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 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.

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 Estimation of drug-likeness properties of GC-MS separated bioactive compounds in rare medicinal Pleione maculata using molecular docking technique and SwissADME insilico tools

2020 ◽  
Author(s):  
HAKANI D SYMPLI
Keyword(s):  
Molecular Docking ◽  
Bioactive Compounds ◽  
Docking Study ◽  
Chromatographic Technique ◽  
Molecular Docking Study ◽  
Lower Solubility ◽  
First Time ◽  
Random Control ◽  
Very High ◽  
High Binding Affinity

Abstract The main aim of present paper is to determine bioactive compounds in Pleione maculata extracts using Gas chromatographic technique and to investigate their drug-likeness potential using molecular docking algorithm and ADME studies on the recent intractable disease for example; SARS-CoV-2. P. maculata sample was prepared for GC-MS analysis. The peak components are identified based on NIST Library. Molecular docking was performed using PatchDock and energy refinement was carried out using FireDock algorithm followed by drug-likeness analysis using Swiss ADME tool. Mass spectrum revealed various pharmacologically important compounds and novel compounds 8-oxatetracyclo{5.2.1.1(2,6). 1(4,10)}Dodecane, 7-tert-Butyl-1,9,9-Trimeth, Cholesterol Isocaproate, Docosane, 2,4-Dimethyl, 7.dehydrocholesterol isocaproate, Kryptogenin 2,4-dinitrophenyl hydrazine, N-decyl-Alpha,D-2-Deoxyglycoside, pyrimidine-2,4,6(1H,3H,5H)-Trione-1-octadecyl) which are reported for the first time. Molecular docking using PatchDock illustrates GC-MS compounds Nor-diazepam,3-{N-hydroxymethyl}aminocarbonyloxy a good docking and high binding affinity with Atomic contact energy -10.95 kcal/mol against SARS-CoV-2 Spike protein S2 subunit. ADME analysis predict Nor-diazepam,3-{N-hydroxymethyl}aminocarbonyloxy and andrographolide showed very high drug-likeness parameters with no metabolism disturbances. The random control anti-viral drug arabidiol revealed a lower binding energy and lower solubility compared to bioactive compounds of P. maculata. The study depicts the first and novel report on various pharmaceutical important GC-MS bioactive compounds and molecular docking study of Pleione maculata having potential against various intractable diseases.

scholarly journals Antibacterial Activities and Molecular Docking of Novel Sulfone Biscompound Containing Bioactive 1,2,3-Triazole Moiety

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4817
Author(s):  
Huda R. M. Rashdan ◽  
Ihsan A. Shehadi ◽  
Mohamad T. Abdelrahman ◽  
Bahaa A. Hemdan
Keyword(s):  
Molecular Docking ◽  
Pathogenic Bacteria ◽  
Analytical Data ◽  
Docking Study ◽  
Antibacterial Activities ◽  
Bactericidal Effect ◽  
Bacterial Strains ◽  
Molecular Docking Study ◽  
Synthetic Compound

In this study, a new synthetic 1,2,3-triazole-containing disulfone compound was derived from dapsone. Its chemical structure was confirmed using microchemical and analytical data, and it was tested for its in vitro antibacterial potential. Six different pathogenic bacteria were selected. MICs values and ATP levels were determined. Further, toxicity performance was measured using MicroTox Analyzer. In addition, a molecular docking study was performed against two vital enzymes: DNA gyrase and Dihydropteroate synthase. The results of antibacterial abilities showed that the studied synthetic compound had a strong bactericidal effect against all tested bacterial strains, as Gram-negative species were more susceptible to the compound than Gram-positive species. Toxicity results showed that the compound is biocompatible and safe without toxic impact. The molecular docking of the compound showed interactions within the pocket of two enzymes, which are able to stabilize the compound and reveal its antimicrobial activity. Hence, from these results, this study recommends that the established compound could be an outstanding candidate for fighting a broad spectrum of pathogenic bacterial strains, and it might therefore be used for biomedical and pharmaceutical applications.

scholarly journals Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

2020 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Sefren Geiner Tumilaar ◽  
Nurdjannah Jane Niode ◽  
Fatimawali Fatimawali ◽  
Billy Johnson Kepel ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Bioactive Compounds ◽  
Binding Free Energy ◽  
Epigallocatechin Gallate ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Ligand Complex ◽  
Main Protease ◽  
Glycoprotein Inhibitors

Since the outbreak of the COVID-19 (Coronavirus Disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants by using a molecular docking approach to inhibit the Main Protease (Mpro) and Spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina as a docking engine. A rule of five (RO5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was done by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding / ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine and hydroxychloroquine sulfate (anti-malarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir, but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. These plant compounds have the potential to be developed as specific therapeutic agents against COVID-19. Several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate which so far are recommended in the treatment of COVID-19. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development lead compounds to treat infections caused by SARS-CoV-2.

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.

scholarly journals In silico docking analysis of selective bioactive compounds of Phyllanthus acidusaqueousfruit extractagainst MAPK1

Biomedicine ◽  
2021 ◽  
Vol 41 (2) ◽  
pp. 349-357
Author(s):  
E. Padmini ◽  
M. Kavitha
Keyword(s):  
Binding Energy ◽  
Cell Survival ◽  
Bioactive Compounds ◽  
In Silico ◽  
Docking Study ◽  
Mitogen Activated Protein Kinase ◽  
Molecular Docking Study ◽  
Ligand Complex ◽  
In Silico Docking ◽  
Methyl Prednisolone

Introduction and Aim: Phyllanthus acidus L.Skeels (Family: Phyllanthaceae) or Star Gooseberry which bears small, edible, juicy, sour, yellow berries fruit is known as a “liver tonic” in ayurvedic medicine. However, the behavior of the plant fruit or its constituents in cell apoptosis/cell survival is unknown. Hence, the purpose of thepresent study was to perform an in silico docking of selective bioactive compounds of aqueous extract of fruit of P.acidus (PAFAE) against MAPK1. Mitogen activated protein kinase is a family of serine threonine specific protein kinases- MAPK1/ERK1/2, JNK1-3, p38MAPK and ERK5.Activation ofMAPK1 promotes cell survival in certain tissues by inhibiting proapoptotic proteins and by stimulating anti apoptotic factors.   Methodology: In silico docking studies was carried out using bioinformatics tools.The active compounds (Trihomovitamin D3; 2Z,6Z,8Z,12E Hexadecatetraenoic acid, Methyl prednisolone, Hydroxysalmeterol and Tridesacetoxykhivorin) ofP.acidus aqueous fruit extract were docked against MAPK1 resulting in receptor-ligand complex.   Results: The binding energy is correlated with the probability of affinity and stable bound between ligand and its receptor.   Conclusion: The molecular docking study of selective bioactive compounds of PAFAE with MAPK1 protein revealed that Tridesacetoxykhivorinand Methyl Prednisolone, is having good interaction in favorable pose with MAPK1 as shownfrom theireffective binding energy(-7.79kcal/mol and -7.19 kcal/mol), strong bond length and interactions with active site of MAPK1.

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.

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