Ultrafast Hot Exciton Nonadiabatic Excited-State Dynamics in Green Fluorescent Protein Chromophore Analogue.

The ultrafast high-energy nonadiabatic excited-state dynamics of the benzylidenedimethylimidazolinone chromophore dimer has been investigated using an electronic structure method coupled with on-the-fly quantitative wave function analysis to gain insight into the photophysics of hot excitons in biological systems. The dynamical simulation provides a rationalization of the behavior of the exciton in a dimer after the photoabsorption of light to higher-energy states. The results suggest that hot exciton localization within the manifold of excited states is caused by the hindrance of torsional rotation due to imidazolinone (I) or phenolate (P) bonds i.e., ΦI- or ΦP-dihedral rotation, in the monomeric units of a dimer. This hindrance arises due to weak π-π stacking interaction in the dimer, resulting in an energetically uphill excited-state barrier for ΦI- and ΦP-twisted rotation, impeding the isomerization process in the chromophore. Thus, this study highlights the potential impact of the weak π-π interaction in regulating the photodynamics of the green fluorescent protein chromophore derivatives.

Dynamic Exchange of Substituents in a Prebiotic Organocatalyst: Initial Steps towards an Evolutionary System.

All evolutionary biological processes lead to a change in heritable traits over successive generations. The responsible genetic information encoded in DNA is altered, selected, and inherited by mutation of the base sequence. While this is well known at the biological level, an evolutionary change at the molecular level of small organic molecules is unknown but represents an important prerequisite for the emergence of life. Here, we present a class of prebiotic imidazolidine-4-thione organocatalysts able to dynamically change their constitution and potentially capable to form an evolutionary system. These catalysts functionalize their building blocks and dynamically adapt to their (self-modified) environment by mutation of their own structure. Depending on the surrounding conditions, they show pronounced and opposing selectivity in their formation. Remarkably, the preferentially formed species can be associated with different catalytic properties, which enable multiple pathways for the transition from abiotic matter to functional biomolecules.

An aromatic imidazoline derived from chloroquinoline triggers cell cycle arrest and inhibits with high selectivity the Trypanosoma cruzi mammalian host-cells infection.

Trypanosoma cruzi is a hemoflagellated parasite causing Chagas disease, which affects 6-8 million people in the Americas. More than one hundred years after the description of this disease, the available drugs for treating the T. cruzi infection remain largely unsatisfactory. Chloroquinoline and arylamidine moieties are separately found in various compounds reported for their anti-trypanosoma activities. In this work we evaluate the anti-T. cruzi activity of a collection of 26 "chimeric" molecules combining choroquinoline and amidine structures. In a first screening using epimastigote forms of the parasite as a proxy for the clinically relevant stages, we selected the compound 7-chloro-4-[4-(4,5-dihydro-1H-imidazol-2-yl)phenoxy]quinoline (named here as A6) that performed better as an anti-T. cruzi compound (IC50 of 2.2 ± 0.3 µM) and showed a low toxicity for the mammalian cell CHO-K1 (CC50 of 137.9 ± 17.3 µM). We initially investigated the mechanism of death associated to the selected compound. The A6 did not trigger phosphatidylserine exposure or plasma membrane permeabilization. Further investigation led us to observe that under short-term incubations (until 6 hours), no alterations of mitochondrial function were observed. However, at longer incubation times (4 days), A6 was able to decrease the intracellular Ca2+, to diminish the intracellular ATP levels, and to collapse mitochondrial inner membrane potential. After analysing the cell cycle, we found as well that A6 produced an arrest in the S phase that impairs the parasite proliferation. Finally, A6 was effective against the infective forms of the parasite during the infection of the mammalian host cells at a nanomolar concentration (IC50(tryps) = 26.7 ± 3.7 nM), exhibiting a selectivity index (SI) of 5,170. Our data suggest that A6 is a promising hit against T. cruzi.

Exploring the binding mode of PQ912 against secretory glutaminyl cyclase through systematic exploitation of conformational ensembles.

Secretory glutaminyl cyclase (sQC) plays an important role in the formation of the pyroglutamate-amyloid beta (pGlu-Aß) peptide, one of the most abundant variants of Aß found in the Alzheimer's disease (AD) brain. This post-translationally modified pGlu-Aß possesses high toxicity and rapid aggregation propensity when compared to the wild-type Aß (WT-Aß). Since pGlu-Aß acts as seed for WT-Aß, the inhibition of sQC limits the formation of pGlu-Aß and reduces the overall load of Aß plaques in the AD brain. PQ912 is a potent inhibitor of sQC and has been enrolled in phase 2b clinical trial of the AD drug development pipeline; however, the binding mode of PQ912 against sQC is not elucidated yet. Understanding the binding mode of PQ912 is important as it helps in the discovery against AD where sQC as a target. To explore the binding mode of PQ912, we employed ensemble docking towards 9 sQC structures that differ either in active site geometry or in the bound ligands. Further pose clustering and binding energy calculations yielded three possible binding modes for PQ912. Finally, all atom molecular dynamics simulations determined the most energetically favorable binding mode for PQ912, in the active site of sQC, which is similar to that of LSB-09, a recently reported sQC inhibitor containing benzimidazole-6-carboxamide moiety.

Synthesis, antiproliferative and antitrypanosomal activities, and DNA binding of novel 6-amidino-2-arylbenzothiazoles.

A series of 6-amidinobenzothiazoles, linked via phenoxymethylene or directly to the 1,2,3-triazole ring with a p-substituted phenyl or benzyl moiety, were synthesised and evaluated in vitro against four human tumour cell lines and the protozoan parasite Trypanosoma brucei. The influence of the type of amidino substituent and phenoxymethylene linker on antiproliferative and antitrypanosomal activities was observed, showing that the imidazoline moiety had a major impact on both activities. Benzothiazole imidazoline 14a, which was directly connected to N-1-phenyl-1,2,3-triazole, had the most potent growth-inhibitory effect (IC50 = 0.25 µM) on colorectal adenocarcinoma (SW620), while benzothiazole imidazoline 11b, containing a phenoxymethylene linker, exhibited the best antitrypanosomal potency (IC90 = 0.12 µM). DNA binding assays showed a non-covalent interaction of 6-amidinobenzothiazole ligands, indicating both minor groove binding and intercalation modes of DNA interaction. Our findings encourage further development of novel structurally related 6-amidino-2-arylbenzothiazoles to obtain more selective anticancer and anti-HAT agents.

Solid-Phase Synthesis of an Insect Pyrokinin Analog Incorporating an Imidazoline Ring as Isosteric Replacement of a trans Peptide Bond.

A facile solid-phase synthetic method for incorporating the imidazoline ring motif, a surrogate for a trans peptide bond, into bioactive peptides is reported. The example described is the synthesis of an imidazoline peptidomimetic analog of an insect pyrokinin neuropeptide via a cyclization reaction of an iminium salt generated from the preceding amino acid and 2,4-diaminopropanoic acid (Dap).

Photophysics of DFHBI bound to RNA aptamer Baby Spinach.

The discovery of the GFP-type dye DFHBI that becomes fluorescent upon binding to an RNA aptamer, termed Spinach, led to the development of a variety of fluorogenic RNA systems that enable genetic encoding of living cells. In view of increasing interest in small RNA aptamers and the scarcity of their photophysical characterisation, this paper is a model study on Baby Spinach, a truncated Spinach aptamer with half its sequence. Fluorescence and fluorescence excitation spectra of DFHBI complexes of Spinach and Baby Spinach are known to be similar. Surprisingly, a significant divergence between absorption and fluorescence excitation spectra of the DFHBI/RNA complex was observed on conditions of saturation at large excess of RNA over DFHBI. Since absorption spectra were not reported for any Spinach-type aptamer, this effect is new. Quantitative modelling of the absorption spectrum based on competing dark and fluorescent binding sites could explain it. However, following reasoning of fluorescence lifetimes of bound DFHBI, femtosecond-fluorescence lifetime profiles would be more supportive of the notion that the abnormal absorption spectrum is largely caused by trans-isomers formed  within the cis-bound DFHBI/RNA complex. Independent of the origin, the unexpected discrepancy between absorption and fluorescence excitation spectra allows for easily accessed screening and insight into the efficiency of a fluorogenic dye/RNA system.

Nickel-Catalyzed Asymmetric Synthesis of α-Arylbenzamides.

A nickel-catalyzed asymmetric reductive hydroarylation of vinyl amides to produce enantioenriched α-arylbenzamides is reported. The use of a chiral bisimidazoline (BIm) ligand, in combination with diethoxymethylsilane and aryl halides, enables the regioselective introduction of aryl groups to the internal position of the olefin, forging a new stereogenic center α to the N atom. The use of neutral reagents and mild reaction conditions provides simple access to pharmacologically relevant motifs present in anticancer, SARS-CoV PLpro inhibitors, and KCNQ channel openers.

The Antibacterial Drug Candidate SBC3 is a Potent Inhibitor of Bacterial Thioredoxin Reductase.

Antibiotic resistance is a growing problem for public health and associated with increasing economic costs and mortality rates. Silver and silver-related compounds have been used for centuries due to their antimicrobial properties. In this work, we show that 1,3-dibenzyl-4,5-diphenyl-imidazol-2-ylidene silver(I) acetate/NHC*-Ag-OAc (SBC3) is a reversible, high affinity inhibitor of E. coli thioredoxin reductase (TrxR; Ki =10.8±1.2 nM). Minimal inhibition concentration (MIC) tests with different E. coli and P. aeruginosa strains demonstrated that SBC3 can efficiently inhibit bacterial cell growth, especially in combination with established antibiotics like gentamicin. Our results show that SBC3 is a promising antibiotic drug candidate targeting bacterial TrxR.

Synthesis and in vitro carbonic anhydrases and acetylcholinesterase inhibitory activities of novel imidazolinone-based benzenesulfonamides.

New imidazolinone-based benzenesulfonamides 3a-e and 4a-e were synthesized in three steps and their chemical structures were confirmed by 1 H NMR (nuclear magnetic resonance), 13 C NMR, and high-resolution mass spectrometry. The benzenesulfonamides used were sulfacetamide (3a, 4a), sulfaguanidine (3b, 4b), sulfanilamide (3c, 4c), sulfadiazine (3d, 4d), sulfamerazine (3e), and sulfathiazole (4e). The compounds were evaluated against carbonic anhydrase (CA) and acetylcholinesterase (AChE) enzymes to obtain possible drug candidate/s. The lead compounds of the series were 3a and 4a against human CA (hCA) I, whereas 3d and 4a were leads against hCA II in terms of Ki values. Series 4 includes more effective CAs inhibitors than series 3 (except 3d). Series 4 compounds having a nitro group (except 4d) were 3.3-4.8 times more selective inhibitors than their corresponding analogues 3a-d in series 3, in which hydrogen was located in place of the nitro group, by considering Ki values against hCA II. Compounds 3c and 4c, where the sulfanilamide moiety is available, were the leads in terms of AChE inhibition with the lowest Ki values. The use of secondary sulfonamides was a more effective modification on CA inhibition, whereas the primary sulfonamide was the effective substitution in terms of AChE inhibitory potency.

Di-aryl guanidinium derivatives: Towards improved α2-Adrenergic affinity and antagonist activity.

Compounds with excellent receptor engagement displaying α2-AR antagonist activity are useful not only for therapeutic purposes (e.g. antidepressants), but also to help in the crystallization of this particular GPCR. Therefore, based on our broad experience in the topic, we have prepared eighteen di-aryl (phenyl and/or pyridin-2-yl) mono- or di-substituted guanidines and 2-aminoimidazolines. The in vitro α2-AR binding affinity experiments in human brain tissue showed the advantage of a 2-aminoimidazolinium cation, a di-arylmethylene core, a conformationally locked pyridin-2-yl-guanidine and a di-substituted guanidinium to achieve good α2-AR engagement. After different in vitro [35S]GTPγS binding experiments in human prefrontal cortex tissue, it was possible to identify that compounds 7a, 7b and 7c were α2-AR partial agonist, whereas 8h was a potent α2-AR antagonist. Docking and MD studies with a model of α2A-AR and two crystal structures suggest that antagonism is achieved by compounds carrying a di-substituted guanidine which substituent occupy a pocket adjacent to TM5 without engaging S2005.42 or S2045.46, and a mono-substituted cationic group, which favorably interacts with E942.65.

Microsecond Exchange Processes Studied by Two-Dimensional ESR at 95 GHz.

Exchange processes which include conformational change, protonation/deprotonation, and binding equilibria are routinely studied by 2D exchange NMR techniques, where information about the exchange of nuclei between environments with different NMR shifts is obtained from the development of cross-peaks. Whereas 2D NMR enables the real time study of millisecond and slower exchange processes, 2D ESR in the form of 2D-ELDOR (two-dimensional electron-electron double resonance) has the potential for such studies over the nanosecond to microsecond real time scales. Cross-peak development due to chemical exchange has been seen previously for semiquinones in ESR, but this is not possible for most common ESR probes, such as nitroxides, studied at typical ESR frequencies because, unlike NMR, the exchanging states yield ESR signals that are not resolved from each other within their respective line widths. But at 95 GHz, it becomes possible to resolve them in many cases because of the increased g-factor resolution. The 95 GHz instrumental developments occurring at ACERT now enable such studies. We demonstrate these new capabilities in two studies: (A) the protonation/deprotonation process for a pH-sensitive imidazoline spin label in aqueous solution where the exchange rate and the population ratio of the exchanging states are controlled by the concentration and pH of the buffer solution, respectively, and (B) a nitroxide radical partitioning between polar (aqueous) and nonpolar (phospholipid) environments in multilamellar lipid vesicles, where the cross-peak development arises from the exchange of the nitroxide between the two phases. This work represents the first example of the observation and analysis of cross-peaks arising from chemical exchange processes involving nitroxide spin labels.

Synthesis and Biological Evaluation of N-Aminoimidazolidin-2-one-Containing Angiotensin-(1-7) Peptidomimetics.

N-Aminoimidazolidin-2-one (Aid)-containing peptides with a constrained backbone present a novel class of peptidomimetics for drug discovery. The introduction of Aid residues into peptide sequences has been achieved by intramolecular Mitsunobu cyclization of a serine side chain onto the α-NH of an aza-glycine residue. The effectiveness of this new strategy was demonstrated by synthesizing six Aid-containing analogues of angiotensin-(1-7) on solid support. The Aid analogues of angiotensin-(1-7) exhibited increased peptidase stability against human ACE and DPP3 and improved anti-inflammation and antiproliferation activity.

Substituted Imidazoline Synthesis: A Diastereo- and Enantioselective aza-Henry Route to a Human Proteasome Modulator.

The first enantio- and diastereoselective synthesis of Tepe's human proteasome modulator is described. Routes to this and other highly substituted chiral imidazolines generally produce racemic material. Key to the route disclosed here is a gram-scale anti-selective aza-Henry reaction of an α-alkyl α-nitro ester nucleophile, catalyzed by a Bis(Amidine) [BAM] chiral proton complex, delivering the key intermediate in high yield as a single stereoisomer. The adduct is reduced to the amino ester and converted to an imidazoline.

Five concomitant polymorphs of a green fluorescent protein chromophore (GFPc) analogue: understanding variations in photoluminescence with π-stacking interactions.

The synthetically modified green fluorescent protein chromophore analogue 3,4,5-trimethoxybenzylidene imidazolinone (1) yielded five polymorphs (I, II, III, IV, V) concomitantly irrespective of the solvent used for crystallization. The pentamorphic modification of 1 is solely due to the interplay of iso-energetic weak intermolecular interactions in molecular associations as well as the conformational flexibility offered by a C-C single bond, which connects the electron-deficient moiety imidazolinone with the electron-rich trimethoxybenzylidene group. A common structural feature observed in all the polymorphs is the formation of a `zero-dimensional' centrosymmetric dimeric unit through a short and linear C-H...O hydrogen bond engaging phenyl C-H and imidazolinone carbonyl oxygen. However, the networking of these dimeric units showed a subtle difference in all the polymorphs. The 2D isostructurality was observed between polymorphs I, II and III, while the other two polymorphs IV and V revealed only `zero-dimensional' isostructurality. The different fluorescence emissions of Form I (blue) and Forms II to V (yellow) were attributed to the differences in π-stacking interactions. It shows that one can modulate the photophysical properties of these smart materials by slightly altering their crystal structure. Such an approach will aid in developing new multi-colour organic fluorescent materials of varying crystal structures for live-cell imaging and fluorescent sensing applications.

Keggin-type Heteropolyacids-Catalyzed Selective Hydrothermal Oxidation of Microalgae for Low Nitrogen Biofuel Production.

Hydrothermal liquefaction (HTL) of microalgae for biofuel production is suffering from low bio-oil yield and high heteroatomic compositions owing to their low efficiency and selectivity to hydrolysis of cellular compounds. Hereby we report Keggin-type (Mo-V-P) heteropolyacids (HPAs)-catalyzed HTL of microalgae for efficient low-nitrogen biocrude production. The increases of reaction temperature, reaction time, and vanadium substitution degrees of HPAs are favorable to biocrude yield initially, whereas a significant decrease of biocrude yield is observed owing to the enhanced oxidation of carbohydrates above the optimum reaction conditions. The maximum biocrude yield of HPAs-catalyzed HTL of microalgae is 29.95 % at reaction temperature of 300 °C, reaction time of 2 h, and 5 wt% of HPA-4, which is about 19.66 % higher than that of control with 71.17 % less N-containing compounds, including 1,3-propanediamine, 1-pentanamine, and 2, 2'-heptamethylene-di-2-imidazoline than that of control. This work reveals that HPAs with Brønsted acidity and reversible redox properties are capable of both enhancing biocrude production via catalyzing the hydrolysis of cellular compounds and reducing their nitrogen content through avoiding the Maillard reactions between the intermediates of hydrolysis of carbohydrates and proteins. HPAs-catalyzed HTL is an efficient strategy to produce low N-containing biofuels, possibly paving the way of their direct use in modern motors.

Design, synthesis, antitrypanosomal activity, DNA/RNA binding and in vitro ADME profiling of novel imidazoline-substituted 2-arylbenzimidazoles.

Novel imidazoline benzimidazole derivatives containing diversely substituted phenoxy moieties were synthesized with the aim of evaluating their antitrypanosomal activity, DNA/RNA binding affinity and in vitro ADME properties. The presence of the diethylaminoethyl subunit in 18a-18c led to enhanced antitrypanosomal potency, particularly for 18a and 18c, which contain unsubstituted and methoxy-substituted phenoxy moieties. They were found to be > 2-fold more potent against African trypanosomes than nifurtimox. Fluorescence and CD spectroscopy, thermal denaturation assays and computational analysis indicated a preference of 18a-18c toward AT-rich DNA and their minor groove binding mode. Replacement of the amidine group with less basic and ionisable nitrogen-containing moieties failed to improve membrane permeability of the investigated compounds. Due to structural diversification, the compounds displayed a range of physico-chemical features resulting in variable in vitro ADME properties, leaving space for further optimization of the biological profiles.

Tag-Free, Temperature Dependent Infrared Spectra of the GFP Chromophore: Revisiting the Question of Isomerism.

We report infrared spectra of a model chromophore of green fluorescent protein, prepared in an ion trap at temperatures ranging from 30 K to room temperature. We compare the changes in the infrared spectrum with predicted infrared spectra for the Z and E isomers of this molecule, and we confirm that the molecule exists as the Z isomer at low temperatures. We revisit the question whether or not it can thermally isomerize in the temperature range of this experiment, and we find no evidence for isomerization.

Discovery, synthesis and characterization of a series of 7-aryl-imidazo[1,2-a]pyridine-3-ylquinolines as activin-like kinase (ALK) inhibitors.

The activin-like kinases are a family of kinases that play important roles in a variety of disease states. Of this class of kinases, ALK2, has been shown by a gain-of-function to be the primary driver of the childhood skeletal disease fibrodysplasia ossificans progressiva (FOP) and more recently the pediatric cancer diffuse intrinsic pontine glioma (DIPG). Herein, we report our efforts to identify a novel imidazo[1,2-a]pyridine scaffold as potent inhibitors of ALK2 with good in vivo pharmacokinetic properties suitable for future animal studies.

A protein-independent fluorescent RNA aptamer reporter system for plant genetic engineering.

Reporter systems are routinely used in plant genetic engineering and functional genomics research. Most such plant reporter systems cause accumulation of foreign proteins. Here, we demonstrate a protein-independent reporter system, 3WJ-4 × Bro, based on a fluorescent RNA aptamer. Via transient expression assays in both Escherichia coli and Nicotiana benthamiana, we show that 3WJ-4 × Bro is suitable for transgene identification and as an mRNA reporter for expression pattern analysis. Following stable transformation in Arabidopsis thaliana, 3WJ-4 × Bro co-segregates and co-expresses with target transcripts and is stably inherited through multiple generations. Further, 3WJ-4 × Bro can be used to visualize virus-mediated RNA delivery in plants. This study demonstrates a protein-independent reporter system that can be used for transgene identification and in vivo dynamic analysis of mRNA.