scholarly journals In Silico Analysis of Extended-Spectrum β-Lactamases in Bacteria

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 812
Author(s):  
Patrik Mlynarcik ◽  
Hana Chudobova ◽  
Veronika Zdarska ◽  
Milan Kolar
Keyword(s):  
In Silico ◽  
Phylogenetic Trees ◽  
Bacterial Resistance ◽  
Public Health Problem ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Extended Spectrum ◽  
Wide Range ◽  
Phosphoethanolamine Transferases ◽  
Silico Analysis

The growing bacterial resistance to available β-lactam antibiotics is a very serious public health problem, especially due to the production of a wide range of β-lactamases. At present, clinically important bacteria are increasingly acquiring new elements of resistance to carbapenems and polymyxins, including extended-spectrum β-lactamases (ESBLs), carbapenemases and phosphoethanolamine transferases of the MCR type. These bacterial enzymes limit therapeutic options in human and veterinary medicine. It must be emphasized that there is a real risk of losing the ability to treat serious and life-threatening infections. The present study aimed to design specific oligonucleotides for rapid PCR detection of ESBL-encoding genes and in silico analysis of selected ESBL enzymes. A total of 58 primers were designed to detect 49 types of different ESBL genes. After comparing the amino acid sequences of ESBLs (CTX-M, SHV and TEM), phylogenetic trees were created based on the presence of conserved amino acids and homologous motifs. This study indicates that the proposed primers should be able to specifically detect more than 99.8% of all described ESBL enzymes. The results suggest that the in silico tested primers could be used for PCR to detect the presence of ESBL genes in various bacteria, as well as to monitor their spread.

scholarly journals Comprehensive In Silico Analysis and Transcriptional Profiles Highlight the Importance of Mitochondrial Dicarboxylate Carriers (DICs) on Hypoxia Response in Both Arabidopsis thaliana and Eucalyptus grandis

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 181
Author(s):  
Pedro Barreto ◽  
Mariana L. C. Arcuri ◽  
Rômulo Pedro Macêdo Lima ◽  
Celso Luis Marino ◽  
Ivan G. Maia
Keyword(s):  
In Silico ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Eucalyptus Grandis ◽  
In Silico Analysis ◽  
Developmental Expression ◽  
Hypoxia Response ◽  
Submergence Stress ◽  
Wide Range ◽  
Silico Analysis

Plant dicarboxylate carriers (DICs) transport a wide range of dicarboxylates across the mitochondrial inner membrane. The Arabidopsis thalianaDIC family is composed of three genes (AtDIC1, 2 and 3), whereas two genes (EgDIC1 and EgDIC2) have been retrieved in Eucalyptus grandis. Here, by combining in silico and in planta analyses, we provide evidence that DICs are partially redundant, important in plant adaptation to environmental stresses and part of a low-oxygen response in both species. AtDIC1 and AtDIC2 are present in most plant species and have very similar gene structure, developmental expression patterns and absolute expression across natural Arabidopsis accessions. In contrast, AtDIC3 seems to be an early genome acquisition found in Brassicaceae and shows relatively low (or no) expression across these accessions. In silico analysis revealed that both AtDICs and EgDICs are highly responsive to stresses, especially to cold and submergence, while their promoters are enriched for stress-responsive transcription factors binding sites. The expression of AtDIC1 and AtDIC2 is highly correlated across natural accessions and in response to stresses, while no correlation was found for AtDIC3. Gene ontology enrichment analysis suggests a role for AtDIC1 and AtDIC2 in response to hypoxia, and for AtDIC3 in phosphate starvation. Accordingly, the investigated genes are induced by submergence stress in A. thaliana and E. grandis while AtDIC2 overexpression improved seedling survival to submergence. Interestingly, the induction of AtDIC1 and AtDIC2 is abrogated in the erfVII mutant that is devoid of plant oxygen sensing, suggesting that these genes are part of a conserved hypoxia response in Arabidopsis.

scholarly journals In Silico Analysis of Laccifer Lacca as a Potential Therapeutic Agent for Cervical, Breast and Lung Cancers

2021 ◽  
Vol 11 (3) ◽  
pp. 79-85
Author(s):  
Ashish Kumar ◽  
Neeraj Kumar ◽  
Balwan Singh
Keyword(s):  
Nitric Oxide ◽  
Molecular Docking ◽  
In Silico ◽  
A549 Cells ◽  
In Silico Analysis ◽  
Wide Range ◽  
Anticancer Therapeutics ◽  
Anti Inflammatory ◽  
Silico Analysis

Laccifer lacca has generally been used as pigmenting, coloring agent and dying in chemical industry. Although, it has wide range of industrial applications, but inappropriately, due to lesser availability of data, it has been ignored. Keeping in mind, the wide application of Laccifer lacca, we tried to report the in-silico anti-cancer effects. The experimental techniques used to determine the structure was X-RAY diffraction. The reported resolution of this entry is 2.80 Å. Percentile scores (ranging between 0-100) for global authentication metrics of the record. In silico have a good pool to explore various parameters in molecular docking. We have performed in silico analysis of the active components of Laccifer lacca against the cervical, breast and lung cancer proteins and also found that lac extract enhances the production of anti-inflammatory markers and the increase is significant when compared to the standard vinblastine. It has been demonstrated by Lala and colleagues that a short lived molecule nitric oxide can result in the progression of human tumours. Therefore, the prominent antioxidant activity of phytochemical that can act as inhibitors of nitric oxide production can act as anticancer therapeutics. Both methanolic and aqueous extract shows significant anticancer effect on the hela, MCF-7 & A549 cells suggesting them as potential anticancer therapeutics for future. Keywords: Laccifer lacca, In-vitro & In-silico analysis, Carcinogenesis, Anti-inflammatory, Molecular Docking.

scholarly journals Potential Biological Activities of Peptides Generated during Casein Proteolysis by Curly Kale (Brassica oleracea L. var. sabellica L.) Leaf Extract: An In Silico Preliminary Study

Foods ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2877
Author(s):  
Magdalena Polak-Berecka ◽  
Magdalena Michalak-Tomczyk ◽  
Katarzyna Skrzypczak ◽  
Katarzyna Michalak ◽  
Kamila Rachwał ◽  
...  
Keyword(s):  
In Silico ◽  
Leaf Extract ◽  
Degradation Products ◽  
Biological Activities ◽  
Protein Profile ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Casein Hydrolysis ◽  
Sds Page ◽  
Silico Analysis

This study is a brief report on the proteolytic activity of curly kale leaf extract against casein. Casein degradation products and an in silico analysis of the biological activity of the peptides obtained was performed. The efficiency of casein hydrolysis by curly kale extract was determined using SDS–PAGE and by peptide concentration determination. The pattern of the enzymatic activity was determined by MALDI–TOF MS analysis. The results showed that α- and β-casein were more resistant to curly kale extract hydrolysis, whereas κ-casein was absent in the protein profile after 8 h of proteolysis, and all casein fractions were completely hydrolyzed after 24 h of incubation. Based on sequence analysis, seven peptides were identified, with molecular mass in the range of 1151–3024 Da. All the peptides were products of β-casein hydrolysis. The identified amino acid sequences were analyzed in BIOPEP, MBPDB, and FeptideDB databases in order to detect the potential activities of the peptides. In silico analysis suggests that the β-casein-derived peptides possess sequences of peptides with ACE inhibitory, antioxidant, dipeptidyl peptidase IV inhibitory, antithrombotic, immunomodulatory, and antiamnesic bioactivity. Our study was first to evaluate the possibility of applying curly kale leaf extract to generate biopeptides through β-casein hydrolysis.

scholarly journals In Vitro Phenotypic Activity and In Silico Analysis of Natural Products from Brazilian Biodiversity on Trypanosoma cruzi

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5676
Author(s):  
Raiza B. Peres ◽  
Ludmila F. de A. Fiuza ◽  
Patrícia B. da Silva ◽  
Marcos M. Batista ◽  
Flávia da C. Camillo ◽  
...  
Keyword(s):  
Natural Products ◽  
Trypanosoma Cruzi ◽  
In Silico ◽  
In Silico Analysis ◽  
Mammalian Host ◽  
Reference Drug ◽  
Wide Range ◽  
Pure Compounds ◽  
Silico Analysis

Chagas disease (CD) affects more than 6 million people worldwide. The available treatment is far from ideal, creating a demand for new alternative therapies. Botanical diversity provides a wide range of novel potential therapeutic scaffolds. Presently, our aim was to evaluate the mammalian host toxicity and anti-Trypanosoma cruzi activity of botanic natural products including extracts, fractions and purified compounds obtained from Brazilian flora. In this study, 36 samples of extracts and fractions and eight pure compounds obtained from seven plant species were evaluated. The fraction dichloromethane from Aureliana fasciculata var. fasciculata (AFfPD) and the crude extract of Piper tectoniifolium (PTFrE) showed promising trypanosomicidal activity. AFfPD and PTFrE presented EC50 values 10.7 ± 2.8 μg/mL and 12.85 ± 1.52 μg/mL against intracellular forms (Tulahuen strain), respectively. Additionally, both were active upon bloodstream trypomastigotes (Y strain), exhibiting EC50 2.2 ± 1.0 μg/mL and 38.8 ± 2.1 μg/mL for AFfPD and PTFrE, respectively. Importantly, AFfPD is about five-fold more potent than Benznidazole (Bz), the reference drug for CD, also reaching lower EC90 value (7.92 ± 2.2 μg/mL) as compared to Bz (23.3 ± 0.6 μg/mL). Besides, anti-parasitic effect of eight purified botanic substances was also investigated. Aurelianolide A and B (compounds 1 and 2) from A. fasciculata and compound 8 from P. tuberculatum displayed the best trypanosomicidal effect. Compounds 1, 2 and 8 showed EC50 of 4.6 ± 1.3 μM, 1.6 ± 0.4 μM and 8.1 ± 0.9 μM, respectively against intracellular forms. In addition, in silico analysis of these three biomolecules was performed to predict parameters of absorption, distribution, metabolism and excretion. The studied compounds presented similar ADMET profile as Bz, without presenting mutagenicity and hepatotoxicity aspects as predicted for Bz. Our findings indicate that these natural products have promising anti-T. cruzi effect and may represent new scaffolds for future lead optimization.

scholarly journals Molecular modeling of the interaction of the dihydroquercetin and its metabolites with cyclooxygenase-2

2019 ◽  
Vol 18 (3) ◽  
pp. 101-106 ◽  
Author(s):  
R. P. Terekhov ◽  
I. A. Selivanova
Keyword(s):  
Molecular Modeling ◽  
In Silico ◽  
In Silico Analysis ◽  
Cyclooxygenase 2 ◽  
Protein Data Bank Code ◽  
Antiinflammatory Drugs ◽  
Study Objective ◽  
Wide Range ◽  
Cox 2 ◽  
Silico Analysis

Background. Dihydroquercetin (DHQ) is a natural flavonoid. It has a wide range of pharmacological effects, which includes anti-inflammatory activity. There is a gap in our knowledge about the biochemical mechanisms of the therapeutic potency implementation of this compound. This fact slows down the process of the drug development using DHQ. Molecular modeling is designed to further translate the research from the fundamental experimentation to the real clinical practice. Purpose. The study objective was to estimate DHQ as a cyclooxygenase-2 (COX-2) inhibitor by using in silico analysis.Materials and methods. The information about the COX-2 structure was obtained from the Protein Data Bank (code 5KIR). The 3D-models of DHQ were generated by using the ChemBioDraw Ultra software. Docking was carried out in the GOLD program after the corresponding validation of molecular modeling algorithms based on experimental data of X-ray diffraction analysis.Results. The design of this study is based on the rational selecting of the virtual ligand structures. It gives an opportunity to optimize the quantum-mechanical calculation. By using in silico analysis, it was shown that DHQ and some of its metabolites demonstrate ability of binding to SER353, SER530, and ARG513 of COX-2 at the catalytic site.Conclusion. Important α-amino acids for intermolecular interaction of DHQ and its metabolites with COX-2 were determined during this study. Our data can be used for the development of new antiinflammatory drugs on the base of DHQ. 

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

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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