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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.

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.