scholarly journals In silico analysis of Trisindoline 1 compound against Mpro SARS-CoV-2 as novel potential drugs candidate

2021 ◽  
Vol 2 (2) ◽  
pp. 42-50
Author(s):  
Fitri Lianingsih
Keyword(s):  
Amino Acid ◽  
Viral Entry ◽  
In Silico ◽  
In Silico Analysis ◽  
Cell Receptor ◽  
The Novel ◽  
Discovery Studio ◽  
Protein Receptors ◽  
Marine Compound ◽  
Novel Coronavirus

The novel coronavirus 2019 (SARS-CoV-2) is one of the viruses that can infect humans and cause high mortality worldwide. The protease (Mpro) is key SARS-CoV-2 an enzyme mediates the viral replication and the transcription. Mpro is currently used as the candidate for the SARS-CoV-2 vaccine because Mpro is one of the key enzymes in the viral life cycle that essential for interactions between the virus and host cell receptor during viral entry. The Mpro can be a target protein to design the novel drug of SARS-CoV-2. The drug design from natural products that are considered to have low toxicity is needed against the virus. The study aims to determines the potential pharmacology of Trisindoline 1 compound from the sponge Hyrtios altum against SARS-CoV-2 and to find the amino acid residues between interaction ligand-protein receptors. The methods of this study use the virtual screening of Auto Dock Vina and visualization the amino acid residue using Bio via Discovery Studio. The result of this study was the selected marine compound from Trisindoline 1 may have potential to developed as inhibitor of SARS-CoV-2.Keywords: In Silico, Mpro, Sars Cov 2, Trisindoline 1, Sponges

scholarly journals Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

2020 ◽  
Author(s):  
Elena Susana Barbieri ◽  
Tamara Rubilar ◽  
Ayelén Gázquez ◽  
Marisa Avaro ◽  
Erina Noé Seiler ◽  
...  
Keyword(s):  
Sea Urchin ◽  
In Silico ◽  
In Silico Analysis ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
Therapeutic Drug ◽  
The Novel ◽  
Novel Coronavirus ◽  
Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br>

scholarly journals Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

2020 ◽  
Author(s):  
Elena Susana Barbieri ◽  
Tamara Rubilar ◽  
Ayelén Gázquez ◽  
Marisa Avaro ◽  
Erina Noé Seiler ◽  
...  
Keyword(s):  
Sea Urchin ◽  
In Silico ◽  
In Silico Analysis ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
Therapeutic Drug ◽  
The Novel ◽  
Novel Coronavirus ◽  
Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br>

The Antiviral and Antimalarial Drug Repurposing in Quest of Chemotherapeutics to Combat COVID-19 Utilizing Structure-Based Molecular Docking

2020 ◽  
Vol 23 ◽  
Author(s):  
Sisir Nandi ◽  
Mohit Kumar ◽  
Mridula Saxena ◽  
Anil Kumar Saxena
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Drug Repurposing ◽  
Clinical Settings ◽  
The Novel ◽  
In Silico Docking ◽  
Biochemical Mechanisms ◽  
Novel Coronavirus ◽  
In Silico Molecular Docking

Background: The novel coronavirus disease (COVID-19) is caused by a new strain (SARS-CoV-2) erupted in 2019. Nowadays, it is a great threat that claims uncountable lives worldwide. There is no specific chemotherapeutics developed yet to combat COVID-19. Therefore, scientists have been devoted in the quest of the medicine that can cure COVID- 19. Objective: Existing antivirals such as ASC09/ritonavir, lopinavir/ritonavir with or without umifenovir in combination with antimalarial chloroquine or hydroxychloroquine have been repurposed to fight the current coronavirus epidemic. But exact biochemical mechanisms of these drugs towards COVID-19 have not been discovered to date. Method: In-silico molecular docking can predict the mode of binding to sort out the existing chemotherapeutics having a potential affinity towards inhibition of the COVID-19 target. An attempt has been made in the present work to carry out docking analyses of 34 drugs including antivirals and antimalarials to explain explicitly the mode of interactions of these ligands towards the COVID-19protease target. Results: 13 compounds having good binding affinity have been predicted towards protease binding inhibition of COVID-19. Conclusion: Our in silico docking results have been confirmed by current reports from clinical settings through the citation of suitable experimental in vitro data available in the published literature.

scholarly journals Colorectal Cancer that Highly Express Both ACE2 and TMPRSS2, Suggesting Severe Symptoms to SARS-CoV-2 Infection

2021 ◽  
Vol 27 ◽  
Author(s):  
Huai Wang ◽  
Jiankang Yang
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Viral Entry ◽  
Colon Adenocarcinoma ◽  
The Novel ◽  
Aberrant Expression ◽  
Systematic Analysis ◽  
More Care ◽  
Novel Coronavirus ◽  
Colorectal Cancer Patients

The epidemic of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) in the world pose a global health emergency. Cancer has been identified as a risk factor for the novel Coronavirus disease 2019 (COVID-19). The ACE2 and TMPRSS2 have been implicated in SARS-CoV-2 infection for mediating viral entry into the host cell. However, a systematic analysis of aberrant expression of ACE2 and TMPRSS2 was not yet reported in multiple human cancers. Here, we analyzed gene expression of ACE2 and TMPRSS2 across 31 types of tumors. Notably, overexpression of ACE2 and TMPRSS2 have been observed in colorectal cancer including colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ). In addition, the colorectal tumors with upregulated gene expressing presented with decreased DNA methylation levels. DNA methylation might be one of the reasons for abnormal expression of ACE2 and TMPRSS2. Conclusively, colorectal cancer was the only cancer with the upregulated expression of ACE2 and TMPRSS2. More care of colorectal cancer patients is needed in multiple cancers affected by the COVID-19 outbreak.

scholarly journals In silico identification of vaccine targets for 2019-nCoV

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 145 ◽  
Author(s):  
Chloe Hyun-Jung Lee ◽  
Hashem Koohy
Keyword(s):  
T Cell ◽  
In Silico ◽  
Vaccine Development ◽  
De Novo ◽  
Cell Receptor ◽  
Binding Potential ◽  
Hla Alleles ◽  
Immunogenic Peptides ◽  
Novel Coronavirus ◽  
Positional Weight

Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China. Methods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0. Results: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential. Conclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline.

In Silico Approaches for Novel Drug Discovery Against Coronavirus by Employing the Hybrid Molecular Technique: A Review

2021 ◽  
pp. 1-8
Author(s):  
Noor ul Amin Mohsin ◽  
Muhammad Irfan ◽  
Muhammad Naeem Aamir
Keyword(s):  
In Silico ◽  
Antiviral Agent ◽  
Molecular Technique ◽  
The Novel ◽  
Hybrid Molecules ◽  
The World ◽  
Being There ◽  
Novel Coronavirus ◽  
Novel Drug ◽  
Day By Day

The coronavirus disease (COVID-19) is causing havoc all around the world. The number of active cases and deaths is increasing day by day. The novel coronavirus (CoV) is the causative agent of this disease. For the time being, there is no specific antiviral agent for the cure of COVID-19. A variety of drugs are being repurposed to counteract this disease. Scientists all over the world are striving to get some ideal molecules against this pandemic. Some hybrid molecules have been designed by coupling the privileged scaffolds of known antiviral and antimalarial drugs. This review deals with the hybrid molecules that have been designed and evaluated against the known targets of CoV by in silico techniques.

In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

2021 ◽  
Vol 24 ◽  
Author(s):  
Ashis Kumar Goswami ◽  
Hemanta Kumar Sharma ◽  
Neelutpal Gogoi ◽  
Ankita Kashyap ◽  
Bhaskar Jyoti Gogoi
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Discovery Studio ◽  
North East ◽  
Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

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