RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.

Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.

Pneumonectomy combined with SU5416 or monocrotaline pyrrole does not cause severe pulmonary hypertension in mice.

In the field of pulmonary hypertension (PH), a well-established protocol to induce severe angioproliferation in rats (SuHx) involves combining the VEGF-R inhibitor Sugen 5416 (SU5416) with 3 wk of hypoxia (Hx). In addition, injecting monocrotaline (MCT) into rats can induce inflammation and shear stress in the pulmonary vasculature, leading to neointima-like remodeling. However, the SuHx protocol in mice is still controversial, with some studies suggesting it yields higher and reversible PH than Hx alone, possibly due to species-dependent hypoxic responses. To establish an alternative rodent model of PH, we hypothesized mice would be more sensitive to hemodynamic changes secondary to shear stress compared with Hx. We attempted to induce severe and irreversible PH in mice by combining SU5416 or monocrotaline pyrrole (MCTP) injection with pneumonectomy (PNx). However, our experiments showed SU5416 administered to mice at various time points after PNx did not result in severe PH. Similarly, mice injected with MCTP after PNx (MPNx) showed no difference in right ventricular systolic pressure or exacerbated pulmonary vascular remodeling compared with PNx alone. These findings collectively demonstrate that C57/B6 mice do not develop severe and persistent PH when PNx is combined with either SU5416 or MCTP.NEW & NOTEWORTHY We attempted to establish a mouse model of severe and irreversible pulmonary hypertension by substituting hypoxia with pulmonary overcirculation. To do so, we treated mice with either SU5416 or monocrotaline pyrrole after pneumonectomy and performed hemodynamic evaluations for PH. Despite this "two-hit" protocol, mice did not exhibit signs of severe pulmonary hypertension or exacerbated pulmonary vascular remodeling compared with PNx alone.

Poly (ADP-ribose) polymerase inhibitor sensitized DNA damage caused by an alkylating pyrrole-imidazole polyamide targeting MYCN in neuroblastoma cells.

MYCN amplification (MYCN-amp) is a significant prognostic factor and early genetic marker of high-risk neuroblastoma (NB). MYCN induces the DNA damage response (DDR) and modulates the insensitivity of NB cells to Poly (ADP-ribose) polymerase (PARP) inhibitors. We previously reported that CCC-002, a DNA-alkylating agent conjugated with pyrrole-imidazole polyamide targeting MYCN, inhibits NB cell proliferation and induces DNA damage signaling. In this study, we investigated the synergistic effects of CCC-002 and PARP inhibitors on MYCN-amp NB cells. Combination treatment with PARP inhibitors significantly enhanced the sensitivity of MYCN-amp NB cells to CCC-002. DNA damage signals, such as phosphorylation of H2AX and RPA32 elicited after CCC-002 treatment, were further enhanced by PARP inhibitors, as detected through western blotting and immunofluorescence analyses. The potent cytotoxicity of this combination treatment was confirmed by the significant increase in the subG0-G1 phase. Although MYCN knockdown showed no synergistic effect with PARP inhibitors, fluorescence in situ hybridization and quantitative PCR analyses indicated that PARP inhibitors enhanced the effect of CCC-002 to reduce MYCN copy number and suppress its expression. Overall, our study provides novel insights into a therapeutic approach that combines CCC-002 and PARP inhibition to effectively induce DNA damage and apoptosis in MYCN-amp NB cells.

A-D-A Type Nonfullerene Acceptors Synthesized by Core Segmentation and Isomerization for Realizing Organic Solar Cells with Low Nonradiative Energy Loss.

Reducing non-radiative recombination energy loss (ΔEnonrad ) in organic solar cells (OSCs) has been considered an effective method to improve device efficiency. In this study, the backbone of PTBTT-4F/4Cl is divided into D1-D2-D3 segments and reconstructed. The isomerized TPBTT-4F/4Cl obtains stronger intramolecular charge transfer (ICT), thus leading to elevated highest occupied molecular orbital (HOMO) energy level and reduced bandgap (Eg ). According to ELoss  = Eg- qVOC , the reduced Eg and enhanced open circuit voltage (VOC ) result in lower ELoss , indicating that ELoss has been effectively suppressed in the TPBTT-4F/4Cl based devices. Furthermore, compared to PTBTT derivatives, the isomeric TPBTT derivatives exhibit more planar molecular structure and closer intermolecular stacking, thus affording higher crystallinity of the neat films. Therefore, the reduced energy disorder and corresponding lower Urbach energy (Eu ) of the TPBTT-4F/4Cl blend films lead to low ELoss and high charge-carrier mobility of the devices. As a result, benefitting from synergetic control of molecular stacking and energetic offsets, a maximum power conversion efficiency (PCE) of 15.72% is realized from TPBTT-4F based devices, along with a reduced ΔEnonrad of 0.276 eV. This work demonstrates a rational method of suppressing VOC loss and improving the device performance through molecular design engineering by core segmentation and isomerization.

Some pyrroles as inhibitors of the pentose phosphate pathways enzymes: An in vitro and molecular docking study.

Glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (6PGD) are pentose phosphate pathway enzymes. Compounds with a heterocyclic pyrrole ring system containing this atom can be derivatized with various functional groups into highly effective bioactive agents. In this study, pyrrole derivatives on these enzyme's activity were investigated. The IC50 values of different concentrations of pyrrole derivatives for G6PD were found in the range of 0.022-0.221 mM Ki values 0.021 ± 0.003-0.177 ± 0.021 and for 6PGD IC50 values 0.020-0.147, mM Ki values 0.013 ± 0.002-0.113 ± 0.030 mM. The 2-acetyl-1-methylpyrrole (1g) showed the best inhibition value for G6PD and 6PGD enzymes. In addition, in silico molecular docking experiments were performed to elucidate how these pyrrole derivatives (1a-g) interact with the binding sites of the target enzymes. The study's findings on pyrrole derivatives could be used to create innovative therapeutics that could be a treatment for many diseases, especially cancer manifestations.

Nucleic acid-based small molecules as targeted transcription therapeutics for immunoregulation.

Transcription therapy is an emerging approach that centers on identifying the factors associated with the malfunctioning gene transcription machinery that causes diseases and controlling them with designer agents. Until now, the primary research focus in therapeutic gene modulation has been on small-molecule drugs that target epigenetic enzymes and critical signaling pathways. However, nucleic acid-based small molecules have gained popularity in recent years for their amenability to be pre-designed and realize operative control over the dynamic transcription machinery that governs how the immune system responds to diseases. Pyrrole-imidazole polyamides (PIPs) are well-established DNA-based small-molecule gene regulators that overcome the limitations of their conventional counterparts owing to their sequence-targeted specificity, versatile regulatory efficiency, and biocompatibility. Here, we emphasize the rational design of PIPs, their functional mechanisms, and their potential as targeted transcription therapeutics for disease treatment by regulating the immune response. Furthermore, we also discuss the challenges and foresight of this approach in personalized immunotherapy in precision medicine.

Conformational and Substitution Effects on the Donor and Reducing Strength of Tin(II) Porphyrinogens.

Meso-octaalkylcalix[4]pyrrolates are a class of redox-active porphyrinogen ligands. They have been well established in d- and f-block chemistry for over three decades but have only recently been introduced as ligands for p-block elements. Here, we present a study on the influence of meso-substituents on the redox chemistry of calix[4]pyrrolato stannate(II) dianions [2R]2- (R=Me, Et). Expansion of the normal-mode structural decomposition (NSD) method, well known for porphyrin chemistry, provides insights into the ligand conformation of a calix[4]pyrrolato p-block complex. Combined with the results of spectroscopic donor scaling, electrochemical studies, and quantum mechanical bond analysis tools, subtle but significant substitution and conformational effects on the electronic structure are revealed. Exploiting this knowledge rationalizes the role of this class of tin(II) dianions to act as potent reducing agents, but can also be expanded for other central elements. Photoexcitation boosts this reactivity further, allowing for the reduction of even challenging chlorobenzene.

Mn(II) Promoted Divergent-Convergent Domino Reaction Giving Dinuclear Tetrasubstituted Pyrrole Complex.

Domino reaction of benzo[d]thiazole-2-methylamine (S1) has been developed in the presence of MnCl2 ⋅ 4H2O, leading to tetrasubstituted pyrrole coordinated dinuclear Mn(II) complex 1 ([MnClP]2, P-=2,3,4,5-tetrakis(benzo[d]thiazol-2-yl)pyrrol-1-ide). The reaction process has been studied by assigning a series of intermediates based on time-dependent mass spectrometry, control experiments, crystallography, and density functional theory (DFT) theoretical calculation. A plausible mechanism involving an unprecedented divergent-convergent domino sequence has been proposed. Compound S1 could be activated by MnCl2 ⋅ 4H2O via coordination, which divergently produces two intermediates imine II (1-(benzo[d]thiazol-2-yl)-N-(benzo[d]thiazol-2-ylmethyl)methanimine) and alkene C (1,2-bis(benzo[d]thiazol-2-yl)ethene) through oxidative self-condensation and free radical coupling followed by elimination, respectively. They could then react with each other convergently via formal [3+2] cycloaddition to give deprotonated tetrasubstituted pyrrole coordinated intermediate [MnClP] after aromatization. Dimerization of [MnClP] produces the final product 1. Three C-C bonds and one C-N bond are formed through this six-step domino sequence. The corresponding organic skeleton (HP: 2,2',2'',2'''-(1H-pyrrole-2,3,4,5-tetrayl)tetrakis(benzo[d]thiazole)) has been obtained from 1 and shows a higher fluorescent quantum yield (52 %) than the reported 3,4-diphenyl substituted analogue 2,2'-(3,4-diphenyl-1H-pyrrole-2,5-diyl)bis(benzo[d]thiazole) (DPB) (42 %).

Unveiling the Ultrafast Excitation Energy Transfer in Tetraarylpyrrolo[3,2-b]pyrrole-BODIPY Dyads.

We have synthesized two dyads (dyad 1 and 2) comprising of tetraarylpyrrolo[3,2-b]pyrrole (TAPP) and BODIPY. In dyad 1, two BODIPYs are directly connected with TAPP moiety whereas in dyad 2, BODIPYs are connected through phenylethynyl linkers. TAPP is a blue energy donor which is easy to synthesize and functionalize as compared to other well-known blue energy donors like pyrene, perylene etc. This is the first report of using TAPP as an energy donor in BODIPY based dyad molecules. Complete quenching of TAPP fluorescence in the dyads suggests fast energy transfer from TAPP to BODIPY unit (ETE ~ 99.9%). Ultrafast fluorescence and transient absorption spectroscopic studies of dyad 1 showed TAPP to BODIPY energy transfer in 125 fs (kET = 8.0 x 1012 s-1) which is one of the fastest energy transfer events in BODIPY based dyad reported so far. Whereas, in dyad 2, energy transfer is almost four times slower (480 fs, kET = 2.1 x 1012 s-1). These results were rationalized by theoretical Förster formulations. This study shows that suitably matched optical properties of TAPP and BODIPY dyes along with their easy syntheses will be the key to develop highly efficient energy transfer systems in future for multiple applications.

Ion-Pairing Assemblies of Anion-Responsive π-Electronic Systems That Have Noncovalently Assisted Expanded Planar Region.

Arylethynyl-substituted dipyrrolyldiketone BF2 complexes as anion-responsive π-electronic molecules exhibited characteristic electronic properties derived from conformation changes upon anion binding, which caused an increase in UV/vis absorption and associated two-photon absorption. The anion complexes showed expanded planar regions assisted by intramolecular interactions, resulting in charge-by-charge ion-pairing assemblies in the solid state.

Binding of Acetylated Lysine by Using a Water Soluble Aryl Extended Calix[4]pyrrole.

Post-translational modifications of lysine in histones, as methylation and acetylation, have well established functions in epigenetics and are emerging as important actors in broader biological regulation. Currently, the detection of acetylated lysine (Kac) in water solution as free amino acid or protein residue remains challenging. Acetylated lysine is a neutral amino acid, and the lack of ion-dipole interactions causes the decrease in binding affinity displayed by synthetic molecular receptors with respect to the other lysine modifications. Here, we report molecular modeling calculations and 1H NMR experiments to investigate the binding properties of two different calix[4]pyrrole receptors towards Kac. Computational analyses reveal that tetra-aryl-extended calix[4]pyrrole (1) preferentially binds the cis-Kac conformer over the trans one due to steric considerations and more favorable interactions. Experimental 1H NMR titration experiments confirm the formation of a 1 : 1 complex between receptor 1 and cis-Kac, with a Ka exceeding 103 M-1. Conversely, the super-aryl-extended calix[4]pyrrole 2 is less efficient in binding Kac, due to unfavorable solvation/desolvation effects, as proven by 1H NMR experiments. Moreover, receptor 1 showed a higher affinity for Kac over other lysine modifications, such as methylated lysines.

Development of multifunctional pyrrole-imidazole polyamides that increase hepatocyte growth factor and suppress transforming growth factor-ß1.

PURPOSE: The DNA recognition peptide compounds pyrrole-imidazole (PI) polyamides bind to the minor groove and can block the binding of transcription factors to target sequences. To develop more PI polyamides as potential treatments for fibrotic diseases, including chronic renal failure, we developed multifunctional PI polyamides that increase hepatocyte growth factor (HGF) and decrease transforming growth factor (TGF)-ß1. METHODS: We designed seven PI polyamides (HGF-1 to HGF-7) that bind to the chicken ovalbumin upstream promoter transcription factor-1 (COUP-TF1) binding site of the HGF promoter sequence. We selected PI polyamides that increase HGF and suppress TGF-ß1 in human dermal fibroblasts (HDFs). FINDINGS: Gel shift assays showed that HGF-2 and HGF-4 bound the appropriate dsDNAs. HGF-2 and HGF-4 significantly inhibited the TGF-ß1 mRNA expression in HDFs stimulated by phorbol 12-myristate 13-acetate. HGF-2 and HGF-4 significantly inhibited the TGF-ß1 protein expression in HDFs with siRNA targeting HGF, indicating that HGF-2 and HGF-4 directly inhibited the expression of TGF-ß1. CONCLUSION: The designed and synthetic HGF PI polyamides targeting the HGF promoter, which increased the expression of HGF and suppressed the expression of TGF-ß, will be a potential practical medicine for fibrotic diseases, including progressive renal diseases.

Carbazole Integrated Tetrakis-(1 H-pyrrole-2-carbaldehyde): A Highly Selective Fluorescent Probe for HP2O73.

A new carbazole-coupled tetrakis-(1 H-pyrrole-2-carbaldehyde) anion receptor 1 has been designed and synthesized. Anion binding studies in organic media using fluorescence and UV-vis spectroscopy revealed that receptor 1 is capable of sensing HP2O73- with high selectivity. Addition of HP2O73- to THF solution of 1 resulted in the emergence of a new broad band at longer wavelength along with quenching of the original emission band forming a ratiometric response. Based on dynamic light scattering (DLS) experiment and fluorescence lifetime measurement, we propose that the emergence of new emission band in the presence of HP2O73- ion is due to the aggregation-induced excimer formation.

Access to 2,4-Disubstituted Pyrrole-Based Polymer with Long-Wavelength and Stimuli-Responsive Properties via Copper-Catalyzed [3+2] Polycycloaddition.

Pyrrole-based polymers (PBPs), a type of fascinating functional polymers, play a crucial role in materials science. However, efficient synthetic strategies of PBPs with diverse structures are mainly focused on conjugated polypyrroles and still remain challenging. Herein, an atom and step economy protocol is described to access various 2,4-disubstituted PBPs by in situ formation of pyrrole core structure via copper-catalyzed [3+2] polycycloaddition of dialkynones and diisocyanoacetates. A series of PBPs is prepared with high molecular weight (Mw up to 18 200 Da) and moderate to good yield (up to 87%), which possesses a fluorescent emission located in the green to yellow light region. Blending the PBPs with polyvinyl alcohol, the stretchable composite films exhibit a significant strengthening of the mechanical properties (tensile stress up to 59 MPa, elongation at break >400%) and an unprecedented stress-responsive luminescence enhancement that over fourfold fluorescent emission intensity is maintained upon stretching up to 100%. On the basis of computational studies, the unique photophysical and mechanical properties are attributed to the substitution of carbonyl chromophores on the pyrrole unit.

Elevating pyrrole derivative synthesis: a three-component revolution.

Pyrrole is an essential chemical with considerable relevance as a pharmaceutical framework for many biologically necessary medications. The growing demand for biologically active compounds calls for a simple one-pot method for generating novel pyrrole derivatives. Nots surprisingly, several multicomponent reactions (MCRs) aim to synthesize pyrrole derivatives. However, this review presents the three-component synthesis of pyrrole derivatives, highlighting the significance of multicomponent reaction in synthesizing eclectic multi-functionalised pyrrole covering the selected literature on the three-component synthesis of substituted pyrrole from 2016 to late 2023. Furthermore, this article classifies the reactions based on the starting material with functional groups involved in the pyrrole ring formation.

Chiral diketopyrrolo[3,4-c]pyrrole-based oligothiophenes: Synthesis and characterization of aggregated states in solution and thin films.

In this work, we synthesized a family of three structurally related chiral oligothiophenes containing a 1,4-diketo-3,6-diarylpyrrolo[3,4-c]pyrrole (DPP) unit as the central core; functionalized with the same (S)-3,7-dimethyl-1-octyl chains on the nitrogen atoms of lactam moieties, they only differ in the number of lateral thiophene units. The aggregation modes of these π-conjugated chiral systems were evaluated by means of UV-Vis absorption and ECD spectroscopies in conditions of solution aggregation (CHCl3 /MeOH mixtures) and as thin films, describing in particular the impact of the π-conjugation length on the chiroptical properties. Interestingly, we found that the variable number of thiophene units attached to the DPP core affects not only the propensity to aggregation but also the aggregates' helicity. ECD revealed information about the supramolecular arrangement of these molecules, that one would not obtain by using conventional optical spectroscopy and microscopy techniques. Thin film samples revealed very different aggregation modes with respect to solution aggregates, casting doubts on the common assumption that these latter may serve as simple models of the former ones.

Denigrins H-L: Sulfated Derivatives of Denigrins D and E from a New Zealand Dictyodendrilla c.f. dendyi Marine Sponge.

Five new sulfated arylpyrrole and arylpyrrolone alkaloids, denigrins H-L (1-5), along with two known compounds, dictyodendrin B and denigrin G, were isolated from an extract of a New Zealand Dictyodendrilla c.f. dendyi marine sponge. Denigrins H-L represent the first examples of sulfated denigrins, with denigrins H and I (1-2), as derivatives of denigrin D, containing a pyrrolone core, and denigrins J-L (3-5), as derivatives of denigrin E (6), containing a pyrrole core. Their structures were elucidated by interpretation of 1D and 2D NMR spectroscopic data, ESI, and HR-ESI-MS spectrometric data, as well as comparison with literature data. Compounds 1-5, along with six known compounds previously isolated from the same extract, showed minimal cytotoxicity against the HeLa cervical cancer cell line.

Marine Streptomyces-Derived Novel Alkaloids Discovered in the Past Decade.

Natural alkaloids originating from actinomycetes and synthetic derivatives have always been among the important suppliers of small-molecule drugs. Among their biological sources, Streptomyces is the highest and most extensively researched genus. Marine-derived Streptomyces strains harbor unconventional metabolic pathways and have been demonstrated to be efficient producers of biologically active alkaloids; more than 60% of these compounds exhibit valuable activity such as antibacterial, antitumor, anti-inflammatory activities. This review comprehensively summarizes novel alkaloids produced by marine Streptomyces discovered in the past decade, focusing on their structural features, biological activity, and pharmacological mechanisms. Future perspectives on the discovery and development of novel alkaloids from marine Streptomyces are also provided.

Fulvanines J-K, two rare lactam pyrrole alkaloids from Hemerocallis fulva.

Two rare jatropham lactam derivatives, named as fulvanines J-K (1-2), together with six known pyrrole alkaloids, 5,5'-oxydi(3-methyl-3-pyrrolin-2-one) (3), (-)-5-hydroxy-3-methyl-3-pyrrolin-2-one (jatropham) (4), (±)-5-O-methyljatropham (5), perlolyrine (6), butyl-2-formyl-5-(hydroxymethyl)-1H-pyrrole-1-butanoate (7), and hemerocallisamine II (8), were isolated from the flower of Hemerocallis fulva. Their structures were elucidated on the basis of spectroscopic methods and compared with the NMR spectra data in the literature. All compounds were evaluated for their anti-complementary activity in vitro, and compounds 1, 4, and 6 exhibited anti-complement effect with CH50 values from 0.61 to 1.42 mM.

Synthesis, Thermal Stability and Antifungal Evaluation of Two New Pyrrole Esters.

To develop new chemicals that are stable at high temperatures with biological activity, a pyrrole intermediate was firstly synthesized using glucosamine hydrochloride as raw materials through cyclization and oxidation. Further, two novel pyrrole ester derivatives were prepared via Steglich esterification from pyrrole intermediate with vanillin and ethyl maltol, respectively. Nuclear magnetic resonance (1 H-NMR, 13 C NMR), infrared spectroscopy (IR) and high resolution mass spectrometry (HRMS) were used to confirm the target compounds. Thermal behavior of the compounds was investigated by thermogravimetry (TG), differential scanning calorimeter (DSC) and the pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) methods. The plausible pyrolytic mechanism was proposed. Additionally, their biological activities against the pathogens Fusarium graminearum, Fusarium oxysporum, Fusarium moniliforme, Phytophthora nicotianae, and Rhizoctonia solani were assessed. These target compounds showed outstanding antifungal activities and the highest inhibitor rates of 62.50 % and 68.75 % against R. solani with EC50 values of 0.0296 and 0.0200 mg mL-1 , respectively. SDHI protein sequence was molecularly docked to identify the binding mechanisms in the active pocket and examine the interactions between both the molecules and the SDHI protein.