Tuberculosis (TB) is a bacterial infection caused by the bacillus Mycobacterium tuberculosis. It usually affects the lungs, but it can also affect other sites (extrapulmonary TB).

In the “Global Tuberculosis Report 2018”, TB is recognized as one of the 10 main causes of death worldwide and the main cause of a single infectious agent (above HIV/AIDS).

By the other hand, medicinal plants have been widely used to treat this disease. Some extracts derived from plants are known to have antimycobacterial properties, and can be of great significance in therapeutic treatments. For that reason, we aimed to evaluate the antimycobacterial activity of Cissus incisa leaves on a sensible strain. Three extracts were prepared from collected leaves of this plant: hexane, chloroform methanol (1:1) and aqueous. The antitubercular activity was evaluated on M. Tuberculosis H37RV strain (ATCC), using Alamar Blue assay. The hexane and chloroform/methanol extracts were the most active (MIC=250 μg/mL). Until the best of our knowledge, there are no studies related to the traditional use of this plant for treat tuberculosis.

The present investigation will contribute to the discovery of potential antibacterial agents derived from plants, and to expand the use of C. incisa in traditional medicine.

Microalgae such as Spirulina (Arthrospira) platensis are the source of several bioactive compounds. C-phycocyanin (C-PC) is one of these compounds and has been widely used in the food industry. Caries disease is multifactorial and causes destruction of dental tissues. The lesions are sugar dependent, with sucrose being the most cariogenic sugar, which is metabolized by bacteria that cause caries. Thus, our objective was to verify through molecular docking the possible binding of C-PC with sucrose and thus create the possibility of adding C-PC in a mouthwash (which enhances the elimination of sucrose from the dental surface). We used the UFSC Chimera for removing heteroatoms from C-PC, AutoDock Tools for preparing protein (C-PC) and ligand (sucrose), AutoDock Vina for docking simulation, PyMol for viewing and converting files and, finally, the LigPlot+ to check the types of bonds between molecules. The C-PC and sucrose connected with a free bonding energy of -7.0 Kcal/mol. In addition, the molecules established 08 hydrogen bonds and 07 hydrophobic interactions. Our results demonstrate the potential for sucrose sequestration of C-PC and the possibility of adding C-PC in a mouthwash as an aid to dental cleaning and caries preventing.

For a long time, scientists have investigated in familiar world to identify novel microbial biocatalysts. However, the mountain soils has been shown as an almost entire reserve of novel enzymes with interesting properties for industrial and environmental applications. Bacillus sp. as a genus of facultative anaerobic bacteria, is widespread in nature. Many species of this genus produce different enzymes used in biodegradation, textiles, bakery, food industry, stationery, biopharmaceutical industries and in many other domains. Thus, the strain KA15 was isolated from Tikjda, in the Djurdjura Mountains, Algeria. The identification of this newly isolated bacterium was carried out using morphological, physiological, and biochemical characteristics. In addition, the 16S rDNA gene was also amplified and sequenced. All the data obtained with regards to the physiological and biochemical properties of the isolate, confirmed that the KA15 strain belonged to the Bacillus genus. The growth temperature was 8-45°C with an optimum Temperature at 25°C, and pH range was 5–8 with an optimum pH around 5. Moreover, the nucleotide sequence and blast analyses confirmed that the KA15 strain (access number GenBank MK874318) was closely related to those of the Bacillus strains. All the results obtained strongly suggested that this isolate should be assigned as Bacillus altitudinis strain KA15.

Looking into the literature and scientific forums, there isn’t any software that can explore the diversity of a database or a sequence subset by applying the similarity measures reported to delimit the twilight zone according all previously mentioned thresholds. So far, in order to retrieve several similarity measures like identity, similarity and scores in an all-vs-all pairwise sequence comparison, users should run previously software like needle (global alignment), water (local alignment), blast (local alignment) and even multiple sequence alignments (MSAs) tools (http://imed.med.ucm.es/Tools/sias.html), then results should be parsed to be presented in a nxn matrix. However, going through all these steps to get at the final similarity matrix require programming skills.

Here, we present SeqDivA, a python-based tool with a friendly GUI allowing non-expert users to run alignment algorithms (water, needle and blast) to compare all vs all protein, DNA and RNA sequences. SeqDivA provides similarity, identity and bit-score matrixes to explore the diversity/homology of the sequences, enabling the delimitation of the twilight zone. The resulting matrixes are visualized using dot plot-like graphs representing pairwise similarity measures (identities, similarity and bit-scores). SeqDivA also allows redundancy reduction by exploring amino acid identities from global alignments and can be connected to the output of software simulating related sequences with a known evolutionary history i.e. ROSE [1] and INDELible [2] in order to get subsets of homologous sequences at different identities or bit-scores ranges. The software can be freely downloaded at https://github.com/eancedeg/SeqDivA. The software was published as part of the paper published at https://doi.org/10.3390/biom10010026

1- Stoye, J., D. Evers, and F. Meyer, Rose: generating sequence families. Bioinformatics, 1998. 14(2): p. 157-163.

2- Fletcher, W. and Z. Yang, INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol, 2009. 26(8): p. 1879-88

The Streptococcus mutans is one of the main causes of pathologies such as caries. To generate its effects, S.mutans has several mechanisms, including adhesion between microorganisms and microorganisms in tooth enamel. Adhesins are surface or cell wall proteins of S. mutans fundamental to the adhesion process. Thus, blocking this type of protein could represent an inhibition or deceleration of the caries process. The Rosemary (R. officinalis L.) can promote several pharmacological effects due to the interaction between the molecules of the plant and the organic systems. The objective of this study was to verify the possible interaction between Rosemary and adhesion protein (antigen I / II) of S. mutans through molecular docking. First, we prepare the receptor (adhesin) by removing the heteroatoms using the UCSF Chimera. Then, we made several preparations in the receptor and in the ligand (Rosemary) using AutoDock Tools. Finally, the docking simulation took place in AutoDock Vina. The V-region of S. mutans antigen I/II (adhesin) and Alecrim connected with a free binding energy of -8.0 Kcal/mol. The molecules established 08 hydrogen bonds and 06 hydrophobic interactions. Considering the anti-microbial action of rosemary associated with its binding potential in adhesins demonstrated in the docking, Rosemary can be a potent aid in combating caries in dental products.

An extracellular acido-thermostable chitinase (called ChiA-Ba43) was hyper-produced and purified to homogeneity from a newly isolated Bacillus altitudinis strain KA15. This strain exhibited the highest chitinase activity (about 10,000 U/mL) after 46 h of incubation in an optimized meduim. Pure enzyme was obtained after ammonium sulphate precipitation (30-60%), followed by sequential column chromatographies on Sephacryl S-200 HR and Mono Q-Sepharose. The purified enzyme is a monomer with a molecular mass of 43,190.05 Da as determined by matrix assisted laser desorption ionization time-of-flight/mass spectrometry (MALDI-TOF/MS). The sequence of the 27 NH₂-terminal residues of ChiA-Ba43 showed high homology with other Bacillus species. Optimal activity was recorded at pH 4.0-5.5 and 85°C. The pure enzyme was inhibited by p-chloromercuribenzoic acid (p-CMB) and N-ethylmaleimide (NEM). Interstingly, ChiA-Ba43 showed higher activity towards colloidal chitin, chitin azure, glycol chitin, glycol chitosane, chitotriose, and chito-oligosaccharide, while it did not hydrolyse chitibiose and amylose. Moreover, ChiA-Ba43 acted as an endo-splitting enzyme as showed by thin-layer chromatography (TLC) from enzymatic catalyzed hydrolysis of chitin-oligosaccharides and colloidal chitin. More interstingly, ChiA-Ba43 showed a high level of catalytic efficiency compared to chitinases ChiA-Mt45, ChiA-Hh59, Chitodextrinase^®, N-acetyl-β-glucosaminidase^®, and ChiA-65. Thanks to its biochemical properties, ChiA-Ba43 may be used for the bioconversion of chitinous waste on an industrial scale.

The Ribonuclease III (RNase III) enzymatic family is implied in many important biological processes from the bacteria until humans. In this sense, they have been selected as drug-target candidates for drug development. Although RNase III members show a high degree of sequence diversity, they generally share common structural and some degree of enzymatic activity. The accessory domains are key determinants for both the substrate selectivity and the biological function of each RNase III type, however, their role is still under study. The in vitro enzymatic activity of three RNase III members from class I (E. coli RNase III, Schizosaccharomyces pombe Pac1 and Saccharomyces cerevisiae Rntp1) and the human Drosha placed in class II was tested against four different substrates. These two RNase III classes encompass members having different domain organization. Enzymatic activity differences were found among members of the class I, which get increased when the human Drosha (class II) was included in the test. The substrate promiscuity of the E. coli RNase III was corroborated in vivo through its expression in S. cerevisiae, as reported previously, but was extended here to Pichia pastoris. The new biochemical data integrated with previous studies confirmed that RNases III substrate specificity is highly influenced by its protein structure architecture. This fact also allowed drawing evolutionary links between RNase III members from their structural and substrate specificity differences. More details about the results can be consulted at DOI: 10.2174/1381612822666160511150416.

Besides COVID-19 can severely affect the health of those infected, this pandemic is also causing several problems in society, such as economic and psychological issues. Thus, preventing new cases is important to minimized these problems. This work developing an app (SMStopCorona) that sending text messages (Short Message Service – SMS) in automated and tailored way, with guidance about prevention and general health tips, aiming to welcome the population about coping pandemic. A multidisciplinary team from Instituto Federal Sul-rio-grandense (IFSul) and Hospital Escola/Universidade Federal de Pelotas (HE/UFPel) prepared the messagens to be sent and registered it in the app. About 500 people from the southern region of Brazil signed up to receive these messages, and then they were imported into the app. SMStopCorona then automatically sends a daily orientation to each person registered via SMS. Preliminary results indicated good acceptance in receiving these messages by registered people. Several people responded to the messages received, thanking for the care and guidance they had received via SMS text message.

The Sars-CoV-2 or new coronavirus is responsible for the coronavirus disease-19 (COVID-19) that causes the current and serious pandemic. There are still no vaccines or well-defined treatments for this disease, making it urgent to investigate molecules capable of preventing and/or treating COVID-19. One of the most important proteins for coronavirus is the Spike. This protein is responsible for the fusion of the virus with the host cell to initiate the pathology. Spike blockade could prevent viral fusion with human cells and act preventively and/or therapeutically. The Rosemary (R. officinalis L.) already had antiviral effects on the Human Immunodeficiency Virus type 1, thus having the potential to inhibit the proliferation of Sars-CoV-2. Our objective was to verify the possible interaction between Rosemary and Spike protein through molecular docking. We prepare the receptor (Spike) by removing the heteroatoms using the UCSF Chimera and we made others preparations in the receptor and in the ligand (Rosemary) using AutoDock Tools. For the docking simulation we used the AutoDock Vina. The Spike of coronavirus and Alecrim connected with a free binding energy of -6.5 Kcal/mol. The molecules established 06 hydrogen bonds and 05 hydrophobic interactions. Considering the antiviral action of Rosemary associated with its binding potential in Spike demonstrated in the docking on this research, Rosemary can be a potent aid against the new coronavirus.

To represent the molecular structure of most nanomaterials by a molecular graph or even simplified molecular input-line entry system (SMILES) is very problematic. Databases that contain a large number of different nanomaterials are not established up to now. Nevertheless, large collections of the behavior of individual nanomaterials under different experimental conditions are available. Namely, the experimental conditions are a tool to define how to influence nanomaterial in order to obtain some attractive effect on different targets such as cells, organisms, or chemical-technological processes. Traditional SMILES provide special codes related to the molecular structure which can be used to build up traditional QSPR/QSAR models. Quasi-SMILES is an extension of the traditional SMILES by means of considering additional codes that reflect experimental conditions. The quasi-SMILES were applied to build up models for different endpoints related to nanomaterials such as mutagenic potential of multiwalled carbon nanotubes (MWCNTs) [1]; cytotoxicity for metal oxide nanoparticles [2,3]; cytotoxicity of MWCNTs [4]; solubility of fullerenes C₆₀ and C₇₀ in various solvents [5]; cell viability of human lung and skin cells exposed to different metal oxide nanomaterials [6]; mutagenic potential of silver nanoparticles [7]. Most probably, quasi-SMILES will find many others applications in the nearest future, e.g. by using the CORAL software [1-7] (http://www.insilico.eu/coral).

References

Toropov AA, Toropova AP. Quasi-QSAR for mutagenic potential of multi-walled carbon-nanotubes. Chemosphere 2015; 124 (1): 40-46. DOI: 10.1016/j.chemosphere.2014.10.067

Toropova AP, Toropov AA, Rallo R, Leszczynska D, Leszczynski J. Optimal descriptor as a translator of eclectic data into prediction of cytotoxicity for metal oxide nanoparticles under different conditions. Ecotoxicol Environ Saf. 2015; 112: 39-45. DOI: 10.1016/j.ecoenv.2014.10.003

Ahmadi S. Mathematical modeling of cytotoxicity of metal oxide nanoparticles using the index of ideality correlation criteria. Chemosphere 2020; 242: 125192. DOI: 10.1016/j.chemosphere.2019.125192

Trinh TX, Choi J-S, Jeon H, Byun H-G, Yoon T-H, Kim J. Quasi-SMILES-Based Nano-Quantitative Structure-Activity Relationship Model to Predict the Cytotoxicity of Multiwalled Carbon Nanotubes to Human Lung Cells. Chem. Res. Toxicol, 2018; 31 (3): 183-190. DOI: 10.1021/acs.chemrestox.7b00303

Toropova AP, Toropov AA. QSPR and nano-QSPR: What is the difference? J Mol Struct. 2019; 1182: 141-149. DOI: 10.1016/j.molstruc.2019.01.040

Choi J-S, Trinh TX, Yoon T-H, Kim J, Byun H-G. Quasi-QSAR for predicting the cell viability of human lung and skin cells exposed to different metal oxide nanomaterials. Chemosphere 2019; 217: 243-249. DOI: 10.1016/j.chemosphere.2018.11.014

Toropov AA, Toropova AP. The Correlation Contradictions Index (CCI): Building up reliable models of mutagenic potential of silver nanoparticles under different conditions using quasi-SMILES. Sci Total Environ. 2019: 681: 102-109. DOI: 10.1016/j.scitotenv.2019.05.114