Acute Lung Injury ()
Acute lung injury (ALI) has a high lethality rate, and interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) contribute most to tissue deterioration in cases of ALI. In this study, we designed and synthesized a new series of thiazolo[3,2-a]pyrimidine derivatives based on a previously identified lead compound, and we evaluated their anti-inflammatory activities. Structure–activity relationship studies led to the discovery of two highly potent inhibitors. The two promising compounds were found to inhibit lipopolysaccharide (LPS)-induced IL-6 and TNF-α release in a dose-dependent manner in mouse primary peritoneal macrophages (MPMs). Furthermore, administration of these compounds resulted in lung histopathological improvements and attenuated LPS-induced ALI in vivo. Taken together, these data indicate that these novel thiazolo[3,2-a]pyrimidine derivatives could be developed as candidate drugs for the treatment of ALI. Breathe easy: Based on lead compound 6, we designed and synthesized a series of thiazolo[3,2-a]pyrimidine derivatives. The most promising compounds, 11 e and 11 l, were found to inhibit lipopolysaccharide (LPS)-induced cytokines with IC50 values in the low- to sub-micromolar range. Further administration of these compounds in mice was found to attenuate LPS-induced acute lung injury.
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Synthesis, DNA Cleavage Activity, Cytotoxicity, Acetylcholinesterase Inhibition, and Acute Murine Toxicity of Redox-Active Ruthenium(II) Polypyridyl Complexes ()
Four mononuclear [(L-L)2Ru(tatpp)]2+ and two dinuclear [(L-L)2Ru(tatpp)Ru(L-L)2]4+ ruthenium(II) polypyridyl complexes (RPCs) containing the 9,11,20,22-tetraazatetrapyrido[3,2-a:2′,3′-c:3′′,2′′-l:2′′′,3′′′-n]pentacene (tatpp) ligand were synthesized, in which L-L is a chelating diamine ligand such as 2,2′-bipyridine (bpy), 1,10-phenanthroline (phen), 3,4,7,8-tetramethyl-1,10-phenanthroline (Me4phen) or 4,7-diphenyl-1,10-phenanthroline (Ph2phen). These Ru–tatpp analogues all undergo reduction reactions with modest reducing agents, such as glutathione (GSH), at pH 7. These, plus several structurally related but non-redox-active RPCs, were screened for DNA cleavage activity, cytotoxicity, acetylcholinesterase (AChE) inhibition, and acute mouse toxicity, and their activities were examined with respect to redox activity and lipophilicity. All of the redox-active RPCs show single-strand DNA cleavage in the presence of GSH, whereas none of the non-redox-active RPCs do. Low-micromolar cytotoxicity (IC50) against malignant H358, CCL228, and MCF7 cultured cell lines was mainly restricted to the redox-active RPCs; however, they were substantially less toxic toward nonmalignant MCF10 cells. The IC50 values for AChE inhibition in cell-free assays and the acute toxicity of RPCs in mice revealed that whereas most RPCs show potent inhibitory action against AChE (IC50 values <15 μm), Ru–tatpp complexes as a class are surprisingly well tolerated in animals relative to other RPCs. Tatpp-ing into antitumor drugs: Ruthenium polypyridyl complexes (RPCs) bearing the redox-active tetraazatetrapyridopentacene (tatpp) ligand show enhanced cytotoxicity and selectivity over other RPCs that lack redox-active ligands toward malignant cells. The RPCs show promising antitumor activity, low murine toxicity, and effect DNA damage. Surprisingly, all RPCs are potent inhibitors of acetylcholinesterase in vitro, but the redox-active complexes show little neuro- or acute toxicity in mice.
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Synthesis and Antineoplastic Evaluation of Mitochondrial Complex II (Succinate Dehydrogenase) Inhibitors Derived from Atpenin A5 ()
Mitochondrial complex II (CII) is an emerging target for numerous human diseases. Sixteen analogues of the CII inhibitor natural product atpenin A5 were prepared to evaluate the structure–activity relationship of the C5 pyridine side chain. The side chain ketone moiety was determined to be pharmacophoric, engendering a bioactive conformation. One analogue, 1-(2,4-dihydroxy-5,6-dimethoxypyridin-3-yl)hexan-1-one (16 c), was found to have a CII IC50 value of 64 nm, to retain selectivity for CII over mitochondrial complex I (>156-fold), and to possess a ligand-lipophilicity efficiency (LLE) of 5.62, desirable metrics for a lead compound. This derivative and other highly potent CII inhibitors show potent and selective anti-proliferative activity in multiple human prostate cancer cell lines under both normoxia and hypoxia, acting to inhibit mitochondrial electron transport. Simplicity in complex inhibition: Ten highly potent inhibitors of mitochondrial complex II (CII) were produced in this study. Compound 16 c was found to be the most drug-like; its combined potency and LLE makes it the best of the CII inhibitors synthesized. It has far greater potency than existing inhibitors while retaining selectivity for CII over mitochondrial complex I. Inhibitor 16 c inhibits mitochondrial electron transport parameters, decreases oxygen consumption rate, basal respiration, ATP production, and maximal respiration. Compounds from this work will be valuable tools to study the effect of CII in cancer and other diseases.
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Identification of Transthyretin Fibril Formation Inhibitors Using Structure-Based Virtual Screening ()
Transthyretin (TTR) is the primary carrier for thyroxine (T4) in cerebrospinal fluid and a secondary carrier in blood. TTR is a stable homotetramer, but certain factors, genetic or environmental, could promote its degradation to form amyloid fibrils. A docking study using crystal structures of wild-type TTR was planned; our aim was to design new ligands that are able to inhibit TTR fibril formation. The computational protocol was thought to overcome the multiple binding modes of the ligands induced by the peculiarity of the TTR binding site and by the pseudosymmetry of the site pockets, which generally weaken such structure-based studies. Two docking steps, one that is very fast and a subsequent step that is more accurate, were used to screen the Aldrich Market Select database. Five compounds were selected, and their activity toward inhibiting TTR fibril formation was assessed. Three compounds were observed to be actives, two of which have the same potency as the positive control, and the other was found to be a promising lead compound. These results validate a computational protocol that is able to archive information on the key interactions between database compounds and TTR, which is valuable for supporting further studies. Rapid and accurate! Inhibitors of transthyretin (TTR) fibril deposition were identified thanks to a structure-based virtual screening of the entire Aldrich Market Select database. The first results of this protocol, despite the unique peculiarity of the TTR site with its symmetry and multi-binding mode, allowed the detection of two very active inhibitors and one scaffold for optimization. Much information, however, is still stored in the outputs.
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Novel, Selective, and Developable Dopamine D3 Antagonists with a Modified “Amino” Region ()
This Minireview describes a presentation made at the XXIV National Meeting in Medicinal Chemistry (NMMC) held in Perugia (Italy), September 11–14, 2016. It relates to the discovery of novel templates of the so-called “amino” region of dopamine D3 receptor antagonists. Moving from the early scaffolds, which were modified in the amine portion, this review discusses the variations that led to the discovery of new systems published in 2016, which allowed the identification of compounds endowed with great selectivity over the dopamine D2 receptor and the human ether-à-go-go-related gene (hERG) ion channel. The main efforts in characterizing these compounds were devoted not only to determining their potency and selectivity relative to closely associated targets (e.g., the dopamine D2 receptor), but to ensure a large therapeutic window versus liability points such as hERG. In particular, we present examples of derivatives with selectivities greater than 2000-fold. Furthermore, much focus is devoted to the overall developability of the scaffolds, ensuring that appropriate physicochemical and pharmacokinetic parameters are present in all compounds progressing through the screening cascade. New scaffolds! This Minireview describes the discovery of novel templates of the so-called “amino” region of dopamine D3 receptor antagonists. Moving from the early scaffolds, which were modified in the amine portion, this review discusses the variations that led to the discovery of new systems published in 2016, which allowed the identification of compounds endowed with great selectivity over the dopamine D2 receptor and hERG channels.
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Cannabinoid Type 1 Receptor (CB1) Ligands with Therapeutic Potential for Withdrawal Syndrome in Chemical Dependents of Cannabis sativa ()
Cannabis sativa withdrawal syndrome is characterized mainly by psychological symptoms. By using computational tools, the aim of this study was to propose drug candidates for treating withdrawal syndrome based on the natural ligands of the cannabinoid type 1 receptor (CB1). One compound in particular, 2-n-butyl-5-n-pentylbenzene-1,3-diol (ZINC1730183, also known as stemphol), showed positive predictions as a human CB1 ligand and for facile synthetic accessibility. Therefore, ZINC1730183 is a favorable candidate scaffold for further research into pharmacotherapeutic alternatives to treat C. sativa withdrawal syndrome. Off the hook: Most drugs used to treat chemical dependence treat the symptoms but not the underlying biological target. This study was designed to identify potential CB1 agonists to treat C. sativa withdrawal syndrome. Pharmacophore-based ligand screening and classification by structural similarity revealed a group of seven compounds for which predictions of pharmacokinetics, toxicology, biological activity, and synthetic accessibility were carried out. One compound stood out as particularly well suited for further development, with the ultimate goal of decreasing the damage caused by drug dependency.
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Structure–Activity Relationships on Cinnamoyl Derivatives as Inhibitors of p300 Histone Acetyltransferase ()
Human p300 is a polyhedric transcriptional coactivator that plays a crucial role in acetylating histones on specific lysine residues. A great deal of evidence shows that p300 is involved in several diseases, including leukemia, tumors, and viral infection. Its involvement in pleiotropic biological roles and connections to diseases provide the rationale to determine how its modulation could represent an amenable drug target. Several p300 inhibitors (i.e., histone acetyltransferase inhibitors, HATis) have been described so far, but they all suffer from low potency, lack of specificity, or low cell permeability, which thus highlights the need to find more effective inhibitors. Our cinnamoyl derivative, 2,6-bis(3-bromo-4-hydroxybenzylidene)cyclohexanone (RC56), was identified as an active and selective p300 inhibitor and was proven to be a good hit candidate to investigate the structure–activity relationship toward p300. Herein, we describe the design, synthesis, and biological evaluation of new HATis structurally related to our hit; moreover, we investigate the interactions between p300 and the best-emerged hits by means of induced-fit docking and molecular-dynamics simulations, which provided insight into the peculiar chemical features that influence their activity toward the targeted enzyme. HAT trick: Histone acetyltransferase (HAT) is an attractive anticancer target. Several HAT inhibitors have been identified, but they all exhibit low potency or pharmacodynamics limits. Herein we report the design and synthesis along with biological evaluations and theoretical investigations of potent and selective cinnamoyl compounds, highlighting the peculiar features required to develop an effective HAT inhibitor.
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A Molecular Dynamics–Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor α ()
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein′s active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand–protein interactions within the complexes. The study was carried out on peroxisome proliferator-activated receptor α (PPARα). Findings derived from the dynamic analysis of interactions were then used as features for pharmacophore generation and constraints for generating the docking grid for use in virtual screening. We found that information derived from short multiple MD simulations using different molecules within the binding pocket of the target can improve the early enrichment of active ligands in the virtual screening process for this receptor. In the end we adopted a consensus scoring based on docking score and pharmacophore alignment to rank our dataset. Our results showed an improvement in virtual screening performance in early recognition when screening was performed with the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach. The MYSHAPE approach is a new way of studying ligand–receptor interactions. In this method, a pharmacophore model is created that exploits information derived from multiple short MD simulations, using different molecules within the binding pocket of the target. Conformational information is retrieved from the full trajectory and not only from clustered frames. This approach can help improve virtual screening performance, especially for the early enrichment of active ligands in the virtual screening process.
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Cover Picture: Target Deconvolution Efforts on Wnt Pathway Screen Reveal Dual Modulation of Oxidative Phosphorylation and SERCA2 (ChemMedChem 12/2017) ()
The front cover picture shows the process of photocrosslinking a small molecule functionalized with a diaziridino group to its putative target upon UV irradiation, a critical step in photoaffinity chemical proteomics and target deconvolution. Though not intended to reflect the mode of binding, this depiction shows the photocrosslinking between a 1,2,3-thiadiazole-5-carboxamide (TDZ) series with SERCA2, one of the binding partners identified after enrichment and mass spectrometry analysis. Cellular effects observed with the TDZ series are consistent with mitochondrial dysfunction and SERCA engagement and modulation being mechanisms of actions. Front cover art created by Matias Casás-Selves and Julie Grouleff. More information can be found in the Full Paper by Andrew X. Zhang, et al. on page 917 in Issue 12, 2017 (DOI: 10.1002/cmdc.201700028).
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Inside Cover: Lanthanide Complexes in Molecular Magnetic Resonance Imaging and Theranostics (ChemMedChem 12/2017) ()
The inside cover picture shows that the versatile magnetic and luminescence features of lanthanide ions can be widely exploited to create molecular imaging agents. The relaxation and chemical exchange saturation transfer properties, thus the magnetic resonance imaging (MRI) efficiency of lanthanide complexes can be influenced via interaction with biomarkers allowing for responsive probes which detect neurotransmitters, enzymes, etc. Complexes targeted to peptides which are the molecular signature of a disease are investigated for early diagnosis, and lanthanides offer also unique opportunities in theranostics. More information can be found in the Minireview by Éva Tóth and Sara Lacerda on page 883 in Issue 12, 2017 (DOI: 10.1002/cmdc.201700210).
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Back Cover: Benzylphenylpyrrolizinones with Anti-amyloid and Radical Scavenging Effects, Potentially Useful in Alzheimer's Disease Treatment (ChemMedChem 12/2017) ()
The back cover picture shows a novel benzylphenylpyrrolizinone agent designed to target both the amyloid aggregation and the oxidative stress implied in the pathogenesis of Alzheimer's Disease. Associated to radical scavenging effects and relevant druggability parameters, these properties could contribute to slow down neurodegeneration and to stem brain damages induced by the disease. Further in vivo experiments will be carried out in this respect to confirm the potential therapeutic interest of this novel series of derivatives. More information can be found in the Communication by Jean-Pierre Jourdan, Christophe Rochais, Patrick Dallemagne et al. on page 913 in Issue 12, 2017 (DOI:10.1002/cmdc.201700102).
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The 52nd International Conference on Medicinal Chemistry (RICT 2016) of the French Medicinal Chemistry Society (SCT) Held in Caen (Normandy) ()
Outstanding Medchem in France: Guest editors Janos Sapi, Luc Van Hjfte, and Patrick Dallemagne look back at the 52nd International Conference on Medicinal Chemistry (RICT 2016) held in Caen, France. They discuss the history of the French Medicinal Chemistry Society (Société de Chimie Thérapeutique, SCT) and provide highlights of last year′s events, including some key presentations now collected in this Special Issue.
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Nucleic Acid Templated Reactions for Chemical Biology ()
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging. From sci-fi to reality: Nucleic acid templated chemical reactions are a unique asset in chemical biology, enabling specific in situ drug synthesis, release, and nucleic acid sensing. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Lanthanide Complexes in Molecular Magnetic Resonance Imaging and Theranostics ()
Lanthanide complexes have attracted much attention in the biomedical field, and today various imaging applications make use of their versatile magnetic and luminescence properties. In this minireview, we give insight into the mechanistic aspects that allow modulation of the relaxation or chemical exchange saturation transfer (CEST) features, and thus the magnetic resonance imaging (MRI) efficiency of paramagnetic lanthanide chelates in order to create agents that are capable of providing an MRI response as a function of a specific biomarker. We focus on the detection of neurotransmitters, enzymatic activities, and amyloid peptides. We also describe two selected theranostic strategies: 1) a novel approach directed at monitoring drug release from liponanoparticles and 2) molecular or nanoparticle probes for the MRI visualization of photosensitizer delivery in photodynamic therapy. With their versatile magnetic and optical properties and rich coordination chemistry, lanthanide complexes offer boundless possibilities to create molecular imaging and theranostic agents. This minireview discusses examples of smart magnetic resonance imaging (MRI) probes with specific responses to neurotransmitters or enzymes, MRI targeting of abundant peptides, luminescence monitoring of nanoparticle integrity, or combining PDT and MRI.
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Targeting DNA-Dependent Protein Kinase for Cancer Therapy ()
The catalytic activity of DNA-dependent protein kinase (DNA-PK) is critical to its ability to repair lethal DNA double-strand breaks (DSBs). This includes repair of DSB lesions resulting from oxidative stress, oncogene-induced transcription, or following therapeutic treatment of cancer cells. Armed with this knowledge, many attempts have been made to identify small-molecule inhibitors of DNA-PK activity as an approach to induce tumour chemo- and radiosensitisation. This review examines the structures of known reversible and irreversible inhibitors, including those based on chromen-4-one, arylmorpholine, and benzaldehyde scaffolds. DNA-PK catalytic inhibitors, such as VX-984 (8-[(1S)-2-[[6-(4,6-dideuterio-2-methylpyrimidin-5-yl)pyrimidin-4-yl]amino]-1-methylethyl]quinoline-4-carboxamide) and M3814 ((S)-[2-chloro-4-fluoro-5-(7-morpholinoquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol), have now progressed into clinical development which should help to further advance our understanding of whether this approach is a promising therapeutic strategy for the treatment of cancer. Stopping the fixer: The catalytic activity of DNA-dependent protein kinase (DNA-PK) is critical to its ability to repair lethal DNA double-strand breaks, and many attempts have been made to identify small-molecule inhibitors of DNA-PK activity as an approach to induce tumour chemo- and radiosensitisation. DNA-PK catalytic inhibitors have now progressed into clinical development, which should help to further advance our understanding of whether this approach is a promising therapeutic strategy for the treatment of cancer.
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Identifying Protein Allosteric Transitions for Drug Discovery with 1D NMR ()
Allosteric drugs present many advantages over orthosteric drugs and are therefore an attractive approach in drug discovery, despite being highly challenging. First, the binding of ligands in protein allosteric pockets do not ensure an allosteric effect, and second, allosteric ligands can possess diverse modes of pharmacology even within a compound family. Herein we report a new method to: 1) detect allosteric communication between protein binding sites, and 2) compare the effect of allosteric ligands on the allosteric transitions of the protein target. The method, illustrated with glycogen phosphorylase, consists of comparing 1D saturation transfer difference (STD) NMR spectra of a molecular spy (here fragments) in the absence and presence of allosteric ligands. The modification of the STD NMR spectrum of the fragment indicates whether the protein dynamics/conformations have been changed in the presence of the allosteric modulator, thereby highlighting allosteric coupling between the binding pocket of the reference compound (in this case the fragment) and the allosteric pocket. The other site: Allosteric drug discovery is an attractive approach for the generation of drugs with improved safety, while being highly challenging. Fundamental issues are the identification of allosterically coupled protein pockets and the observation of the allosteric effect resulting from ligand binding. Herein we report a method for the detection and comparison of ligand-induced allosteric transitions based on 1D NMR spectroscopy.
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1,3,5-Trisubstituted Pyrazoles as Potent Negative Allosteric Modulators of the mGlu2/3 Receptors ()
The metabotropic glutamate subtype 2 (mGlu2) receptor is a presynaptic membrane receptor distributed widely in brain that provides feedback inhibitory control of glutamate release. Inhibition of the mGlu2 receptor function with a negative allosteric modulator (NAM) enhances activity-dependent glutamate release, which may be of therapeutic benefit for the treatment of neurological and psychiatric disorders. An attractive pyrazole hit was identified after a high-throughput screening (HTS) campaign. The evolution of this hit is described by structure–activity relationship (SAR) studies on specific parts of the molecule. From near micromolar potency we could obtain compounds with single-digit nanomolar activity in the mGlu2 NAM GTPγS assay. In addition to SAR on in vitro potency, a more detailed overview is given with a specific set of compounds on the excellent agreement between in vitro potency, free brain concentration, and ex vivo mGlu2 receptor occupancy. Finally, to obtain improved drug-like compounds, plans for future research are suggested toward increasing free brain concentration while maintaining high in vitro potency. Much positive in the negative: A medicinal chemistry exploration of the high-throughput screening hit 1 resulted in compounds 17 and 19, both of which have single-digit nanomolar potency against the metabotropic glutamate 2 receptor (mGluR2) and excellent correlation with unbound brain fraction at ED50 from ex vivo occupancy assays. These findings support the development of mGluR2 negative allosteric modulators (NAMs) to treat neurological and psychiatric disorders.
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Benzylphenylpyrrolizinones with Anti-amyloid and Radical Scavenging Effects, Potentially Useful in Alzheimer's Disease Treatment ()
Herein we describe the drug design steps developed to increase the radical scavenging and β-amyloid aggregation inhibitory activities of a previously described series of benzylidenephenylpyrrolizinones. Among the newly synthesized derivatives, some benzylphenylpyrrolizinones exhibited interesting results in regard to those activities. Initial druggability parameters were measured, and suggest these compounds as a suitable starting point for potential alternatives in treating Alzheimer's disease. Pick up & break up: This study aimed at increasing the radical scavenging and anti-Aβ-aggregation activities of a series of benzylidenephenylpyrrolizinones. Some of the new derivatives showed promising results in this regard. These compounds could serve as a good starting point for new drugs to treat Alzheimer's disease.
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Target Deconvolution Efforts on Wnt Pathway Screen Reveal Dual Modulation of Oxidative Phosphorylation and SERCA2 ()
Wnt signaling is critical for development, cell proliferation and differentiation, and mutations in this pathway resulting in constitutive signaling have been implicated in various cancers. A pathway screen using a Wnt-dependent reporter identified a chemical series based on a 1,2,3-thiadiazole-5-carboxamide (TDZ) core with sub-micromolar potency. Herein we report a comprehensive mechanism-of-action deconvolution study toward identifying the efficacy target(s) and biological implication of this chemical series involving bottom-up quantitative chemoproteomics, cell biology, and biochemical methods. Through observing the effects of our probes on metabolism and performing confirmatory cellular and biochemical assays, we found that this chemical series inhibits ATP synthesis by uncoupling the mitochondrial potential. Affinity chemoproteomics experiments identified sarco(endo)plasmic reticulum Ca2+-dependent ATPase (SERCA2) as a binding partner of the TDZ series, and subsequent validation studies suggest that the TDZ series can act as ionophores through SERCA2 toward Wnt pathway inhibition. Waste not, Wnt not: We identified a 1,2,3-thiadiazole-5-carboxamide chemical series in a Wnt pathway inhibition screen. We generated chemical probes to identify the targets of this series based on our efforts to optimize potency and physical properties. Using a combination of biochemical, cell biology, and chemoproteomics methods, we found two previously unreported mechanisms for this pharmacophore: uncouplers of the mitochondrial potential and Ca2+ ionophores through interaction with SERCA2.
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A Time-Resolved FRET Cell-Based Binding Assay for the Apelin Receptor ()
Analogues of apelin-13 carrying diverse spacers and an ad hoc DY647-derived fluorophore were designed and synthesized by chemoselective acylation of α-hydrazinopeptides. The resulting probes retain very high affinity and efficacy for both the wild-type and SNAP-tagged apelin receptor (ApelinR). They give a time-resolved FRET (TR-FRET) signal with rare-earth lanthanides used as donor fluorophores grafted onto the SNAP-tagged receptor. This specific signal allowed the validation of a binding assay with a high signal-to-noise ratio. In such an assay, the most potent sub-nanomolar fluorescent probe was found to be competitively displaced by the endogenous apelin peptides with binding constants similar to those obtained in a classical radioligand assay. We have thus validated the first TR-FRET cell-based binding assay for ApelinR with potential high-throughput screening applications. The search is on! There is still a need for the rapid discovery of apelin receptor ligands for use as pharmacological probes and precursors of drug candidates. As an alternative to radioligand binding assays, we report herein an unprecedented, efficient, robust, and safe time-resolved binding assay to investigate ligand–apelin receptor interactions at the cell surface with potential application for high-throughput screening.
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Structure-Based Design and Synthesis of Harmine Derivatives with Different Selectivity Profiles in Kinase versus Monoamine Oxidase Inhibition ()
Dual-specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) is an emerging biological target with implications in diverse therapeutic areas such as neurological disorders (Down syndrome, in particular), metabolism, and oncology. Harmine, a natural product that selectively inhibits DYRK1A amongst kinases, could serve as a tool compound to better understand the biological processes that arise from DYRK1A inhibition. On the other hand, harmine is also a potent inhibitor of monoamine oxidase A (MAO-A). Using structure-based design, we synthesized a collection of harmine analogues with tunable selectivity toward these two enzymes. Modifications at the 7-position typically decreased affinity for DYRK1A, whereas substitution at the 9-position had a similar effect on MAO-A inhibition but DYRK1A inhibition was maintained. The resulting collection of compounds can help to understand the biological role of DYRK1A and also to assess the interference in the biological effect originating in MAO-A inhibition. Choosing sides: The different orientations of harmine in the X-ray structures of this natural product bound to DYRK1A and monoamine oxidase A (MAO-A) suggest chemical ways to fine-tune the selectivity profile of this compound class. These structure-guided transformations led to the abolition of DYRK1A and/or MAO-A inhibition in harmine derivatives as well as to the synthesis of dual inhibitors of mixed inhibition ratio.
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Synthesis and Antiproliferative Effect of Ethyl 4-[4-(4-Substituted Piperidin-1-yl)]benzylpyrrolo[1,2-a]quinoxalinecarboxylate Derivatives on Human Leukemia Cells ()
Acute leukemia is a hematological malignancy with high incidence and recurrence rates and is characterized by an accumulation of blasts in bone marrow due to proliferation of immature lymphoid or myeloid cells associated with a blockade of differentiation. The heterogeneity of leukemia led us to look for new specific molecules for leukemia subtypes or for therapy-resistant cases. Among heterocyclic derivatives that attracted attention due to their wide range of biological activities, we focused our interest on the pyrrolo[1,2-a]quinoxaline heterocyclic framework that has been previously identified as an interesting scaffold for antiproliferative activities against various human cancer cell lines. In this work, new ethyl 4-[4-(4-substituted piperidin-1-yl)]benzylpyrrolo[1,2-a]quinoxalinecarboxylate derivatives (1 a–o) were designed, synthesized, and evaluated against five different leukemia cell lines, including Jurkat and U266 (lymphoid cell lines) and K562, U937, and HL60 (myeloid cell lines), as well as on normal human peripheral blood mononuclear cells (PBMCs). This new pyrrolo[1,2-a]quinoxaline series showed interesting cytotoxic potential against all tested leukemia cell lines. In particular, pyrroloquinoxalines 1 a and 1 m,n seem to be interesting due to their high activity against leukemia and their low activity against normal hematopoietic cells, leading to a high index of selectivity. An antileukemia army: New ethyl 4-[4-(4-substituted piperidin-1-yl)]benzylpyrrolo[1,2-a]quinoxalinecarboxylate derivatives were designed, synthesized, and evaluated against five leukemia cell lines, as well as normal human peripheral blood mononuclear cells. These new pyrrolo[1,2-a]quinoxalines showed interesting cytotoxic potential against all leukemia cell lines tested, with three pyrroloquinoxalines having particularly high activity against leukemia and low activity against normal hematopoietic cells.
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Molecular Features of the YAP Inhibitor Verteporfin: Synthesis of Hexasubstituted Dipyrrins as Potential Inhibitors of YAP/TAZ, the Downstream Effectors of the Hippo Pathway ()
Porphyrin derivatives, in particular verteporfin (VP), a photosensitizer initially designed for cancer therapy, have been identified as inhibitors of the YAP–TEAD interaction and transcriptional activity. Herein we report the efficient convergent synthesis of the dipyrrin half of protoporphyrin IX dimethyl ester (PPIX-DME), in which the sensitive vinyl group was created at the final stage by a dehydroiodination reaction. Two other dipyrrin derivatives were synthesized, including dipyrrin 19 [(Z)-2-((3,5-dimethyl-4-vinyl-2H-pyrrol-2-ylidene)methyl)-3,5-dimethyl-4-vinyl-1H-pyrrole], containing two vinyl groups. We found that VP and dipyrrin 19 showed significant inhibitory effects on TEAD transcriptional activity in MDA-MB-231 human breast cancer cells, whereas other compounds did not show significant changes. In addition, we observed a marked decrease in both YAP and TAZ levels following VP treatment, whereas dipyrrin 19 treatment primarily decreased the levels of YAP and receptor kinase AXL, a downstream target of YAP. Together, our data suggest that, due to their chemical structures, porphyrin- and dipyrrin-related derivatives can directly target YAP and/or TAZ proteins and inhibit TEAD transcriptional activity. Directed dipyrrins: An efficient convergent synthesis yielded hexasubstituted dipyrrins structurally related to verteporfin (VP), with a sensitive vinyl group created at the final stage by a dehydroiodination reaction. While VP showed a direct effect on YAP and TAZ levels, one dipyrrin affected only YAP levels, suggesting that dipyrrin-related compounds may directly affect the expression of YAP and/or TAZ.
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Rational Design and Synthesis of 1-(Arylideneamino)-4-aryl-1H-imidazole-2-amine Derivatives as Antiplatelet Agents ()
Based on previous studies indicating the pharmacophoric role of a hydrazone group and azole rings for antiplatelet aggregation activity, a few series of compounds with both hydrazone and an azole (imidazole) ring in their structures were synthesized, and their platelet aggregation inhibitory effects were evaluated. Two of these 1-(arylideneamino)-4-aryl-1H-imidazole-2-amine derivatives, compounds 4 a [(E)-1-(benzylideneamino)-4-phenyl-1H-imidazol-2-amine] and 4 p [(E)-4-phenyl-1-((thiophen-2-ylmethylene)amino)-1H-imidazol-2-amine], exhibited IC50 values similar to that of acetylsalicylic acid against collagen as a platelet aggregation inducer. Structural comparison of the synthesized compounds revealed that those with a para-substituted phenyl ring on the imidazole were among the most active compounds against platelet aggregation induced by arachidonic acid (AA), and the presence of a thiophene ring in these compounds maximized their antiplatelet activity. Put a ring on it: Cyclization of aromatic guanylhydrazones with phenacyl bromide was found to increase the antiplatelet activity against arachidonic acid (AA) and collagen as platelet aggregation inducers. Phenyl ring substituents at imidazole position 4 decreased activity against collagen-induced aggregation, whereas a para-substituted phenyl ring on the imidazole increased activity against AA-induced aggregation. Changes did not affect adenosine diphosphate (ADP)-induced platelet aggregation.
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1,2,4-Triazole-3-thione Compounds as Inhibitors of Dizinc Metallo-β-lactamases ()
Metallo-β-lactamases (MBLs) cause resistance of Gram-negative bacteria to β-lactam antibiotics and are of serious concern, because they can inactivate the last-resort carbapenems and because MBL inhibitors of clinical value are still lacking. We previously identified the original binding mode of 4-amino-2,4-dihydro-5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione (compound IIIA) within the dizinc active site of the L1 MBL. Herein we present the crystallographic structure of a complex of L1 with the corresponding non-amino compound IIIB (1,2-dihydro-5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione). Unexpectedly, the binding mode of IIIB was similar but reverse to that of IIIA. The 3 D structures suggested that the triazole–thione scaffold was suitable to bind to the catalytic site of dizinc metalloenzymes. On the basis of these results, we synthesized 54 analogues of IIIA or IIIB. Nineteen showed IC50 values in the micromolar range toward at least one of five representative MBLs (i.e., L1, VIM-4, VIM-2, NDM-1, and IMP-1). Five of these exhibited a significant inhibition of at least four enzymes, including NDM-1, VIM-2, and IMP-1. Active compounds mainly featured either halogen or bulky bicyclic aryl substituents. Finally, some compounds were also tested on several microbial dinuclear zinc-dependent hydrolases belonging to the MBL-fold superfamily (i.e., endonucleases and glyoxalase II) to explore their activity toward structurally similar but functionally distinct enzymes. Whereas the bacterial tRNases were not inhibited, the best IC50 values toward plasmodial glyoxalase II were in the 10 μm range. Active duty: A series of 1,2,4-triazole-3-thiones were synthesized and evaluated on a panel of metallo-β-lactamases involved in bacterial resistance. Some of them were found to have IC50 values in the micromolar range toward IMP-1, NDM-1, and VIM-2. Structural requirements for activity are discussed. The crystal structure of L1–IIIB is reported, and the activity on other metalloenzymes belonging to the metallo-β-lactamase-fold superfamily is also evaluated.
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Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation ()
Thiazolylaminomannosides (TazMan) are FimH antagonists with anti-adhesive potential against adherent-invasive Escherichia coli (AIEC) promoting gut inflammation in patients with Crohn's disease. The lead TazMan is highly potent in vitro, but shows limited in vivo efficiency, probably due to low pH stability and water solubility. We recently developed a second generation of stable TazMan, but the anti-adhesive effect was lower than the first. Herein we report a co-crystal structure of the lead TazMan in FimH, revealing that the anomeric NH group and the second thiazole moiety provide a positive hydrogen bonding interaction with a trapped water molecule, and π-stacking with Tyr48 of FimH, respectively. Consequently, we developed NeoTazMan homologated with a methylene group for low-pH and mannosidase stability with a conserved NH group and bearing various heterocyclic aglycones. Microencapsulation of the lead NeoTazMan in γ-cyclodextrin dramatically improved water solubility without disrupting the affinity for FimH or the anti-adhesive effect against AIEC isolated from patients with Crohn's disease. TazMania! We developed a new generation of potent anti-adhesives that target pathogenic Escherichia coli strains which promote gut inflammation in Crohn's disease. The neo-thiazolylmannosides were homologated by a methyl group and included in a γ-cyclodextrin carrier to form a water-soluble NeoTazMan@γCD complex with anti-adhesive effects against E. coli.
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Chemoproteomics-Aided Medicinal Chemistry for the Discovery of EPHA2 Inhibitors ()
The receptor tyrosine kinase EPHA2 has gained attention as a therapeutic drug target for cancer and infectious diseases. However, EPHA2 research and EPHA2-based therapies have been hampered by the lack of selective small-molecule inhibitors. Herein we report the synthesis and evaluation of dedicated EPHA2 inhibitors based on the clinical BCR-ABL/SRC inhibitor dasatinib as a lead structure. We designed hybrid structures of dasatinib and the previously known EPHA2 binders CHEMBL249097, PD-173955, and a known EPHB4 inhibitor in order to exploit both the ATP pocket entrance as well as the ribose pocket as binding epitopes in the kinase EPHA2. Medicinal chemistry and inhibitor design were guided by a chemical proteomics approach, allowing early selectivity profiling of the newly synthesized inhibitor candidates. Concomitant protein crystallography of 17 inhibitor co-crystals delivered detailed insight into the atomic interactions that underlie the structure–affinity relationship. Finally, the anti-proliferative effect of the inhibitor candidates was confirmed in the glioblastoma cell line SF-268. In this work, we thus discovered a novel EPHA2 inhibitor candidate that features an improved selectivity profile while maintaining potency against EPHA2 and anticancer activity in SF-268 cells. Chemoproteomics-guided drug discovery: Chemical proteomics was used to guide a drug discovery program toward novel inhibitors that target the receptor tyrosine kinase EPHA2. We discovered compound 4 a as a valuable inhibitor with low nanomolar affinity, an improved selectivity profile, and promising anti-proliferative effects.
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