In Silico Study of miR-132 with mRNA of Acetylcholinesterase to Investigate the Binding Affinity for Interaction

2018 ◽  
Vol 08 (02) ◽  
Author(s):  
Sabahat Sohail
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
In Silico Study

Coumarins and Quinolones as Effective Multiple Targeted Agents Versus Covid-19: An in Silico Study

2021 ◽  
Vol 17 ◽  
Author(s):  
Mojgan Nejabat ◽  
Razieh Ghodsi ◽  
Farzin Hadizadeh
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Oral Absorption ◽  
Antiviral Agent ◽  
In Vivo Studies ◽  
Reference Drug ◽  
Viral Proteases ◽  
In Silico Study

Background: The Covid-19 virus emerged a few months ago in China and infections rapidly escalated into a pandemic. Objective: To date, there is no selective antiviral agent for the management of pathologies associated with covid-19 and the need for an effective agent against it is essential. Method: In this work two home-made databases from synthetic quinolines and coumarins were virtually docked against viral proteases (3CL and PL), human cell surface proteases (TMPRSS2 and furin) and spike proteins (S1 and S2). Chloroquine, a reference drug without a clear mechanism against coronavirus was also docked on mentioned targets and the binding affinities compared with title compounds. Result: The best compounds of synthetic coumarins and quinolines for each target were determined. All compounds against all targets showed binding affinity between -5.80 to -8.99 kcal/mol in comparison with the FDA-approved drug, Chloroquine, with binding affinity of -5.7 to -7.98 kcal/mol. Two compounds, quinoline-1 and coumarin-24, were found to be effective on three targets – S2, TMPRSS2 and furin – simultaneously, with good predicted affinity between -7.54 to -8.85 kcal/mol. In silico ADME studies also confirmed good oral absorption for them. Furthermore, PASS prediction was calculated and coumarin-24 had higher probable activity (Pa) than probable inactivity (Pi) with acceptable protease inhibitory as well as good antiviral activity against Hepatitis C virus (HCV), Human immunodeficiency virus (HIV) and influenza. Conclusion: Quinoline-1 and Coumarin-24 have the potential to be used against Covid-19. Hence these agents could be useful in combating covid-19 infection after further in vitro and in vivo studies.

scholarly journals IN SILICO STUDY OF APIGENIN AND APIGETRIN AS INHIBITOR OF 3-HYDROXY-3-METHYL-GLUTAYL-COENZYME A REDUCTASE

2017 ◽  
Vol 10 (11) ◽  
pp. 284
Author(s):  
Dwintha Lestari ◽  
Elin Yulinah Sukandar ◽  
Irda Fidrianny
Keyword(s):  
Binding Site ◽  
Binding Affinity ◽  
In Silico ◽  
Coenzyme A ◽  
Inhibition Constant ◽  
Two Dimensional ◽  
Binding Interaction ◽  
Docking Result ◽  
Binding Process ◽  
In Silico Study

  Objective: The objectives of this research were to investigate in silico interaction between apigenin and apigetrin with 3-hydroxy-3-methyl-glutayl-coenzyme A (HMG Co-A) reductase, to find the most favorable binding site as well as to predict the binding mode.Materials and Methods: Docking calculation was performed by branded Sony Vaio PC Linux Ubuntu 14.04 LTS. The binding process based on the best docking result with HMG Co-A reductase was presented in two-dimensional diagram. Statin, atorvastatin, and R-mevalonate were used as standard.Results: Binding affinity and inhibition constant of R-mevalonate were Ei=−4.2 kcal/mol, Ki=836.78 μM; apigenin Ei=−7.0 kcal/mol, Ki=7.43 μM; apigetrin Ei=−5.9 kcal/mol, Ki=47.53 μM; simvastatin Ei=−8.2 kcal/mol; Ki=0.98 μM; atorvastatin Ei=−8.4 kcal/mol; Ki=0.7 μM. Apigenin had better binding interaction than apigetrin.Conclusion: Apigenin could be developed as anticholesterol.

In silico Study of the Active Compounds of Lindera aggregata (Sims) Kosterm. as Anti-coronavirus

2020 ◽  
Vol 16 ◽  
Author(s):  
Elok R. Firdiana ◽  
Elga Renjana ◽  
Linda W. Ningrum ◽  
Melisnawati H. Angio ◽  
Muhamad Nikmatullah ◽  
...  
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Chinese Government ◽  
Docking Analysis ◽  
Target Proteins ◽  
Rate Of Spread ◽  
Inhibitory Mechanisms ◽  
In Silico Study ◽  
New Type ◽  
Coronavirus Infection

Background: Covid-19, caused by a new type of coronavirus named SARS-CoV-2, has become a pandemic. Together with SARS-CoV and MERS-CoV, Covid-19 is a large global outbreak of coronavirus infection; however, its rate of spread is much higher. Since the vaccines and anti-SARS-CoV-2 have not been found, a faster control mechanism is needed. Traditional herbs have shown the potential for this purpose, as has been demonstrated by the Chinese Government with a high success rate. One of the herbs used was Lindera aggregata, which is part of the collection in Purwodadi Botanic Garden. Objectives: Through in silico study, this research aims to reveal the secondary metabolites contained in L. aggregata that have the potential to serve as anti-SARS-CoV-2 medication as well as showcase their inhibitory mechanisms. Methods: The research was conducted through molecular docking analysis of terpenoids and alkaloids contained in the root of L. aggregata, with target proteins 3CLpro, PLpro, Spike, and ACE 2 playing a role in SARS-CoV-2 infection. Result: All analyzed compounds tended to interact with all four target proteins with different binding affinity values, but the interaction seemed stronger with 3CLpro and Spike. Terpenoids, linderane and linderalactone, had the strongest interaction tendency with 3CLpro, PLpro, and Spike; the compound norboldine, an alkaloid, had the strongest interaction with ACE 2, with a binding affinity value of -8.2 kcal/mol. Conclusion: Terpenoids and alkaloids contained in the root of L. aggregata, which caused inhibition of adsorption and replication of SARS-CoV-2, could serve as anti-SARS-CoV-2.

Missense mutations involvement in COX-2 structure, and protein-substrate binding affinity: in-silico study

2021 ◽  
pp. 1-19
Author(s):  
Tahereh Zahedi ◽  
Abasalt Hosseinzadeh Colagar ◽  
Habibollah Mahmoodzadeh ◽  
Jahan-Bakhsh Raoof
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Substrate Binding ◽  
Missense Mutations ◽  
Protein Substrate ◽  
In Silico Study ◽  
Cox 2

Human Transthyretin Binding Affinity of Halogenated Thiophenols and Halogenated Phenols: an in Vitro and in Silico Study

Chemosphere ◽  
2021 ◽  
pp. 130627
Author(s):  
Xianhai Yang ◽  
Wang Ou ◽  
Songshan Zhao ◽  
Lianjun Wang ◽  
Jingwen Chen ◽  
...  
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
In Silico Study ◽  
Halogenated Phenols

In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

2013 ◽  
Vol 13 (10) ◽  
pp. 1407-1414 ◽  
Author(s):  
L. Fabian ◽  
V. Sulsen ◽  
F. Frank ◽  
S. Cazorla ◽  
E. Malchiodi ◽  
...  
Keyword(s):  
In Silico ◽  
Sesquiterpene Lactones ◽  
Trypanocidal Activity ◽  
In Silico Study

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.

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