Immunoinformatics and analysis of antigen distribution of Ureaplasma diversum strains isolated from different Brazilian states

Abstract Background Ureaplasma diversum has numerous virulence factors that contribute to pathogenesis in cattle, including Lipid-associated membrane proteins (LAMPs). Therefore, the objectives of this study were to evaluate in silico important characteristics for immunobiological applications and for heterologous expression of 36 LAMPs of U. diversum (UdLAMPs) and, also, to verify by conventional PCR the distribution of these antigens in strains of Brazilian states (Bahia, Minas Gerais, São Paulo, and Mato Grosso do Sul). The Manatee database was used to obtain the gene and peptide sequences of the antigens. Similarity and identity studies were performed using BLASTp and direct antigenicity was evaluated by the VaxiJen v2.0 server. Epitope prediction for B lymphocytes was performed on the BepiPred v2.0 and CBTOPE v1.0 servers. NetBoLApan v1.0 was used to predict CD8+ T lymphocyte epitopes. Subcellular location and presence of transmembrane regions were verified by the software PSORTb v3.0.2 and TMHMM v2.2 respectively. SignalP v5.0, SecretomeP v2.0, and DOLOP servers were used to predict the extracellular excretion signal. Physico-chemical properties were evaluated by the web-software ProtParam, Solpro, and Protein-sol. Results In silico analysis revealed that many UdLAMPs have desirable properties for immunobiological applications and heterologous expression. The proteins gudiv_61, gudiv_103, gudiv_517, and gudiv_681 were most promising. Strains from the 4 states were PCR positive for antigens predicted with immunogenic and/or with good characteristics for expression in a heterologous system. Conclusion These works contribute to a better understanding of the immunobiological properties of the UdLAMPs and provide a profile of the distribution of these antigens in different Brazilian states.

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Discovering Health Benefits of Phytochemicals with Integrated Analysis of the Molecular Network, Chemical Properties and Ethnopharmacological Evidence

Nutrients ◽

10.3390/nu10081042 ◽

2018 ◽

Vol 10 (8) ◽

pp. 1042 ◽

Cited By ~ 10

Author(s):

Sunyong Yoo ◽

Kwansoo Kim ◽

Hojung Nam ◽

Doheon Lee

Keyword(s):

Health Effects ◽

Molecular Analysis ◽

In Silico ◽

Health Benefits ◽

Chemical Properties ◽

In Silico Analysis ◽

Integrated Analysis ◽

Screening Methods ◽

Potential Health

Identifying the health benefits of phytochemicals is an essential step in drug and functional food development. While many in vitro screening methods have been developed to identify the health effects of phytochemicals, there is still room for improvement because of high cost and low productivity. Therefore, researchers have alternatively proposed in silico methods, primarily based on three types of approaches; utilizing molecular, chemical or ethnopharmacological information. Although each approach has its own strength in analyzing the characteristics of phytochemicals, previous studies have not considered them all together. Here, we apply an integrated in silico analysis to identify the potential health benefits of phytochemicals based on molecular analysis and chemical properties as well as ethnopharmacological evidence. From the molecular analysis, we found an average of 415.6 health effects for 591 phytochemicals. We further investigated ethnopharmacological evidence of phytochemicals and found that on average 129.1 (31%) of the predicted health effects had ethnopharmacological evidence. Lastly, we investigated chemical properties to confirm whether they are orally bio-available, drug available or effective on certain tissues. The evaluation results indicate that the health effects can be predicted more accurately by cooperatively considering the molecular analysis, chemical properties and ethnopharmacological evidence.

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Molecular cloning, characterization, heterologous expression and in-silico analysis of disordered boiling soluble stress-responsive wBsSRP protein from drought tolerant wheat cv.PBW 175

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2016.12.017 ◽

2017 ◽

Vol 112 ◽

pp. 29-44 ◽

Cited By ~ 6

Author(s):

Gurmeen Rakhra ◽

Tarandeep Kaur ◽

Dhiraj Vyas ◽

Arun Dev Sharma ◽

Jatinder Singh ◽

...

Keyword(s):

Heterologous Expression ◽

Molecular Cloning ◽

In Silico ◽

In Silico Analysis ◽

Drought Tolerant ◽

Silico Analysis

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An in silico Analysis of Protein Targeted by Glycyrrhizin in Common Dental Pathogens

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2020/v32i1530640 ◽

2020 ◽

pp. 170-178

Author(s):

S. Balamithra ◽

Smiline Girija ◽

J. Vijayashree Priyadharsini

Keyword(s):

Virulence Factors ◽

In Silico ◽

In Silico Analysis ◽

Subcellular Location ◽

Functional Class ◽

Treponema Denticola ◽

Peptic Ulcers ◽

Upper Respiratory Tract ◽

Tannerella Forsythia ◽

Medicinal Uses

Glycyrrhizin is a phytocompound which is derived from Glycyrrhiza glabra. It is used in treating the upper respiratory tract disease like cough, bronchitis, laryngitis, sore throat, etc. It has various medicinal uses in rheumatism, peptic ulcers, asthma, allergies, and inflammation. Glycyrrhizin has been reported to possess antibacterial, antiviral, antioxidant, anti inflammatory properties. In view of the above facts, the present in silico study was designed to demonstrate the molecular mechanism underlying the antimicrobial activity of glycyrrhizin against common dental pathogens such as Streptococcus mutans, Porphyromonas gingivalis, Treponema denticola, Enterococcus faecalis and Tannerella forsythia. The STITCH tool was used to identify the drug-protein interaction. The functional class of the protein was deduced using VICMPred, followed by the identification of epitopes on the virulence factors using BepiPred. Further, the subcellular location of the virulence factors were also studied using PSORTb software. The computational analysis performed identified several virulence factors viz., short chain dehydrogenase/reductase family oxidoreductase of Treponema denticola and D-mannonate oxidoreductase of Tannerella forsythia which were found to interact with glycyrrhizin. Interestingly, phosphopyruvate hydratase was found to be the protein present in all the five genera was shown to interact with glycyrrhizin. Thus the present study reveals the target proteins on the dental pathogens which were shown to interact with glycyrrhizin. Furthermore, experimental validation of the results are warranted to provide substantial details on the anti-microbial activity of glycyrrhizin against common dental pathogens.

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The adpA-like regulatory gene from Actinoplanes teichomyceticus: in silico analysis and heterologous expression

World Journal of Microbiology and Biotechnology ◽

10.1007/s11274-015-1882-6 ◽

2015 ◽

Vol 31 (8) ◽

pp. 1297-1301 ◽

Cited By ~ 8

Author(s):

Bohdan Ostash ◽

Oleksandr Yushchuk ◽

Stepan Tistechok ◽

Halyna Mutenko ◽

Lilia Horbal ◽

...

Keyword(s):

Heterologous Expression ◽

In Silico ◽

Regulatory Gene ◽

In Silico Analysis ◽

Actinoplanes Teichomyceticus ◽

Silico Analysis

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Novel Fluorinated Imidazolium Ionic Liquids: Eco-friendly, Facile and Efficient Construction, Characterization, in vitro Anticancer Activity, Toxicity and in silico Analysis

Asian Journal of Chemistry ◽

10.14233/ajchem.2020.22491 ◽

2020 ◽

Vol 32 (3) ◽

pp. 690-696 ◽

Cited By ~ 2

Author(s):

Ahmed H. Albalawi ◽

Saud M. Almutairi ◽

Ateyatallah Aljuhani ◽

Pramod K. Sahu ◽

Praveen K. Sahu ◽

...

Keyword(s):

Ionic Liquids ◽

In Silico ◽

Human Cancer ◽

Chemical Properties ◽

In Silico Analysis ◽

Human Cancer Cell Lines ◽

Ic50 Values ◽

Efficient Construction ◽

Silico Analysis

An efficient and facile synthesis of novel fluorinated imidazolium-tagged ionic liquids under microwave irradiation is described. Novel prepared ionic liquids was identified and confirmed by spectroscopic and elemental analysis. Synthesized ionic liquids (1-12) was explored for their antiproliferative inhibition potency against three selected human cancer cell lines (MCF-7, HepG-2 and CACO2). Screening results have revealed that some tested ionic liquids exhibited promising activity compared with standard drugs, especially compounds 5 and 6 which consistently produced low IC50 values. Preliminary structure activity relationship (SAR) studies have been performed to identify the relation between molecular structure and activity. in silico Analysis of ionic liquids was carried out based on ADME, Lipinski rule, drug likeness, toxicity profiles and other physico-chemical properties. All compounds were safe in toxicity profile and computed LD50 values were in accepted range (2.55-2.89 mol/kg). in silico Results have shown that Lipinski rule of five was in accept range, except compound 1 and 2.

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A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

Seminars in Oncology ◽

10.1053/j.seminoncol.2020.02.012 ◽

2020 ◽

Vol 47 (6) ◽

pp. 398-408

Author(s):

Sonam Tulsyan ◽

Showket Hussain ◽

Balraj Mittal ◽

Sundeep Singh Saluja ◽

Pranay Tanwar ◽

...

Keyword(s):

Systematic Review ◽

Gallbladder Carcinoma ◽

In Silico ◽

In Silico Analysis ◽

Transcriptomic Profile ◽

Silico Analysis

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In Silico Analysis of Single Nucleotide Polymorphism in Human Prothrombin Gene

10.1055/s-0039-1680245 ◽

2019 ◽

Author(s):

I. Farah ◽

A. El-Mubark ◽

M. Osman ◽

A. Soliman ◽

F. Ali ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

In Silico ◽

In Silico Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Prothrombin Gene ◽

Silico Analysis

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Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

Current Medicinal Chemistry ◽

10.2174/0929867327666200727114410 ◽

2020 ◽

Vol 27 (38) ◽

pp. 6523-6535 ◽

Cited By ~ 3

Author(s):

Antreas Afantitis ◽

Andreas Tsoumanis ◽

Georgia Melagraki

Keyword(s):

Data Analysis ◽

Virtual Screening ◽

In Silico ◽

Model Development ◽

In Silico Analysis ◽

Material Design ◽

Efficient Solutions ◽

Biological Data ◽

Cost Efficient ◽

Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

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In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

Current Proteomics ◽

10.2174/1570164616666190401204009 ◽

2020 ◽

Vol 17 (1) ◽

pp. 40-50

Author(s):

Farzane Kargar ◽

Amir Savardashtaki ◽

Mojtaba Mortazavi ◽

Masoud Torkzadeh Mahani ◽

Ali Mohammad Amani ◽

...

Keyword(s):

Phylogenetic Tree ◽

In Silico ◽

Alpha Helix ◽

In Silico Analysis ◽

Glycogen Storage ◽

Docking Studies ◽

Random Coil ◽

Special Topic ◽

Industrial Biotechnology ◽

In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

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