scholarly journals Antioxidant Activity and In-Silico Study of Anthraquinone Glycosides Extracted from Cassia Fistula Against the Main Protease (7BUY) In SARS-COV2

2021 ◽  
Vol 14 (3) ◽  
pp. 1669-1674
Author(s):  
Yessar A. Dawood ◽  
Sabaa Ali Mohammed Al.Fadal ◽  
Ula M. i Noor Almousaw ◽  
Murtakab Y Al-Hejjaj
Keyword(s):  
Hydrogen Peroxide ◽  
Docking Study ◽  
Inhibition Assay ◽  
Cassia Fistula ◽  
Energy Score ◽  
Main Protease ◽  
Anthraquinone Glycosides ◽  
In Silico Study ◽  
The World ◽  
Aloe Emodin

With the spreading of Covid-19 and seeking for a drug that helps people around the world to cure this disease.In this article, we used a plant(Cassia fistula) which is rich in anthraquinone glycosides to control the causative agent. Anthraquinone was extracted from Cassia fistula pods using alcohol method.Antioxidant activity of the extracted anthraquinone was analysed by using hydrogen peroxide scavenging assay.The best inhibition assay was 70% at100mg/mlconcentration. The docking study introduced atheoretical explanation for an interaction between two types of anthraquinone glycosides (rhein and aloe-emodin) in Cassia fistula against the main protease (7BZ5) in SARS-COV-2 virus, which gave a good binding energy score as -5.36491489 and -5.48040009 for rhein and aloe-emodin, respectively.

scholarly journals In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease

2021 ◽  
Vol 8 ◽  
Author(s):  
Osvaldo Yañez ◽  
Manuel Isaías Osorio ◽  
Eugenio Uriarte ◽  
Carlos Areche ◽  
William Tiznado ◽  
...  
Keyword(s):  
Experimental Studies ◽  
Ligand Efficiency ◽  
Infected People ◽  
High Affinity ◽  
Main Protease ◽  
In Silico Study ◽  
The World ◽  
Low Toxicity ◽  
Viral Maturation ◽  
New Treatments

The pandemic that started in Wuhan (China) in 2019 has caused a large number of deaths, and infected people around the world due to the absence of effective therapy against coronavirus 2 of the severe acute respiratory syndrome (SARS-CoV-2). Viral maturation requires the activity of the main viral protease (Mpro), so its inhibition stops the progress of the disease. To evaluate possible inhibitors, a computational model of the SARS-CoV-2 enzyme Mpro was constructed in complex with 26 synthetic ligands derived from coumarins and quinolines. Analysis of simulations of molecular dynamics and molecular docking of the models show a high affinity for the enzyme (∆Ebinding between −5.1 and 7.1 kcal mol−1). The six compounds with the highest affinity show Kd between 6.26 × 10–6 and 17.2 × 10–6, with binding affinity between −20 and −25 kcal mol−1, with ligand efficiency less than 0.3 associated with possible inhibitory candidates. In addition to the high affinity of these compounds for SARS-CoV-2 Mpro, low toxicity is expected considering the Lipinski, Veber and Pfizer rules. Therefore, this novel study provides candidate inhibitors that would allow experimental studies which can lead to the development of new treatments for SARS-CoV-2.

scholarly journals A molecular docking study of SARS-CoV-2 main protease against phytochemicals of Siddha Medicinal herb Vilvam (Aegle marmelos)

2021 ◽  
Vol 12 (3) ◽  
pp. 506-512
Author(s):  
Nagappan A G ◽  
Krishnaveni M ◽  
Monika T ◽  
Thillaivanan S ◽  
Selvamoorthy G
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Medicinal Herb ◽  
Aegle Marmelos ◽  
Ligand Complex ◽  
Main Protease ◽  
Study Results ◽  
The World ◽  
Novel Coronavirus

Background: In December of 2019, mysterious pneumonia was reported. A novel coronavirus (nCoV) was identified as the causative agent for this pneumonia; it is now known as coronavirus 2. This pandemic has caused widespread alarm around the world. Now, countries around the world are preparing for the third and fourth waves of COVID-19. Objective: This research aims to conduct In Silico computational studies of phytoconstituents in leaf extracts of the Siddha medicinal herb Aegle marmelos (Vilvam), which are commonly used in the treatment of viral fever and respiratory infectious diseases and may be effective against the current pandemic novel coronavirus disease. Methodology: In Silico molecular docking analysis was performed for all the active compounds present in the herb Aegle marmelos (Vilvam) with potential targets SARS-CoV-2 Main Protease (PDB ID: 7JQ5). The ligand structures were prepared and optimized by AutoDockTools. The active sites docking study was performed using Autodock Vina for all the compounds. The inhibitor compound MPI8 bound inSARS-CoV-2 main protease Protein-Ligand complex (PDB ID: 7JQ5) is considered as the reference inhibitor molecule of this study. Results: Molecular docking of the 14 bioactive phytochemicals compounds from Aegle marmelos leaves carried out towards the active site of SARS-CoV-2 Main Protease protein (PDB ID: 7JQ5). The interactions of these compounds were comparatively analyzed with the reference inhibitor MPI8 bound inSARS-CoV-2 Main Protease protein-ligand complex (PDB ID: 7JQ5). These phytochemicals exhibited effective molecular interactions with the active residues enumerating their differential inhibition potency. Conclusion: Further research and clinical trials are needed whether this herb can be implemented to effectively treat and manage COVID-19. 

scholarly journals DFT Calculations and In silico Study of Chlorogenic, Ellagic and Quisqualic acids as Potential Inhibitors of SARS-CoV-2 Main Protease Mpro

2021 ◽  
Vol 12 (1) ◽  
pp. 61-73
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Density Functional Theory Calculations ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Strong Inhibitor ◽  
Quantum Molecular Descriptors ◽  
Main Protease ◽  
In Silico Study ◽  
Potential Inhibitors

In the present work, at first, density functional theory calculations were performed to investigate the molecular structure of the Chlorogenic, Ellagic, and Quisqualic acids by CAM-B3LYP/MidiX level of theory. A detail of quantum molecular descriptors of the title compounds such as ionization potential (IP) and Electron Affinities (EA), Hardness (η), Softness (S), Electronegativity (μ), Electrophilic Index (ω), Electron Donating Power (ω-), Electron Accepting Power (ω+) and Energy Gap (Eg) have been calculated. Pharmacokinetic properties of the title compounds and their bioactivity were investigated. In the following, a molecular docking study was carried out to screen for an effective available compound that may work as a strong inhibitor for the SARS-CoV-2 main protease Mpro. The binding energy between SARS-CoV-2 main protease Mpro and title organic acids showed a good binding affinity. Therefore, the Chlorogenic, Ellagic, and Quisqualic acids can be used for potential application against the SARS-CoV-2 main protease Mpro.

Comparative docking of SARS-CoV-2 receptors antagonists from repurposing drugs

2020 ◽  
Author(s):  
Micael Davi Lima de Oliveira ◽  
Kelson Mota Teixeira de Oliveira
Keyword(s):  
World Health Organisation ◽  
World Health ◽  
Lung Cells ◽  
The Novel ◽  
High Modulation ◽  
Main Protease ◽  
The World ◽  
Novel Coronavirus ◽  
Viral Receptors ◽  
Theoretical Results

According to the World Health Organisation, until 16 June, 2020, the number of confirmed and notified cases of COVID-19 has already exceeded 7.9 million with approximately 434 thousand deaths worldwide. This research aimed to find repurposing antagonists, that may inhibit the activity of the main protease (Mpro) of the SARS-CoV-2 virus, as well as partially modulate the ACE2 receptors largely found in lung cells, and reduce viral replication by inhibiting Nsp12 RNA polymerase. Docking molecular simulations were performed among a total of 60 structures, most of all, published in the literature against the novel coronavirus. The theoretical results indicated that, in comparative terms, paritaprevir, ivermectin, ledipasvir, and simeprevir, are among the most theoretical promising drugs in remission of symptoms from the disease. Furthermore, also corroborate indinavir to the high modulation in viral receptors. The second group of promising drugs includes remdesivir and azithromycin. The repurposing drugs HCQ and chloroquine were not effective in comparative terms to other drugs, as monotherapies, against SARS-CoV-2 infection.

Identification of Main Protease of Coronavirus SARS-CoV-2 (Mpro)Inhibitors from Melissa officinalis

2020 ◽  
Vol 17 ◽  
Author(s):  
Olusola O. Elekofehinti ◽  
Opeyemi Iwaloye ◽  
Courage D. Famusiwa ◽  
Olanrewaju Akinseye ◽  
Joao B. T. Rocha
Keyword(s):  
Qsar Model ◽  
Computational Approach ◽  
Melissa Officinalis ◽  
Lead Compounds ◽  
Main Protease ◽  
The World ◽  
Recent Outbreak ◽  
Global Concern ◽  
Catalytic Dyad ◽  
Potential Therapeutic Intervention

Background: he recent outbreak of Coronavirus SARS-CoV-2 (Covid-19) which has rapidly spread around the world in about three months with tens of thousands of deaths recorded so far is a global concern. An urgent need for potential therapeutic intervention is of necessity. Mpro is an attractive druggable target for the development of anti-COVID-19 drug development. Compounds previously characterized from Melissa officinalis were queried against main protease of coronavirus SARS-CoV-2 using computational approach. Results: Melitric acid A and salvanolic acid A had higher affinity than lopinavir and ivermectin using both AutodockVina and XP docking algorithms. The computational approach was employed in the generation of QSAR model using automated QSAR, and in the docking of ligands from Melissa officinalis with SARS-CoV-2 Mpro inhibitors. The best model obtained was KPLS_Radial_28 (R2 = 0.8548 and Q2=0.6474, and was used in predicting the bioactivity of the lead compounds. Molecular mechanics based MM-GBSA confirmed salvanolic acid A as the compound with the highest free energy and predicted bioactivity of 4.777; it interacted with His-41 of the catalytic dyad (Cys145-His41) of SARS-CoV-2 main protease (Mpro), as this may hinder the cutting of inactive viral protein into active ones capable of replication. Conclusion: Salvanolic acid A can be further evaluated as potential Mpro inhibitor.

scholarly journals Reduction of Constipating Scoring System Among Women Aged 18-25 Years Old as A Result of Decocted Trengguli (Cassia fistula L.)

2017 ◽  
Vol 1 (2) ◽  
pp. 58
Author(s):  
Isnaini Nur Jannah ◽  
Arifa Mustika ◽  
Edith Frederika Puruhito
Keyword(s):  
Scoring System ◽  
Bowel Movement ◽  
Wilcoxon Test ◽  
Cassia Fistula ◽  
School Of Medicine ◽  
Large Size ◽  
Anthraquinone Glycosides ◽  
The Family ◽  
Post Test ◽  
Quasi Experimental

Background: Constipation is a condition when someone has difficulty to defecate. Constipation is indicated by hard and large size stool as well as a decrease frequency of bowel movement. Commonly, constipation is indicated by anxiety during bowel movement due to disruption defecation. Constipation can cause severe stress resulting from discomforts for patient. The severity of the constipation can be measured using the Constipation Scoring System (CSS). CSS is a scoring system for patient, which based on the answers about the symptoms being asked in the questionnaire. One of the herbs to handle the problem of constipation that have a laxative effect is Trengguli (Cassia fistula L.) originate from the family Fabaceae. The part that can be used for a laxative is a Trengguli fruit. A decocta method to Trengguli flesh of the fruit for a laxative, since decocta method generates the highest total anthraquinone glycosides for the use of laxatives. Purpose: The purpose of this study was to prove the effectiveness of decocta pulp of trengguli for the reduction of constipation scoring system among women aged 18- 25 years old with constipation problem. Methods: The method used is quasi-experimental design using a design of one group pre-post test. The study was conducted in December at the clinic Battra Airlangga University School of Medicine with 26 responded. Data were analyzed using SPSS with the Wilcoxon test. Result: The results of this study showed that the decocta pulp of trengguli(Cassia fistula L.) has significant effectiveness with p = 0.000 with p <0.05 on a decrease in constipation scoring sytem for constipation treatment among women aged 18-25 years.

scholarly journals A Computational and Literature-Based Evaluation for a Combination of Chiral Anti-CoV Drugs to Block and Eliminate SARS-CoV-2 Safely

2021 ◽  
Author(s):  
Mohd. Suhail
Keyword(s):  
Side Effects ◽  
Jc Virus ◽  
Computational Study ◽  
Human Cells ◽  
The Body ◽  
Binding Affinities ◽  
Chiral Drugs ◽  
Main Protease ◽  
The World ◽  
Second Wave

<p><a>It has been a great challenge for scientists to develop an anti-covid drug/vaccine with fewer side effects, since the coronavirus began. Of course, the prescription of chiral drugs (chloroquine or hydroxychloroquine) has been proved wrong because these chiral drugs neither kill the virus nor eliminate it from the body, but block SARS-CoV-2 from binding to human cells. Another hurdle in front of the world, is not only the positive test of the patient recovered from coronavirus but also the second wave of Covid 19. Hence, the word demands such a drug or drug combination which not only prevents the entry of SARS-CoV-2 in the human cell but also eliminates it or its material from the body completely. The presented computational study explains (i) why the prescription of chiral drugs was not satisfactory (ii) what types of modification can make their prescription satisfactory (iii) the mechanism of action of chiral drugs (chloroquine and hydroxychloroquine) to block SARS-CoV-2 from binding to human cells, and (iv) the strength of mefloquine to eliminate SARS-CoV-2. As the main protease (M<b><sup>pro</sup></b>) of microbes is considered as an effective target for drug design and development, the binding affinities of mefloquine with the main proteases (M<sup>pros</sup>) of JC virus and SARS-CoV-2, were calculated, and then compared to know the eliminating strength of mefloquine against SARS-CoV-2. The main protease (M<sup>pro</sup>) of JC virus was taken because mefloquine has already shown a tremendous result of eliminating it from the body. The current study includes the docking results and literature data in support of the prescription of a combination of S-(+)-hydroxychloroquine and (+) mefloquine. Besides, the presented study also confirms that the prescription of only hydroxychloroquine would not be so effective as in combined form with mefloquine.</a></p>

scholarly journals Molecular Docking Study of the Potential Relevance of the Natural Compounds Isoflavone and Myricetin to COVID-19

2021 ◽  
Vol 25 (3) ◽  
pp. 271-282
Author(s):  
Didik Priyandoko ◽  
◽  
Wahyu Widowati ◽  
Mawar Subangkit ◽  
Diana Jasaputra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Severe Acute Respiratory Syndrome ◽  
Active Sites ◽  
Docking Study ◽  
Binding Mode ◽  
Molecular Docking Study ◽  
Wuhan City ◽  
The World ◽  
Novel Coronavirus ◽  
Proteins Interactions

The 2019 novel coronavirus (2019-nCoV) or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly from its origin in Wuhan City, Hubei Province, China, to the rest of the world. The efficacy of herbal treatment in the control of contagious disease was demonstrated during the 2003 outbreak of severe acute respiratory syndrome (SARS). Natural compound used for this study were isoflavone and myricetin. Molecular docking was performed to analyze binding mode of the compounds towards 12 proteins related to COVID-19. The prediction shows that isoflavone and myricetin have moderate probability of antiviral activity. All of the docked compounds occupied the active sites of the proteins related to COVID-19. Based on QSAR and molecular docking, interactions were predicted with 10 out of 12 potential COVID-19 proteins for myricetin and with 9 out of 12 proteins interactions for isoflavone. A potential disease alleviating action is suggested for isoflavone and myricetin in the context of COVID-19 infection.

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

Sign in / Sign up

Export Citation Format

Share Document