Selective, broad-spectrum antiviral photodynamic disinfection with dicationic imidazolyl chlorin photosensitizers.

The COVID-19 pandemic exposes our vulnerability to viruses that acquire the ability to infect our cells. Classical disinfection methods are limited by toxicity. Existing medicines performed poorly against SARS-CoV-2 because of their specificity to targets in different organisms. We address the challenge of mitigating known and prospective viral infections with a new photosensitizer for antimicrobial photodynamic therapy (aPDT). Photodynamic inactivation is based on local oxidative stress, which is particularly damaging to enveloped viruses. We synthesized a cationic imidazolyl chlorin that reduced by > 99.999% of the percentage inhibition of amplification of SARS-CoV-2 collected from patients at 0.2 µM concentration and 4 J cm-2. Similar results were obtained in the prevention of infection of human ACE2-expressing HEK293T cells by a pseudotyped lentiviral vector exhibiting the S protein of SARS-CoV-2 at its surface. No toxicity to human epidermal keratinocytes (HaCaT) cells was found under similar conditions. aPDT with this chlorin offers fast and safe broad-spectrum photodisinfection and can be repeated with low risk of resistance.

Reactivity of ethyl nitrosoacrylate toward pyrrole, indole and pyrrolo[3,2-c]carbazole: an experimental and theoretical study.

Nitrosoalkenes react with 8-methyl-1,6-dihydropyrrolo[3,2-c]carbazole to give both 2- and 3-alkylated products via hetero-Diels-Alder reaction followed by the cycloadduct ring-opening. Quantum chemical calculations, at DFT level of theory, were carried out to investigate the regioselectivity of the cycloaddition of ethyl nitrosoacrylate with 1,6-dihydropyrrolo[3,2-c]carbazoles as well as with pyrrole and indole, allowing a more comprehensive analysis of the reactivity pattern of nitrosoalkenes with five-membered heterocycles. Furthermore, theoretical calculations confirmed that ethyl nitrosoacrylate reacts with these heterocycles via a LUMOheterodiene-HOMOdienophile controlled cycloaddition. The reactivity of one of the oxime-functionalized 1,6-dihydropyrrolo[3,2-c]carbazole was explored and a new hexahydropyrido[4',3':4,5]pyrrolo[3,2-c]carbazole system was obtained in high yield via a one-pot, two-step procedure.

Fluorinated Mn(III)/(II)-Porphyrin with Redox-Responsive 1 H and 19 F Relaxation Properties.

A new fluorinated manganese porphyrin, (Mn-TPP-p-CF3 ) is reported capable of providing, based on the Mn(III)/Mn(II) equilibrium, dual 1 H relaxivity and 19 F NMR response to redox changes. The physical-chemical characterization of both redox states in DMSO-d6 /H2 O evidenced that the 1 H relaxometric and 19 F NMR properties are appropriate for differential redox MRI detection. The Mn(III)-F distance (dMn-F =9.7-10 Å), as assessed by DFT calculations, is well tailored to allow for adequate paramagnetic effect of Mn(III) on 19 F T1 and T2 relaxation times. Mn-TPP-p-CF3 has a reversible Mn(II)/Mn(III) redox potential of 0.574 V vs. NHE in deoxygenated aqueous HEPES/ THF solution. The reduction of Mn(III)-TPP-p-CF3 in the presence of ascorbic acid is slowly, but fully reversed in the presence of air oxygen, as monitored by UV-Vis spectrometry and 19 F NMR. The broad 1 H and 19 F NMR signals of Mn(III)-TPP-p-CF3 disappear in the presence of 1 equivalent ascorbate replaced by a shifted and broadened 19 F NMR signal from Mn(II)-TPP-p-CF3 . Phantom 19 F MR images in DMSO show a MRI signal intensity decrease upon reduction of Mn(III)-TPP-p-CF3 , retrieved upon complete reoxidation in air within ~24 h. 1 H NMRD curves of the Mn(III)/(II)-TPP-p-CF3 chelates in mixed DMSO/water solvent have the typical shape of Mn(II)/Mn(III) porphyrins.

Antibacterial Photodynamic Inactivation of Antibiotic-Resistant Bacteria and Biofilms with Nanomolar Photosensitizer Concentrations.

Gram-negative bacteria and bacteria in biofilms are very difficult to eradicate and are the most antibiotic-resistant bacteria. Therapeutic alternatives less susceptible to mechanisms of resistance are urgently needed to respond to an alarming increase of resistant nosocomial infections. Antibacterial photodynamic inactivation (PDI) generates oxidative stress that triggers multiple cell death mechanisms that are more difficult to counteract by bacteria. We explore PDI of multidrug-resistant bacterial strains collected from patients and show how positive charge distribution in the photosensitizer drug impacts the efficacy of inactivation. We demonstrate the relevance of size for drug diffusion in biofilms. The designed meso-imidazolyl porphyrins of small size with positive charges surrounding the macrocycle enabled the inactivation of bacteria in biofilms by 6.9 log units at 5 nM photosensitizer concentration and 5 J cm-2, which offers new opportunities to treat biofilm infections.

Computational Approaches in Theranostics: Mining and Predicting Cancer Data.

The ability to understand the complexity of cancer-related data has been prompted by the applications of (1) computer and data sciences, including data mining, predictive analytics, machine learning, and artificial intelligence, and (2) advances in imaging technology and probe development. Computational modelling and simulation are systematic and cost-effective tools able to identify important temporal/spatial patterns (and relationships), characterize distinct molecular features of cancer states, and address other relevant aspects, including tumor detection and heterogeneity, progression and metastasis, and drug resistance. These approaches have provided invaluable insights for improving the experimental design of therapeutic delivery systems and for increasing the translational value of the results obtained from early and preclinical studies. The big question is: Could cancer theranostics be determined and controlled in silico? This review describes the recent progress in the development of computational models and methods used to facilitate research on the molecular basis of cancer and on the respective diagnosis and optimized treatment, with particular emphasis on the design and optimization of theranostic systems. The current role of computational approaches is providing innovative, incremental, and complementary data-driven solutions for the prediction, simplification, and characterization of cancer and intrinsic mechanisms, and to promote new data-intensive, accurate diagnostics and therapeutics.

Adsorption of charged macromolecules upon multicomponent responsive surfaces.

Adsorption of polyions onto charged surfaces has long been recognized as a crucial phenomenon in biological and technological applications. An intuitive model relating polyelectrolyte adsorption with the imposed features of polarizable surfaces of different compositions and charges is proposed based on Monte Carlo simulations using a coarse-grained approach. The excellent performance of the equation allows simultaneously describing a wide range of adsorption regimes and accounting for specific non-monotonic trends. For a constant surface charge density, the surface composition governs adsorption, promoting variations exceeding 100%. Adsorption increases with the number of attractive charges in the surface until reaching a maximum, decreasing thereafter due to the presence of polyanion-like charged particles. The presence of crowders hampers adsorption. These results can be used to efficiently predict and modulate the interaction between charged macromolecules and different substrates with direct implications in de novo designs of vehicles and biomedical devices.

A novel Pd-catalysed sequential carbonylation/cyclization approach toward bis-N-heterocycles: rationalization by electronic structure calculations.

An unprecedented palladium-catalysed sequential aminocarbonylation/cyclization synthetic strategy, using carbon monoxide and structurally different aliphatic diamines as N-nucleophiles, gives access, in one pot, to a new family of indole-based N-heterocyclic derivatives (hydropyrazinones, benzodiazepinones and hydroquinoxalines). Optimization of the reaction conditions towards double carbonylation (P CO = 30 bar, T = 80°C, iodoindole/diamine ratio = 1 : 1.5, toluene as solvent) allowed the target cyclic products, which are formed in situ via intramolecular cyclization of the ketocarboxamide intermediates, to be obtained through a nucleophilic addition/elimination reaction with the pendant terminal amine groups. The structure of the diamine nucleophile was revealed to affect the reaction's selectivity, with the best yields for the cyclic products being obtained in the presence of (1S,2S)-(+)-cyclohexane-1,2-diamine (a) as the nucleophile, using either 5- or 7-iodoindole as the substrate. The reaction's selectivity was rationalized based on electronic structure calculations, which explain the effect of the diamine structure on the predominant formation of the cyclic products.

Critical Role of the Spacer Length of Gemini Surfactants on the Formation of Ionic Liquid Crystals and Thermotropic Behavior.

Numerous reports have shown that the self-assembling properties of 12-s-12 bis(quaternary ammonium) gemini surfactants in aqueous solution are significantly influenced by s, the number of methylene groups in the covalent spacer. However, the role played by s on the phase behavior of the single compounds has not been investigated in a similarly systematic way. Here, we report on the thermotropic phase behavior of the anhydrous compounds with s = 2-6, 8, 10, and 12, resorting to differential scanning calorimetry (DSC), polarized light microscopy (PLM), and X-ray diffraction (XRD). All of the compounds show a stepwise melting behavior, decomposing at 200 °C. As the spacer length increases, nonmonotonic trends are observed for the thermodynamic parameters of the thermotropic phase transitions, mesophase formation, and solid-state d00l spacings. In particular, the number and type of mesophases (ordered smectic phases and/or fluid smectic liquid crystals) depend critically on s. Further, upon heating molecules with s < 8 decompose before the liquid phase, while those with long spacers, s = 8-12, reach the isotropization (clearing) temperature, hence forming both ionic liquid crystals and ionic liquid phases. We demonstrate that the melting behavior and type of ionic mesophases formed by gemini molecules can be usefully manipulated by a simple structural parameter like the length of the covalent linker.

Free-energy patterns in inclusion complexes: the relevance of non-included moieties in the stability constants.

Inclusion complexes play a definite role in a variety of applications, ranging from drug solubilization to smart materials. This work presents a series of studies based on molecular dynamics, including potential of mean force calculations, and aiming at understanding the factors that govern inclusion. Naphthalene and its derivatives are used as guests for a common host, ß-cyclodextrin. It is observed that the substitution of naphthalene promotes an increase in the complexation constant (up to 100-fold), irrespective of the nature of the substituent, the latter comprising small hydrophobic and hydrophilic (including charged) groups. It is also seen that entropy does not favor inclusion, the order of magnitude of the binding free energy being given by the enthalpic component, with a dominating guest-host interaction contribution. Desolvation penalizes the inclusion process, and is not observed in the vicinity of the hydrophilic and charged groups, which remain exposed to the solvent. Results suggest that substantial modulation of the inclusion complexes can be achieved imposing different substituents, with direct transposition for the modulation of properties in supramolecular structures based on these complexes.

Methyl-ß-cyclodextrin Inclusion Complex with ß-Caryophyllene: Preparation, Characterization, and Improvement of Pharmacological Activities.

ß-Caryophyllene (BCP) is a sesquiterpene that shows high potential in pharmacological applications. However, these have been drastically limited by the respective volatility and poor water solubility. The present study investigates the formation of inclusion complexes between BCP and methyl-ß-cyclodextrin (MßCD) and shows that these complexes promote a significant improvement of the anti-inflammatory, gastric protection, and antioxidant activities relative to neat BCP. It is shown that the solubility of BCP is significantly increased through complexation in phase solubility studies. Inclusion complexes with MßCD in solid state were prepared by three different methods, kneading, rotary evaporation, and lyophilization, with the latter confirmed by differential scanning calorimetry, Fourier transformed infrared spectroscopy, scanning electron microscopy, 1H NMR spectroscopy, and molecular dynamics studies. This study provides for the first time a full characterization of inclusion complexes between BCP and MßCD and highlights the impact of complex formation upon pharmacological activity.

Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study.

Bubbles in DNA are involved in many important biological processes. In this work, a coarse-grained model is used for characterizing bubbles formed in DNA melting. The model resorts only to electrostatic interactions at the Debye-Hückel level, in combination with a short-ranged attractive interaction within a base pair. In spite of also omitting atomistic details, the model is able to capture experimentally established trends in persistence length and radius of gyration. By applying it on different systems, it is possible to conclude that there is a minimum size for stable bubbles, in the interval between 12 and 20 bp, which agrees well with previously published experimental findings. Simulated scattering data distinguishes between different bubbles and detects conformational changes in the melting process. Therefore, SAXS is regarded as useful for bubble formation studies, while simulations provide a molecular understanding.

Synthesis of chiral hexacyclic steroids via [8π + 2π] cycloaddition of diazafulvenium methides.

First examples of [8π + 2π] cycloaddition of 16-dehydropregnenolone (16-DPA) acetate with diazafulvenium methides leading to chiral 4,5,6,7-tetrahydropyrazolo[1,5-a]pyridine-fused steroids are reported. These hexacyclic steroids were obtained exclusively or selectively with the approach of the 1,7-dipole by the less hindered α-face of 16-DPA. Quantum chemical calculations at the DFT level were carried out, using the cycloaddition of 1-methyl- and 1-benzyl-diazafulvenium methides with N-phenylmaleimide as model reactions, in order to rationalize the stereochemistry outcome. The results indicate that endo cycloadditions of the more stable dipole conformation, having the 1-substituent pointing outward, are significantly more favorable than the alternative exo cycloaddition.

Confined polyelectrolytes: The complexity of a simple system.

The interaction between polyelectrolytes and counterions in confined situations and the mutual relationship between chain conformation and ion condensation is an important issue in several areas. In the biological field, it assumes particular relevance in the understanding of the packaging of nucleic acids, which is crucial in the design of gene delivery systems. In this work, a simple coarse-grained model is used to assess the cooperativity between conformational change and ion condensation in spherically confined backbones, with capsides permeable to the counterions. It is seen that the variation on the degree of condensation depends on counterion valence. For monovalent counterions, the degree of condensation passes through a minimum before increasing as the confining space diminishes. In contrast, for trivalent ions, the overall tendency is to decrease the degree of condensation as the confinement space also decreases. Most of the particles reside close to the spherical wall, even for systems in which the density is higher closer to the cavity center. This effect is more pronounced, when monovalent counterions are present. Additionally, there are clear variations in the charge along the concentric layers that cannot be totally ascribed to polyelectrolyte behavior, as shown by decoupling the chain into monomers. If both chain and counterions are confined, the formation of a counterion rich region immediately before the wall is observed. Spool and doughnut-like structures are formed for stiff chains, within a nontrivial evolution with increasing confinement.

Reactions of nitrosoalkenes with dipyrromethanes and pyrroles: insight into the mechanistic pathway.

The reactivity of nitrosoalkenes toward dipyrromethanes, pyrrole, and 2,5-dimethylpyrrole is described. 1-(p-Bromophenyl)nitrosoethylene shows a different chemical behavior with these heterocycles than the previously reported reactions of ethyl nitrosoacrylate, which proceeds via a Diels-Alder reaction. 1-(p-Bromophenyl)nitrosoethylene reacts with dipyrromethanes and pyrrole to afford two isomeric oximes via conjugate addition followed by rearomatization of the pyrrole unit. On the other hand, this nitrosoalkene reacts with 2,5-dimethylpyrrole through an initial conjugate addition followed by intramolecular O- and N-nucleophilic addition with the formation of the corresponding bicyclic oxazine and five-membered cyclic nitrone, respectively. Quantum chemical calculations, at the DFT level of theory, indicate that the barriers associated with the Diels-Alder reactions of ethyl nitrosoacrylate are over 30 kJ/mol lower than those that would be required for the cycloadditions of 1-(p-bromophenyl)nitrosoethylene. Thus, calculations predict that the Diels-Alder reaction is privileged in the case of ethyl nitrosoacrylate and point to a different reaction pathway for 1-(p-bromophenyl)nitrosoethylene, corroborating the experimental findings.

Interpreting the rich behavior of ternary DNA-PEI-Fe(III) complexes.

This work aims to shed light on the mechanism of interaction between components of ternary DNA-PEI-Fe(III) complexes, using experimental and theoretical approaches. In the experimental part, the chelation between PEI-Fe(III) was inspected by potentiometry and electrical conductance measurements and the respective importance for the condensation of DNA analyzed. To this end, three different mixing protocols for the components were imposed using different PEIs, branched (bPEI1.2 and bPEI10) and linear (lPEI2.5 and lPEI25). A delay in DNA condensation was observed when PEI and Fe(III) were premixed and then added to DNA. The set of observations was complemented by determination of the amount of Fe(III) included in the polyplexes, which was found to be dependent on the order of mixture and on the type of PEI used, decreasing with intrinsic PEI condensation efficiency. Overall, a coherent picture in which Fe(III) compensates PEI, probably modulating the respective charge, emerges. Some points arisen from the experimental part were rationalized using Monte Carlo simulations. Different architectured polycation (PC) chains were modeled and an interaction between PC and multivalent ions, mimicking the chelation of Fe(III) by the PEI, was imposed. It was found that chelation enhances polyanion (PA) compaction, irrespective of the PC architecture and charge density. The amount of multivalent ions in each polyplex compensates the negative charge unbalanced by the PC. The charge density and the ability of chelation of each PC dictate the disposition of each condensing agent along the PA backbone, and their coexistence strengthens PA compaction. The deep understanding of these ternary mixtures is a step forward in the optimization of such systems for application in gene delivery.

A new perspective on correlated polyelectrolyte adsorption: positioning, conformation, and patterns.

This work focuses on multiple chain deposition, using a coarse-grained model. The phenomenon is assessed from a novel perspective which emphasizes the conformation and relative arrangement of the deposited chains. Variations in chain number and length are considered, and the surface charge in the different systems ranges from partially neutralized to reversed by backbone deposition. New tools are proposed for the analysis of these systems, in which focus is given to configuration-wise approaches that allow the interpretation of correlated multi-chain behavior. It is seen that adsorption occurs, with a minimal effect upon the bulk conformation, even when overcharging occurs. Also, chain ends create a lower electrostatic potential, which makes them both the least adsorbed region of the backbone, and the prevalent site of closer proximity with other chains. Additionally, adsorption into the most favorable region of the surface overrides, to a large degree, interchain repulsion.

Nonrandom adsorption of polyelectrolyte chains on finite regularly charged surfaces.

Adsorption phenomena are relevant in a wide variety of subjects, from biophysics to technological applications. Different aspects, such as molecular recognition, multilayer deposition, and dynamics of polymer adsorption have been addressed. The methodologies used range from analytical and numerical methods to molecular dynamics or Monte Carlo simulations. In this work, a coarse-grained model is used to explore the adsorption of charged backbones to oppositely charged regions of a surface. These regions encompass those small enough to prevent complete adsorption, but extend to surfaces sufficiently large to promote adsorption with minimal effect on the three-dimensional conformation in bulk. Apart from the different surface areas explored, variations on the surface charge density, polyelectrolyte chain length, and chain stiffness were also considered. The degree of compaction of the polyelectrolyte, on adsorption, is different from that found in the bulk. Also, results indicate an nonuniform adsorption pattern on regularly charged surfaces.

Conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution.

This work presents an investigation on the conformational preferences of alpha,alpha-trehalose in gas phase and aqueous solution. Eighty-one systematically selected structures were studied at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level, giving rise to 40 unique conformers. The 19 lower energy structures and some selected other were further re-optimized at the B3LYP/6-311++G(d,p) level. The main factors accounting for the conformer's stability were pointed out and discussed. NBO and QTAIM analyses were performed in some selected conformers in order to address the anomeric and exo-anomeric effects as well as intramolecular hydrogen bonding. The effect of solvent water on the relative stability of the conformers was accounted for by applying the conductor-like polarizable continuum model, CPCM.

Erythritol: crystal growth from the melt.

The structural changes occurring on erythritol as it is cooled from the melt to low temperature, and then heated up to the melting point have been investigated by differential scanning calorimetry (DSC), polarized light thermal microscopy (PLTM), X-ray powder diffraction (PXRD) and Fourier transform infrared spectroscopy (FTIR). By DSC, it was possible to set up the conditions to obtain an amorphous solid, a crystalline solid, or a mixture of both materials in different proportions. Two crystalline forms have been identified: a stable and a metastable one with melting points of 117 and 104 degrees C, respectively. The fusion curve decomposition of the stable form revealed the existence of three conformational structures. The main paths of the crystallization from the melt were followed by PLTM. The texture and colour changes allowed the characterization of the different phases and transitions in which they are involved on cooling as well as on heating processes. The type of crystallization front and its velocity were also followed by microscopic observation. These observations, together with the data provided by PXRD, allowed elucidating the transition of the metastable form into the stable one. The structural changes occurring upon the cooling and subsequent heating processes, namely those arising from intermolecular hydrogen bonds, were also accompanied by infrared spectroscopy. Particular attention was given to the spectral changes occurring in the OH stretching region.

A study of the structure of the pindolol based on infrared spectroscopy and natural bond orbital theory.

Beta-adrenoceptor-blocking agents (beta-blockers) are on the list of the top selling drugs. Pindolol is a representative of this type of compound, either from the structural point of view, or as reference for comparison of the pharmacokinetic properties of the beta-blockers. A study of the pindolol structure based on infrared spectroscopy and natural bond orbital (NBO) theory is the main aim of the present research. FTIR spectra of the solid pindolol were recorded from 4000 to 400cm(-1), at temperatures between 25 and -170 degrees C. For spectral interpretation, the theoretical vibrational spectra of the conformer present in the solid was obtained at the B3LYP/6-31G* level of theory. NBO analysis of the reference conformer, before and after optimization, was carried out at the same level of theory referred above. Characteristic absorption vibrational bands of the spectra of solid pindolol and of the isolated conformer were identified. Intra- and intermolecular interactions in pindolol were confirmed by the frequency shift of the vibrational modes and by the NBO theory. A detailed molecular picture of pindolol and of its intermolecular interactions was obtained from spectroscopy and NBO theory. The combination of both methods gives a deeper insight into the structure.