Promotion of Water as Solvent in Amination of 4-Chloropyrrolopyrimidines and Related Heterocycles under Acidic Conditions.

A switch of reaction medium from organic solvents to water can improve the safety and lower the cost of production processes. Hydrochloric acid-promoted amination of fused pyrimidines has been studied using 4-chloro-7H-pyrrolo[2,3-d]pyrimidine and aniline as model compounds. Higher rate was observed in water than in four alcoholic solvents and DMF. An important aspect is that the amount of acid should be kept low to minimize the competing solvolysis. The substrate scope for the amination in water was evaluated by reacting 4-chloro-7H-pyrrolo[2,3-d]pyrimidine with 20 aniline derivatives with variance in steric and electronic properties. Preparative useful reactions were seen for 14 of the 20 derivatives. Unsuited nucleophiles are ortho-substituted anilines with a pKa below 1. Amination of the corresponding quinazoline, thienopyrimidine, and purine also proceeded well in water. Highly lipophilic and crystalline compounds are more efficiently aminated in 2-propanol. Aliphatic and benzylic amines react poorly under acidic conditions, but these aminations can be done in water without acid.

Pyrrolopyrimidine based CSF1R inhibitors: Attempted departure from Flatland.

The colony-stimulating factor 1 receptor (CSF1R) is an attractive target for inflammation disorders and cancers. Based on a series of pyrrolo[2,3-d]pyrimidine containing two carbo-aromatic rings, we have searched for new CSF1R inhibitors having a higher fraction of sp3-atoms. The phenyl unit in the 4-amino group could efficiently be replaced by tetrahydropyran (THP) retaining inhibitor potency. Exchanging the 6-aryl group with cyclohex-2-ene units also resulted in highly potent compounds, while fully saturated ring systems at C-6 led to a loss of activity. The structure-activity relationship study evaluating THP containing pyrrolo[2,3-d]pyrimidine derivates identified several highly active inhibitors by enzymatic studies. A comparison of 11 pairs of THP and aromatic compounds showed that inhibitors containing THP had clear benefits in terms of enzymatic potency, solubility, and cell toxicity. Guided by cellular experiments in Ba/F3 cells, five CSF1R inhibitors were further profiled in ADME assays, indicating the para-aniline derivative 16t as the most attractive compound for further development.

Activation of multiple stress responses in Staphylococcus aureus substantially lowers the minimal inhibitory concentration when combining two novel antibiotic drug candidates.

The past few decades have been plagued by an increasing number of infections caused by antibiotic resistant bacteria. To mitigate the rise in untreatable infections, we need new antibiotics with novel targets and drug combinations that reduce resistance development. The novel ß-clamp targeting antimicrobial peptide BTP-001 was recently shown to have a strong additive effect in combination with the halogenated pyrrolopyrimidine JK-274. In this study, the molecular basis for this effect was examined by a comprehensive proteomic and metabolomic study of the individual and combined effects on Staphylococcus aureus. We found that JK-274 reduced activation of several TCA cycle enzymes, likely via increasing the cellular nitric oxide stress, and BTP-001 induced oxidative stress in addition to inhibiting replication, translation, and DNA repair processes. Analysis indicated that several proteins linked to stress were only activated in the combination and not in the single treatments. These results suggest that the strong additive effect is due to the activation of multiple stress responses that can only be triggered by the combined effect of the individual mechanisms. Importantly, the combination dose required to eradicate S. aureus was well tolerated and did not affect cell viability of immortalized human keratinocyte cells, suggesting a species-specific response. Our findings demonstrate the potential of JK-274 and BTP-001 as antibiotic drug candidates and warrant further studies.

A highly selective purine-based inhibitor of CSF1R potently inhibits osteoclast differentiation.

The colony-stimulating factor 1 receptor (CSF1R) plays an important role in the regulation of many inflammatory processes, and overexpression of the kinase is implicated in several disease states. Identifying selective, small-molecule inhibitors of CSF1R may be a crucial step toward treating these disorders. Through modelling, synthesis, and a systematic structure-activity relationship study, we have identified a number of potent and highly selective purine-based inhibitors of CSF1R. The optimized 6,8-disubstituted antagonist, compound 9, has enzymatic IC50 of 0.2 nM, and displays a strong affinity toward the autoinhibited form of CSF1R, contrasting that of other previously reported inhibitors. As a result of its binding mode, the inhibitor shows excellent selectivity (Selectivity score: 0.06), evidenced by profiling towards a panel of 468 kinases. In cell-based assays, this inhibitor shows dose-dependent blockade of CSF1-mediated downstream signalling in murine bone marrow-derived macrophages (IC50 = 106 nM) as well as disruption of osteoclast differentiation at nanomolar levels. In vivo experiments, however, indicate that improve metabolic stability is needed in order to further progress this compound class.

Directed Lithiation of Protected 4-Chloropyrrolopyrimidine: Addition to Aldehydes and Ketones Aided by Bis(2-dimethylaminoethyl)ether.

Pyrrolopyrimidines are important scaffolds for the preparation of bioactive molecules. Therefore, developing efficient and flexible ways for selective functionalization of the pyrrolopyrimidine skeleton is of interest. We have investigated lithiation-addition at C-6 of protected 4-chloro-7H-pyrrolo [2,3-d]pyrimidine as a route to new building blocks for medicinal chemistry. It was found that bis(2-dimethylaminoethyl) ether as an additive increased the yield in the additional reaction with benzaldehyde. Deuterium oxide quench experiments showed that this additive offered both a higher degree of lithiation and increased stability of the lithiated intermediate. The substrate scope of the protocol was investigated with 16 aldehydes and ketones, revealing the method to be excellently suited for reaction with aldehydes, cyclohexanone derivatives and 2,2,2-trifluoroacetophenone, while being less efficient for acetophenones. Yields in the range of 46-93% were obtained.

Synthetic Efforts to Investigate the Effect of Planarizing the Triarylamine Geometry in Dyes for Dye-Sensitized Solar Cells.

The geometry of a dye for dye-sensitized solar cells (DSSCs) has a major impact on its optical and electronic properties. The dye structure also dictates the packing properties and how well the dye insulates the metal-oxide surface from oxidants in the electrolyte. The aim of this work is to investigate the effect of planarizing the geometry of the common triarylamine donor, frequently used in dyes for DSSC. Five novel dyes were designed and prepared; two employ conventional triarylamine donors with thiophene and furan π-spacers, two dyes have had their donors planarized through one sulfur bridge (making two distinct phenothiazine motifs), and the final dye has been planarized by forming a double phenoxazine. The synthesis of these model dyes proved to be quite challenging, and each required specially designed total syntheses. We demonstrate that the planarization of the triarylamine donor can have different effects. When planarization was achieved by a 3,7-phenothiazine and double phenoxazine structures, improved absorption properties were noted, and a panchromatic absorption was achieved by the latter. However, an incorrect linking of donor and acceptor moieties has the opposite effect. Further, electrochemical impedance spectroscopy revealed clear differences in charge recombination depending on the structure of the dye. A drawback of planarized dyes in relation to DSSC is their low oxidation potentials. The best photovoltaic performance was achieved by 3,7-phenothazine with furan as a π-spacer, which produces a power conversion efficiency of 5.2% (J sc = 8.8 mA cm-2, V oc = 838 mV, FF = 0.70).

Halogenated Pyrrolopyrimidines with Low MIC on Staphylococcus aureus and Synergistic Effects with an Antimicrobial Peptide.

Currently, there is a world-wide rise in antibiotic resistance causing burdens to individuals and public healthcare systems. At the same time drug development is lagging behind. Therefore, finding new ways of treating bacterial infections either by identifying new agents or combinations of drugs is of utmost importance. Additionally, if combination therapy is based on agents with different modes of action, resistance is less likely to develop. The synthesis of 21 fused pyrimidines and a structure-activity relationship study identified two 6-aryl-7H-pyrrolo [2,3-d] pyrimidin-4-amines with potent activity towards Staphylococcus aureus. The MIC-value was found to be highly dependent on a bromo or iodo substitution in the 4-benzylamine group and a hydroxyl in the meta or para position of the 6-aryl unit. The most active bromo and iodo derivatives had MIC of 8 mg/L. Interestingly, the most potent compounds experienced a four-fold lower MIC-value when they were combined with the antimicrobial peptide betatide giving MIC of 1-2 mg/L. The front runner bromo derivative also has a low activity towards 50 human kinases, including thymidylate monophosphate kinase, a putative antibacterial target.

Adamantyl Side Chains as Anti-Aggregating Moieties in Dyes for Dye-Sensitized Solar Cells.

Designing and evaluating novel dye concepts is crucial for the development of the field of dye-sensitized solar cells (DSSCs). In our recent report, the novel concept of tethering the anti-aggregation additive chenodeoxycholic acid (CDCA) to dyes for DSSC was introduced. Based on the performance improvements seen for this modification, the aim of this study is to see if a simplified anti-aggregation unit could achieve similar results. The following study reports the synthesis and photovoltaic characterization of two novel dyes decorated with the steric ethyladamantyl moiety on the π-spacer, and on the triarylamine donor. This modification is demonstrated to be successful in increasing the photovoltages in devices employing copper-based electrolytes compared to the non-modified reference dye. The best photovoltaic performance is achieved by a device prepared with the adamantyl decorated donor dye and CDCA, this device achieves a power conversion efficiency of 6.1 % (Short-circuit current=8.3 mA cm-2 , Open-circuit voltage=1054 mV, Fill factor=0.69). The improved photovoltaic performance seen for the adamantyl decorated donor demonstrate the potential of ethyladamantyl side chains as a tool to ensure surface protection of TiO2 .

Synthesis of Novel 3,6-Dithienyl Diketopyrrolopyrrole Dyes by Direct C‒H Arylation.

Direct C‒H arylation coupling is potentially a more economical and sustainable process than conventional cross-coupling. However, this method has found limited application in the synthesis of organic dyes for dye‒sensitized solar cells. Although direct C‒H arylation is not an universal solution to any cross-coupling reactions, it efficiently complements conventional sp2‒sp2 bond formation and can provide shorter and more efficient routes to diketopyrrolopyrrole dyes. Here, we have applied palladium catalyzed direct C‒H arylation in the synthesis of five new 3,6-dithienyl diketopyrrolopyrrole dyes. All prepared sensitizers display broad absorption from 350 nm up to 800 nm with high molar extinction coefficients. The dye‒sensitized solar cells based on these dyes exhibit a power conversion efficiency in the range of 2.9 to 3.4%.

Effect of Auxiliary Donors on 3,8-Phenothiazine Dyes for Dye-Sensitized Solar Cells.

Phenothiazines are one of the more common dye scaffolds for dye-sensitized solar cells. However, these sensitizers are exclusively based on a 3,7-substitution pattern. Herein, we have synthesized and characterized novel 3,8-substituted phenothiazine dyes in order to evaluate the effect of auxiliary donor groups on the performance of this new dye class. The power conversion efficiency increased by 7%-10% upon insertion of an auxiliary donor in position 8 of the phenothiazine, but the structure of the auxiliary donor (phenyl, naphthyl, pyrene) had a low impact when electrodes were stained with chenodeoxycholic acid (CDCA) additive. In the absence of CDCA, the highest power conversion efficiency was seen for the phenyl-based sensitizer attributed to a higher quality dye-monolayer. By comparing the novel dyes to their previously reported 3,7- analogues, only subtle differences were seen in photophysical, electrochemical, and performance measurements. The most notable difference between the two geometries is a lowering of the oxidation potentials of the 3,8-dyes by 40-50 mV compared to the 3,7-analogues. The best auxiliary donor for the 3,8-phenothiazine dyes was found to be pyrenyl, with the best device delivering a power conversion efficiency of 6.23% (99 mW cm-2, 10 eq. CDCA, JSC = 10.20 mA cm-2, VOC = 791 mV, and FF = 0.765).

Potent and selective EGFR inhibitors based on 5-aryl-7H-pyrrolopyrimidin-4-amines.

The epidermal growth factor receptor represents an important target in cancer therapy, and low molecular weight inhibitors based on quinazolines have reached the marked. Herein we report on a new scaffold, 5-aryl-7H-pyrrolo[2,3-d]pyrimidin-4-amines, and show that when employing (S)-phenylglycinol as C-4 substituent, potent inhibitors can be made. The two most active inhibitors have suitable druglike properties, were equipotent with Erlotinib in Ba/F3 cell studies, and showed lower cross reactivity than Erlotinib in a panel of 50 kinases.

Identification of fused pyrimidines as interleukin 17 secretion inhibitors.

Inhibiting the interleukin 17 pathway is of interest in a number of autoimmune diseases. Herein, 42 fused pyrimidines have been evaluated as interleukin 17 secretion inhibitors using a phenotypic assay with peripheral blood mononuclear cells. 7H-Pyrrolo [2,3-d]pyrimidin-4-amines having aryl groups at C-5 or C-6 were found more active than the corresponding thieno- and furopyrimidines. Low cytotoxicity was seen for the most active inhibitors. However, the pyrrolopyrimidines also inhibit interleukin 5 secretion, suggesting that selective interleukin 17 inhibitors should rather be based on furopyrimidines. Profiling towards a panel of 51 kinases and assays towards the retinoic acid receptor-related orphan receptor gamma were performed in order to identify the compounds mode of action.

Is literature data useful for identifying enzyme catalysts for new substrates? A case study on reduction of 1-aryl-2-alkanoates.

The use of literature data to identify catalysts for a novel transformation is a commonly used approach. Herein, we have evaluated if this is a viable strategy in enzyme catalysis, using asymmetric reduction of 1-aryl-2-alkanoates asa model system. The study, which includes data from 24 ketone substrates and 108 enzymes, clearly identifies pitfalls with this approach, but anyhow shows that literature data is highly useful for identification of enantioselective catalysts. By combining data for selectivity and rate useful catalyst for converting different substrates to their corresponding (R)- and (S)-enantiomers are highlighted.

Solvent Effects on Optical Rotation: On the Balance between Hydrogen Bonding and Shifts in Dihedral Angles.

Optical rotations of several conformers of four fluorinated molecules containing the 1-naphthalene or 4-(benzyloxy)phenyl group at the stereocenter have been calculated both in the gas phase and in an aqueous environment. For the compounds containing the 4-(benzyloxy)phenyl group, solvent effects on the optical rotations have also been investigated in chloroform as solvent. Optical rotations have been obtained by time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the aug-cc-pVDZ basis set at λ = 589 nm. Implicit and explicit solvent effects were investigated through the polarizable continuum model (PCM) and a microsolvation approach in conjunction with PCM, respectively. In the latter model, solvent molecules are considered as an explicit solvent and their positions are obtained by geometry optimizations for different conformers of the chiral molecule. For molecules containing the 1-naphthalene group, this model gives the same optical rotation signs for all conformers as compared to both gas phase and PCM results and reduces absolute deviations between calculations and experiment. Also, the microsolvation model reproduces the sign of the experimental optical rotations for the molecules containing the 4-(benzyloxy)phenyl group using both water and chloroform as solvent. In a microsolvation model, however, the water and chloroform solvent molecules have similar hydrogen bonds but different effects on the conformation and thereby on the optical rotation since one dihedral angle, having a large effect on the optical rotation, is strongly sensitive to hydrogen bonding to water but not to chloroform. Our investigations demonstrate that a microsolvation approach in conjunction with PCM predicts optical rotations in reasonable agreements with experiments for both sign and magnitude.

Changes in cellular signaling proteins in extracts from A549, H460, and U2OS cells treated with cisplatin or docetaxel.

Cell extracts from A549, H460, and U2OS human cancer cell lines treated with cisplatin and docetaxel were analyzed by mass spectrometry (MS) proteomic analysis. The extracts were enriched for cellular signaling proteins using a mix of three different immobilized kinase inhibitors (Purvalanol B, Bisindolylmaleimide X, and (R)-3-(4-((1-Phenylethyl)amino)thieno[2,3-d]pyrimidin-6-yl)benzoic acid (SB6-060-05)) on sepharose bead columns. Raw data is deposited in the PRIDE database [1], project number PXD005286. Data presented () shows changes relative to untreated control for each biological replicate for the three cell lines.

On-column trypsinization allows for re-use of matrix in modified multiplexed inhibitor beads assay.

The Multiplexed Inhibitor Bead (MIB) assay is a previously published quantitative proteomic MS-based approach to study cellular kinomes. A rather extensive procedure, need for multiple custom-made kinase inhibitors and an inability to re-use the MIB-columns, has limited its applicability. Here we present a modified MIB assay in which elution of bound proteins is facilitated by on-column trypsinization. We tested the modified MIB assay by analyzing extract from three human cancer cell lines treated with the cytotoxic drugs cisplatin or docetaxel. Using only three immobilized kinase inhibitors, we were able to detect about 6000 proteins, including ∼40% of the kinome, as well as other signaling, metabolic and structural proteins. The method is reproducible and the MIB-columns are re-usable without loss of performance. This makes the MIB assay a simple, affordable, and rapid assay for monitoring changes in cellular signaling.

Balancing potency, metabolic stability and permeability in pyrrolopyrimidine-based EGFR inhibitors.

The present study describes our continuous effort to develop epidermal growth factor receptor (EGFR) inhibitors based on the 6-aryl-pyrrolo[2,3-d]pyrimidin-4-amine scaffold. The activity-ADME space has been evaluated by synthesizing 43 new structures, including four variations of the 4-amino group and 34 different substitution patterns in the 6-aryl moiety. Most of the new pyrrolopyrimidines were highly active, with twelve analogues possessing lower IC50 values than the commercial drug Erlotinib in enzymatic assays. Ten EGFR inhibitors were also profiled in cell studies using the Ba/F3-EGFRL858R reporter cells, and all revealed nanomolar activity. However, some of the privileged structures in terms of potency had ADME short-comings: compounds containing amides, sulfonamides, amine and hydroxymethyl substituents in the 6-aryl group had low permeability and high efflux, derivatives having (R)-3-amino-3-phenylpropan-1-ol at C-4 induced hERG inhibition properties, and metabolic lability was seen for compounds having (S)-2-methoxy-1-phenylethan-1-amine at C-4. Based on a trade-off between enzymatic activity, cellular potency and ADME properties, (S)-2-phenyl-2-((6-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino)ethan-1-ol appeared as the most promising drug candidate. Cellular studies indicate this compound to have therapeutic use in EGFR driven diseases.

Optical Rotation Calculations for Fluorinated Alcohols, Amines, Amides, and Esters.

We have calculated the optical rotation at λ = 589 nm for 45 fluorinated alcohols, amines, amides, and esters using both time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional and the second-order approximate coupled-cluster singles and doubles (CC2) method, where the aug-cc-pVDZ basis set was adopted in both methods. Comparison of CAM-B3LYP and CC2 results to experiments illustrates that both methods are able to reproduce the experimental optical rotation results for both sign and magnitude. Several conformers for molecules containing the benzyloxy and naphthalene groups needed to be considered to obtain consistent signs with experiments, and these conformers are discussed in detail. We have also used a two-point inverse power extrapolation of the basis set to investigate the optical rotation in the basis set limit at the CC2 level, however, we only found small differences compared to the aug-cc-pVTZ results. Our results demonstrate that the least computationally expensive method investigated here, the CAM-B3LYP functional with the aug-cc-pVDZ basis set, is a reliable method to predict the optical rotation for large molecules and thereby the absolute configuration of chiral molecules.

Chiral 6-aryl-furo[2,3-d]pyrimidin-4-amines as EGFR inhibitors.

Epidermal growth factor receptor inhibitors are of importance in cancer therapy and possibly in the management of pain. Herein, we report a structure-activity relationship study with 29 new 6-aryl-furo[2,3-d]pyrimidin-4-amines, involving modification of the 4-amino group and 6-aryl function. The EGFR activity was especially dependent on having a chiral 4-benzylamino group with correct stereochemistry. Molecular dynamics indicate this to be due to favourable cation-π interactions. The most active inhibitor identified, equipotent to Erlotinib, was substituted with (R)-1-phenylethylamine at C-4 and a N(1), N(1)-dimethyl-1,2-diamine group in para position of the 6-aryl moiety. These new furopyrimidines had a different off-target kinase profile when compared to Erlotinib, and also possessed high activity towards Ba/F3 EGFR(L858R) reporter cells. Further, comparing the EGFR data of the furo[2,3-d]pyrimidin-4-amines with that of the corresponding thieno- and pyrrolopyrimidines concludes the furopyrimidine scaffold to be highly useful for development of new epidermal growth factor receptor antagonists.

Extended structure-activity study of thienopyrimidine-based EGFR inhibitors with evaluation of drug-like properties.

Thieno[2,3-d]pyrimidines are attractive derivatives for cancer treatment, among others through regulation of the epidermal growth factor receptor tyrosine kinase (EGFR-TK). In an extended SAR study, 44 new compounds of this class have been evaluated as inhibitors, while simultaneously focussing on ADME properties. Through the application of bioisosters, hybrid structures, solubilizing tails, and a combination approach several successful alterations in terms of activity and physiochemical properties were accomplished. Compounds based on benzylamines were found superior to aniline hybrid structures with respect to activity and ADME profile. Exploration of the former class revealed meta- and para amides as favourable 6-aryl substituents, contributing to an increase in activity and acting as a linker for solubilizing tails. Next, combinations of activity-inducing groups on the same scaffold resulted in new drug candidates. Compounds containing 6-aryls with the (2-(dimethylamino)ethyl)carbamoyl substituent were found equipotent to Erlotinib. Compared to this commercial drug, improved solubility and metabolic stability were observed. However, the thieno[2,3-d]pyrimidines with a solubilizing tail was by Caco-2 experiments found to have permeability issues, making further drug development difficult. Selected compounds were further analysed for toxicity and teratogenicity in zebrafish embryos. Two thienopyrimidines were both found to be less lethal than Erlotinib and to perform as well in terms of teratogenicity. Finally, the most promising thienopyrimidine drug was evaluated in a panel of human cancer cell lines, showing a clear potential for thienopyrimidines as anti-cancer agents.