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The interaction between two nitrosyl ruthenium complexes [Ru (NH.NHq-COOH)(tpy)NO](PF6 )3 (RuBDQ) and [Ru (NH.NHq-H)(tpy)NO](PF6 )3 (RuBD) and human serum albumin (HSA) was investigated using spectroscopic and computational methods. From fluorescence experiments, a dynamic quenching mechanism and binding constants at a single site demonstrated the higher stability of the RuBDQ-HSA system at 308 K compared with RuBD-HSA. Thermodynamic parameters indicated that binding of RuBDQ and RuBD to HSA was mainly driven by hydrophobic interaction and hydrogen bonding, respectively. Synchronous fluorescence and FT-IR results suggested that interactions between both nitrosyl ruthenium complexes and HSA affected protein conformation. Competition experiments revealed that RuBDQ and RuBD bound to Sudlow sites I and II, respectively. Molecular docking results showed that RuBDQ interacted with Ser-192 and Ala-291 residues via hydrogen bonding and polar contact, respectively, whereas RuBD associated with Asn-391 via a polar interaction. Noncovalent interaction results suggested that van der Waals interactions were the main binding forces for both systems, i.e. RuBDQ associated with Trp-214 via van der Waals interaction and with Ty-150 via dipole-dipole bonding, whereas RuBD associated with Tyr-452 via van der Waals forces. The Asp-391 residue interacted with the nitrosyl ligand via polar contact and the terpyridine ligand via van der Waals interaction.

With the advancement of computational and sequencing methods, a large amount of biological data are generated by using various techniques, such as high-throughput screening, next-generation sequencing, Chipseq analysis, microarray analysis, and mass spectroscopy. These generated data sets (genome, transcriptome, proteome, and metabolome) are very complex and provide a holistic view of the biological mechanisms. The biological data have genes, proteins, RNA, and metabolome, which are interconnected with each other and regulate each other’s activation, repression, and in general the expression. Hence, dealing with complex biological networks and extracting the meaningful picture requires newly emerging techniques, such as systems biology. It is an emerging field that provides a top-down approach (whole cell to gene level) for big data analysis. However, the bottom-up approach is also applicable and implemented in systems biology. Hence, in this chapter, we have summarized various big data resources and how that data can be used for the systems biology analysis.

The total impact of the worldwide COVID-19 pandemic is still emerging, changing all relationships as a result, including those with pet animals. In the infection process, the use of Angiotensin-converting enzyme 2 (ACE2) as a cellular receptor to the spike protein of the new coronavirus is a fundamental step. In this sense, understanding which residue plays what role in the interaction between SARS-CoV-2 spike glycoprotein and ACE2 from cats, dogs, and ferrets is an important guide for helping to choose which animal model can be used to study the pathology of COVID-19 and if there are differences between these interactions and those occurring in the human system. Hence, trying to help to answer these questions, we performed classical molecular dynamics simulations to evaluate, from an atomistic point of view, the interactions in these systems. Our results show that there are significant differences in the interacting residues between the systems from different animal species, and the role of ACE2 key residues are different in each system and can assist in the search for different inhibitors for each animal.

The DC-SIGN glycoprotein is responsible for the initial adhesion of dengue virus (DENV) to immune cells by the carbohydrate recognition domain (CRD). There are thirteen soluble and membrane-bound DC-SIGN isoforms, but the role of soluble isoforms in the DENV internalization process is not known. Five isoforms with an altered or absent CRD were identified, and three different soluble isoforms were used to confirm the interactions with mannose residues. The results show the loss of binding ability of one soluble isoform and binding ability of two of them. All of them will be used to verify their role in the DENV internalization process.

The computation of accurate electron affinity (EA) remains one of the most difficult tasks in quantum chemistry. A major source of error in EA calculations is the inadequacy of the basis set (BS) to represent the anionic system, since the Gaussian exponents are normally optimized for the neutral atom energy. To overcome this problem, one must augment the BSs with diffuse functions, which allow a better description of long-range interactions in anionic systems. Here, we report a new methodology to generate BSs for accurate EA computation that consists in the direct optimization of the Gaussian exponents in an anionic environment. By using the anionic basis sets (ABSs), we substantially reduce the errors in EA calculation for boron, carbon, oxygen and fluorine. A graphical analysis of the ABS parameters shows that their exponents are able to span important regions for short- and long-ranged interactions, which permit the ABSs to properly describe both neutral and anionic systems.

The interaction between two nitrosyl ruthenium complexes [Ru (NH.NHq-COOH)(tpy)NO](PF

Streptococcus pneumoniae is a pathogen that resides in the upper respiratory tract of healthy individuals, maintaining a commensal relationship with its host. However, the virulent form may be the etiology of pneumonia, meningitis, bacteremia, and other respiratory tract infections. Streptococcal diseases are preventable by vaccination; but currently available vaccines have some drawbacks, especially due to the high capsule variability of streptococci strains. Thus, an effective prevention strategy continues to be the focus of extensive research. In our work, several bioinformatics tools were used to identify immunogenic peptides from a selected pool of 46 conserved proteins from Streptococcus pneumoniae. In silico analysis showed that 10 proteins had epitopes with affinity for B and T lymphocytes, which were present in at least 26 different pathogens serotypes and were considered promiscuous. The multi-epitope protein, designated HC44, was designed based on these epitopes and specific linkers to improve stability and exposure to T lymphocytes. The recombinant HC44 protein was expressed in E.coli and Swiss-Webster mice were immunised by intraperitoneal injection. Immunisation with the multi-epitope HC44 protein resulted in the production of very high levels of IgG with title superior to 1/1.200.000. However, subtype IgG was highly unbalanced toward IgG1 and no protection was afforded after challenge with S.pneumoniae in a sepsis model. Thus, our strategy has been effective in constructing a highly antigenic protein but novel immunisation strategies should be investigated to reorient the immune system toward a protective response.

In prokaryotic cells, the UvrB protein plays a central role in nucleotide excision repair, which is involved in the recognition of bulky DNA lesions generated by chemical or physical agents. The present investigation aimed to characterize the uvrB gene of Corynebacterium pseudotuberculosis (CpuvrB) and evaluate its involvement in the DNA repair system of this pathogenic organism. In computational analysis, the alignment of the UvrB protein sequences of Escherichia coli, Mycobacterium tuberculosis, Bacillus caldotenax and Corynebacterium pseudotuberculosis showed high similarity and the catalytic amino acid residues and functional domains are preserved. A CpUvrB model was constructed by comparative modeling and presented structural similarity with the UvrB of E. coli. Moreover, in molecular docking analysis CpUvrB showed favorable interaction with EcUvrA and revealed a preserved ATP incorporation site. Heterologous functional complementation assays using E. coli uvrB-deficient cells exposed to UV irradiation showed that the CpUvrB protein contributed to an increased survival rate in relation to those in the absence of CpUvrB. Damaged oligonucleotides containing thymine dimer or 8-oxoguanine lesion were synthesized and incubated with CpUvrB protein, which was able to recognize and excise UV irradiation damage but not 8-oxoguanine. These results suggest that CpUvrB is involved in repairing lesions derived from UV light and encodes a protein orthologous to EcUvrB.

Schistosomiasis is the second leading cause of death due to parasitic diseases in the world. Seeking an alternative for the control of disease, the World Health Organization funded the genome sequencing of the major species related to schistosomiasis to identify potential vaccines and therapeutic targets. Therefore, the aim of this work was to select T and B-cell epitopes from Schistosoma mansoni through computational analyses and evaluate the immunological potential of epitopes in vitro. Extracellular regions of membrane proteins from the Schistosoma mansoni were used to predict promiscuous epitopes with affinity to different human Major Histocompatibility Class II (MHCII) molecules by bioinformatics analysis. The three-dimensional structure of selected epitopes was constructed and used in molecular docking to verify the interaction with murine MHCII H2-IAb . In this process, four epitopes were selected and synthesized to assess their ability to stimulate proliferation of CD4+ T lymphocytes in mice splenocyte cultures. The results showed that Sm041370 and Sm168240 epitopes induced significant cell proliferation. Additionally, the four epitopes were used as antigens in the Indirect Enzyme-Linked Immunosorbent Assay (ELISA) to assess the recognition by serum from individuals infected with Schistosoma mansoni. Sm140560, Sm168240, and Sm041370 epitopes were recognized by infected individuals IgG antibodies. Therefore, Sm041370 and Sm168240 epitopes that stood out in in silico and in vitro analyses could be promising antigens in schistosomiasis vaccine development or diagnostic kits. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:804-814, 2017.

Midazolam (MID) is a sedative drug which can be added in beverage samples as drug-facilitated-sexual assault (date rape drug). This type of drug has short half-life in biological fluids (not detectable) which often prevents the correlation between drug abuse and crime. In this work, we described a simple and low-cost method for fast screening and selective determination of MID in beverage samples (vodka, whiskey and red wine). For the first time, the electrochemical oxidation of MID was used for this purpose. The oxidation mechanism was studied using electrochemical techniques (cyclic and square-wave voltammetry) and computational simulations (density functional theory calculations). Differential-pulse voltammetry, boron-doped diamond electrode (BDDE), and Britton-Robinson (BR) buffer (pH = 2) were selected as electrochemical analysis technique, working electrode and supporting electrolyte, respectively. Different linear response ranges (4–25 μmol L−1 with r = 0.9972; 1–10 μmol L−1 with r = 0.9951; 1–15 μmol L−1 with r = 0.9982) and limits of detection (0.46, 0.43 and 0.33 μmol L−1) were obtained for the analysis of vodka, whisky, and red wine solutions, respectively. The precision and accuracy were satisfactory considering the low relative standard deviation values (RSD

Schistosomiasis remains an important parasitic disease that affects millions of individuals worldwide. Despite the availability of chemotherapy, the occurrence of constant reinfection demonstrates the need for additional forms of intervention and the development of a vaccine represents a relevant strategy to control this disease. With the advent of genomics and bioinformatics, new strategies to search for vaccine targets have been proposed, as the reverse vaccinology. In this work, computational analyses of Schistosoma mansoni membrane proteins were performed to predict epitopes with high affinity for different human leukocyte antigen (HLA)-DRB1. Ten epitopes were selected and along with murine major histocompatibility complex (MHC) class II molecule had their three-dimensional structures optimized. Epitope interactions were evaluated against murine MHC class II molecule through molecular docking, electrostatic potential, and molecular volume. The epitope Sm141290 and Sm050890 stood out in most of the molecular modeling analyses. Cellular proliferation assay was performed to evaluate the ability of these epitopes to bind to murine MHC II molecules and stimulate CD4+ T cells showing that the same epitopes were able to significantly stimulate cell proliferation. This work showed an important strategy of peptide selection for epitope-based vaccine design, achieved by in silico analyses that can precede in vivo and in vitro experiments, avoiding excessive experimentation.

Malaria is responsible for more deaths around the world than any other parasitic disease. Due to the emergence of strains that are resistant to the current chemotherapeutic antimalarial arsenal, the search for new antimalarial drugs remains urgent though hampered by a lack of knowledge regarding the molecular mechanisms of artemisinin resistance. Semisynthetic compounds derived from diterpenes from the medicinal plant Wedelia paludosa were tested in silico against the Plasmodium falciparum Ca2+-ATPase, PfATP6. This protein was constructed by comparative modelling using the three-dimensional structure of a homologous protein, 1IWO, as a scaffold. Compound 21 showed the best docking scores, indicating a better interaction with PfATP6 than that of thapsigargin, the natural inhibitor. Inhibition of PfATP6 by diterpene compounds could promote a change in calcium homeostasis, leading to parasite death. These data suggest PfATP6 as a potential target for the antimalarial ent-kaurane diterpenes.

Human schistosomiasis is a neglected tropical disease of great importance in public health. A large number of people are infected with schistosomiasis, making vaccine development and effective diagnosis important control strategies. A rational epitope prediction workflow using Schistosoma mansoni hypothetical proteins was previously presented by our group, and an improvement to that approach is presented here. Briefly, immunodominant epitopes from parasite membrane proteins were predicted by reverse vaccinology strategy with additional in silico analysis. Furthermore, epitope recognition was evaluated using sera of individuals infected with S. mansoni. The epitope that stood out in both in silico and in vitro assays was used to compose a rational chimeric molecule to improve immune response activation. Out of 2185 transmembrane proteins, four epitopes with high binding affinities for human and mouse MHCII molecules were selected through computational screening. These epitopes were synthesized to evaluate their ability to induce TCD4+ lymphocyte proliferation in mice. Sm204830e and Sm043300e induced significant TCD4+ proliferation. Both epitopes were submitted to enzyme-linked immunosorbent assay to evaluate their recognition by IgG antibodies from the sera of infected individuals, and epitope Sm043300 was significantly recognized in most sera samples. Epitope Sm043300 also showed good affinity for human MHCII molecules in molecular docking, and its sequence is curiously highly conserved in four S. mansoni proteins, all of which are described as G-protein-coupled receptors. In addition, we have demonstrated the feasibility of incorporating this epitope, which showed low similarity to human sequences, into a chimeric molecule. The stability of the molecule was evaluated by molecular modeling aimed at future molecule production for use in diagnosis and vaccination trials.

Dengue virus (DENV) has been characterized as having great clinical importance in the world, as there is no specific treatment against this virus. The NS2B-NS3pro complex is essential for the replication and maturation of DENV and is a potential pharmacological target. The present study aims to evaluate and understand the interactions and affinities (via molecular docking/AutoDock Vina) of 16 peptidomimetic derivatives applied to a NS2B-NS3pro DENV-2 complex constructed by homology modeling (via SWISS-MODEL). Two compounds were selected as potential inhibitors of this protein complex. In addition, these compounds possess important interactions involving Ser135, Gly169 and Tyr161, which have been described previously to be fundamental to the recognition of inhibitors directed to this receptor. Thus, the involvement of these residues is significant pharmacologically because they may contribute to the inhibitory action of this molecular target against DENV.

The barley HvAACT1 gene codes for a citrate transporter associated with tolerance to acidic soil. In this report, we describe a single nucleotide polymorphism (SNP) in the HvAACT1 coding region that was detected as T-1,198 (in genotypes with lower root growth on acidic soil) or G-1,198 (greater root growth) and resulted in a single amino acid change (L/V-172). Molecular dynamic analysis predicted that HvAACT1 proteins with L or V-172 were stable, although the substitution led to structural changes within the protein. To evaluate the effect of the SNP on tolerance to acidic soil, barley accessions were separated into haplotypes based on the presence of a 1 kb insertion in the HvAACT1 promoter and a 21 bp insertion/deletion. These markers and the SNP-1,198 allowed the identification of five haplotypes. Short-term soil experiments showed no difference in root growth for most of the accessions containing the 21 bp insertion and T or G-1,198. In contrast, genotypes showing both the 21 bp deletion and G-1,198, with one of them having the 1 kb insertion, showed greater root growth. These results indicate that the SNP was not advantageous or deleterious when genotypes from the same haplotype were compared. The occurrence of the SNP was highly correlated with the 21 bp insertion/deletion that, together with the 1 kb insertion, explained most of the barley tolerance to acidic soil.

A series of novel long-chain alkyltriazoles were prepared from commercial diols in a rapid process with good yields. The compounds were evaluated in vitro for their anticancer potential against two human cancer cell lines: colon carcinoma (RKO) and uterine carcinoma (HeLa). The results of colorimetric MTT assays showed that six of fourteen compounds tested decreased cell viability in these cell lines. Compounds 5e and 6a were the most active against RKO cells, with IC50 values of 16.70 and 14.57 μM, respectively. The same compounds, 5e and 6a, were the most active in HeLa cells as well, with IC50 values of 11.05 and 12.77 μM, respectively. In addition, compound 5e was found to induce apoptosis in RKO cells, as assessed by TUNEL assay. The results suggest that compound 5e may be a promising prototype anticancer agent.

Herein, we report the antimalarial activity of nine 4-methoxychalcone derivatives 1a–i and an initial analysis of their ADMET properties. All compounds showed potent activity against the P. falciparum chloroquine-resistant clone W2, with IC50 values ranging from 1.96 µM to 10.99 µM, with moderate or low cytotoxicity against the HeLa cell line. The compound 1a (IC50 = 2.06 µM) had the best selectivity index (9.0). All the sulfonamide 4-metychalcone derivatives synthesized had cLogP values between 2 and 5 (mean value 3.79) and molecular weights (MWs) below 500. The substitution of the pyrrolidine group in 1i by a morpholine group in 1a reduced the cLogP value from 3.05 in compound 1i to 2.34 in compound 1a. Indeed, compound 1a had the highest LipE value. The binding free energy of compound 1a showed it to be the most optimal chalcone derivative for plasmepsin-2 (−7.3 Kcal/mol). The physicochemical properties and LipE analysis of the dataset allowed us to establish that compound 1a is the highest quality compound of the series and a potential oral lead candidate.

macrocycles was evaluated by the differencebetween the respective binding energies. The first-row metal binding energy is higher to polyethermacrocycle than to polyamine one. In the case of second-row transition metals, the polyamine lig-and has a higher binding energy than the polyether macrocycle. This behavior is in good agreementwith the macrocyclic cavity dimension, which has a direct relation to the ring size and metal ionsize. While the oxygen–oxygen distances are close to4Ainthepolyether macrocycle cavity, in thepolyamine one the nitrogen–nitrogen distances are close to 5 A.

The expression in silico, which means performed on computer or via computer simulation, has been seen with increasing frequency, in almost every area of knowledge, in scientific papers published in the last few years. This is particularly true with regard to biochemistry; it is quite hard to imagine any area in which in silico analysis has not been employed, isolated or hand-in-hand with experimental analysis, to predict the structure and/or energetic behavior, in such a way that it furnishes a relatively detailed vision of the behavior of specific molecules in biochemical systems. The term “in silico analyses” embraces a series of techniques, which can be used for atomic and for molecular systems. These techniques may use the principles and methods of quantum or Newtonian mechanics, depending on the level of analyses desired. Bioinformatics applies neither quantum nor Newtonian mechanics, but it is included in in silico analysis once it uses a computer to analyze biological data, such as the information of genome and proteome projects, searching for similarity in protein sequences, reverse vaccinology, etc. The description made here is about the current status of spider toxin deposits in public databases, the techniques of bioinformatics used in the study of such peptides, molecular docking, and molecular dynamics. Initially, a short introduction in the techniques in this area is given, followed by the list of some of the studies that have applied these techniques to spider toxins.

Artemisinin (Qinghaosu) is a sesquiterpene lactone with an endoperoxide function being currently used against strains of Plasmodium falciparum. These compounds are supposed to act on heme leading to reduction of the peroxide bond and production of radicals that can kill the parasite. The main goal of this study was the identification of new potential antimalarial drugs from natural sources as well as to find possible correlations between in silico parameters and experimental data. Thus, the interactions of 51 peroxides with heme were studied by molecular docking following refinement by conformational analysis and semiempirical parametric method 6. As a result, correlation between complex energy and dissociation constant (Kd) was found to be significant. The results indicate that compounds 5 and 24 are promising antimalarial agent. © 2012 Wiley Periodicals, Inc.

Several medicinal plants have been studied in recent years in Brazil. However, despite many efforts, the pharmacological mechanisms of many natural products are still unknown. Several biological assays in vivo and in vitro are needed to further address this issue, which increases the cost of these studies. The main goal of this study was to apply the methodology of inverse virtual screening (IVS), followed by docking studies, and refinement by molecular dynamics (MD) simulation and quantum mechanical/molecular mechanical to determine the pharmacological receptors for five selected natural products with the exception of the benzoxazinone isolated from the exudate of the radicle of the crop species which were mainly isolated from the Cerrado species, obtained from Cerrado, a typical Brazilian biome. Initially, the structures of the natural compounds were generated using the online software program sc-PDB, which searches for molecular targets deposited in the protein data bank. The ligands were docked against target proteins found in IVS step-forming complexes, which were refined again using MD simulations by ff03 force field for 1 ns. Finally, the binding energy for each complex was obtained by the ONIOM (PM6:UFF) method. As a result, these calculations suggested possible molecular targets for these natural compounds. Among the targets found were 1EH4, 2A4Z, 1H49, 1JT2, 2BNJ, and 3FW9, which are involved in cancer and rheumatoid arthritis pathologies, indicating that they are promising molecular targets. In this study, we proposed a biological assay for these natural compounds. The results indicate that structural changes may be proposed to generate compounds that are able to bind more strongly to the receptor and become new drug candidates, thus optimizing the search for lead natural compounds. © 2012 Wiley Periodicals, Inc.

The culture of cacao in Brazil was highly harmed by Moniliophthora perniciosa, the fungus that causes witches' broom disease of cocoa. This disease decreases significantly the cocoa production. An important strategy for control of the witches' broom is the molecular study of the interaction between cacao–M. perniciosa. However, there is little information about of the mechanism of molecular interaction involved in resistance/vulnerability of cacoa tree. To address this problem, the Genome Project showed genes of cysteine protease involved in the mechanism of resistance/vulnerability. Cysteine protease is expressed during the process of the maturation of the seed and it is present in necrofitics period of the disease. Furthermore, proteases have a wide application in feed products, detergents, and pharmaceutical industries. This work constructed the three-dimensional structure of the cysteine protease of Theobroma cacao by comparative modeling. Thus, the primary sequence of the cysteine protease of T. cacao was submitted to BLASTp obtaining the protein 1PCI with 36% of structural similarity. The model was refined and validated by AMBER 11.0; and evaluated by PROCHECK and ANOLEA software, respectively. This model consists of 171 amino acids, formed by 2693 atoms linked by 2719 chemical bonds. The 3D structure of this enzyme has seven α-helix, 23 turns, and two β-sheets. The region of the conserved active site is represented by residues Cys25 and His159. From this model, a mutant model was then generated by replacing His159/Gly. This also was evaluated showing similar characteristics. Studies of the interaction between the mutant structure with the metal ions such as Zn+2, Cu+1, Cu+2, and Cd+2 were performed by Quantum Mechanical/Molecular Mechanical (QM/MM) approach implemented in Gaussian 09W. As a result, the mutant protein is able to complex with all of them, principally with Cd+2 by −3.04 Kcal/mol. This is potentially toxic element present in the environment. Therefore this study suggests that changes in the sequence of the cysteine protease of T. Cacao can lead to development new products of commercial interest. © 2012 Wiley Periodicals, Inc.

In this study, the aim was to determine the complete sequence of the Copaifera langsdorffii trypsin inhibitor (CTI)-1 using 2-dimensional (2D)-PAGE, matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF), and quadrupole time-of-flight (QTOF) spectrometry. Spots A (CTI-1) and F (CTI-2) were submitted to enzymatic digestions with trypsin, SV8, and clostripain. The accurate mass of the peptide obtained from each digest was determined by mass spectrometry (MS) using MALDI-TOF. The most abundant peptides were purified and sequenced in a liquid chromatograph connected to an electrospray ionization-QTOF MS. When the purified trypsin inhibitor was submitted to 2D electrophoresis, different spots were observed, suggesting that the protein is composed of 2 subunits with microheterogeneity. Isoelectric points of 8.0, 8.5, and 9.0 were determined for the 11 kDa subunit and of 4.7, 4.6, and 4.3 for the 9 kDa subunit. The primary structure of CTI-1, determined from the mass of the peptide of the enzymatic digestions and the sequence obtained by MS, indicated 180 shared amino acid residues and a high degree of similarity with other Kunitz (KTI)-type inhibitors. The peptide also contained an Arg residue at the reactive site position. Its 3-dimensional structure revealed that this is because the structural discrepancies do not affect the canonical conformation of the reactive loop of the peptide. Results demonstrate that a detailed investigation of the structural particularities of CTI-1 could provide a better understanding of the mechanism of action of these proteins, as well as clarify its biologic function in the seeds. CTI-1 belongs to the KTI family and is composed of 2 polypeptide chains and only 1 disulfide bridge.

Malaria is the most prevalent parasitic disease in the world. Currently, an effective vaccine for malaria does not exist, and chemotherapy must be used to treat the disease. Because of increasing resistance to current antimalarial drugs, new treatments must be developed. Among the many potential molecular targets, the hexose transporter of Plasmodium falciparum (PfHT) is particularly promising because it plays a vital role in glucose transport for the parasite. Thus, this study aims to determine the three-dimensional structure of PfHT and to describe the intermolecular interactions between active glycoside derivatives and PfHT. Such information should aid in the development of new antimalarial drugs. The receptor PfHT was constructed from primary sequences deposited in the SWISS MODEL database. Next, molecular docking simulations between O-(undec-10-en)-l-D-glucose and the constructed active site models were performed using Autodock Vina. The glycoside derivative-PfHT complexes were then refined using the hybrid QM/MM (PM3/ff03) method within the AMBER package. The models were then evaluated using Ramachandran plots, which indicated that 93.2% of the residues in the refined PfHT models (P5) were present in favorable regions. Furthermore, graphical plots using ANOLEA showed that the potential energies of interaction for atoms unbonded to P5 were negative. Finally, the O-(undec-10-en)-l-D-glucose-PfHT complex was evaluated using 20-ns Molecular Dynamics simulations with an ff03 force field. Docking and QM/MM studies revealed the amino acids essential for molecular recognition of and activity on glycosides. Inhibition of glucose transporters may prevent the development and metabolism of P. falciparum, so a description of the receptor’s structure is a critical step towards rational drug design.

Cardiotonic steroids (CS), natural compounds with traditional use in cardiology, have been recently suggested to exert potent anticancer effects. However, the repertoire of molecules with Na,K-ATPase activity and anticancer properties is limited. This paper describes the synthesis of 6 new digoxin derivatives substituted (on the C17-butenolide) with γ-benzylidene group and their cytotoxic effect on human fibroblast (WI-26 VA4) and cancer (HeLa and RKO) cell lines as well as their effect on Na,K-ATPase activity and expression. As digoxin, compound BD-4 was almost 100-fold more potent than the other derivatives for cytotoxicity with the three types of cells used and was also the only one able to fully inhibit the Na,K-ATPase of HeLa cells after 24h treatment. No change in the Na,K-ATPase α1 isoform protein expression was detected. On the other hand it was 30-40 fold less potent for direct Na,K-ATPase inhibition, when compared to the most potent derivatives, BD-1 and BD-3, and digoxin. The data presented here demonstrated that the anticancer effect of digoxin derivatives substituted with γ-benzylidene were not related with their inhibition of Na,K-ATPase activity or alteration of its expression, suggesting that this classical molecular mechanism of CS is not involved in the cytotoxic effect of our derivatives.

Accurate Gaussian basis sets for atoms from H to Ba were obtained by means of the generator coordinate Hartree-Fock (GCHF) method based on a polynomial expansion to discretize the Griffin-Wheeler-Hartree-Fock equations (GWHF). The discretization of the GWHF equations in this procedure is based on a mesh of points not equally distributed in contrast with the original GCHF method. The results of atomic Hartree-Fock energies demonstrate the capability of these polynomial expansions in designing compact and accurate basis sets to be used in molecular calculations and the maximum error found when compared to numerical values is only 0.788 mHartree for indium. Some test calculations with the B3LYP exchange-correlation functional for N2, F2, CO, NO, HF, and HCN show that total energies within 1.0 to 2.4 mHartree compared to the cc-pV5Z basis sets are attained with our contracted bases with a much smaller number of polarization functions (2p1d and 2d1f for hydrogen and heavier atoms, respectively). Other molecular calculations performed here are also in very good accordance with experimental and cc-pV5Z results. The most important point to be mentioned here is that our generator coordinate basis sets required only a tiny fraction of the computational time when compared to B3LYP/cc-pV5Z calculations.

The prolapse-free relativistic adapted Gaussian basis sets (RAGBSs), developed by our research group on the basis of the four-component approach, are used for the first time in Douglas–Kroll–Hess 2nd order scalar relativistic calculations (DKH2) of simple diatomic molecules containing Hydrogen and the halogens from Fluorine up to Iodine: HX and X 2 , where X = F, Cl, Br, and I. To this end, the RAGBSs were contracted with the general contraction scheme to triple-, quadruple-, and quintuple-zeta sets. Polarization functions were also added to the basis sets by optimization with the configuration interaction method including single and double excitations into the DKH2 environment, DKH2-CISD. The molecular properties were then calculated with the coupled cluster electronic correlation treatment and the DKH2 scalar relativistic method, DKH2-CCSD(T), and indicated that our RAGBSs should be contracted as quadruple-zeta basis sets. The results achieved with the DKH2-CCSD(T) calculations and the selected quadruple-zeta RAGBSs are able to reproduce the experimental data of equilibrium distances, dissociation energies, and harmonic vibrational frequencies with root-mean-square (rms) errors of 0.015 A, 3.6 kcal mol −1 , and 21.7 cm −1 , respectively.

Prolapse-free relativistic Gaussian basis sets are presented for all the closed-shell elements up to nobelium, using the spherical nuclear model. These relativistic Gaussian basis sets were generated using the polynomial version of the generator coordinate Dirac–Fock (p-CGDF) method with the goal of obtaining an energy difference with respect to numerical results in the millihartree order of magnitude, resulting in a good balance between cost and accuracy. The discretization parameters for generating the Gaussian exponents are also presented. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Cardiotonic steroids are used to treat heart failure and arrhythmia and have promising anticancer effects. The prototypic cardiotonic steroid ouabain may also be a hormone that modulates epithelial cell adhesion. Cardiotonic steroids consist of a steroid nucleus and a lactone ring, and their biological effects depend on the binding to their receptor, Na,K-ATPase, through which, they inhibit Na+ and K+ ion transport and activate of several intracellular signaling pathways. In this study, we added a styrene group to the lactone ring of the cardiotonic steroid digoxin, to obtain 21-benzylidene digoxin (21-BD), and investigated the effects of this synthetic cardiotonic steroid in different cell models. Molecular modeling indicates that 21-BD binds to its target Na,K-ATPase with low affinity, adopting a different pharmacophoric conformation when bound to its receptor than digoxin. Accordingly, 21-DB, at relatively high µM amounts inhibits the activity of Na,K-ATPase α1, but not α2 and α3 isoforms. In addition, 21-BD targets other proteins outside the Na,K-ATPase, inhibiting the multidrug exporter Pdr5p. When used on whole cells at low µM concentrations, 21-BD produces several effects, including: 1) up-regulation of Na,K-ATPase expression and activity in HeLa and RKO cancer cells, which is not found for digoxin, 2) cell specific changes in cell viability, reducing it in HeLa and RKO cancer cells, but increasing it in normal epithelial MDCK cells, which is different from the response to digoxin, and 3) changes in cell-cell interaction, altering the molecular composition of tight junctions and elevating transepithelial electrical resistance of MDCK monolayers, an effect previously found for ouabain. These results indicate that modification of the lactone ring of digoxin provides new properties to the compound, and shows that the structural change introduced could be used for the design of cardiotonic steroid with novel functions.

Fitases (EC 3.1.3.8), quando presentes em racoes para animais, aumentam a qualidade nutricional por aumentar a biodisponibilidade de fosfatos. Entretanto, seu uso e restrito, pois sofrem rapida degradacao pelo suco gastrico. Com objetivo de desenvolver fitase acido resistente, um modelo da fitase de Yersinia foi construido por modelagem comparativa. Inicialmente, uma busca por estruturas moldes seguida da construcao do modelo foi realizada pelo programa SWISS MODEL. O modelo construido foi avaliado quanto a estereoquimica da cadeia principal pelo PROCHECK. Finalmente, o modelo foi refinado simulacao de dinâmica molecular por 8 nanosegundos atraves do programa AMBER. Como resultado, o modelo possui as mesmas caracteristicas da estrutura molde, fitase de Escherichia coli, PDB: 1DKQ. Alem disso, o modelo resultante mostra que o residuo de histidina e capaz de interagir com o grupamento fosfato presente no fitato. Este modelo permitira realizar estudos de mutagenese dirigida in silico, capaz de desenvolver fitases com propriedades fisico-quimicas mais adequadas.

Schistosomiasis is a serious public health problem in Brazil and worldwide. Although the drugs used to treatment schistosomiasis are effective, the disease continues to expand in all endemic countries due to constant reinfection, poor sanitation, and the lack of effective programs for disease control. However, advances generated through genome projects have provided important information that has improved the understanding of the biology of this parasite. These advances, associated with the advent of bioinformatic analysis, are becoming an important tool in reverse vaccinology. Through database access to the DNA and protein sequences of Schistosoma mansoni and the use of bioinformatics programs, fourteen epitopes were identified. Five epitopes were obtained from proteins whose immunogenic potential had already been assessed in other studies (KP), and nine whose immunogenic potential is unknown (UP). To improve stimulation of the host immune system, the selected epitopes were modeled with a sugar moiety. After this addition, all of the epitopes showed structures similar to those observed in the native proteins, but only eleven of the peptides presented thermodynamically stable structures. Prediction analysis and molecular modeling showed that the glycopeptides presented here are important targets in the search for a vaccine against schistosomiasis. Additionally, they suggest that these molecules may be used in immunological assays to evaluate the level of protection, the effect on pathology reduction and the profile of cytokines and antibodies induced by them.

A asma é caracterizada como um distúrbio inflamatório crônico das vias aéreas, provocada pela contração da musculatura lisa dos bronquíolos, ocasionando obstrução parcial dos mesmos e dificultando a respiração. A Organização Mundial de Saúde (OMS) estima que 300 milhões de pessoas atualmente sofram de asma, sendo que as crianças estão entre as mais acometidas. Somente em 2005, 255.000 pessoas morreram de asma. Dentre os mediadores envolvidos no processo asmático, os leucotrienos cisteínicos, derivados do ácido araquidônico, são considerados os mais potentes entre aqueles envolvidos no processo asmático, indicados como principais mediadores da inflamação reversível das vias aéreas. Nos últimos 20 anos, grandes esforços têm sido realizados para identificar e desenvolver antagonistas dos receptores de leucotrienos na busca de melhorar o tratamento da asma, limitar a sua morbidade, e reduzir os efeitos dos medicamentos atuais. Portanto, o presente estudo propôs a construção de um modelo teórico do receptor do leucotrienos cisteínicos denominado CysLT1 por Modelagem Comparativa. Conclui-se que o modelo obtido através das metodologias computacionais e apresentado no presente estudo pode auxiliar em futuros testes, principalmente em metodologias que empregam ancoragem molecular e de novo design testando, in silico, ligantes de diversas fontes contra o receptor CysLT1.

A detailed theoretical study of the 1,7,1l,17-tetraoxa-2,6,12,16-tetraaza-cycloeicosane ligand ([20]AneN4O4) coordinated to Fe2+, Co2+, Ni2+, Ru2+, Rh2+, and Pd2+ transition metal ions was carried out with the B3LYP method. Two different cases were performed: when nitrogen is the donor atom (1aq) and also with the oxygen as the donor atom (1bq). For all the cases performed in this study 1aq structures were always more stable than the 1bq ones. Considering each row is possible to see that the energy increases with the increase of the atomic number. The M2+ cation binding energies for the 1aq complexes increase with the following order: Fe2+ < Ru2+ < Co2+ < Ni2+ < Rh2+ < Pd2+.

A Triagem Virtual Inversa, ou Triagem Inversa, consiste em uma busca em banco de dados de estruturas proteicas, sendo estas de relevância farmacologica, de maneira a evidenciar in silico, os receptores farmacologicos de atuacao para um determinado ligante de interesse. A plataforma utilizada denomina-se sc-PDB, o qual e um software on-line que abriga somente alvos farmacologicos, sendo selecionadas a partir do PDB. O principal objetivo deste estudo e realizar o processo de TVI para neurotransmissores cujos receptores encontram-se descritos no PDB. Este estudo preliminar busca validar o metodo de TVI para uma posterior aplicacao em compostos naturais. A estrutura dos neurotransmissores da adrenalina, serotonina e adenosina foram submetidos ao programa on-line sc-PDB. Onze variaveis foram estudadas, cada uma separadamente, mantendo as demais segundo o default do programa. Apos esse procedimento foi estabelecido um protocolo, o qual sera utilizado na busca de receptores de compostos naturais. Nesse protocolo ficou estabelecido o procedimento que encontra maior numero de ligantes, na qual a molecula deve ser gerada sem os seus hidrogenios, sem estereoquimica, definindo como parâmetro de entrada subestrutura, e sem considerar variaveis como numero de ligacoes rotaveis, de aneis ou de grupos doadores e receptores de ligacao hidrogenio. 10.5216/ref.v8i1.10561

Dopamine (DA) is an important neurotransmitter in the Central Nervous System (CNS) of mammals being found in significant quantities in the brain. In a low concentration is associated with Parkinson's disease [1], which makes it important detection. However, a major problem in determining DA is its joint resolution with coexisting species such as ascorbic acid (AA). In traditional solid electrodes, AA is oxidized at a potential close to that of DA, resulting in an overlapping voltammetric response [2]. Therefore, improving the selectivity of the monitoring techniques of AD has been the focus of much research. [3] Thus, ionic liquids at ambient temperatures (RTILs) tetrafluoroborate and 1-butyl-3-methylimidazolium (BMI.BF4) can be used as electrolytes for different electrochemical reactions, which have important properties, the selectivity of them, making the technique voltammetric more efficient. Our focus as this work is to analyze the behavior of these molecules (DA and AA) amid BMI.BF4 compared to conventional solvents, using a method known as Molecular Dynamics (MD), being a powerful tool for obtaining properties structural and thermodynamic properties of these substances. MD simulations were carried out for systems in DA [BMI.BF4] and AA [BMI.BF4]. For comparison, simulations were also carried out in water. All simulations were performed using the AMBER 9 package. We also used PTRAJ to perform analyses on the data we collected, such as calculating density, total energy, RDFs and self-diffusion coefficients, and we used xmgrace and gnuplot to aid us in visualizing the data. As part of evaluating the interference between molecules (AA and DA), we show the results of analyzes of AA. In this case the average density is 1.0768 cc / mol, while the water density is 1.027 cc / mole. As the total energy of the two systems have different values and constants (-19.5 kcal / mol in the midst of water and -12.5 kcal / mol among LI) along the dynamics. This difference in energy is given by unfavorable interactions that AA has with the molecules of the LI. For a better understanding of the systems were calculated the radial distribution functions for each of statepoints. The results presented in both solvent were similar, demonstrating that the AA is added in both LI well as for water, ie they have good solvation. Regarding the results of diffusivity, the 298K and 1 atm the coefficient of self-diffusion (MSD) showed lower values compared to the water in the same conditions. This result reveals the MSD in a higher viscosity of the LI and so may be an important property for separation of molecules (AA and DA) and therefore important in electrochemical process.

A malaria e uma doenca de importância mundial. A necessidade pela busca de novas alternativas terapeuticas e reforcada devido a crescente resistencia adquirida pelo parasito aos farmacos atuais. O transportador de hexoses de Plasmodium falciparum (PfHT) tem apresentado suporte genetico para que PfHT seja utilizado como alvo para o desenvolvimento de antimalaricos, podendo com isso inibir a absorcao de glicose e eliminar os parasitas. Com o objetivo de avaliar a conformacao farmacoforica do ligante previamente ancorado ao receptor antes e apos a simulacao de dinâmica (DM) molecular. Desta forma foi possivel analisar que o processo de dinâmica molecular permitiu ao modelo estabilidade bem como caracteristicas de viabilidade mais proximas a sua utilizacao biologica. O que demonstra a impotância de ferramentas de bioinformatica em estudos de moleculas bioativas com possivel potencial farmacologico.

A malaria e uma doenca para a qual e necessario o desenvolvimento de novos antimalaricos com maior eficacia devido a crescente resistencia que o parasito vem adquirindo. O objetivo deste trabalho foi realizar uma triagem in silico a fim de encontrar compostos com maior afinidade com o receptor transportador de hexose do Plasmodium falciparum (PfHT), considerado um novo alvo molecular contra a malaria. Assim, estudos de ancoragem molecular foram realizados utilizando o software AutoDock Vina a fim de avaliar as energias de ligacao e as interacoes receptor-ligante. Os resultados mostraram que os compostos analisados podem ser potenciais antimalaricos, no entanto os compostos 28951446 e 59797532 sao os que possuem melhores energias de ligacao e interacoes entre ligante-receptor, c onstituindo assim, potenciais farmacos antimalaricos.

Devido a grande resistencia do Plasmodium falciparum as terapias ja existentes, e necessario desenvolver antimalaricos mais eficazes. Estudos anteriores tem mostrado que o receptor transportador de hexose do Plasmodium falciparum (PfHT) tem grande relevância para novos estudos, pois, a sua inibicao diminui a absorcao da glicose e, consequentemente, elimina o parasito. Nosso estudo teve como objetivos construir um modelo do receptor da PfHT capaz de descrever a atividade biologica e a conformacao farmacoforica de derivados de glicose atraves de estudos de acoplamento molecular entre ligante-receptor.

A malaria e um dos principais problemas de saude publica no mundo. A crescente resistencia adquirida pelo parasito aos farmacos atuais endossa a necessidade pela busca de novos antimalaricos. A PfHT tem se mostrado como importante alvo molecular no desenvolvimento de novos antimalaricos, por inibir a absorcao de glicose levando a morte do parasito. Com o objetivo de estudar as interacoes de receptores com a PfHT, visando o planejamento de novas moleculas bioativas que bloqueiam a biossintese e induzam a morte o parasita foram realizados estudos de dinâmica molecular das interacoes proteina-ligante da PfHT. Os resultados preliminares motivam a utilizacao do modelo do receptor da PfHT como inibidor no transporte de hexose no ciclo de vida do parasita por apresentarem estabilidade durante a interacao. Assim, novos compostos prototipos poderao ser planejados, os quais poderao ser capazes de se ligarem a este receptor de forma mais efetiva e seletiva.

A esquistossomose humana e uma doenca cronica e debilitante causada por helmintos com maior taxa de mortalidade no mundo. Neste estudo foram selecionados epitopos de proteinas da superficie do Schistosoma mansoni para construcao de uma proteina quimerica com capacidade de induzir uma resposta imune e reducao da patologia. Analises in silico foram feitas para obtencao da sequencia proteica, avaliacao de parâmetros fisicos e quimicos, e modelagem da estrutura 3D. Atraves da modelagem comparativa foram construidos modelos 3D da quimera. As analises foram refinadas por calculos moleculares seguidas de simulacao da dinâmica molecular. Os modelos refinados das estrutura das quimeras forneceu informacoes sobre a sua dobragem e a estabilidade termodinâmica. Considerando que e um modelo termodinamicamente estavel, foi realizada a sintese e expressao da quimera em linhagem de bacterias E. coli DE3-Rosetta para futuros ensaios de purificacao e analise de imunogenicidade.

A dengue e a Arbovirose mais prevalente do mundo. O virus infecta anualmente cerca de 50 a 100 milhoes depessoas, das quais 500 000 evoluem para quadros mais graves como a dengue hemorragica e a sindrome do choque da dengue, cujo indice de mortalidade atinge os 20% em alguns casos. Nao existe vacina licenciado ou terapia antiviral especifica. Na tentativa de se desenvolver estrategias terapeuticas a NS5 metiltransferase converge em um potencial alvo farmacologico para o desenvolvimento racional de farmacos,uma vez ser ela essencial para os processos de replicacao do virus na celula hospedeira. A triagem virtual de compostos em banco de dados fornece uma ferramenta importante para a obtencao de estruturas quimicas com potencial atividade farmacologica, e acoplada a analises em modelagem molecular, pode-se predizer a atividade destes compostos, reduzindo assim os gastos com a sintese e testes biologicos de moleculas candidatas a farmacos.

O virus da dengue (DENV) caracteriza-se como virus de grande importância clinica, uma vez que acometem milhoes de pessoas anualmente em todo o mundo. Estrategias para o desenvolvimento de medicamentos voltados para o combate e controle do DENV tornam-se de extrema relevância e necessidade, uma vez que ate o momento nao se tem disponivel nenhum tratamento especifico contra o mesmo. Nesse contexto, destaca-se o complexo NS2B-NS3pro, essencial para replicacao e maturacao do DENV, sendo um potencial alvo farmacologico. O presente estudo tem como objetivo avaliar os resultados de ancoragem molecular, realizada na presenca e ausencia de moleculas de agua, desenvolvido para avaliar a afinidade potenciais candidatos a inibidores de NS2B-NS3pro.

Os bancos de dados sao uma ferramenta importante de gerenciamento de informacoes. A organizacao de alvos moleculares em um banco especifico possibilita a rapida triagem de compostos prototipos e agiliza os ensaios biologicos, diminuindo os custos e o tempo de pesquisa de novos compostos bioativos. A criacao do banco de alvos moleculares ira contribuir para a maior integracao e eficiencia da pesquisa de novos farmacos na UFSJ/CCO.

DOI 10.5433/2316-5200.2013v2n4p59 Malaria e a doenca parasitaria que mais acomete o homem. Segundo a Organizacao Mundial de Saude (OMS), o aparecimento de cepas de Plasmodium resistentes a artemisinina tornam a busca de novos alvos e compostos com acao antimalarica extremamente necessaria. Neste estudo relatamos aspectos historicos, ciclo biologico, atuais farmacos, alvos moleculares passiveis de intervencao terapeutica e recentes receptores farmacologicos. Esta revisao conclui com uma breve discussao das perspectivas e dificuldades contribuindo para o avanco no desenvolvimento de novos antimalaricos.