scholarly journals A study on catalytic and non-catalytic sites of H5N1 and H1N1 neuraminidase as the target for chalcone inhibitors

2021 ◽  
Vol 64 (1) ◽  
Author(s):  
Pandu Hariyono ◽  
Jasvidianto Chriza Kotta ◽  
Christophorus Fideluno Adhipandito ◽  
Eko Aprilianto ◽  
Evan Julian Candaya ◽  
...  
Keyword(s):  
In Silico ◽  
H1n1 Pandemic ◽  
Inhibitor Development ◽  
Pharmacokinetic Profiles ◽  
Common Drug ◽  
In Silico Study ◽  
Catalytic Sites ◽  
Competitive Inhibitors ◽  
The World ◽  
Better Than

AbstractThe H1N1 pandemic in 2009 and the H5N1 outbreak in 2005 have shocked the world as millions of people were infected and hundreds of thousands died due to the infections by the influenza virus. Oseltamivir, the most common drug to block the viral life cycle by inhibiting neuraminidase (NA) enzyme, has been less effective in some resistant cases due to the virus mutation. Presently, the binding of 10 chalcone derivatives towards H5N1 and H1N1 NAs in the non-catalytic and catalytic sites was studied using molecular docking. The in silico study was also conducted for its drug-like likeness such as Lipinski Rule, mutagenicity, toxicity and pharmacokinetic profiles. The result demonstrates that two chalcones (1c and 2b) have the potential for future NA inhibitor development. Compound 1c inhibits H5N1 NA and H1N1 NA with IC50 of 27.63 µM and 28.11 µM, respectively, whereas compound 2b inhibits NAs with IC50 of 87.54 µM and 73.17 µM for H5N1 and H1N1, respectively. The in silico drug-like likeness prediction reveals that 1c is 62% better than 2b (58%) in meeting the criteria. The results suggested that 1c and 2b have potencies to be developed as non-competitive inhibitors of neuraminidase for the future development of anti-influenza drugs.

scholarly journals In silico Analysis of Phylogeny and Virulence Genes in STEC Strains Associated with Outbreaks

2021 ◽  
Author(s):  
Mehmet Demirci ◽  
Akın Yiğin ◽  
Fadile Yıldız Zeyrek
Keyword(s):  
Foodborne Pathogens ◽  
In Silico ◽  
Virulence Genes ◽  
Genomic Analysis ◽  
In Silico Analysis ◽  
Comparative Genomic ◽  
Phylogeny Analysis ◽  
In Silico Study ◽  
The World ◽  
Different Parts

Objective: Shiga toxin-producing E. coli (STEC) strains are important foodborne pathogens. Significant outbreaks with STEC strains can be encountered, even if the geography, time or resources were different. The aim of our in silico study was to compare the virulance factors and phylogeny of STEC strains such as EDL933 and Sakai, which have been identified as an agent in important outbreaks in different parts of the world and whole genomic data were in open databases. Method: Genomic NCBI data of eight strains were included in our study, including seven different STEC strains associated with significant epidemics in different parts of the world, and one supershedder strain obtained from cattle feces. Results: According to phylogeny analysis, the most similar strain to EDL933 strain was TW14588, with 96.4% similarity. The most distant similarity was Sakai strains with 79.2%. According to the virulence genes analysis; the presence of 333 genes that constitute virulence factors under nine headings were detected. In the first STEC origin, EDL933, 45% of all virulence genes were found to be active. Adherence genes such as Ecp, Elf, Hcp and toxin genes such as clyA were active in all strains except stx genes. Conclusion: In our in silico study of comparative genomic analysis of STEC strains which are associated with outbreaks, it was determined that STEC strains used different virulence genes besides the stx gene. Indeed, they used certain virulence genes, even their sources, time and locations were different, in the pathogenesis

Phytochemicals as Therapeutics Against COVID-19: An In-Silico Study

2020 ◽  
Author(s):  
Debraj Koiri ◽  
Ditam Chakraborty ◽  
Pranotosh Das ◽  
Rajkumar Rana ◽  
Soumyanil Chatterjee ◽  
...  
Keyword(s):  
In Silico ◽  
Therapeutic Agents ◽  
Binding Energies ◽  
Daily Lives ◽  
Lab Experiments ◽  
In Silico Studies ◽  
In Silico Study ◽  
The World ◽  
Wet Lab ◽  
Low Costs

Since December 2019, the worldwide spread of COVID-19 has brought the majority of the world to a standstill, affecting daily lives as well as economy. Under these conditions, it is imperative to develop a cure as soon as possible. On account of some of the adverse side effects of the existing conventional drugs, researchers all around the world are screening natural antiviral phytochemicals as potential therapeutic agents against COVID-19. This paper aims to review interactions of some specific phytochemicals with the receptor binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2 and suggest their possible therapeutic applications. Literature search was done based on the wide array of in-silico studies conducted using broad spectrum phytochemicals against SARS-CoV-2 and other viruses. We shortlisted 26 such phytochemicals specifically targeting the S protein and its interactions with host receptors. To validate the previously published results, we also conducted molecular docking using the AutoDockVina application and identified 6 high potential phytochemicals for therapeutic use based on their binding energies. Besides this, availability of these compounds, their mode of action, toxicity data and cost-effectiveness were also taken into consideration. Our review specifically identifies 6 phytochemicals that can be used as potential treatments for COVID-19 based on their availability, toxicology results and low costs of production. However, all these compounds need to be further validated by wet lab experiments and should be approved for clinical use only after appropriate trials.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating them as potentials candidates for muti-target drugs for COVID-19.

The Use of Bioinformatics and Big Data for the In Silico Study of Psychiatric Disorders

2021 ◽  
pp. 255-268
Author(s):  
Wei Zhang ◽  
Gabriel R. Fries ◽  
Joao Quevedo
Keyword(s):  
Big Data ◽  
Psychiatric Disorders ◽  
In Silico ◽  
Integrated Analysis ◽  
Data Sets ◽  
In Silico Study ◽  
The World ◽  
Ongoing Development ◽  
Psychiatry Disorders ◽  
Mental And Behavioral Disorders

Mental and behavioral disorders are becoming the leading cause of disability across the world. Along with the ongoing development of biomedical and computational technologies, more and more data are being constantly produced, including genomic, transcriptomic, metabolomic, proteomic, clinical, and imaging resources. As a consequence, scientists in the psychiatric field are actively changing their research ways from studies focused on individual investigators to large international consortia, which accelerate the data accumulation and increase its size. This chapter discusses the current publicly available data sets on psychiatry disorders and neuroscience, as well as their integrated analysis. The authors also list some studies using novel types of data, which will further extent the potential of big data in the study of psychiatric disorders.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating them as potentials candidates for muti-target drugs for COVID-19.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating that they are potentials candidates for muti-target drugs for COVID-19.

scholarly journals Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

2020 ◽  
Author(s):  
Romulo O. Barros ◽  
Fabio L. C. C. Junior ◽  
Wildrimak S. Pereira ◽  
Neiva M. N. Oliveira ◽  
Ricardo Ramos
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Social Health ◽  
Research Institutions ◽  
Health Measures ◽  
In Silico Study ◽  
The World ◽  
Anti Hiv ◽  
Society Research

The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for the COVID-19. In this work, molecular docking was used to study (in silico) the interaction of twenty-four ligands, divided into four groups, with four important SARS-CoV-2 receptors. The results showed that Metaquine (group 01), antimalarial substance and the anti-HIV antiretroviral Saquinavir (group 03), presented interaction with all the studied receptors, indicating them as potentials candidates for muti-target drugs for COVID-19.

Anti-Inflammation Prediction of Orthosiphon Stamineus Extract Against Covid19 (In Silico Study)

2021 ◽  
Vol 8 (1) ◽  
pp. 14-18
Author(s):  
Mahdi Nazari V ◽  
Masoumeh Nazari ◽  
Soodabeh Arabani ◽  
Mansoureh NazariI V
Keyword(s):  
Active Site ◽  
In Silico ◽  
The Other ◽  
Active Compounds ◽  
Orthosiphon Stamineus ◽  
In Silico Study ◽  
Asian People ◽  
In Silico Molecular Docking ◽  
Anti Inflammation ◽  
Better Than

Orthosiphon stamineus Benth (OS) due to its anti-inflammation effect is one of the possible options to fight the outbreak of coronavirus disease in 2019 (COVID-19). In this article, we evaluate in silico (molecular docking) properties of active compounds available in OS which is generally consumed by south east asian people and compare its effect with remdesivir and favipiravir as positive compounds based on docking properties. The main active compounds were grouped based on their major roles in OS. The results demonstrated that most of the studied main compounds perform better than selected drugs in inhibition of the spike protein in COVID-19. According to the combined scores in binding affinity, the drug-likeness properties of the ligand, revealed to be the best possible covid19 inhibitor as compared to the other ligands. The analysis of active site also demonstrated that OS active compounds may have the therapeutic effect against COVID19.

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