Probing Mastoparan-like Antimicrobial Peptides Interaction with Model Membrane Through Energy Landscape Analysis.

Antimicrobial Peptides (AMPs) have emerged as promising alternatives to conventional antibiotics due to their capacity to disrupt the lipid packing of bacterial cell membranes. This mechanism of action may prevent the development of resistance by bacteria. Understanding their role in lipid packing disruption and their structural properties upon interaction with bacterial membranes is highly desirable. In this study, we employed Molecular Dynamics simulations and the Energy Landscape Visualization Method (ELViM) to characterize and compare the conformational ensembles of mastoparan-like Polybia-MP1 and its analogous H-MP1, in which histidines replace lysine residues. Two situations were analyzed: (i) the peptides in their free state in an aqueous solution containing water and ions and (ii) the peptides spontaneously adsorbing onto an anionic lipid bilayer, used as a bacteria membrane mimetic. ELViM was used to project a single effective conformational phase space for both peptides, providing a comparative analysis. This projection enabled us to map the conformational ensembles of each peptide in an aqueous solution and assess the structural effects of substituting lysines with histidines in H-MP1. Furthermore, a single conformational phase space analysis was employed to describe structural changes during the adsorption process using the same framework. We show that ELViM provides a comprehensive analysis, able to identify discrepancies in the conformational ensembles of these peptides that may affect their affinity to the membrane and adsorption kinetics.

Integrative approach reveals the identity of Brazilian specimens previously recognized as Anastrepha dissimilis Stone, 1942 (Diptera: Tephritidae).

Anastrepha dissimilis is currently considered to be widely distributed in Brazil, occurring in 20 of 27 states. However, morphological differences between the holotype (from Plaisance, Haiti) and a paratype (from Pernambuco, Brazil) suggest that the Brazilian specimens are not A. dissimilis, because their aculeus tip is similar to the paratype not to the holotype. Therefore, considering the importance of integrative taxonomy for species delimitation, we used geometric and linear morphometrics and cytochrome c oxidase subunit I sequences integrated with the morphology of the aculeus tip to clarify the identity of populations previously identified as A. dissimilis from multiple Brazilian localities. Morphological data show a uniform pattern among the Brazilian populations, with some variation among specimens from the south and northeast. In addition, the geometric and linear morphometrics suggest considerable geographic variation among these populations, suggesting the existence of at least two morphs. The molecular analysis revealed that specimens from Brazil previously identified as A. dissimilis belong to Anastrepha chiclayae Greene, with a genetic distance ranging from 0.00 to 0.015%. According to our integrative analyses, specimens from Brazil formerly identified as A. dissimilis actually are A. chiclayae. Therefore, this is the first record of A. chiclayae in Brazil, and we also report that A. dissimilis does not occur in Brazil.

Modified Atmosphere Does Not Reduce the Efficacy of Phytosanitary Irradiation Doses Recommended for Tephritid Fruit Flies.

Phytosanitary irradiation (PI) has been successfully used to disinfest fresh commodities and facilitate international agricultural trade. Critical aspects that may reduce PI efficacy must be considered to ensure the consistency and effectiveness of approved treatment schedules. One factor that can potentially reduce PI efficacy is irradiation under low oxygen conditions. This factor is particularly important because storage and packaging of horticultural commodities under low oxygen levels constitute practices widely used to preserve their quality and extend their shelf life. Hence, international organizations and regulatory agencies have considered the uncertainties regarding the efficacy of PI doses for insects infesting fresh commodities stored under low oxygen levels as a rationale for restricting PI application under modified atmosphere. Our research examines the extent to which low oxygen treatments can reduce the efficacy of phytosanitary irradiation for tephritids naturally infesting fruits. The effects of normoxia (21% O2), hypoxia (~5% O2), and severe hypoxia (< 0.5% O2) on radiation sensitivity of third instars of Anastrepha fraterculus (sensu lato), A. ludens (Loew), Bactrocera dorsalis (Hendel), and Ceratitis capitata (Wiedemann) were evaluated and compared at several gamma radiation doses. Our findings suggest that, compared to normoxia, hypoxic and severe-hypoxic conditioning before and during irradiation can increase adult emergence and contribute to advancement of larval development of tephritid fruit flies only at low radiation doses that are not used as phytosanitary treatments. With phytosanitary irradiation doses approved internationally for several tephritids, low oxygen treatments applied before and during irradiation did not increase the emergence rates of any fruit fly species evaluated, and all treated insects died as coarctate larvae. Thus, the findings of our research support a re-evaluation of restrictions related to phytosanitary irradiation application under modified atmospheres targeting tephritid fruit flies.

Molecular Aspects of the Dengue Virus Infection Process: A Review.

BACKGROUND: At the present time, dengue is one of the most important arboviruses affecting man, becoming a serious global public health problem, especially in subtropical and tropical countries, where environmental conditions favor the development and proliferation of the mosquito Aedes aegypti. Dengue is caused by a type of flavivírus, which is an enveloped virus of spherical geometry. Nowadays, it is one of the diseases with the highest incidence in Brazil, reaching the population of all states, regardless of social class. Several papers address the molecular aspects of infection of human cell by the viruses, which are reviewed in this work. CONCLUSION: Analyzing the three-dimensional structures of the fusion peptide of dengue virus protein E, we observed that the fusion peptide presents a region rich in hydrophobic residues and a "collar" of charged, polar residues. Probably, this hydrophilic collar plays an important role in the fusion process between the dengue virus and the cell membrane. In order for this disease to cease being a serious global public health problem, we must deepen our knowledge about the fusion process between the dengue virus and the cell membrane through further experimental and, especially, computational studies to find ways to inhibit the mechanism of virus infection.

Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes.

The human respiratory syncytial virus (hRSV) is the major cause of lower respiratory tract infection in children and elderly people worldwide. Its genome encodes 11 proteins including SH protein, whose functions are not well known. Studies show that SH protein increases RSV virulence degree and permeability to small compounds, suggesting it is involved in the formation of ion channels. The knowledge of SH structure and function is fundamental for a better understanding of its infection mechanism. The aim of this study was to model, characterize, and analyze the structural behavior of SH protein in the phospholipids bilayer environment. Molecular modeling of SH pentameric structure was performed, followed by traditional molecular dynamics (MD) simulations of the protein immersed in the lipid bilayer. Molecular dynamics with excited normal modes (MDeNM) was applied in the resulting system in order to investigate long time scale pore dynamics. MD simulations support that SH protein is stable in its pentameric form. Simulations also showed the presence of water molecules within the bilayer by density distribution, thus confirming that SH protein is a viroporin. This water transport was also observed in MDeNM studies with histidine residues of five chains (His22 and His51), playing a key role in pore permeability. The combination of traditional MD and MDeNM was a very efficient protocol to investigate functional conformational changes of transmembrane proteins that act as molecular channels. This protocol can support future investigations of drug candidates by acting on SH protein to inhibit viral infection. Graphical Abstract The ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domainᅟ.

Synthesis, cytotoxicity and in vitro antileishmanial activity of naphthothiazoles.

The leishmaniasis is a spectral disease caused by the protozoan Leishmania spp., which threatens millions of people worldwide. Current treatments exhibit high toxicity, and there is no vaccine available. The need for new lead compounds with leishmanicidal activity is urgent. Considering that many lead leishmanicidal compounds contain a quinoidal scaffold and the thiazole heterocyclic ring is found in a number of antimicrobial drugs, we proposed a hybridization approach to generate a diverse set of semi-synthetic heterocycles with antileishmanial activity. We found that almost all synthesized compounds demonstrated potent activity against promastigotes of Leishmania (Viannia) braziliensis and reduced the survival index of Leishmania amastigotes in mammalian macrophages. Furthermore, the compounds were not cytotoxic to macrophages at fivefold higher concentrations than the EC50 for promastigotes. All molecules fulfilled Lipinski's Rule of Five, which predicts efficient orally absorption and permeation through biological membranes, the in silico pharmacokinetic profile confirmed these characteristics. The potent and selective activity of semi-synthetic naphthothiazoles against promastigotes and amastigotes reveals that the 2-amino-naphthothiazole ring may represent a scaffold for the design of compounds with leishmanicidal properties and encourage the development of drug formulation and new compounds for further studies in vivo.

On the search for potential anti-Trypanosoma cruzi drugs: synthesis and biological evaluation of 2-hydroxy-3-methylamino and 1,2,3-triazolic naphthoquinoidal compounds obtained by click chemistry reactions.

Five 2-hydroxy-3-substituted-aminomethyl naphthoquinones, nine 1,2,3-triazolic para-naphthoquinones, five nor-ß-lapachone-based 1,2,3-triazoles, and several other naphthoquinonoid compounds were synthesized and evaluated against the infective bloodstream form of Trypanosoma cruzi, the etiological agent of Chagas disease, continuing our screening program for new trypanocidal compounds. Among all the substances, 16-18, 23, 25-29 and 30-33 were herein described for the first time and fifteen substances were identified as more potent than the standard drug benznidazole, with IC(50)/24h values in the range of 10.9-101.5 µM. Compounds 14 and 19 with Selectivity Index of 18.9 and 6.1 are important structures for further studies.

Combined crystallographic and solution molecular dynamics study of allosteric effects in ester and ketone p-tert-butylcalix[4]arene derivatives and their complexes with acetonitrile, Cd(II), and Pb(II).

We describe here a procedure to bridge the gap in the field of calixarene physicochemistry between solid-state atomic-resolution structural information and the liquid-state low-resolution thermodynamics and spectroscopic data. We use MD simulations to study the kinetics and energetics involved in the complexation of lower rim calix[4]arene derivatives (L), containing bidentate ester (1) and ketone (2) pendant groups, with acetonitrile molecule (MeCN) and Cd(2+) and Pb(2+) ions (M(2+)) in acetonitrile solution. On one hand, we found that the prior inclusion of MeCN into the calix to form a L(MeCN) adduct has only a weak effect in preorganizing the hydrophilic cavity toward metal ion binding. On the other hand, the strong ion-hydrophilic cavity interaction produces a wide open calix which enhances the binding of one MeCN molecule (allosteric effect) to stabilize the whole (M(2+)) L(MeCN) bifunctional complex. We reach two major conclusions: (i) the MD results for the (M(2+)) 1(MeCN) binding are in close agreement with the "endo", fully encapsulated, metal complex found by X-ray diffraction and in vacuo MD calculations, and (ii) the MD structure for the more flexible 2 ligand, however, differs from the also endo solid-state molecule. In fact, it shows strong solvation effects at the calixarene lower bore by competing MeCN molecules that share the metal coordination sphere with the four CO oxygens of an "exo" (M(2+)) 2(MeCN) complex.

Development of new Cd2+ and Pb2+ Lennard-Jones parameters for liquid simulations.

We present new Lennard-Jones parameters for Cd2+ and Pb2+ ion-water interactions and describe a general methodology to obtain these parameters for any ion. Our strategy is based on the adjustment of ion parameters to reproduce simultaneously experimental absolute hydration free energy and structural properties, namely, g(r) and coordination numbers, obtained from X-ray liquid scattering and quantum mechanical/molecular mechanical (QM/MM) calculations. The validation of the obtained parameters is made by the calculation of dynamical properties and comparing them with experimental values and theoretical results from the literature. The transferability of parameters is checked by the calculation of thermodynamic, structural, and dynamical properties cited above with four different water models. The results obtained for Cd2+ and Pb2+ show an overall agreement with reference values. The absolute hydration free energy calculated with the TIP3P, SPC/E, SPC, and TIP4P water models presents, respectively, percent differences of 3.8, 3.0, 4.3, and 7.2% for lead(II) and 9.8, 8.4, 10.2, and 14.1% for cadmium(II) when compared with experimental values. Ion-water mean distance and coordination numbers for the first coordination shell are in good agreement with experimental and QM/MM results for both ions. Cd2+ shows a lesser diffusion coefficient compared to that of Pb2+ despite its smaller atomic radius, indicating a more persistent first coordination shell for the cadmium(II) ion, a result confirmed with calculations of the mean residence time of water molecules in the first coordination shell.