scholarly journals EVOLUTIONARY RELATIONSHIP AND REPURPOSING OF SARS INHIBITORS AGAINST SURFACE GLYCOPROTEIN OF SARS-COV-2

2021 ◽  
pp. 272-279
Author(s):  
PRIYANKA RAJBHAR ◽  
DIKSHANT SINGH ◽  
RUKHSAR FATIMA ◽  
RUCHI YADAV
Keyword(s):  
Phylogenetic Tree ◽  
Human Life ◽  
Bootstrap Method ◽  
Evolutionary Relationship ◽  
Docking Studies ◽  
Surface Glycoprotein ◽  
High Rate ◽  
Membrane Glycoprotein ◽  
Upper Respiratory Tract ◽  
Spike Glycoprotein

Objective: Coronaviruses are a group of similar viruses which cause fatal infection and responsible for affecting the upper respiratory tract in many organisms. Throughout the time these viruses have been found to affect human life by causing major pandemics like SARS, MERS and COVID-19 due to their high rate of mutation and zoonotic transmission. Repurposing of a drug could be a solution for this challenge, as many previously available drugs hold great potential to act as a drug molecule. Interfering this interaction could be a potent mechanism to stop the viral infection and propagation. Methods: In the current study we have predicted the evolutionary relationship of nCoV using three viral proteins Nucleocapsid phosphoprotein, membrane glycoprotein and Envelop protein with accession number YP_009724397, YP_009724393 and YP_009724392 respectively. Phylogenetic tree was constructed and evaluated using the bootstrap method. Homology modeling and docking studies has been done to identify the interaction and binding affinity of SARS drugs. Results: Phylogenetic tree shows that Nucleocapsid phosphoprotein is originated from Hypsugo Bat Coronavirus, Membrane glycoprotein is originated from MERS Corona Virus and Envelop proteins have originated from Ferret coronavirus. From the docking result we concluded that Precose (glide score-8.372) shows that it has stable and strong interaction with Spike glycoprotein. Conclusion: Precose which is commonly known as Acarbose can act as a potential inhibitor for the spike glycoprotein. This paper described and highlighted the importance of repurposing of the previously available drug to act as a potent inhibitor in the newly discovered or novel diseases.

Hydroxychloroquine (HCQ) exhibits better binding to the main protease (Mpro) compared to spike protein (S protein) of SARS-CoV-2: An in-silico analysis

2021 ◽  
Vol 08 ◽  
Author(s):  
Deepa R. Bandi ◽  
SubbaRao V. Tulimilli ◽  
Durai Ananda Kumar T. ◽  
Chandi Kumari Chitturi ◽  
Anjalidevi S. Bettadapura ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico Analysis ◽  
Protein S ◽  
Data Bank ◽  
Docking Studies ◽  
Surface Glycoprotein ◽  
Spike Glycoprotein ◽  
S Protein ◽  
Discovery Studio ◽  
Main Protease

Background: Despite various efforts in preventing and treating SARS-CoV-2 infections; transmission and mortality have been increasing at alarming rates globally. Since its first occurrence in Wuhan, China, in December 2019, the number of cases and deaths due to SARS-CoV-2 infection continues to increase across 220 countries. Currently, there are about 228 million cases and 4.6 million deaths recorded globally. Although several vaccines/drugs have been reported to prevent or treat SARS-CoV-2, their efficacy to protect against emerging variants and duration of protection are not fully known. Hence, more emphasis is given to repurpose the existing pharmacological agents to manage the infected individuals. One such agent is hydroxychloroquine (HCQ), which is a more soluble derivative of antimalarial drug chloroquine. HCQ has been tested in clinical trials to mitigate SARS-CoV-2 infection-induced complications while reducing the time to clinical recovery (TTCR). However, several concerns and questions about the utility and efficacy of HCQ for treating SARS-CoV-2 infected individuals still persist. Identifying key proteins regulated by HCQ is likely to provide vital clues required to address these concerns. Objective: The objective of this study is to identify the ability of HCQ for binding to the most widely studied molecular targets of SARS-CoV-2 viz., spike glycoprotein (S protein), and main protease (Mpro, also referred as chymotrypsin like protease) using molecular docking approaches and correlate the results with reported mechanisms of actions of HCQ. Methods: X-ray crystallographic structures of spike glycoprotein and main protease of SARS-CoV-2 were retrieved from Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). The structure of Hydroxychloroquine was retrieved from the PubChem compound database. The binding interactions of the HCQ with target proteins were predicted using C-Docker algorithm, and visualized using Discovery studio visualizer. Results: Data from molecular docking studies showed very strong binding of HCQ to the main protease compared to spike glycoprotein. Conclusion: The antiviral activity of HCQ is attributed to its ability to bind to the main protease compared to surface glycoprotein. Therefore, future studies should focus more on developing a combination agent/strategy for targeting surface glycoprotein and main protease together.

Sequencing Analysis and Phylogenetic Tree of HPV Isolated from Breast Cancer Patients at Thi-Qar Province/Iraq

2020 ◽  
pp. 37-40
Keyword(s):  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Breast Cancer Patients ◽  
The North ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
History Of

Genetic variety examination has demonstrated fundamental to the understanding of the epidemiological and developmental history of Papillomavirus (HPV), for the development of accurate diagnostic tests and for efficient vaccine design. The HPV nucleotide diversity has been investigated widely among high-risk HPV types. To make the nucleotide sequence of HPV and do the virus database in Thi-Qar province, and compare sequences of our isolates with previously described isolates from around the world and then draw its phylogenetic tree, this study done. A total of 6 breast formalin-fixed paraffin-embedded (FFPE) of the female patients were included in the study, divided as 4 FFPE malignant tumor and 2 FFPE of benign tumor. The PCR technique was implemented to detect the presence of HPV in breast tissue, and the real-time PCR used to determinant HPV genotypes, then determined a complete nucleotide sequence of HPV of L1 capsid gene, and draw its phylogenetic tree. The nucleotide sequencing finding detects a number of substitution mutation (SNPs) in (L1) gene, which have not been designated before, were identified once in this study population, and revealed that the HPV16 strains have the evolutionary relationship with the South African race, while, the HPV33 and HPV6 showing the evolutionary association with the North American and East Asian race, respectively.

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

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.

A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

2021 ◽  
Vol 9 (1) ◽  
pp. 49-55
Author(s):  
Vanlal hruaia ◽  
◽  
Lal rinmuana ◽  
J Lalbiaknunga ◽  
Laldinfeli Ralte
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Flowering Plants ◽  
Morphological Features ◽  
Total Evidence ◽  
Pictorial Representation ◽  
Phenetic Analysis ◽  
Morphological Relationship

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

Molecular Analysis of Hepatitis B Virus in Mothers-Children Pairs

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chatzidaki V ◽  
◽  
Perdikogianni C ◽  
Galanakis E ◽  
Paraskevis D ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Phylogenetic Tree ◽  
Surface Glycoprotein ◽  
Phylogenetic Tree Analysis ◽  
Source Of Infection ◽  
B Virus ◽  
Maximum Likelihood Methods ◽  
Infection Source ◽  
Relationship Of

ackground: Vertical transmission of Hepatitis B Virus (HBV) is the primary infection source for infants, but little is known on the proportion of children that have acquired HBV from their mothers. Objective: We investigated the relationship of HBV sequencing in HBVpositive children and their mothers and explored the HBV phylogenetic tree. Methods: Serum-extracted HBV-DNA from 38 individuals (13 children paired to nine mothers, 16 unpaired infected children) was amplified by polymerase chain reaction and the target region HBV surface glycoprotein (amino acids 40-171) was directly sequenced. Following editing and alignment of these sequences, phylogenetic tree analysis was performed using the neighbourjoining and maximum-likelihood methods. Results: Analysis was successfully performed in 29 subjects (23 children and six mothers), including six mother-child pairs. All individuals were infected by genotype D. Subgenotype adw3 prevailed (21, 72.4%), followed by ayw2 (4, 13.8%) and ayw3 (4, 13.8%). Among six mother-child pairs, three had identical and three had different subgenotypes. Phylogenetic analysis revealed that HBV sequences from three children did not cluster with their siblings suggesting a different source of infection. Conclusion: Our findings suggest that HBV subgenotypes in infected children may not be identical to their mothers’ and point to non-vertical HBV transmission in childhood.

scholarly journals Optimized Pseudotyping Conditions for the SARS-COV-2 Spike Glycoprotein

2020 ◽  
Vol 94 (21) ◽  
Author(s):  
Marc C. Johnson ◽  
Terri D. Lyddon ◽  
Reinier Suarez ◽  
Braxton Salcedo ◽  
Mary LePique ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Neutralizing Antibodies ◽  
Particle Production ◽  
Surface Glycoprotein ◽  
Spike Protein ◽  
Target Cells ◽  
Spike Glycoprotein ◽  
Infectious Particle ◽  
Pathogenic Virus ◽  
Hiv 1

ABSTRACT The severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) Spike glycoprotein is solely responsible for binding to the host cell receptor and facilitating fusion between the viral and host membranes. The ability to generate viral particles pseudotyped with SARS-COV-2 Spike is useful for many types of studies, such as characterization of neutralizing antibodies or development of fusion-inhibiting small molecules. Here, we characterized the use of a codon-optimized SARS-COV-2 Spike glycoprotein for the generation of pseudotyped HIV-1, murine leukemia virus (MLV), and vesicular stomatitis virus (VSV) particles. The full-length Spike protein functioned inefficiently with all three systems but was enhanced over 10-fold by deleting the last 19 amino acids of the cytoplasmic tail. Infection of 293FT target cells was possible only if the cells were engineered to stably express the human angiotensin-converting enzyme 2 (ACE2) receptor, but stably introducing an additional copy of this receptor did not further enhance susceptibility. Stable introduction of the Spike-activating protease TMPRSS2 further enhanced susceptibility to infection by 5- to 10-fold. Replacement of the signal peptide of the Spike protein with an optimal signal peptide did not enhance or reduce infectious particle production. However, modifications D614G and R682Q further enhanced infectious particle production. With all enhancing elements combined, the titer of pseudotyped HIV-1 particles reached almost 106 infectious particles/ml. Finally, HIV-1 particles pseudotyped with SARS-COV-2 Spike were successfully used to detect neutralizing antibodies in plasma from coronavirus disease 2019 (COVID-19) patients, but not in plasma from uninfected individuals. IMPORTANCE In work with pathogenic viruses, it is useful to have rapid quantitative tests for viral infectivity that can be performed without strict biocontainment restrictions. A common way of accomplishing this is to generate viral pseudoparticles that contain the surface glycoprotein from the pathogenic virus incorporated into a replication-defective viral particle that contains a sensitive reporter system. These pseudoparticles enter cells using the glycoprotein from the pathogenic virus, leading to a readout for infection. Conditions that block entry of the pathogenic virus, such as neutralizing antibodies, will also block entry of the viral pseudoparticles. However, viral glycoproteins often are not readily suited for generating pseudoparticles. Here, we describe a series of modifications that result in the production of relatively high-titer SARS-COV-2 pseudoparticles that are suitable for the detection of neutralizing antibodies from COVID-19 patients.

Comparative genomic analysis ofAcidithiobacillus ferrooxidansstrains using theA. ferrooxidansATCC 23270 whole-genome oligonucleotide microarray

2009 ◽  
Vol 55 (5) ◽  
pp. 587-598 ◽  
Author(s):  
Hailang Luo ◽  
Li Shen ◽  
Huaqun Yin ◽  
Qian Li ◽  
Qijiong Chen ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Oligonucleotide Microarray ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Mining Areas ◽  
Main Factor

Acidithiobacillus ferrooxidans is an important microorganism used in biomining operations for metal recovery. Whole-genomic diversity analysis based on the oligonucleotide microarray was used to analyze the gene content of 12 strains of A. ferrooxidans purified from various mining areas in China. Among the 3100 open reading frames (ORFs) on the slides, 1235 ORFs were absent in at least 1 strain of bacteria and 1385 ORFs were conserved in all strains. The hybridization results showed that these strains were highly diverse from a genomic perspective. The hybridization results of 4 major functional gene categories, namely electron transport, carbon metabolism, extracellular polysaccharides, and detoxification, were analyzed. Based on the hybridization signals obtained, a phylogenetic tree was built to analyze the evolution of the 12 tested strains, which indicated that the geographic distribution was the main factor influencing the strain diversity of these strains. Based on the hybridization signals of genes associated with bioleaching, another phylogenetic tree showed an evolutionary relationship from which the co-relation between the clustering of specific genes and geochemistry could be observed. The results revealed that the main factor was geochemistry, among which the following 6 factors were the most important: pH, Mg, Cu, S, Fe, and Al.

The relationship of social phobia and personality characters in colleague students

2017 ◽  
Vol 41 (S1) ◽  
pp. S414-S415
Author(s):  
M. Mokhtaree ◽  
P. Aghamohammad Hasani
Keyword(s):  
Social Phobia ◽  
Human Life ◽  
Pearson Correlation ◽  
High Rate ◽  
Questionnaire Data ◽  
Medical Sciences ◽  
Academic Courses ◽  
Competing Interest ◽  
Relationship Of ◽  
The Relationship

Social anxiety disorder, pervasive and debilitating disorder with a high rate that affects many aspects of human life. The aim of the study was to assess the relation between social phobia and personality traits of Rafsanjan University of medical sciences students. By using Cochran formula and random stratified sampling, 284 person of Rafsanjan University of medical sciences students selected. Participants responded to questions of the NEO Personality and Social Phobia questionnaire. Data analyzed with Pearson correlation coefficient, analysis of variance and regression. Among the individuals, 11.6% had severe social phobia and 4.6% very severe. The relationship between social phobia and neuroticism was reversed and significant and other personality characters were significantly. Neuroticism and openness predicted social phobia significantly. The academic courses in terms of social phobia had not different with them but there were significant differences in the character of personality. It seems that dimensions of personality associated with Social phobia and be able to explain it.Disclosure of interestThe authors have not supplied their declaration of competing interest.

scholarly journals Molecular Systematic Investigations of Three Fin Fish Cichlid Species of Oreochromis niloticus (Nile Tilapia), Genetically Improved Farmed Tilapia (GIFT) and Astronotus ocellatus (Oscar Cichlid)

2021 ◽  
Vol 10 (4) ◽  
pp. 2850-2860
Keyword(s):  
Phylogenetic Tree ◽  
Nile Tilapia ◽  
Evolutionary Relationship ◽  
Aquatic Organisms ◽  
Recent Common Ancestor ◽  
Farmed Fish ◽  
Molecular Systematic ◽  
Cichlid Species ◽  
Astronotus Ocellatus ◽  
The World

Fisheries in India contribute significantly to the total GDP of agriculture and earn significant foreign exchange. Aquaculture is playing an important role in India and is bestowed with a huge biodiversity of aquatic organisms. India ranks second in total fish production in the world. Nile tilapia has become the world’s second most popular farmed fish, after carps. Oscars is a popular aquarium fish around the world. In the present study, efforts were made to analyze the extent of divergence or similarity among three cichlid finfishes (Nile Tilapia, GIFT Tilapia, and Oscar Cichlid) using molecular biology techniques such as Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP). The Phylogenetic tree was constructed using PhyElph software to study the evolutionary relationship between the three cichlid finfish species. The Phylogenetic or evolutionary relationship was established for the three fishes, Nile tilapia, GIFT, and Oscar cichlid, with the Phylogenetic tree. It was found that Nile tilapia and GIFT share a recent common ancestor, while Oscar cichlid does not share any evolutionary relationship with Nile tilapia and GIFT.

Sign in / Sign up

Export Citation Format

Share Document