scholarly journals Herbal Compounds from Syzygium aromaticum and Cassia acutifolia as a Shield against SARS-CoV-2 Mpro: a Molecular Docking Approach

2021 ◽  
Vol 11 (6) ◽  
pp. 14853-14865
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
New Drugs ◽  
In Vivo Studies ◽  
Syzygium Aromaticum ◽  
Amino Acid Residues ◽  
Ligand Interaction ◽  
Docking Approach ◽  
Novel Coronavirus

Novel coronavirus (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2) was first identified in China in December 2019. Currently, the novel coronavirus disease 2019 (COVID-19) is the most infectious disease worldwide. In the absence of a vaccine or drug, herbal compounds may be used to treat or control this disease. To explore novel potent inhibitors that suppress this virus's growth, we performed molecular docking studies on SARS-CoV-2 Mpro using 17 effective herbal compounds, along with three reference drugs. Docking results showed that crategolic acid from Syzygium aromaticum (clove) had the highest binding affinity with SARS-CoV-2 Mpro protease, followed by sennoside (A, B, C, and D) compounds from Cassia acutifolia (Sana Makki). Crategolic acid and sennoside (A, B, C, and D) contain amino acid residues and hydrogen bonds involved in the protein-ligand interaction. The present study confirms that crategolic acid and sennoside represent the strongest potential inhibitors of SARS-CoV-2 Mpro. This study's results may help in vivo studies validate the usefulness of compounds from clove and Sana Makki in preparing herbal medicine for the treatment of COVID-19. This analysis supports the production of new drugs for the treatment and control of COVID-19.

Homology Modeling of Mus Musculus CDK5 and Molecular Docking Studies with Flavonoids

2017 ◽  
Vol 9 (6) ◽  
Author(s):  
Sowmya Suri ◽  
Rumana Waseem ◽  
Seshagiri Bandi ◽  
Sania Shaik
Keyword(s):  
Molecular Docking ◽  
3D Model ◽  
Structural Features ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Cyclin Dependent Kinase ◽  
Ligand Complex ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Cyclin Dependent Kinase 5

A 3D model of Cyclin-dependent kinase 5 (CDK5) (Accession Number: Q543f6) is generated based on crystal structure of P. falciparum PFPK5-indirubin-5-sulphonate ligand complex (PDB ID: 1V0O) at 2.30 Å resolution was used as template. Protein-ligand interaction studies were performed with flavonoids to explore structural features and binding mechanism of flavonoids as CDK5 (Cyclin-dependent kinase 5) inhibitors. The modelled structure was selected on the basis of least modeler objective function. The model was validated by PROCHECK. The predicted 3D model is reliable with 93.0% of amino acid residues in core region of the Ramachandran plot. Molecular docking studies with flavonoids viz., Diosmetin, Eriodictyol, Fortuneletin, Apigenin, Ayanin, Baicalein, Chrysoeriol and Chrysosplenol-D with modelled protein indicate that Diosmetin is the best inhibitor containing docking score of -8.23 kcal/mol. Cys83, Lys89, Asp84. The compound Diosmetin shows interactions with Cys83, Lys89, and Asp84.

Promising Anti-stroke Signature of Voglibose: Investigation through In- Silico Molecular Docking and Virtual Screening in In-Vivo Animal Studies

2020 ◽  
Vol 20 (3) ◽  
pp. 223-235
Author(s):  
Pooja Shah ◽  
Vishal Chavda ◽  
Snehal Patel ◽  
Shraddha Bhadada ◽  
Ghulam Md. Ashraf
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Reductase Activity ◽  
Infarct Volume ◽  
Docking Studies ◽  
Serum Glucose ◽  
In Vivo Studies ◽  
In Silico Molecular Docking

Background: Postprandial hyperglycemia considered to be a major risk factor for cerebrovascular complications. Objective: The current study was designed to elucidate the beneficial role of voglibose via in-silico in vitro to in-vivo studies in improving the postprandial glycaemic state by protection against strokeprone type 2 diabetes. Material and Methods: In-Silico molecular docking and virtual screening were carried out with the help of iGEMDOCK+ Pymol+docking software and Protein Drug Bank database (PDB). Based on the results of docking studies, in-vivo investigation was carried out for possible neuroprotective action. T2DM was induced by a single injection of streptozotocin (90mg/kg, i.v.) to neonates. Six weeks after induction, voglibose was administered at the dose of 10mg/kg p.o. for two weeks. After eight weeks, diabetic rats were subjected to middle cerebral artery occlusion, and after 72 hours of surgery, neurological deficits were determined. The blood was collected for the determination of serum glucose, CK-MB, LDH and lipid levels. Brains were excised for determination of brain infarct volume, brain hemisphere weight difference, Na+-K+ ATPase activity, ROS parameters, NO levels, and aldose reductase activity. Results: In-silico docking studies showed good docking binding score for stroke associated proteins, which possibly hypotheses neuroprotective action of voglibose in stroke. In the present in-vivo study, pre-treatment with voglibose showed a significant decrease (p<0.05) in serum glucose and lipid levels. Voglibose has shown significant (p<0.05) reduction in neurological score, brain infarct volume, the difference in brain hemisphere weight. On biochemical evaluation, treatment with voglibose produced significant (p<0.05) decrease in CK-MB, LDH, and NO levels in blood and reduction in Na+-K+ ATPase, oxidative stress, and aldose reductase activity in brain homogenate. Conclusion: In-silico molecular docking and virtual screening studies and in-vivo studies in MCAo induced stroke, animal model outcomes support the strong anti-stroke signature for possible neuroprotective therapeutics.

scholarly journals Effect of Harmine against Parkinson’s Disease Protein (PARK7) through Molecular Docking Studies

2021 ◽  
Vol 9 (VI) ◽  
pp. 5479-5485
Author(s):  
Love Kumar
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Molecular Docking ◽  
Neurodegenerative Disorder ◽  
Docking Studies ◽  
In Vivo Studies ◽  
Receptor Protein ◽  
Unknown Etiology

Parkinson’s disease (PD) is a common known neurodegenerative disorder with unknown etiology. It was estimated about 0.3% prevalence in the U.S population and enhance to 4 to 5% in older than 85 years. All studies were depending on the molecular docking where all ligands and protein PARK7 (PDB ID: 2RK3) were interacted by docked process. Some natural compounds was selected such as Harmine, Alloxan, Alpha spinasterol, Myrcene, and Vasicinone and PARK7 (PDB ID: 2RK3) protein. According to the PyRx and SWISS ADME result, Harmine was the only ligand which was showing minimum binding affinity. AutoDock Vina software was used for docking process between ligand (Harmine) and receptor protein PARK7 (PDB ID: 2RK3). The result was visualized under PyMol. Harmine was inhibiting the activity of PARK7 (PDB ID: 2RK3) and it may be used for the treatment of PD in future prospect after its in vitro and in vivo studies.

scholarly journals Evaluation of Lens culinaris phytochemicals in binding to the 3C-like protease of SARS-CoV-2 – A molecular docking approach

2020 ◽  
Vol 72 ◽  
pp. 173-176
Author(s):  
Anamul Hasan ◽  
Rownak Jahan ◽  
Khoshnur Jannat ◽  
Tohmina Afroze Bondhon ◽  
Md Shahadat Hossan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Lens Culinaris ◽  
Docking Studies ◽  
Polyphenolic Compounds ◽  
Binding Affinities ◽  
The Novel ◽  
Molecular Docking Studies ◽  
Docking Approach ◽  
Novel Coronavirus ◽  
Scientific Attention

The novel coronavirus known as SARS-CoV-2 and the virus-induced disease COVID-19 has caused widespread concerns due to its contagiousness, fatality rate, and the absence of drug(s). This study investigated Lens culinaris and its phytochemicals, especially the flavonoids. The compounds were assessed through molecular docking studies for their binding abilities with the major protease of the novel coronavirus, SARS-CoV-2 (PDB: 6LU7). A total of 42 phytochemicals of Lens culinaris were analyzed through molecular docking studies for their binding affinities to COVID 3C-like protease. Of them, 23 compounds were found to have binding affinities to the protease of −7.5 kcal/mol or higher. Our study indicates that Lens culinaris contains a number of polyphenolic compounds as well as phytosterols, which can bind to the active site of the protease, and so merits further scientific attention on trials for use as potential anti-COVID-19 drugs.

Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19)

2020 ◽  
Vol 23 ◽  
Author(s):  
Raghvendra Dubey ◽  
Kushagra Dubey
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Studies ◽  
Molecular Docking Studies ◽  
Molegro Virtual Docker ◽  
Main Protease ◽  
Docking Approach ◽  
Inhibitory Potential ◽  
Efficacy Parameters ◽  
Novel Coronavirus

Background: COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many of the patients have been contaminated by environmental contamination and transmission from one human to another. Objective: The objective of work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein) , using molecular docking approach. Method: The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. Result: The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore and H Bond score of nicotiflorin and standard inhibitor X77 was observed as -173.058, -127.302, -21.9398 and -156.913,- 121.296,-5.7369, respectively. Conclusion: Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.

scholarly journals Synthesis, Hypoglycemic Effect, Antimicrobial and Molecular Docking Studies of Organotin(IV) Complexes Derived from N-Phthalimido β-Amino Acid Derivatives

2021 ◽  
Author(s):  
Muhammad Ahmed ◽  
Nagina Riaz ◽  
Muhammad Kashif ◽  
Muhammad Ashfaq ◽  
Muhammad Arshad ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Docking Studies ◽  
Hypoglycemic Agents ◽  
Amino Acid Derivatives ◽  
Propanoic Acid ◽  
Ionization Mass ◽  
Amino Acid Residues ◽  
Diabetic Rabbits

N-Phthalimido β-amino acid derivatives, 3-phthalimido-3(2-hydroxyphenyl) propanoic acid (P2HPA) and 3-phthalimido-3(2-nitrophenyl) propanoic acid (P2NPA) with new series of diand triorganotin(IV) complexes (1-12) have been designed and synthesized. All the ligands and organotin(IV) complexes were characterized by elemental analysis, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (1H, 13C, 119Sn) spectroscopy and electron ionization mass spectrometry (EI-MS). Synthesized ligands and complexes were screened to determine the antibacterial activity and results showed that the triorganotin(IV) complexes have better activity compared to diorganotin(IV) complexes and ligands. In addition, molecular docking analysis of ligands on the catalytic pocket of sortase A (PDB ID 1T2W) showed that the ligands can bind the active amino acid residues in the pocket. The antioxidant activity was also performed by the DPPH (1,1-diphenyl-2-picrylhydrazyl radical) method and complexes showed better results than ligands. The compounds were also tested in vivo to determine the hypoglycemic activities on different groups of alloxan induced diabetic rabbits. The complexes (1-6) were found better hypoglycemic agents as they stabilized the glucose level to about 175-105 mg dL-1 as compared to ligand P2HPA.

scholarly journals Molecular docking studies of deacetylbisacodyl with intestinal sucrase-maltase enzyme

2017 ◽  
Vol 2 (12) ◽  
pp. 191 ◽  
Author(s):  
Ramchander Merugu ◽  
Uttam Kumar Neerudu ◽  
Karunakar Dasa ◽  
Kalpana V. Singh
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Electrostatic Interactions ◽  
Docking Studies ◽  
Amino Acid Residues ◽  
Interaction Study ◽  
Ligand Interaction ◽  
Docking Analysis ◽  
Protein Ligand Interaction ◽  
Intestinal Sucrase

Molecular docking of sucrase-isomaltase with ligand deacetylbisacodyl when subjected to docking analysis using docking server, predicted in-silico result with a free energy of -3.36 Kcal/mol which was agreed well with physiological range for protein-ligand interaction, making bisacodyl probable potent anti-isomaltase molecule. According to docking server Inhibition constant is 5.98Mm. which predicts that the ligand is going to inhibits enzyme and result in a clinically relevant drug interaction with a substrate for the enzyme. Hydrogen bond with bond length 3.45is formed between Pro 64 (A) of target and of ligand, which is again indicative of the docking between target and ligand. Excellent electrostatic interactions of polar, hydrophobic, pi-pi and Van der walls are observed. The proteinligand interaction study showed 6 amino acid residues interaction with the ligand.

scholarly journals Evaluation of Traditional Ayurvedic Preparation for Prevention and Management of the Novel Coronavirus (SARS-CoV-2) Using Molecular Docking Approach

2020 ◽  
Author(s):  
Dharmendra Kumar Maurya ◽  
Deepak Sharma
Keyword(s):  
Molecular Docking ◽  
Transmission Rate ◽  
Black Pepper ◽  
Virus Multiplication ◽  
New Drugs ◽  
Pharmacological Agents ◽  
Target Proteins ◽  
Prevention And Treatment ◽  
Docking Approach ◽  
Novel Coronavirus

<p>Since the emergence of novel Coronavirus (SARS-CoV-2) infection in Wuhan, China in December 2019, it has now spread to over 205 countries. The ever-growing list of globally spread corona virus-19 disease (COVID19) patients has demonstrated the high transmission rate among human population. Although 12 new drugs are being tried for management of COVID19, currently there are no FDA approved drugs or vaccines to prevent and treat the infection of the SARS-CoV-2. Considering the current state of affairs, there is an urgent unmet medical need to identify novel and effective approaches for prevention and treatment of COVID19 by re-evaluating the knowledge of traditional medicines and repurposing of drugs. Here, we used molecular docking approach to explore the beneficial roles of an array of phytochemicals and active pharmacological agents present in the Indian herbs (Tulsi, Haldi, Giloy, Black pepper, Ginger, Clove, Cardamom, lemon, and Ashwagandha) which are widely used in the preparation of Ayurvedic medicines in the form of <i>Kadha </i>to control various respiratory disorders such as cough, cold and flu. The evaluation was made based on the docking scores calculated by AutoDock Vina. Our study has identified an array of phytochemicals present in these herbs which have significant docking scores and potential to inhibit different stages of SARS-CoV-2 infection as well as other Coronavirus target proteins. Molecular docking also indicated that, the phytochemicals present in these herbs possess significant anti-inflammatory property. Overall our study provides scientific justification in terms of binding of active ingredients present in different plants used in <i>Kadha</i> preparation with viral proteins and target proteins for prevention and treatment of the COVID19. This preparation can boost individual’s immunity and inhibit the viral severity by interfering at different stages of virus multiplication in the infected person.<b></b></p>

scholarly journals MOLECULAR DOCKING AND SCREENING OF DRUGS FOR 6LU7 PROTEASE INHIBITOR AS A POTENTIAL TARGET FOR COVID-19

2022 ◽  
pp. 100-105
Author(s):  
MANOJ GADEWAR ◽  
BHARAT LAL
Keyword(s):  
Molecular Docking ◽  
Data Bank ◽  
Docking Study ◽  
In Vivo Studies ◽  
Molecular Docking Study ◽  
Potential Target ◽  
Novel Coronavirus ◽  
Potential Inhibitors

Objective: The aim of present investigation is docking of various existing antiviral, anti-tubercular and anti-malarial drugs on 6LU7 receptor of SARS-CoV-2 in the treatment of COVID-19. Methods: In this study, the structure of coronavirus binding protein and ligands for various drugs were collected from the protein data bank and pub chem. Molecular docking was carried out using Schrodinger 9.0 software. In molecular docking study, 19 different drugs of various categories like antiviral, anti-malarial and anti-tubercular were investigated for analyzing binding to 6LU7 receptors of COVID-19. Results: The docking result showed a high affinity of zanamivir, montelukast, ramdesvir, ritonavir, cobicistat and favipravir to the 6LU7 receptor of novel coronavirus. Thus the combination of these drugs may be useful in preventing further infection and can be used as a potential target for further in vitro and in vivo studies of SARS-CoV-2. Conclusion: Treatment of COVID-19 has been challenge due to the non-availability of effective drug therapy. In this study, we reported drugs for targeting 6LU7 Mpro/3Clpro protein, which showed prominent effects as potential inhibitors of COVID-19 Mpro.

scholarly journals Structural and therapeutic insights from the species specificity and in vivo antithrombotic activity of a novel αIIb-specific αIIbβ3 antagonist

Blood ◽  
2009 ◽  
Vol 114 (1) ◽  
pp. 195-201 ◽  
Author(s):  
Robert Blue ◽  
M. Anna Kowalska ◽  
Jessica Hirsch ◽  
Marta Murcia ◽  
Christin A. Janczak ◽  
...  
Keyword(s):  
Molecular Docking ◽  
High Throughput Screening ◽  
Binding Pocket ◽  
Docking Studies ◽  
In Vivo Studies ◽  
Rgd Peptides ◽  
Molecular Docking Studies ◽  
Antithrombotic Effects ◽  
Rat Platelets

Abstract We previously reported on a novel compound (Compound 1; RUC-1) identified by high-throughput screening that inhibits human αIIbβ3. RUC-1 did not inhibit αVβ3, suggesting that it interacts with αIIb, and flexible ligand/rigid protein molecular docking studies supported this speculation. We have now studied RUC-1's effects on murine and rat platelets, which are less sensitive than human to inhibition by Arg-Gly-Asp (RGD) peptides due to differences in the αIIb sequences contributing to the binding pocket. We found that RUC-1 was much less potent in inhibiting aggregation of murine and rat platelets. Moreover, RUC-1 potently inhibited fibrinogen binding to murine platelets expressing a hybrid αIIbβ3 receptor composed of human αIIb and murine β3, but not a hybrid receptor composed of murine αIIb and human β3. Molecular docking studies of RUC-1 were consistent with the functional data. In vivo studies of RUC-1 administered intraperitoneally at a dose of 26.5 mg/kg demonstrated antithrombotic effects in both ferric chloride carotid artery and laser-induced microvascular injury models in mice with hybrid hαIIb/mβ3 receptors. Collectively, these data support RUC-1's specificity for αIIb, provide new insights into the αIIb binding pocket, and establish RUC-1's antithrombotic effects in vivo.

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