scholarly journals In Silico Approach of Potential Phytochemical Inhibitor from Moringa oleifera, Cocos nucifera, Allium cepa, Psidium guajava, and Eucalyptus globulus for the treatment of COVID-19 by Molecular Docking

2020 ◽  
Author(s):  
Ika Nur Fitriani ◽  
Wiji Utami ◽  
Adi Tiara Zikri ◽  
Pugoh Santoso
Keyword(s):  
Molecular Docking ◽  
Medicinal Plants ◽  
Oleanolic Acid ◽  
Allium Cepa ◽  
Bioactive Compounds ◽  
In Silico ◽  
Eucalyptus Globulus ◽  
Moringa Oleifera ◽  
Cocos Nucifera ◽  
Psidium Guajava

Abstract Background Coronavirus disease 2019 (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2. COVID-19 has devastating effects on people in all countries and getting worse. We aim to investigate an in-silico docking analysis of phytochemical compounds from medicinal plants that used to combat inhibition of the COVID-19 pathway. There are several phytochemicals in medicinal plants, however, the mechanism of bioactive compounds remains unclear. These results are obtained from in silico research provide further information to support the inhibition of several phytochemicals. Methods Molecular docking used to determine the best potential COVID-19 M pro inhibitor from several bioactive compounds in Moringa oleifera, Allium cepa, Cocos nucifera, Psidium guajava, and Eucalyptus globulus. Molecular docking was conducted and scored by comparison with standard drugs remdesivir. ADME properties of selected ligands were evaluated using the Lipinski Rule. The interaction mechanism of the most recommended compound predicted using the STITCH database. Results There was no recommended compound in Moringa oleifera as a potential inhibitor for COVID-19. Oleanolic acid in Allium cepa, α-tocotrienol in Cocos nucifera, asiatic acid in Psidium guajava and culinoside in Eucalyptus globulus were the most recommended compound in each medicinal plant. Oleanolic acid was reported to exhibit anti-COVID-19 activity with binding energy was − 9.20 kcal/mol. This score was better than remdesivir as standard drug. Oleanolic acid interacted through the hydrogen bond with HIS41, THR25, CYS44, GLU166. Oleanolic acid binding with CASP-3, CASP-9, and XIAP signaling pathway. Conclusions Oleanolic acid in Allium cepa found as a potential inhibitor of COVID-19 M-pro that should be examined in future studies. These results suggest that oleanolic acid may be useful in COVID-19 treatment.

scholarly journals Potential Phytochemical Inhibitor from Allium cepa for the Medication of COVID-19 using In-Silico Approach

2021 ◽  
Vol 4 (2) ◽  
pp. 80-87
Author(s):  
Ika Nur Fitriani ◽  
Wiji Utami
Keyword(s):  
Medicinal Plants ◽  
Oleanolic Acid ◽  
Allium Cepa ◽  
In Silico ◽  
Interaction Network ◽  
Standard Drug ◽  
Docking Score ◽  
Future Studies ◽  
Network Process ◽  
Pathway Inhibition

Infection of extreme acute respiratory syndrome coronavirus 2 triggers Coronavirus disease 2019 (COVID-19). COVID-19 has adverse consequences on persons and is getting worse in all nations. The aim of this research is to investigate the development of in-silico approach of phytochemical inhibitor used to fight COVID-19 pathway inhibition. In medicinal plants, there are many phytochemicals, however the bioactive mechanism remains uncertain.  In-silico experiments offer additional evidence to confirm the inhibition of medicinal plants. Molecular docking was used to evaluate phytoconstituents from Allium cepa as COVID-19 M-pro inhibitor, compared to remdesivir (standard drug). STITCH database used to predict the interaction network process of the most potential compound. The most potential compound was oleanolic acid. Oleanolic acid with a docking score of -9.20 kcal/mol was reported as anti-COVID-19 activity. This docking score was higher than remdesivir. Oleanolic acid interacted with GLU166, CYS44, HIS41, and THR25 via the hydrogen bond. From STITCH Database, oleanolic acid interact with CASP-9, XIAP, CASP-3 signalling pathway. Oleanolic acid from Allium cepa has been reported as a possible COVID-19 M-pro inhibitor and should be studied in future studies. The experiment indicates that phytochemical inhibitor can be helpful in the medication of COVID-19.

scholarly journals A Review of Medicinal Plants with Antiviral Activity Available in Bangladesh and Mechanistic Insight Into Their Bioactive Metabolites on SARS-CoV-2, HIV and HBV

2021 ◽  
Vol 12 ◽  
Author(s):  
Sitesh C. Bachar ◽  
Kishor Mazumder ◽  
Ritesh Bachar ◽  
Asma Aktar ◽  
Mamun Al Mahtab
Keyword(s):  
Medicinal Plants ◽  
Antiviral Activity ◽  
Oleanolic Acid ◽  
Bioactive Compounds ◽  
In Silico ◽  
Hepatitis Virus ◽  
Antiviral Drug ◽  
Antiviral Drugs ◽  
Bioactive Metabolites ◽  
Antiviral Activities

Currently, viral infection is the most serious health issue which causing unexpected higher rate of death globally. Many viruses are not yet curable, such as corona virus-2 (SARS-CoV-2), human immunodeficiency virus (HIV), hepatitis virus, human papilloma virus and so others. Furthermore, the toxicities and ineffective responses to resistant strains of synthetic antiviral drugs have reinforced the search of effective and alternative treatment options, such as plant-derived antiviral drug molecules. Therefore, in the present review, an attempt has been taken to summarize the medicinal plants reported for exhibiting antiviral activities available in Bangladesh along with discussing the mechanistic insights into their bioactive components against three most hazardous viruses, namely SARS-CoV-2, HIV, and HBV. The review covers 46 medicinal plants with antiviral activity from 25 families. Among the reported 79 bioactive compounds having antiviral activities isolated from these plants, about 37 of them have been reported for significant activities against varieties of viruses. Hesperidin, apigenin, luteolin, seselin, 6-gingerol, humulene epoxide, quercetin, kaempferol, curcumin, and epigallocatechin-3-gallate (EGCG) have been reported to inhibit multiple molecular targets of SARS-CoV-2 viral replication in a number of in silico investigations. Besides, numerous in silico, in vitro, and in vivo bioassays have been demonstrated that EGCG, anolignan-A, and B, ajoene, curcumin, and oleanolic acid exhibit anti-HIV activity while piperine, ursolic acid, oleanolic acid, (+)-cycloolivil-4′-O-β-d-glucopyranoside, quercetin, EGCG, kaempferol, aloin, apigenin, rosmarinic acid, andrographolide, and hesperidin possess anti-HBV activity. Thus, the antiviral medicinal plants and the isolated bioactive compounds may be considered for further advanced investigations with the aim of the development of effective and affordable antiviral drugs.

scholarly journals Characterization of α-Glucosidase Inhibitors from Psychotria malayana Jack Leaves Extract Using LC-MS-Based Multivariate Data Analysis and In-Silico Molecular Docking

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5885
Author(s):  
Tanzina Sharmin Nipun ◽  
Alfi Khatib ◽  
Zalikha Ibrahim ◽  
Qamar Uddin Ahmed ◽  
Irna Elina Redzwan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Data Analysis ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
In Silico ◽  
Multivariate Data Analysis ◽  
Multivariate Data ◽  
Partial Least Square ◽  
Protein Data Bank Code ◽  
Glucosidase Inhibitors

Psychotria malayana Jack has traditionally been used to treat diabetes. Despite its potential, the scientific proof in relation to this plant is still lacking. Thus, the present study aimed to investigate the α-glucosidase inhibitors in P.malayana leaf extracts using a metabolomics approach and to elucidate the ligand–protein interactions through in silico techniques. The plant leaves were extracted with methanol and water at five various ratios (100, 75, 50, 25 and 0% v/v; water–methanol). Each extract was tested for α-glucosidase inhibition, followed by analysis using liquid chromatography tandem to mass spectrometry. The data were further subjected to multivariate data analysis by means of an orthogonal partial least square in order to correlate the chemical profile and the bioactivity. The loading plots revealed that the m/z signals correspond to the activity of α-glucosidase inhibitors, which led to the identification of three putative bioactive compounds, namely 5′-hydroxymethyl-1′-(1, 2, 3, 9-tetrahydro-pyrrolo (2, 1-b) quinazolin-1-yl)-heptan-1′-one (1), α-terpinyl-β-glucoside (2), and machaeridiol-A (3). Molecular docking of the identified inhibitors was performed using Auto Dock Vina software against the crystal structure of Saccharomyces cerevisiae isomaltase (Protein Data Bank code: 3A4A). Four hydrogen bonds were detected in the docked complex, involving several residues, namely ASP352, ARG213, ARG442, GLU277, GLN279, HIE280, and GLU411. Compound 1, 2, and 3 showed binding affinity values of −8.3, −7.6, and −10.0 kcal/mol, respectively, which indicate the good binding ability of the compounds towards the enzyme when compared to that of quercetin, a known α-glucosidase inhibitor. The three identified compounds that showed potential binding affinity towards the enzymatic protein in molecular docking interactions could be the bioactive compounds associated with the traditional use of this plant.

scholarly journals Molecular Docking Senyawa Asam Askorbat dan Kuersetin pada Tumbuhan Jambu Biji Merah (Psidium guajava L.) Sebagai Pencegah COVID-19

2021 ◽  
Vol 9 (2) ◽  
Author(s):  
Inggrid V. Gandu ◽  
Fona D. H. Budiarso ◽  
Billy J. Kepel ◽  
. Fatimawali ◽  
Aaltje Manampiring ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Ascorbic Acid ◽  
Molecular Docking ◽  
Immune System ◽  
Binding Affinity ◽  
In Silico ◽  
Preventive Measure ◽  
Psidium Guajava ◽  
Positive Control ◽  
Important Thing

Abstract: Coronavirus Disease 2019 or COVID-19 is an infectious disease first identified in Wuhan, China in December 2019. Prevention of COVID-19 infection is an important thing to do in reducing the spread of this virus. Boosting the body's immune system can be done as a preventive measure, one of which is by consuming natural plants such as red guava. This study aims to determine the molecular docking of red guava (Psidium guajava L.) as a plant to prevent COVID-19. This was an in silico with computerized methods. The samples in this study were ascorbic acid and quercetin compounds in red guava plants obtained from the PubChem website. The results showed that the binding affinity of ascorbic acid is -5.4 and the binding affinity of quercetin is -7.6. Remdesivir which was used as a positive control had a binding affinity of -7.3. In conclusion, quercetin compounds have better results than ascorbic acid compounds and remdesivir.Keywords: COVID-19, red guava, molecular docking  Abstrak: Coronavirus Disease 2019 atau COVID-19 merupakan suatu penyakit menular yang pertama kali ditemukan di Wuhan, Tiongkok pada Desember 2019. Pencegahan infeksi COVID-19 merupakan hal yang penting untuk dilakukan dalam mengurangi penyebaran dari virus ini. Meningkatkan sistem imun tubuh dapat dilakukan sebagai tindakan pencegahan salah satunya dengan mengonsumsi tumbuhan-tumbuhan alami seperti jambu biji merah. Penelitian ini bertujuan untuk mengetahui molecular docking jambu biji merah (Psidium guajava L.) sebagai tanaman pencegah COVID-19. Jenis penelitian ialah in silico dengan metode komputerisasi. Sampel penelitian yaitu senyawa asam askorbat dan kuersetin pada tumbuhan jambu biji merah yang diperoleh dari website pubchem. Hasil penelitian mendapatkan binding affinity dari senyawa asam askorbat yaitu -5.4 dan binding affinity dari senyawa kuersetin yaitu -7.6. Remdesivir yang dijadikan sebagai kontrol positif mendapatkan hasil binding affinity yaitu -7.3. Simpulan penelitian ini ialah senyawa kuersetin memiliki hasil yang lebih baik daripada senyawa asam askorbat dan juga obat remdesivir.Kata kunci: COVID-19, jambu biji merah, molecular docking

scholarly journals An In silico Analysis of Some Bioactive Compounds of Psidium guajava against Target Proteins of Vibrio cholerae

2020 ◽  
pp. 14-24
Author(s):  
Yakubu Gambo Hamza ◽  
Aminu Ibrahim Danyaya ◽  
Mudassir Lawal
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Vibrio Cholerae ◽  
Bioactive Compounds ◽  
Psidium Guajava ◽  
The Body ◽  
In Vivo Studies ◽  
Watery Diarrhea ◽  
Ligand Interaction ◽  
Acute Watery Diarrhea

Introduction: Cholera is a destructive disease that causes extreme and intense water loss in the body. It takes between 12 hours and 5 days for an individual to show symptoms after ingesting contaminated food or water. It causes acute watery diarrhea in children and adults and if left untreated, it can lead to death within hours. Unfortunately, children are the most severely affected. In this study, molecular interactions of 24 bioactive compounds of Psidium guajava leaves against Vibrio cholerae targets proteins namely: Alanine racemase (PDB ID: 4BEQ), Cholera enterotoxin, A chain (PDB ID: 1S5F) and ToxT (PDB ID: 3GBG) were evaluated. Methods: Molecular docking study was conducted and the 3D structures of bioactive compounds, Enzymes and the Enzyme-ligand interaction were visualized while Swiss ADME was employed to assess other physiochemical properties of these bioactive compounds. Results and Discussion: The results from the molecular docking revealed that five bioactive compounds showed promising inhibitory activity, which include Spathulenol (Binding energy; -7.5, -6.5 and -9.1 kcal/mol in 4BEQ, 1S5F and 3GBG ), Humulene oxide II (Binding energy; -7.1, -6.0 and -8.5 kcal/mol in 4BEQ, 1S5F and 3GBG), Globulol(-)-Globulol were -7.2, -6.5 and -9.0 kcal/mol in 4BEQ, 1S5F and 3GBG), Cadala-1(10),3,8-triene (Binding energy; -7.8, -6.8 and -9.8 kcal/mol in 4BEQ, 1S5F and 3GBG) and Bicyclo[5.3.0]decane, 2-methylene-5-(1-methylvinyl)-8-methyl (Binding energy; -6.9, -6.7 and -9.4 kcal/mol in 4BEQ, 1S5F and 3GBG) respectively. Conclusion: In this study, it has been revealed that the carefully chosen bioactive compounds have the potential to be used alone or in combination with other natural products for developing potent antibacterial drugs (against cholera). They can be further subjected to fractionation and isolation to confirm their activity towards in vitro and in vivo studies and can be commercialized as a potent antibacterial agent.

scholarly journals The in vitro antimicrobial and antioxidant activity of leaves of medicinal plants with phytobiotic potential in animal production

2021 ◽  
Author(s):  
Roisbel Aroche ◽  
Xianren Jiang ◽  
Yordan Martínez ◽  
Román Rodríguez ◽  
Xilong Li ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Medicinal Plants ◽  
Secondary Metabolites ◽  
Moringa Oleifera ◽  
Psidium Guajava ◽  
Anacardium Occidentale ◽  
Morinda Citrifolia ◽  
Bacterial Strains ◽  
Antimicrobial And Antioxidant Activity

Abstract Little is known about which secondary metabolites are responsible for inhibiting pathogenic bacteria and reducing the pro-oxidant effect on the leaves of four medicinal plants used as phytobiotic in animal production. The aim of this study was to evaluate the antimicrobial and antioxidant activity of four medicinal plants (Anacardium occidentale, Psidium guajava, Morinda citrifolia and Moringa oleifera.) in vitro. A total of six bacterial strains were inoculated, then minimum bactericidal concentration (MBC) was evaluated in fine powder and minimum inhibitory concentration (MIC) and MBC were determined on the aqueous extract. Also, the in vitro antioxidant activity was evaluated through 1,1-diphenyl-2-picryl-hydrazyl, as well as the main secondary metabolites were identified and quantified by chromatographic analysis. The results showed that Anacardium occidentale and Psidium guajava leaves had higher antimicrobial activity against all bacterial strains. In addition, Morinda citrifolia inhibited S. aureus in the aqueous extract, although without in vitro bactericidal effect, while Moringa oleifera leaf did not show antimicrobial effect. All plants showed antioxidant capacity, standing out Anacardium occidentale and Psidium guajava. Mainly the leaves of Anacardium occidentale showed high concentrations of quercetin 3-O-glucoside-7-O-rhamnoside, kaempeferol-7-O-glucoside, quercetin, caffeic acid, and cinnamic acid. Apparently, the antimicrobial and antioxidant activity are due to the main polyphenolic compounds identified in medicinal plants (mainly Anacardium occidentale and Psidium guajava); however, further studies are necessary to elucidate the exact mechanism.

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