Specific and nonspecific collapse in protein folding funnels

Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse transitions are concurrent or whether a nonspecific collapse precedes folding. Many earlier studies have focused on the limit in which collapse is fast compared to the folding time; in this work we focus on the opposite limit where, at the folding temperature, collapse and folding occur simultaneously. Real proteins exist in both of these limits. The folding mechanism varies substantially in these two regimes. In the regime of concurrent folding and collapse, nonspecific collapse now occurs at a temperature below the folding temperature (but slightly above the glass transition temperature).     

Heterocyclic compounds as antiviral drugs: Synthesis,structure–activity relationship and traditional applications

A virus outbreak challenges the economic, medical, and public health infrastructure worldwide. More than one virus capable of triggering diseases have been identified per year since 1972, which requires the development of new ways of treatment and prevention, however, such processes are not rapid and easy. With the pandemic scenario experienced since early 2020, several drugs with well-known purposes have gained prominence, due to speculation of their use in the treatment against the new coronavirus. Among the main drugs studied, the vast majority contain a heterocyclic structure. In this review, we presented the traditional and efficient synthesis of 15 drugs that have been studied for the COVID-19 treatment, containing in their structure heterocycles like indole, quinoline, pyrimidone, tetrahydrofuran, pyrrolidine, triazole, pyridazine, pyrazole, pyrrolopyrimidine, azetidine, pyrrolotriazine, pyrazine, tetrahydropyran, benzofuran, spiroketal, and thiazole. Furthermore, we have shown the original applications, as well as their structure–activity relationship and what is their situation as a drug candidate against COVID-19. Thus, the objective was to consolidate the main synthetic and pharmacological aspects involving clinically developed heterocycles that at some point were presented as promising against SARS-CoV-2.     

Olefin Cyclopropanation by Radical Carbene Transfer Reactions Promoted by Cobalt(II)/Porphyrinates: Active‐Metal‐Template Synthesis of [2]Rotaxanes

A Co^II/porphyrinate‐based macrocycle in the presence of a 3,5‐diphenylpyridine axial ligand functions as an endotopic ligand to direct the assembly of [2]rotaxanes from diazo and styrene half‐threads, by radical‐carbene‐transfer reactions, in excellent 95 % yield. The method reported herein applies the active‐metal‐template strategy to include radical‐type activation of ligands by the metal‐template ion during the organometallic process which ultimately yields the mechanical bond. A careful quantitative analysis of the product distribution afforded from the rotaxane self‐assembly reaction shows that the Co^II/porphyrinate subunit is still active after formation of the mechanical bond and, upon coordination of an additional diazo half‐thread derivative, promotes a novel intercomponent C?H insertion reaction to yield a new rotaxane‐like species. This unexpected intercomponent C?H insertion illustrates the distinct reactivity brought to the Co^II/porphyrinate catalyst by the mechanical bond.     

Molecular dynamics simulations of a nucleoside analogue of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid synthesized as a potential antiviral agent: Conformational studies in vacuum and in water

Conformational analysis of nucleosides may have direct applications to the structure–activity relationship (SAR) studies and in the design of new drug candidates. Although conformational analysis may be accessed in many different ways, in this work it was performed using molecular dynamics (MD) simulation in order to study the dynamic behavior of a nucleoside derivative of 1,4-dihydro-4-oxoquinoline-3-carboxylic acid, synthesized by our group as a potential antiviral agent. The MD simulation was carried out during 10 ns in vacuum and in a box of water at two different temperatures (i.e., 300 and 600 K) using the AMBER force field. The in vacuum MD simulation results are in agreement with the crystallographic structure and with the DFT calculations of the nucleoside, revealing the anti conformer as the more stable one. The simulation in water, however, shows that both conformers may exist at 300 K, the temperature of the in vivo and in vitro assays, revealing that both the syn and anti conformers should be considered in a MD simulation study of the inhibitor–enzyme complex. Simulations are also in agreement with the NOE experiment, which shows that the anti conformer is the preferential one in DMSO-d6 solution at 298 K.     

Conformational analysis: a new approach by means of chemometrics

In conformational analysis, the systematic search method completely maps the space but suffers from the combinatorial explosion problem because the number of conformations increases exponentially with the number of free rotation angles. This study introduces a new methodology of conformational analysis that controls the combinatorial explosion. It is based on a dimensional reduction of the system through the use of principal component analysis. The results are exactly the same as those obtained for the complete search but, in this case, the number of conformations increases only quadratically with the number of free rotation angles. The method is applied to a series of three drugs: omeprazole, pantoprazole, lansoprazole-benzimidazoles that suppress gastric-acid secretion by means of H+, K+-ATPase enzyme inhibition.     

The chemical ecology of cyanobacteria

This review covers the literature on the chemically mediated ecology of cyanobacteria, including ultraviolet radiation protection, feeding-deterrence, allelopathy, resource competition, and signalling. To highlight the chemical and biological diversity of this group of organisms, evolutionary and chemotaxonomical studies are presented. Several technologically relevant aspects of cyanobacterial chemical ecology are also discussed.     

Synthesis of New Chlorin e6 Trimethyl and Protoporphyrin IX Dimethyl Ester Derivatives and Their Photophysical and Electrochemical Characterizations

In view of increasing demands for efficient photosensitizers for photodynamic therapy (PDT), we herein report the synthesis and photophysical characterizations of new chlorin e₆ trimethyl ester and protoporphyrin IX dimethyl ester dyads as free bases and Zn^II complexes. The synthesis of these molecules linked at the β‐pyrrolic positions to pyrano[3,2‐c]coumarin, pyrano[3,2‐c]quinolinone, and pyrano[3,2‐c]naphthoquinone moieties was performed by using the domino Knoevenagel hetero Diels–Alder reaction. The α‐methylenechromanes, α‐methylenequinoline, and ortho‐quinone methides were generated in situ from a Knoevenagel reaction of 4‐hydroxycoumarin, 4‐hydroxy‐6‐methylcoumarin, 4‐hydroxy‐N‐methylquinolinone, and 2‐hydroxy‐1,4‐naphthoquinone, respectively, with paraformaldehyde in dioxane. All the dyads as free bases and as Zn^II complexes were obtained in high yields. All new compounds were fully characterized by 1D and 2D NMR techniques, UV/Vis spectroscopy, and HRMS. Their photophysical properties were evaluated by measuring the fluorescence quantum yield, the singlet oxygen quantum yield by luminescence detection, and also the triplet lifetimes were correlated by flash photolysis and intersystem crossing (ISC) rates. The fluorescence lifetimes were measured by a time‐correlated single photon count (TCSPC) method, fluorescence decay associated spectra (FDAS), and anisotropy measurements. Magnetic circular dichroism (MCD) and circular dichroism (CD) spectra were recorded for one Zn^II complex in order to obtain information, respectively, on the electronic and conformational states, and interpretation of these spectra was enhanced by molecular orbital (MO) calculations. Electrochemical studies of the Zn^II complexes were also carried out to gain insights into their behavior for such applications.     

Black hole bombs and explosions: from astrophysics to particle physics

Black holes are the elementary particles of gravity, the final state of sufficiently massive stars and of energetic collisions. With a 40-year long history, black hole physics is a fully-blossomed field which promises to embrace several branches of theoretical physics. Here I review the main developments in highly dynamical black holes with an emphasis on high energy black hole collisions and probes of particle physics via superradiance. This write-up, rather than being a collection of well known results, is intended to highlight open issues and the most intriguing results.     

Compact stars in Eddington inspired gravity

A new, Eddington inspired theory of gravity was recently proposed by Ba?ados and Ferreira. It is equivalent to general relativity in vacuum, but differs from it inside matter. This viable, one-parameter theory was shown to avoid cosmological singularities and turns out to lead to many other exciting new features that we report here. First, for a positive coupling parameter, the field equations have a dramatic impact on the collapse of dust, and do not lead to singularities. We further find that the theory supports stable, compact pressureless stars made of perfect fluid, which provide interesting models of self-gravitating dark matter. Finally, we show that the mere existence of relativistic stars imposes a strong, near optimal constraint on the coupling parameter, which can even be improved by observations of the moment of inertia of the double pulsar.     

Floating and sinking: the imprint of massive scalars around rotating black holes

We study the coupling of massive scalar fields to matter in orbit around rotating black holes. It is generally expected that orbiting bodies will lose energy in gravitational waves, slowly inspiraling into the black hole. Instead, we show that the coupling of the field to matter leads to a surprising effect: because of superradiance, matter can hover into "floating orbits" for which the net gravitational energy loss at infinity is entirely provided by the black hole's rotational energy. Orbiting bodies remain floating until they extract sufficient angular momentum from the black hole, or until perturbations or nonlinear effects disrupt the orbit. For slowly rotating and nonrotating black holes floating orbits are unlikely to exist, but resonances at orbital frequencies corresponding to quasibound states of the scalar field can speed up the inspiral, so that the orbiting body sinks. These effects could be a smoking gun of deviations from general relativity.