A comprehensive phytochemical, biological, toxicological and molecular docking evaluation of Suaeda fruticosa (L.) Forssk.: An edible halophyte medicinal plant

2021 ◽  
pp. 112348
Author(s):  
Hammad Saleem ◽  
Umair Khurshid ◽  
Muhammad Sarfraz ◽  
Muhammad Imran Tousif ◽  
Abdulwahab Alamri ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Suaeda Fruticosa

scholarly journals Anticancer Screening of the Phytochemicals Present in the Medicinal Plant Vitex Negundo Against Mutant Anaplastic Lymphoma Kinase (ALK) Protein: An In-Silico Approach

2019 ◽  
Vol 12 (2) ◽  
pp. 993-1000 ◽  
Author(s):  
D. Anusha ◽  
S. Sharanya ◽  
Ramya Ramya ◽  
Darling Chellathai David
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Anaplastic Lymphoma Kinase ◽  
Natural Compounds ◽  
Binding Energies ◽  
Vitex Negundo ◽  
Molecular Docking Study ◽  
Selective Toxicity ◽  
Molegro Virtual Docker ◽  
Anaplastic Lymphoma

The lymphomas are a heterogeneous group of cancer of the lymphocytes and the lymphatic system and accounts for up to 3% of all malignancies.1 Most of the drugs currently used for the treatment of lymphoma produce various side effects, hence in this study, we focus on natural compounds, obtained from the medicinal plant Vitex negundo, which exhibits selective toxicity against cancer cells. The objective of this research was to formulate the binding energies and interaction of selected phytochemicals present in the medicinal plant Vitex negundo2 against anaplastic lymphoma kinase protein, which is overexpressed in an anaplastic large cell lymphoma.3, 4,5 The structure of mutant human anaplastic lymphoma kinase protein was retrieved from the Protein Data Bank (PDB ID:4ANL ) and the 3D chemical structure of the phytochemicals present in the medicinal plant Vitex negundo was obtained from the PubChem database. Molecular docking study was performed for these natural compounds to evaluate and analyze their anti-lymphoma-cancer activity. A total of 16 compounds present in Vitex negundo, based on a comprehensive literature survey was selected for this molecular screening. Molecular docking analysis was carried out by Molegro Virtual Docker software, to screen the 16 chosen compounds and rank them according to their binding affinity towards the site of interaction of the oncoprotein, anaplastic lymphoma kinase. Out of the 16 screened phytocompounds, only 4 compounds showed promising interactions against the oncoprotein ALK (4ANL). 6’-p-hydroxybenzoyl mussaenosidic acid exhibited a very good binding with a molecular docking score of -127.723 kcal/mol, ranking first among the compounds screened. This was followed by Betulinic acid, Viridiflorol and protocatechuic acid with molecular docking scores of -95.596 kcal/mol, -76.1648 kcal/mol and -63.0854 kcal/mol and - respectively. The docking scores from the above study shows that the phytocompounds present in Vitex negundo extract exhibits an effective inhibitory effect against anaplastic lymphoma kinase protein that is over expressed in lymphoma.

scholarly journals In-silico screening of active molecules from medicinal plant resources for controlling SARS-CoV-2 infection

2020 ◽  
Vol 6 (3) ◽  
pp. 149-153
Author(s):  
Rajdeep Ghosh ◽  
◽  
Satadru Palbag ◽  
Debasish Ghosh ◽  
◽  
...  
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
In Silico ◽  
Human Population ◽  
Treatment Strategies ◽  
Viral Proteins ◽  
Spike Protein ◽  
Plant Resources ◽  
In Silico Screening ◽  
Life Threatening

The entire human population is under treat of SARS-Cov-2 virus causing life threatening complicacies. Three proteins namely papain-like protease (PLpro), 3C-like protease (3CLpro) and spike protein isolated from the virus have been targeted for formulating the antiviral medicament. Ayurvedic medicinal plants with established antiviral efficacy are great choice to design immediate treatment strategies in this trying time. Here, 9 active molecules from ayurvedic medicinal plant resources were selected, out of which only 6 have screened through ADME analysis and molecular docking was performed with the three viral proteins to understand their antiviral performances in in silico model. Outcome of this study will surely open up a floodgate of thousand new possibilities in exploiting the existing natural herbs in COVID 19 treatments.

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals Molecular Docking Studies of Coronavirus Proteins with Medicinal Plant Based Phytochemicals

2021 ◽  
Vol 6 (1) ◽  
pp. 57-63
Author(s):  
Avinash Marwal ◽  
Mukesh Meena ◽  
RK Gaur
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Rna Binding ◽  
Data Bank ◽  
Black Pepper ◽  
Docking Studies ◽  
Ligand Docking ◽  
Main Protease ◽  
Pubchem Database ◽  
In Silico Molecular Docking

In this study, we presented an in silico molecular docking between the SARS-CoV-2 four proteins [(a) SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (6M3M), (b) Nsp9 RNA binding protein of SARS CoV-2 (6W4B), (c) The crystal structure of COVID-19 main protease in apo form (6M03), and (d) Structure of the 2019-nCoV HR2 Domain (6LVN)] available in the PDB (Protein Data Bank), and the medicinal plant-based phytochemicals (retrieved from PubChem database) as ligand molecules i.e. Piperine (Black Pepper), Eugenol (Clove), Alliin (Garlic), Gingerol (Ginger) and Curcumin (Turmeric). All these ligand molecules showed good docking with their respective receptor molecules and their scores range from -8.195 to -5.263. DockThor Portal (a receptor ligand-docking server) which was recently developed and published this year were used in the current study. The obtained results might help in the wet lab conditions to develop better antiviral compounds against SARS-CoV-2.

scholarly journals Norditerpenoids with Selective Anti-Cholinesterase Activity from the Roots of Perovskia atriplicifolia Benth.

2020 ◽  
Vol 21 (12) ◽  
pp. 4475 ◽  
Author(s):  
Sylwester Ślusarczyk ◽  
F. Sezer Senol Deniz ◽  
Renata Abel ◽  
Łukasz Pecio ◽  
Horacio Pérez-Sánchez ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Neurodegenerative Diseases ◽  
In Silico ◽  
Cholinesterase Activity ◽  
Treatment Strategies ◽  
Lead Compounds ◽  
Central Asian ◽  
Neurodegenerative Dementias ◽  
Anticholinesterase Properties

Inhibition of cholinesterases remains one of a few available treatment strategies for neurodegenerative dementias such as Alzheimer’s disease and related conditions. The current study was inspired by previous data on anticholinesterase properties of diterpenoids from Perovskia atriplicifolia and other Lamiaceae species. The acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition by the three new natural compounds—(1R,15R)-1-acetoxycryptotanshinone (1), (1R)-1-acetoxytanshinone IIA (2), and (15R)-1-oxoaegyptinone A (3)—as well as, new for this genus, isograndifoliol (4) were assessed. Three of these compounds exhibited profound inhibition of butyrylcholinesterase (BChE) and much weaker inhibition of acetylcholinesterase (AChE). All compounds (1–4) selectively inhibited BChE (IC50 = 2.4, 7.9, 50.8, and 0.9 µM, respectively), whereas only compounds 3 and 4 moderately inhibited AChE (IC50 329.8 µM and 342.9 µM). Molecular docking and in silico toxicology prediction studies were also performed on the active compounds. Natural oxygenated norditerpenoids from the traditional Central Asian medicinal plant P. atriplicifolia are selective BChE inhibitors. Their high potential makes them useful candidate molecules for further investigation as lead compounds in the development of a natural drug against dementia caused by neurodegenerative diseases.

scholarly journals Molecular docking data of E3 ubiquitin-protein ligase WWP1 with compounds from a medicinal plant Justicia adhatoda L.

2021 ◽  
Vol 17 (1) ◽  
pp. 162-166
Author(s):  
Jayaraman Selvaraj ◽  
Keyword(s):  
Molecular Docking ◽  
Oral Cancer ◽  
Medicinal Plant ◽  
Ubiquitin Protein Ligase ◽  
Justicia Adhatoda

It is known that E3 ubiquitin-protein ligase WWP1 is linked to oral cancer. Therefore, it is of interest to document molecular docking data of E3 ubiquitin-protein ligase WWP1 with compounds ((Stigmasterol, Pyrazinamide, Vasicinone and Ethambutol)) from a medicinal plant Justicia adhatoda L for further consideration

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