A comprehensive examination of ACE-2 receptor and prediction of spike glycoprotein and ACE-2 interaction based on in silico analysis of ACE-2 receptor

10.22541/au.163155023.33302207/v1 ◽

2021 ◽

Author(s):

Nehir Özdemir Özgentürk ◽

EMRE Aktaş

Keyword(s):

Physical Properties ◽

Critical Role ◽

Transmembrane Helix ◽

In Silico Analysis ◽

Active Role ◽

Vital Role ◽

Surface Glycoprotein ◽

Bioinformatic Tools ◽

Essential Resource ◽

Silico Analysis

ACE-2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in some diseases. Studies have been carried out on the interactions of ACE-2- SARS-CoV proteins. However, comprehensive research has not been conducted on ACE2 protein by using bioinformatic tools. The present study especially two places, G104 and L108 points, which are effective in protecting the structure of the ACE-2 protein, play a critical role in the biological functioning of this protein, and play an essential role in determining the chemical-physical properties of this protein, and play a crucial role for ACE-2 protein-SARS CoV surface glycoprotein, were determined. It was also found that the G104 and L108 regions were more prone to possible mutations or deletions than the other ACE-2 protein regions. Moreover, it was determined that all possible mutations or deletions in these regions affect the chemical-physical properties, biological functions, and structure of the ACE-2 protein. Having a negative GRAVY value, one transmembrane helix, a significant molecular weight, a long-estimated half-life as well as most having unstable are results of G104 and L108 points mutations or deletions. Finally, it was determined that LQQNGSSVLS, which belong to the ACE-2 protein, may play an active role in binding the spike protein of SARS-CoV. All possible docking score results were estimated. It is thought that this study will bring a different perspective to ACE-2 _SARS-CoV interaction and other diseases in which ACE-2 plays an important role and will also be an essential resource for studies on ACE-2 protein.

Download Full-text

Potential Compounds for the Inhibition of TMPRSS2

10.26434/chemrxiv.12727787.v1 ◽

2020 ◽

Author(s):

Muhammad Roomi ◽

Yaser Khan

Keyword(s):

In Silico Analysis ◽

Chemical Compounds ◽

Vital Role ◽

Large Sets ◽

Potential Inhibitors ◽

Key Residues ◽

And Control ◽

Silico Analysis ◽

High Binding Affinity ◽

Cell Fusions

The ongoing search to contain and control the spread of COVID-19 disease focuses on discovering drugs or vaccines that can play an essential role in treating this contagious disease. This paper focuses on natural compounds that can play a vital role in the treatment of Covid-19. The study spans over the chemicals that have the potential to bind with the key residues of type II Transmembrane Protease Serine (TMPRSS2). TMPRSS2 can be termed as the catalyst that cleaves the spike glycoproteins of Sars-Cov-2, which causes the replication and spread of virus inside the human body by facilitating virus-cell fusions. Drugs like Camostat Mesylate, Aprotinin, and Rimantadine have been proposed as potential inhibitors of TMPRSS2. After screening large sets of phytochemicals and flavonoids extracted from plants, potential compounds have been tested, and a set of most effective and suitable compounds are chosen for further studies. These selected compounds are further analyzed in terms of binding with key residues as well as high binding affinity with TMPRSS2. The in silico analysis of possible chemical compounds is carried out by using docking, screening analysis, Molecular Dynamics, and Electrostatic Potential Simulations. Chemicals extracted from different plants are comparatively analyzed with drugs like Aprotinin, Camostat Mesylate, and Rimantadine.

Download Full-text

Genetics A Comprehensive In Silico Analysis of Deleterious SNPs of Paraplegin Protein Associated with Hereditary Spastic Paraplegia through Mitochondrial Dysfunction

BioScientific Review ◽

10.32350/bsr.0202.01 ◽

2020 ◽

Vol 2 (2) ◽

pp. 1-14

Author(s):

Ammara Akhtar ◽

Sobia Nazir Choudhry ◽

Rana Muhammad Mateen ◽

Mureed Hussain

Keyword(s):

Hereditary Spastic Paraplegia ◽

In Silico ◽

Mitochondrial Protein ◽

In Silico Analysis ◽

Missense Mutations ◽

Spastic Paraplegia ◽

Bioinformatic Tools ◽

Pathogenic Variants ◽

Structural And Functional Properties ◽

Silico Analysis

Hereditary spastic paraplegia (HSP) is a heterogenous neurological disorder primarily associated with progressive spasticity. Paraplegin is a mitochondrial protein and mutations in this protein can lead to HSP. In this study, in silico analysis was carried out to identify the pathogenic variants of SPG7 (paraplegin protein). To find novel pathogenic mutations, missense and splicing variants were collected from gnomAD database and passed through a detailed and stringent analysis with the help of a variety of bioinformatic tools. The list of mutations was examined and compared in ClinVar. Altogether, 14 missense mutations and 18 splicing mutations were obtained and these mutations were predicted to have the potential of disrupting the normal structural and functional properties of paraplegin protein.

Download Full-text

In silico Analysis of the Immunological Landscape of Hippocampi in Alzheimer’s Disease

Dementia and Geriatric Cognitive Disorders ◽

10.1159/000508283 ◽

2020 ◽

Vol 49 (3) ◽

pp. 252-254

Author(s):

Sai Batchu

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Dendritic Cells ◽

Cd8 T Cells ◽

Immune Cells ◽

Critical Role ◽

In Silico Analysis ◽

Expression Data ◽

Immune Signature ◽

Silico Analysis

Introduction: Accumulating evidence suggests a relationship between neuroinflammation and neurodegenerative pathologies such as Alzheimer’s disease (AD). This study sought to investigate the immunological composition of hippocampi in patients afflicted with AD. Methods: CIBERSORTx RNA deconvolution was applied on gene expression data developed from hippocampi of 38 AD patients and 17 controls to infer the relative proportions of 22 subsets of immune cells. Results: AD-afflicted hippocampi were found to have greater relative abundances of M2 macrophages and CD8 T cells. AD-afflicted hippocampi were also composed of significantly more active dendritic cells and significantly fewer resting dendritic cells than control samples. Conclusion: AD-afflicted hippocampi present with a distinct immune signature and dendritic cells may play a critical role in the pathogenesis of AD in this brain component.

Download Full-text

Cloning, Sequencing and In Silico Analysis of Omp C of Salmonella Typhimurium

ISRN Veterinary Science ◽

10.5402/2012/512848 ◽

2012 ◽

Vol 2012 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Richa Jha ◽

Anil Kumar ◽

Anjani Saxena ◽

Shantanu Tamuly ◽

M. K. Saxena

Keyword(s):

Dna Vaccine ◽

Outer Membrane Proteins ◽

In Silico Analysis ◽

Broad Host Range ◽

Coding Region ◽

Bioinformatic Tools ◽

Poultry Products ◽

Histocompatibility Complex ◽

Cell Mediated Immune Response ◽

Silico Analysis

Salmonella Typhimurium is an important pathogen having a broad host range. In human population it causes mostly gastroenteritis but there are reports in which it was found to be responsible to cause several lethal diseases like endocarditis and meningitis. Poultry products are the major sources of this organism in India as these are consumed at various stages of cooking. The available vaccines have their own limitations such as short-term immunity. Outer membrane proteins have shown some promising potential, so in the present study Omp C of Salmonella Typhimurium was cloned and sequenced to explore the possibility of development of r-DNA vaccine against Salmonella Typhimurium for poultry. The sequence of Omp C was studied for antigenic indexing, epitope mapping, and MHC mapping using various bioinformatic tools. The ORF analysis revealed a complete coding region of approximately 1000 bp. Five major and 13 minor B-cell epitopes were identified having an antigenic index of 1.7. The sequences also showed major histocompatibility complex (MHC) class I and class II binding region indicating a potential of eliciting cell-mediated immune response. The findings indicate that Omp C may be proven as promising candidate for development of r-DNA vaccine against Salmonella Typhimurium.

Download Full-text

In silico analysis of relative rareness, codon usage, and enzyme-substrate docking of Lampyroidea maculata luciferase

Current Proteomics ◽

10.2174/1570164617999200905132355 ◽

2020 ◽

Vol 17 ◽

Author(s):

Mojtaba Mortazavi ◽

Saman Hosseinkhani ◽

Masoud Torkzadeh-Mahani ◽

Safa Lotfi ◽

Rahman Emamzadeh ◽

...

Keyword(s):

Codon Usage ◽

Binding Site ◽

In Silico ◽

Critical Role ◽

3D Structure ◽

In Silico Analysis ◽

Living Organism ◽

Industrial Biotechnology ◽

Rare Codons ◽

Silico Analysis

: Bioluminescence is the production and emission of light by the luciferase enzymes in a living organism. The luciferases were identified in different domains of life, but the Lampyridae luciferases are considered for biotechnological and clinical applications. Recently, the new Iranian luciferase gene from the Lampyroidea maculata has been cloned and characterized. In this study, in silico analysis of this enzyme as the codon usage bias parameters (CAI, CBI, ENC, and rare codons) were conducted. Furthermore, the 3D structure of this enzyme was modeled in the I-TASSER web server and the status of these rare codons in this model was studied using SPDBV and PyMOL software. In the following, the substrate-binding site was studied using the AutoDock Vina. By molecular modeling, some rare codons were identified that may have a critical role in the structure and function of this enzyme. The GC3% of the CDs was 17/304 and GC3 Skewness was 0.115. The molecular docking analysis recognizes some residues that yield closely related to the DLSA binding site. By these analyses, a new understanding of the sequence and structure of this enzyme was created, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an important role in the design of the new recombinant enzyme.

Download Full-text

Potential Compounds for the Inhibition of TMPRSS2

10.26434/chemrxiv.12727787 ◽

2020 ◽

Author(s):

Muhammad Roomi ◽

Yaser Khan

Keyword(s):

In Silico Analysis ◽

Chemical Compounds ◽

Vital Role ◽

Large Sets ◽

Potential Inhibitors ◽

Key Residues ◽

And Control ◽

Silico Analysis ◽

High Binding Affinity ◽

Cell Fusions

The ongoing search to contain and control the spread of COVID-19 disease focuses on discovering drugs or vaccines that can play an essential role in treating this contagious disease. This paper focuses on natural compounds that can play a vital role in the treatment of Covid-19. The study spans over the chemicals that have the potential to bind with the key residues of type II Transmembrane Protease Serine (TMPRSS2). TMPRSS2 can be termed as the catalyst that cleaves the spike glycoproteins of Sars-Cov-2, which causes the replication and spread of virus inside the human body by facilitating virus-cell fusions. Drugs like Camostat Mesylate, Aprotinin, and Rimantadine have been proposed as potential inhibitors of TMPRSS2. After screening large sets of phytochemicals and flavonoids extracted from plants, potential compounds have been tested, and a set of most effective and suitable compounds are chosen for further studies. These selected compounds are further analyzed in terms of binding with key residues as well as high binding affinity with TMPRSS2. The in silico analysis of possible chemical compounds is carried out by using docking, screening analysis, Molecular Dynamics, and Electrostatic Potential Simulations. Chemicals extracted from different plants are comparatively analyzed with drugs like Aprotinin, Camostat Mesylate, and Rimantadine.

Download Full-text

The expression of miR-513c and miR-3163 was downregulated in tumor tissues compared with normal adjacent tissue of patients with breast cancer

BMC Medical Genomics ◽

10.1186/s12920-021-01029-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Soheila Delgir ◽

Khandan Ilkhani ◽

Asma Safi ◽

Yazdan Rahmati ◽

Vahid Montazari ◽

...

Keyword(s):

Breast Cancer ◽

In Silico ◽

Target Genes ◽

Critical Role ◽

In Silico Analysis ◽

Glutamine Metabolism ◽

Biological Processes ◽

Tumor Tissues ◽

In Silico Studies ◽

Silico Analysis

Abstract Background Breast cancer (BC) is the most invasive cancer with different subtypes that its metabolism is unique compared with normal cells. Glutamine is considered critical nutrition that many cancer cells, particularly BC cells, are dependent on it for growth and proliferation. Therefore, targeting glutamine metabolism, especially enzymes that are related to this pathway, can be beneficial to design anti-cancer agents. Recent evidence has shown that microRNAs (miRNAs), with a short length and single-strand properties, play a prominent role in regulating the genes related to glutamine metabolism, which may control the development of cancer. Methods In silico analysis confirmed that miR-513c and miR-3163 might be involved in glutamine metabolism. The expression level of these two miRNAs was evaluated in eighty BC tissues and normal adjacent tissues. Furthermore, GSE38167, GSE38867, GSE42128, GSE45666, and GSE53179 were employed from gene expression omnibus (GEO). The Limma package was utilized to identify differentially expressed miRNAs (DEMs) of mentioned datasets to evaluate miR-513c and miR-3163 expression. Further, in silico analysis was utilized to predict the potential biological processes and molecular pathways of miR-513c and miR-3163, based on their target genes. Results In silico studies revealed top categories of biological processes and cellular pathways that might play a critical role in metabolism reprogramming and cancer development and were target genes for miR-513c and miR-3163. The current study showed that miR-513c (p value = 0.02062 and FC = − 2.3801) and miR-3163 (p value = 0.02034 and FC = − 2.3792) were downregulated in tumor tissues compared to normal adjacent tissues. The analysis of GEO microarray datasets showed that miR-513c was downregulated in GSE38167, GSE38867, GSE42128, GSE45666 and GSE53179, whereas there was a significant downregulation of miR-3163 in only two studies, including GSE38867 and GSE42128 that they were in accordance with our experimental results. Furthermore, the subgroup analysis did not show any substantial relationship between expression levels of these two miRNAs and factors such as age, family history of cancer, and abortion history. Conclusion MiR-513c and miR-3163 were downregulated in BC tissues, which might serve as tumor suppressors. They are suggested as potential therapeutic targets for patients with BC.

Download Full-text