Structure-Based Design of a Potent and Selective YTHDC1 Ligand.

N6-Adenosine methylation (m6A) is a prevalent post-transcriptional modification of mRNA, with YTHDC1 being the reader protein responsible for recognizing this modification in the cell nucleus. Here, we present a protein structure-based medicinal chemistry campaign that resulted in the YTHDC1 inhibitor 40, which shows an equilibrium dissociation constant (Kd) of 49 nM. The crystal structure of the complex (1.6 Å resolution) validated the design. Compound 40 is selective against the cytoplasmic m6A-RNA readers YTHDF1-3 and YTHDC2 and shows antiproliferative activity against the acute myeloid leukemia (AML) cell lines THP-1, MOLM-13, and NOMO-1. For the series of compounds that culminated into ligand 40, the good correlation between the affinity in the biochemical assay and antiproliferative activity in the THP-1 cell line provides evidence of YTHDC1 target engagement in the cell. The binding to YTHDC1 in the cell is further supported by the cellular thermal shift assay. Thus, ligand 40 is a tool compound for studying the role of YTHDC1 in AML.

Analysis of omarigliptin forced degradation products by ultra-fast liquid chromatography, mass spectrometry, and in vitro toxicity assay.

Omarigliptin (OMG) is an antidiabetic drug indicated for the treatment of type 2 diabetes mellitus. Forced degradation studies are practical experiments to evaluate the stability of drugs and to establish degradation profiles. Herein, we present the investigation of the degradation products (DPs) of OMG formed under various stress conditions. OMG was subjected to hydrolytic (alkaline and acidic), oxidative, thermal, and photolytic forced degradation. A stability-indicating ultra-fast liquid chromatography method was applied to separate and quantify OMG and its DPs. Five DPs were adequately separated and detected in less than 6 min, while other published methods detected four DPs. MS was applied to identify and obtain information on the structural elucidation of the DPs. Three m/z DPs confirmed previously published research, and two novel DPs were described in this paper. The toxicity of OMG and its DPs were investigated for the first time using in vitro cytotoxicity assays, and the sample under oxidative conditions presented significant cytotoxicity. Based on the results from forced degradation studies, OMG was found to be labile to hydrolysis, oxidation, photolytic, and thermal stress conditions. The results of this study contribute to the quality control and stability profile of OMG.

Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases.

Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3ß, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.

Design, synthesis, and molecular docking study of novel cinnoline derivatives as potential inhibitors of tubulin polymerization.

The preparation of a novel 4-methylbenzo[h] cinnolines entity via a three-step synthetic protocol is described. Cyclization of the naphthylamidrazones, in the presence of polyphosphoric acid (PPA), furnishes the respective target benzo[h]cinnolines directly. This one-pot synthesis involves intramolecular Friedel-Crafts acylation followed by instant elimination under heating conditions. It is noteworthy that the yield of the product from this step decreases dramatically if the heating is extended beyond 3 h. The target novel cinnolone derivatives were identified by mass spectrometry and their structures elucidated by spectroscopic techniques. Subsequently, molecular docking was performed to shed light on the putative binding mode of the newly synthesized cinnolines. The docking results indicate that these derivatives are potential inhibitors of tubulin polymerization and the best interaction was achieved with a computational ki = 0.5 nM and posed correctly over the lexibulin.

Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway.

Chemoproteomic profiling of cysteines has emerged as a powerful method for screening the proteome-wide targets of cysteine-reactive fragments, drugs, and natural products. Herein, we report the development and an in-depth evaluation of a tetrafluoroalkyl benziodoxole (TFBX) as a cysteine-selective chemoproteomic probe. We show that this probe features numerous key improvements compared to the traditionally used cysteine-reactive probes, including a superior target occupancy, faster labeling kinetics, and broader proteomic coverage, thus enabling profiling of cysteines directly in live cells. In addition, the fluorine "signature" of probe 7 constitutes an additional advantage resulting in a more confident adduct-amino acid site assignment in mass-spectrometry-based identification workflows. We demonstrate the utility of our new probe for proteome-wide target profiling by identifying the cellular targets of (-)-myrocin G, an antiproliferative fungal natural product with a to-date unknown mechanism of action. We show that this natural product and a simplified analogue target the X-ray repair cross-complementing protein 5 (XRCC5), an ATP-dependent DNA helicase that primes DNA repair machinery for nonhomologous end joining (NHEJ) upon DNA double-strand breaks, making them the first reported inhibitors of this biomedically highly important protein. We further demonstrate that myrocins disrupt the interaction of XRCC5 with DNA leading to sensitization of cancer cells to the chemotherapeutic agent etoposide as well as UV-light-induced DNA damage. Altogether, our next-generation cysteine-reactive probe enables broader and deeper profiling of the cysteinome, rendering it a highly attractive tool for elucidation of targets of electrophilic small molecules.

Discovery of cinnoline derivatives as potent PI3K inhibitors with antiproliferative activity.

Cinnoline is a potential pharmacophore which has rarely been reported for uses as PI3K inhibitors. In this study, a series of cinnoline derivatives were developed as PI3K inhibitors and evaluated for enzymatic and cellular activities. Most compounds displayed nanomolar inhibitory activities against PI3Ks, among which 25 displayed high LLE and micromolar inhibitory potency against three human tumor cell lines (IC50 = 0.264 µM, 2.04 µM, 1.14 µM).

Rh(iii)-Catalysed synthesis of cinnolinium and fluoranthenium salts using C-H activation/annulation reactions: organelle specific mitochondrial staining applications.

The construction of a novel class of indazolo[2,1-a]cinnolin-7-ium and diazabenzofluoranthenium salts was developed by using Rh(iii)-catalyzed C-H activation/annulation reactions with 2-phenyl-2H-indazole, and internal alkynes, which resulted in structurally important polycyclic heteroaromatic compounds (PHAs). This reaction uses mild reaction conditions and has a high efficiency, low catalyst loading, and wide substrate scope. The overall catalytic process involves C-H activation followed by C-C/C-N bond formation. Furthermore, the synthesised cinnolinium/fluoranthenium salts exhibit potential fluorescence properties and 5i was targeted in particular for specific mitochondrial staining in order to investigate cancer cell lines.

Generalized-ensemble method study: A helix-mimetic compound inhibits protein-protein interaction by long-range and short-range intermolecular interactions.

A heterocyclic compound mS-11 is a helix-mimetic designed to inhibit binding of an intrinsic disordered protein neural restrictive silence factor/repressor element 1 silencing factor (NRSF/REST) to a receptor protein mSin3B. We apply a generalized ensemble method, multi-dimensional virtual-system coupled molecular dynamics developed by ourselves recently, to a system consisting of mS-11 and mSin3B, and obtain a thermally equilibrated distribution, which is comprised of the bound and unbound states extensively. The lowest free-energy position of mS-11 coincides with the NRSF/REST position in the experimentally-determined NRSF/REST-mSin3B complex. Importantly, the molecular orientation of mS-11 is ordering in a wide region around mSin3B. The resultant binding scenario is: When mS-11 is distant from the binding site of mSin3B, mS-11 descends the free-energy slope toward the binding site maintaining the molecular orientation to be advantageous for binding. Then, finally a long and flexible hydrophobic sidechain of mS-11 fits into the binding site, which is the lowest-free-energy complex structure inhibiting NRSF/REST binding to mSin3B.

Dissipation, adsorption-desorption, and potential transformation products of pinoxaden in soil.

This study established and validated a simple and sensitive analytical approach for determining pinoxaden residues in soil. The dissipation and adsorption-desorption of pinoxaden in four kinds of Chinese soil were comprehensively investigated for the first time, and the possible metabolic products and pathways were identified. The developed method was successfully applied in dissipation and adsorption-desorption trials. Several influential factors, including temperature, organic matter, and moisture content, affected the dissipation rate of pinoxaden in soil. During the dissipation process, 1 hydrolytic intermediate and 13 possible transformation products were identified, and predicted metabolic pathways were composed of electron rearrangement, oxidation, cyclization, carboxylation, and so on. Both the adsorption and desorption isotherms of pinoxaden in four kinds of Chinese soil followed the Freundlich equation, and the Freundlich Kf values were positively correlated with the soil cation exchange capacity. According to the calculated Gibbs free energies, the adsorption of pinoxaden was an endothermic reaction and mainly a physical process. These results could provide some useful data for the determination of pinoxaden in other matrices and the evaluation of the environmental fate of pinoxaden in soil and other ecosystems.

Discovery of a σ1 receptor antagonist by combination of unbiased cell painting and thermal proteome profiling.

Phenotypic screening for bioactive small molecules is typically combined with affinity-based chemical proteomics to uncover the respective molecular targets. However, such assays and the explored bioactivity are biased toward the monitored phenotype, and target identification often requires chemical derivatization of the hit compound. In contrast, unbiased cellular profiling approaches record hundreds of parameters upon compound perturbation to map bioactivity in a broader biological context and may link a profile to the molecular target or mode of action. Herein we report the discovery of the diaminopyrimidine DP68 as a Sigma 1 (σ1) receptor antagonist by combining morphological profiling using the Cell Painting assay and thermal proteome profiling. Our results highlight that integration of complementary profiling approaches may enable both detection of bioactivity and target identification for small molecules.

Investigating the effects of the core nitrogen atom configuration on the thermodynamic solubility of 6,5-bicyclic heterocycles.

Physicochemical properties, such as solubility, are important when prioritising compounds for progression on a drug discovery project. There is limited literature around the systematic effects of core changes on thermodynamic solubility. This work details the synthesis of nitrogen containing 6,5-bicyclic heterocyclic cores which are common scaffolds in medicinal chemistry and the analysis of their physicochemical properties, particularly, thermodynamic solubility. Crystalline solids were obtained where possible to enable a robust comparison of the thermodynamic solubility. Other parameters such as pKa, melting point and lipophilicity were also measured to determine the key factors affecting the observed solubility.

The impact of radiochemistry in drug projects: The use of C-14 label in the AZD8529, AZD7325, and AZD6280 projects.

Understanding the metabolic transformations of a potential drug molecule is important to understanding the safety profile of a drug candidate. Liquid chromatography-mass spectrometry is a standard method for detecting metabolites in the drug discovery stage, but this can lead to an incomplete understanding of the molecule's metabolism. In this manuscript, we highlight the role radiolabeling played in determining the metabolism and in quantifying the metabolites of AZD8529, AZD7325, and AZD6280. A quantitative whole-body autoradiography study can detect covalent adducts in vivo as was the case with AZD5248 in which the compound was bound to the aorta. Ultimately another compound free of aortic binding was developed, AZD7986.

The status of isocyanide-based multi-component reactions in Iran (2010-2018).

Isocyanides as key intermediates and magic reactants have been widely applied in organic reactions for direct access to a broad spectrum of remarkable organic compounds. Although the history of these magical compounds dates back more than 100 years, it still has been drawing widespread attention of chemists who confirmed their versatility and effectiveness. Because of their wide spectrum of pharmacological, industrial and synthetic applications, many reactions with the utilization of isocyanides are reported in the literature. In this context, Iranian scientist played a significant role in the growth of isocyanides chemistry. The present review article covers literature from the period starting from 2010 onward and encompasses new synthetic routes and organic transformation involving isocyanides by Iranian researchers. During this period, a diverse range of isocyanide-based multi-component reactions (I-MCRs) has been reported such as a new modification of Ugi, post-Ugi, Passerini and Groebke-Blackburn-Bienayme condensation reactions, isocyanide-based [1 + 4] cycloaddition reactions, isocyanide-acetylene-based MCRs, isocyanide and Meldrum's acid-based MCRs, several unexpected reactions besides green mediums and novel catalytic systems for the synthesis of diverse kinds of pharmaceutically and industrially remarkable heterocyclic and linear organic compounds. This review also emphasizes the neoteric applications of I-MCR for the synthesis of valuable peptide and pseudopeptide scaffolds, enzyme immobilization and functionalization of materials with tailorable properties that can play important roles in the plethora of applications.

Solid-Supported Amplification of Aggregation Emission: A Tetraphenylethylene-Cucurbit[6]uril@Hydroxyapatite-Based Supramolecular Sensing Assembly for the Detection of Spermine and Spermidine in Human Urine and Blood.

The development of sensitive and selective tools for the detection and quantification of biomarkers is important in the diagnosis and treatment of clinical diseases. Spermine (SP) and spermidine (SPD) act as biomarkers for early-stage diagnosis of cancer in humans as their increased levels in urine are indicative of abnormal biological processes associated with this fatal disease. In this study, we introduced a strategy for solid-supported amplification of the effective aggregation-induced-emission (AIE) effect of a water-soluble tetraphenylethylene (TPE)-based probe in developing a supramolecular sensing platform for the rapid, sensitive, and selective detection of SP and SPD in water. The nonemissive TPE derivative (TPEHP) forms a less emissive conjugate with hydroxyl cucurbit[6]uril (CB[6]OH) in water, which undergoes several-fold enhancement of effective emission upon electrostatic interaction with the solid surface of hydroxyapatite nanoparticles (HAp NPs), dispersed in the aqueous media. The corresponding three-component supramolecular assembly disrupts by the intrusion of SP and SPD in the CB[6] portal because of the stronger binding ability with CB[6], resulting in a turn-off fluorescence sensor for SP and SPD with enhanced sensitivity. The assembly-disassembly-based sensing mechanism was thoroughly demonstrated by carrying out isothermal titration calorimetry (ITC), spectroscopic, and microscopic experiments. The sensing system showed low limits of detection (LODs) of 1.4 × 10-8 and 3.6 × 10-8 M for SP and SPD, respectively, which are well below the required range for the early diagnosis of cancer. Besides, a good linear relationship was obtained for both SP and SPD. Nominal interference from various metal ions, anions, common chemicals, amino acids, and other biogenic amines makes this sensing platform suitable for the real-time, low-level measurement of spermine (and spermidine) in human urinary and blood samples.

Importance of Fluorine in Benzazole Compounds.

Fluorine-containing heterocycles continue to receive considerable attention due to their unique properties. In medicinal chemistry, the incorporation of fluorine in small molecules imparts a significant enhancement their biological activities compared to non-fluorinated molecules. In this short review, we will highlight the importance of incorporating fluorine as a basic appendage in benzothiazole and benzimidazole skeletons. The chemistry and pharmacological activities of heterocycles containing fluorine during the past years are compiled and discussed.

Radioiodination and in vivo assessment of the potential of newly synthesized pyrrolizine-5-carboxamides derivative in tumor model.

Recently, pyrrolizine derivatives have been reported to possess numerous anticancer activities. In a previous study, (EZ)-6-((4-chlorobenzylidene)-amino)-7-cyano-N-(p-tolyl)-2,3-dihydro-1H-pyrrolizine carboxamide (EZPCA) compound was synthesized and the cytotoxic activity of EZPCA toward COX-2 enzyme (overexpressed in cancer cells) was reported. In order to assess the suitability of this compound as a promising pilot structure for in vivo applications, EZPCA was radiolabeled with radioiodine-131 (131I) and various factors affecting radiolabeling process were studied. Quality control studies of [131I]iodo-EZPCA were performed using paper chromatography and HPLC was used as a co-chromatographic technique for confirming the radiochemical yield. Biodistribution studies of [131I]iodo-EZPCA were undertaken in normal and tumor bearing mice. The radiochemical yield percentage of [131I]iodo-EZPCA was 94.20 ± 0.12%. The biodistribution results showed evident tumor uptake of [131I]iodo-EZPCA with promising target/non-target (T/NT) ratios. As a conclusion, these data suggest that [131I]iodo-EZPCA had high binding efficiency, high tumor uptake and sufficient stability to be used be used in diagnostic studies.

Enantioselective [3+2] annulation of isatin-derived MBH-carbonates and 3-nitroindoles enabled by a bifunctional DMAP-thiourea.

A highly enantioselective [3+2] annulation of isatin-derived Morita-Baylis-Hillman (MBH) carbonates and 3-nitroindoles was enabled by a chiral DMAP-thiourea bifunctional catalyst, affording the corresponding polycyclic spirooxindoles bearing three consecutive stereocenters with good to excellent yields and enantioselectivities. Transformations of the annulation product were subsequently elaborated and the preliminary biological assays demonstrated that these artificial spirooxindoles potentially inhibited pancreatic lipase in a dose-dependent manner.

Excretion, Mass Balance, and Metabolism of [14C]LY3202626 in Humans: An Interplay of Microbial Reduction, Reabsorption, and Aldehyde Oxidase Oxidation That Leads to an Extended Excretion Profile.

The mass balance, excretion, and metabolism of LY3202626 were determined in healthy subjects after oral administration of a single dose of 10 mg of (approximately 100 µCi) [14C]LY3202626. Excretion of radioactivity was slow and incomplete, with approximately 75% of the dose recovered after 504 hours of sample collection. The mean total recovery of the radioactive dose was 31% and 44% in the feces and urine, respectively. Because of low plasma total radioactivity, plasma metabolite profiling was conducted by accelerator mass spectrometry. Metabolism of LY3202626 occurred primarily via O-demethylation (M2) and amide hydrolysis (M1, M3, M4, and M5). Overall, parent drug, M1, M2, and M4 were the largest circulating components in plasma, and M2 and M4 were the predominant excretory metabolites. The slow elimination of total radioactivity was proposed to result from an unusual enterohepatic recirculation pathway involving microbial reduction of metabolite M2 to M16 in the gut and reabsorption of M16, followed by hepatic oxidation of M16 back to M2. Supporting in vitro experiments showed that M2 is reduced to M16 anaerobically in fecal homogenate and that M16 is oxidized in the liver by aldehyde oxidase to M2. LY3202626 also showed a potential to form a reactive sulfenic acid intermediate. A portion of plasma radioactivity was unextractable and presumably bound covalently to plasma proteins. In vitro incubation of LY3202626 in human liver microsomes in the presence of NADPH with dimedone as a trapping agent implicated the formation of the proposed sulfenic acid intermediate. SIGNIFICANCE STATEMENT: The excretion of radioactivity in humans after oral administration of a single dose of 10 mg of [14C]LY3202626 was very slow. The results from in vitro experiments suggested that an interplay between microbial reduction, reabsorption, and aldehyde oxidase oxidation (M2 → M16 → M2) could be a reason for extended radioactivity excretion profile. In vitro metabolism also showed that LY3202626 has the potential to form a reactive sulfenic acid intermediate that could potentially covalently bind to plasma protein and result in the observed unextractable radioactivity from plasma.

Design, Synthesis, and Evaluation of a Series of Novel Super Long-Acting DPP-4 Inhibitors for the Treatment of Type 2 Diabetes.

In the present work, a novel series of trifluoromethyl-substituted tetrahydropyran derivatives were rationally designed and synthesized as potent DPP-4 inhibitors with significantly improved duration time of action over current commercially available DPP-4 inhibitors. The incorporation of the trifluoromethyl group on the 6-position of the tetrahydropyran ring of omarigliptin with the configuration of (2R,3S,5R,6S) not only significantly improves the overall pharmacokinetic profiles in mice but also maintains comparable DPP-4 inhibition activities. Further preclinical development of compound 2 exhibited its extraordinary efficacy in vivo and good safety profile. Clinical studies of compound 2 (Haisco HSK7653) are now ongoing in China, which revealed that inhibitor 2 could serve as an efficient candidate with a once-biweekly therapeutic regimen.

Design, synthesis and biological evaluation of novel dual-acting modulators targeting both estrogen receptor α (ERα) and lysine-specific demethylase 1 (LSD1) for treatment of breast cancer.

Breast cancer is a multi-factor disease, thus more and more drug combination therapies are applied in the treatment. However, there are undeniable disadvantages in drug combination therapy. Therefore, the development of new dual-targeting drugs has become a new strategy. In this study, we have developed a series of dual-acting agents targeting both estrogen receptor α (ERα) and histone demethylase based on a privileged OBHS pharmacophore scaffold developed previously by our laboratory. These novel OBHS-LSD1i conjugates showed excellent ERα binding affinity and selectivity, and exhibited potent inhibitory activity against lysine specific demethylase 1 (LSD1). Several conjugates showed higher antiproliferative efficacy in MCF-7 breast cancer cell line compared to 4-hydroxytamoxifen in vitro. Among them, the best compound 11g displayed potent inhibitory activity against LSD1 and MCF-7 cells with IC50 values of 1.55 µM and 8.79 µM, respectively. Flow cytometry analysis of apoptosis of 11g suggested that the effect of this type compounds on MCF-7 cells is partly caused by inducing apoptosis. Moreover, the molecular docking of 11g with ERα and the active site of LSD1/CoREST complex provides practical way for understanding the dual mechanism actions of this kind of compounds with the targets. As such, these compounds have shown potential to become promising leads for the development of highly efficient dual-acting modulators for breast cancer therapies.