scholarly journals Molecular Docking Study of drug molecules from Drug Bank database against COVID-19 Mpro protein

2020 ◽  
Author(s):  
Tushar Joshi ◽  
Shalini Mathpal ◽  
Priyanka Sharma ◽  
Tanuja Joshi ◽  
Hemlata Pundir ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Drug Repurposing ◽  
Economic Loss ◽  
Docking Study ◽  
New Drugs ◽  
High Morbidity ◽  
Molecular Docking Study ◽  
Drug Molecules ◽  
Therapeutic Development

Aims: SARS-CoV-2 which is NovelCoronavirushas been disseminated all over the world and causing Coronavirus disease (COVID-19) resulting in many deaths as well as economic loss in several countries.This virus is showinga considerable amount of high morbidity and mortality.Currently, no drugs are available againstSARS-CoV-2. Therefore,for the treatment of disease, researchers are looking fornew drugs that can treat the disease and prevent it to be spread.In this regard,drug repurposingmay help scientists for treating and preventing infections associated with SARS-CoV-2. Drug repurposingis a strategy that can identify new targets for existing drugs that are already approved for the treatment of a disease.Main methods: In this study, we present a virtual screening procedure employing deep lerning regression method in 9101 drugs from Drug bank database against the target Main protease (Mpro) for the treatment of COVID-19. 500 screened compounds were subjected to docking.Key findings: Among those 500 drugs, 10 best drugs were selected, which had better binding energy as compared to the reference molecule. Based on the Binding energy score, we can suggest that the identified drug may be considered for therapeutic development against the virus.Significance: Drug repurposing has many advantages as it could shorten the time and reduce the cost of new drug discovery. This research will help to get new drugs against COVID-19 and help humans against this pandemic disease. Keyword- Drug Repurposing, Deep learning, Molecular Docking, COVID-19, Drug bank database, MPro

scholarly journals Molecular docking study of the phytol and its derivatives against COX-2 induced inflammation: A combined density functional study

2020 ◽  
pp. 1-5
Author(s):  
Muhammad Torequl Islam ◽  
Pranta Ray ◽  
Abul Bashar Ripon Khalipha ◽  
SM Hafiz Hassan ◽  
Md. Roich Khan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Docking Study ◽  
Functional Study ◽  
Molecular Docking Study ◽  
Study Results ◽  
Homo And Lumo ◽  
Cox 2

This study aimed to determine the activity of PYT and its derivatives against COX-2, including 5IKR protein induced inflammation by using the computational tools. PYT and its derivatives have been designed by utilizing density functional theory (DFT) and the performance of the drugs was also evaluated by molecular docking study. Results suggest that the NH2 derivative of PYT (D-NH2) showed binding energy -6.4 (Kcal/mol) with protein 5IKR of COX-2 compared to the main drug (D) that showed binding energy -5.1 (Kcal/mol) with the same protein. HOMO and LUMO energy values were also calculated to determine the chemical reactivity of all the modified drugs. Non-covalent interactions of PYT and its derivatives were essential in improving the performance. In conclusion, D-NH2 showed better preference in inhibiting to the protein 5IKR of COX-2 compared to other modified drugs and it can be claimed that D-NH2 will be the best conformer for COX-2 induced inflammation.

scholarly journals MOLECULAR DOCKING STUDY OF NATURALLY OCCURRING COMPOUNDS AS INHIBITORS OF COVID -19

2021 ◽  
pp. 69-71
Author(s):  
SREEDEVI A ◽  
MALAR RETNA A ◽  
ROBIN KUMAR SAMUEL
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Discovery Studio ◽  
Naturally Occurring ◽  
Short Period ◽  
The Right ◽  
Native Ligand ◽  
Made In

Objectives: The worldwide spread of COVID-19 is an emergent issue to be tackled. Currently, several works in various field have been made in rather short period. The present study aimed to assess bioactive compounds found in medicinal plants as potential COVID-19 Mpro inhibitors using molecular docking study. Methods: The docking analyses were performed by using Autodock, Discovery Studio Visualiser and Igemdock. Results: The binding energy obtained from the docking of 6LU7 with native ligand cupressuflavone is -8.9 kcal/mol. Conclusion: These findings will provide the opportunities to identify the right drug to combat COVID-19.

In silico investigation of Alliin as potential activator for AMPA receptor

2021 ◽  
Author(s):  
Hilal Ozturk ◽  
N. Yorulmaz ◽  
Mustafa Durgun ◽  
Harun Basoglu
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ampa Receptor ◽  
Docking Study ◽  
Binding Energies ◽  
Molecular Docking Study ◽  
Gaba A ◽  
Docking Method ◽  
Ampa And Nmda Receptors ◽  
The Central Nervous System

Abstract Natural products from plants, such as flavonoids, arouse immense interest in medicine because of the therapeutic and many other bioactive properties. The molecular docking is a very useful method to screen the molecules based on their free binding energies and give important structural suggestions about how molecules might activate or inhibit the target receptor by comparing reference molecules. Alliin and Allicin differ from many other flavonoids because of containing no benzene rings and having nitrogen and sulfur atoms in their structure. In this study Alliin and Allicin affinity on AMPA, NMDA and GABA-A receptors were evaluated in the central nervous system by using the molecular docking method. Both Alliin and Allicin indicated no inhibitory effects. However Alliin showed significant selectivity to human AMPA receptor (3RN8) as an excitatory. The binding energy of glutamate to 3RN8 was -6.61 kcal/mol, while the binding energy of Allin was -8.08 kcal/mol. Furthermore Alliin’s affinity to the other AMPA and NMDA receptors is quite satisfactory compared to the reference molecule glutamate. In conclusion based on the molecular docking study, Alliin can be useful for synaptic plasticity studies whereas might be enhance seizure activity because of the increased permeability to cations. It also can be beneficial to improve learning and memory and can be used as a supportive product to the hypofunction of NMDA associated problems.

scholarly journals A Comparative Study of Approved Drugs for SARS-CoV-2 by Molecular Docking

2021 ◽  
Vol 1 (1) ◽  
pp. 25-31
Author(s):  
Achal Mishra ◽  
Radhika Waghela
Keyword(s):  
Molecular Docking ◽  
Docking Study ◽  
Docking Studies ◽  
Target Protein ◽  
Molecular Docking Study ◽  
Discovery Studio ◽  
Drug Molecules ◽  
Main Protease ◽  
New Type ◽  
Approved Drugs

SARS-CoV-2, a new type of Coronavirus, has affected more millions of people worldwide. From the spread of this infection, many studies related to this virus and drug designing for the treatment have been started. Most of the studies target the SARS-CoV-2 main protease, spike protein of SASR-CoV-2, and some are targeting the human furin protease. In the current work, we chose the clinically used drug molecules remdesivir, favipiravir, lopinavir, hydroxychloroquine, and chloroquine onto the target protein SARS-CoV-2 main protease. Docking studies were performed using Arguslab, while Discovery Studio collected 2D and 3D pose views with the crystal structure of COVID-19 main protease in complex with an inhibitor N3 with PDB ID 6LU7. Computational studies reveal that all ligands provided good binding affinities towards the target protein. Among all the chosen drugs, lopinavir showed the highest docking score of -11.75 kcal/mol. The results from this molecular docking study encourage the use of lopinavir as the first-line treatment drug due to its highest binding affinity.

scholarly journals Molecular Docking Study on Some Isonicotinoyl Hydrazide Derivatives as Potential Inhibitors of COVID-19

2020 ◽  
Vol 9 (3) ◽  
pp. 1217-1224
Keyword(s):  
Molecular Docking ◽  
Active Sites ◽  
Antiviral Agent ◽  
Docking Study ◽  
Biologically Active ◽  
New Drugs ◽  
Molecular Docking Study ◽  
Docking Score ◽  
Protease Enzyme ◽  
Potential Inhibitors

Coronavirus (COVID-19) is more than a health disaster;it is the greatest challenge that the world confrontsnowadays. There is a race to slow the spread of this disease. Searching for an antiviral agent to stop COVID-19 is an essential demand since there is no approved drug for COVID-19 till now. Molecular docking is a powerful tool in predicting new drugs. In this study, Favpiravir (Avigan), Hydroxychloroquine, and a series of biologically active compounds derived from iso-nicotinoyl hydrazide have been chosen for molecular docking study. Molecular docking was carried out by theMolegro virtual docker program on proteaseenzyme of COVID-19.The results showed that all the studied molecules are located in the active sites of protease after molecular docking. The tested nicotinoyl hydrazide derivatives showed a higher ranking docking score than Favpiravir (Avigan). According to the docking score ranking rearrangement, Hydroxychloroquine comes the third, and Favpiravir comes the last among the tested compounds. N(2-iso-nicotinoyl hydrazine-carbonthioyl)benzamide(2) and the enol form of (E)-N-(1-phenylethylidene)-nicotinohydrazide(7) have shown the highest docking score (123.23 and -123.12 kcal/mol respectively) among the tested compounds. Ligands (2) and (7) are expected to be potential inhibitors of the main protease enzyme of coronavirus.

scholarly journals TEA BIOACTIVE COMPOUNDS AS INHIBITOR OF MRSA PENICILLIN BINDING PROTEIN 2a (PBP2a): A MOLECULAR DOCKING STUDY

2021 ◽  
Vol 3 (2) ◽  
pp. 70
Author(s):  
Marko Jeremia Kalalo ◽  
Fatimawali Fatimawali ◽  
Tekla Kalalo ◽  
Christani I J Rambi
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Bioactive Compounds ◽  
Docking Study ◽  
Antibacterial Activities ◽  
Multidrug Resistant ◽  
Tea Polyphenols ◽  
Resistant Bacteria ◽  
Molecular Docking Study ◽  
Docking Approach

ABSTRACT Methicillin-Resistant Staphylococcus aureus (MRSA) is a hypervirulent multidrug- resistant bacteria. It is spreading around the globe and starting to be a global health problem. It causes bacteremia, infective endocarditis, and bloodstream infection. PBP2a is a protein responsible for MRSA’s resistance to antibiotics, especially beta-lactams. Tea contains bioactive compounds such as polyphenols. It is known to have great antibacterial activities. Therefore, this study aims to find potentials antibacterial compounds from tea polyphenols that can inhibit PBP2a in MRSA with better binding energy than the currently available drugs using the molecular docking approach. We found that theaflavin (-9,7 kcal/mol), as one of the tea polyphenols compound, has a better binding energy with ceftaroline (9,5 kcal/mol) therefore predicted to have better antibacterial activity. (−)- Epigallocatechingallate (-9,1 kcal/mol), (−)-epicatechingallate (-8,8 kcal/mol), myricetin (- 8,7 kcal/mol), quercetin (-8,5 kcal/mol), (−)-epicatechin (-8,3 kcal/mol), (−)- epigallocatechin (-8,3 kcal/mol), kaempferol (-8,3 kcal/mol), procyanidin B2 (-8,1), and theflavindigallate (-7,6 kcal/mol) also have the potential to inhibit MRSA due to its low binding energy. Key words : Molecular docking, MRSA, PBP2a, Tea polyphenols.

scholarly journals In silico Drug Repurposing of FDA-Approved Artemisinins as Potent Chemotherapeutics Targeting Bcl-2, CDK-6 & VEGFR-2: Density Functional Exploration and Molecular Docking Study

2020 ◽  
Vol 11 (2) ◽  
pp. 9604-9618
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Chemical Reactivity ◽  
Lethal Dose ◽  
Drug Repurposing ◽  
Cancer Therapeutics ◽  
Docking Study ◽  
Molecular Docking Study

The strategy of using existing drugs originally developed for one disease to treat other indications has found success across medical fields. This paper focuses on drug repurposing of artemisinin and its derivatives (artenimol, artemether, artemotil, and artesunate) that kill malaria parasites for anticancer agents, specifically targeting Bcl-2, CDK-6, and VEGFR-2. The Artemisinins 1-5 were analyzed for compliance with Lipinski’s drug-likeness rule and optimum ADME parameters. The results of which revealed all calculated physicochemical descriptors and pharmacokinetic properties are within the expected thresholds. Toxicity in terms of predicted median lethal dose (LD50) in mg/kg weight of investigated Artemisinins 1-5 is also reported. Artemisinins 1-5 were subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of Bcl-2, CDK-6, and VEGFR-2. The molecular docking study revealed that Artemisinins 1-5 were able to target CDK-6 and VEGFR-2. DFT/B3LYP theoretical calculations for optimization, DFT, frequency, and HOMO/LUMO were performed to obtain electronic and structural properties, chemical reactivity descriptors. Hence, these findings will be highly beneficial in optimizing the utility of the development of Artemisinins 1-5 for cancer therapeutics, specifically targeting CDK-6 and VEGFR-2.

scholarly journals Targeting CoV-2 Spike RBD and ACE-2 Interaction with Flavonoids of Anatolian Propolis byin silicoandin vitroStudies in terms of possible COVID-19 therapeutics

2021 ◽  
Author(s):  
Halil Ibrahim Guler ◽  
Fulya Ay Sal ◽  
Zehra Can ◽  
Yakup Kara ◽  
Oktay Yildiz ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Caffeic Acid ◽  
In Silico ◽  
Docking Study ◽  
Caffeic Acid Phenethyl Ester ◽  
Elisa Test ◽  
Molecular Docking Study ◽  
Inhibitory Potential

ABSTRACTPropolis is a multi-functional bee product with a rich in polyphenols. In this study, the inhibition effect of Anatolian propolis against SARS coronavirus-2 (SARS CoV-2) was investigated asin vitroandin silico. Raw and commercial of propolis samples were used in the study and it was found that both of were rich in caffeic acid, p-coumaric acid, ferulic acid, t-cinnamic acid, hesperetin, chrysin, pinocembrin and caffeic acid phenethyl ester (CAPE) by HPLC-UV analysis. The ethanolic propolis extracts (EPE) were used in the screening ELISA test against the spike S1 protein (SARS Cov-2): ACE-2 inhibition KIT forin vitrostudy. Binding energy constants of these polyphenols to the CoV-2 Spike S1 RBD and ACE-2proteinwere calculated separately as molecular docking study using AutoDock 4.2 molecular docking software. In addition, pharmacokinetics and drug-likeness properties of these eight polyphenols were calculated according to the SwissADME tool. Binding energy constant of pinocembrin was the highest for both of the receptors, followed by chrysin, CAPE and hesperetin.In silicoADME behavior of the eight polyphenols were found potential ability to work effectively as novel drugs. The findings of both studies showed that propolis has a high inhibitory potential against Covid-19 virus. However, further studies are needed.

scholarly journals Synthesis, spectroscopic characterization, structural studies, thermal analysis and molecular docking of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine, a precursor for drug design against chronic myeloid leukemia

2021 ◽  
Vol 77 (10) ◽  
Author(s):  
Rodolfo Moreno-Fuquen ◽  
Kevin Arango-Daraviña ◽  
Alan R. Kennedy
Keyword(s):  
Molecular Docking ◽  
Drug Design ◽  
Nitro Group ◽  
Spectroscopic Characterization ◽  
Shape Index ◽  
Docking Study ◽  
New Drugs ◽  
Myelogenous Leukemia ◽  
Molecular Docking Study ◽  
Dispersion Energy

The synthesis, crystal structure and spectroscopic and electronic properties of N-(2-methyl-5-nitrophenyl)-4-(pyridin-2-yl)pyrimidin-2-amine (NPPA), C16H13N5O2, a potential template for drug design against chronic myelogenous leukemia (CML), is reported. The design and construction of the target molecule were carried out starting from the guanidinium nitrate salt (previously synthesized) and the corresponding enaminone. X-ray diffraction analysis and a study of the Hirshfeld surfaces revealed important interactions between the nitro-group O atoms and the H atoms of the pyridine and pyrimidine rings. A crystalline ordering in layers, by the stacking of rings through interactions of the π–π type, was observed and confirmed by a study of the shape-index surfaces and dispersion energy calculations. Quantitative electrostatic potential studies revealed the most positive value of the molecule on regions close to the N—H groups (34.8 kcal mol−1); nevertheless, steric impediments and the planarity of the molecule do not allow the formation of hydrogen bonds from this group. This interaction is however activated when the molecule takes on a new extended conformation in the active pocket of the enzyme kinase (PDB ID 2hyy), interacting with protein residues that are fundamental in the inhibition process of CML. The most negative values of the molecule are seen in regions close to the nitro group (−35.4 and −34.0 kcal mol−1). A molecular docking study revealed an energy affinity of ΔG = −10.3 kcal mol−1 for NPPA which, despite not having a more negative value than the control molecule (Imatinib; ΔG = −12.8 kcal mol−1), shows great potential to be used as a template for new drugs against CML.

scholarly journals Effects Of Herbicides And Fungicides On The Soil Chitinolytic Activity. A Molecular Docking Approach

2015 ◽  
Vol 22 (3) ◽  
pp. 439-450
Author(s):  
Diana Larisa Vlădoiu ◽  
Marioara Nicoleta Filimon ◽  
Vasile Ostafe ◽  
Adriana Isvoran
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Sites ◽  
Soil Microorganisms ◽  
Docking Study ◽  
Chitinolytic Activity ◽  
Molecular Docking Study ◽  
Receptor Ligand ◽  
Docking Approach ◽  
Inhibitory Potential

Abstract A molecular docking study was undertaken using the programs SwissDock and PatchDock to assess the interactions of the bacterial chitinases belonging to the GH18 and GH19 families with two herbicides (chlorsulfuron and nicosulfuron) and two fungicides (difenoconazole and drazoxolon). Both molecular docking programs predict that all considered pesticides bind to the active sites of chitinases produced by soil microorganisms. There are correlations for predicted binding energy values for receptor-ligand complexes obtained using the two programs consolidating the prediction of the chitinases-pesticides interactions. The interactions of chitinases with pesticides involve the same residues as their interactions with known inhibitors suggesting the inhibitory potential of pesticides. Pesticides interact stronger with chitinases belonging to the GH18 family, their active sites reflecting higher polarity than those of the GH19 chitinases. Also, herbicides reveal a higher inhibitory potential to bacterial chitinases than fungicides.

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