scholarly journals ANTI-PARKINSON POTENTIAL OF PERSEA AMERICANA SEED EXTRACTS THROUGH IN-SILICO DOCKING STUDY

2020 ◽  
pp. 152-155
Author(s):  
RACHAEL EVANGELINE ◽  
NIHAL AHMED
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Water Extract ◽  
Docking Study ◽  
Persea Americana ◽  
Ligand Docking ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Free Binding Energy

Objective: The aim of this study is to investigate the potential of Persea americana extracts for their Anti-Parkinson application through an in-silico docking study. Methods: PubChem and protein data bank databases were used to retrieve 3D structures. AutoDock4 was used to perform protein-ligand docking analysis. PyMOL was used to visualize the docking results. Results: Among the 30 ligand, the highest affinity was demonstrated by Hesperidin with a free binding energy of −6.8 kcal/mol and formation of five hydrogen bonds. The second highest significance was demonstrated by Biphenyl 4-(4-diethylaminobenzylidenamino) with a free binding energy of −5.9 kcal/mol with the formation of 2 hydrogen bonds. Among the three sets of phytochemicals from different solvent extracts, water extract demonstrated the highest potential as Anti-Parkinson active. Conclusion: P. americana extracts were analyzed for their Anti-Parkinson potential, and among the three extracts, the aqueous extract was predicted to have significant Anti-Parkinson potential, based on in silico docking analysis, due to the presence of active phytochemicals such as Hesperidin and others.

scholarly journals ANTI-METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS POTENTIAL OF PHYTOCHEMICALS IN TERMINALIA CATAPPA AND THEIR PROPOSED IN SILICO MECHANISM OF ACTION

2019 ◽  
pp. 133-137
Author(s):  
LOKESH RAVI ◽  
DIVYA JINDAM ◽  
SUGANYA KUMARESAN ◽  
VENKATESH SELVARAJ ◽  
JAYARAMA REDDY
Keyword(s):  
Staphylococcus Aureus ◽  
Binding Energy ◽  
Hydrogen Bonds ◽  
Mechanism Of Action ◽  
In Silico ◽  
Ethanol Extract ◽  
Docking Study ◽  
Ligand Docking ◽  
Methicillin Resistant ◽  
Antibacterial Potential

Objective: The objective of this study was to investigate the antibacterial potential of leaves of this Terminalia catappa and identify the mechanism of action for those phytochemicals present in this leaves. Methods: Phytochemicals were extracted using maceration and the extracts were analyzed using gas chromatography–mass spectrometry (GC-MS) to identify the chemical structure. Antibacterial potential was evaluated using agar well diffusion. The phytochemicals were subjected to in silico protein–ligand docking study to identify the mechanism of action. Results: In vitro antibacterial study demonstrated that the ethanol extract of the leaves has significant antibacterial activity against Staphylococcus aureus (SA) and methicillin-resistant SA (MRSA) with a zone of inhibition of 16 mm and 18 mm, respectively, at a concentration of 2 mg/ml. The chloroform and hexane extracts of the leaves did not demonstrate any significant activity. Based on GC-MS analysis and literature review, 12 phytochemicals were identified to be present in the ethanol extract of the T. catappa leaves. These molecules were subjected to in silico protein–ligand docking study against common drug target proteins of SA and MRSA. Among the studied ligands, granatin A demonstrated the highest significance to inhibit topoisomerase IV with a binding energy of −11.3 kcal/mol and produced 7 hydrogen bonds, followed by punicalin with −10.7 kcal/mol binding energy toward penicillin-binding protein 2a with 6 hydrogen bonds. Conclusion: Phytochemicals of T. catappa demonstrates significant drug ability potential against drug-resistant MRSA pathogen and demands further investigation on their individual activity and mechanism.

IN VITRO AND IN SILICO ALPHA-AMYLASE INHIBITION POTENTIAL (ANTI-DIABETIC ACTIVITY) OF PSEUDERANTHEMUM BICOLOR (SIMS) RADIK

2020 ◽  
pp. 157-161
Author(s):  
RAMESH BS ◽  
LOKESH RAVI
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Ethyl Acetate ◽  
Bioactive Compounds ◽  
Methyl Ether ◽  
Docking Study ◽  
Alpha Amylase ◽  
Ligand Docking ◽  
Standard Drug ◽  
Reference Drug

Objective: Aim of this study is to evaluate theanti-diabetic activity of Pseuderanthemum bicolor commonly called limang-sugat by inhibiting alpha-amylase protein. Methods: Leaves of P. bicolor were extracted with methanol, chloroform, and ethyl acetate. The extracts were subjected for alpha-amylase inhibition assay and gas chromatography–mass spectrometry (GC–MS) analysis. Phytochemical compounds identified by GC-MS were subjected for protein-ligand docking study against alpha-amylase protein. Acarbose was used as a positive standard drug. Results: The major bioactive compounds obtained from methanol, chloroform, and ethyl acetate extracts were 1,6;2,3-Dianhydro-4-Deoxy-Beta-D-Ribo-Hexopyranose, Pseduosarsasapogenin-5,20-Dien, methyl ether/Hexatriacontane, Di-N-decylsulfone/Octadecanal, and squalene, respectively. A total of 19 secondary metabolites were subjected for protein–ligand docking study against the alpha-amylase protein. The reference drug acarbose demonstrated binding energy of −7.8 Kcal/mol and formed 20 hydrogen bonds with the enzyme. Acarbose signified high polar interaction with the amylase enzyme. Among the 19 test ligands, “2,2-Dibromocholestanone” from ethyl acetate extract exemplified the highest binding energy of −9.3 Kcal/mol. The next highest remarkable inhibition was showed by “Pseduosarsasapogenin-5,20-Dien Methyl Ether” present in the methanol extract, with a binding energy of -9.3 Kcal/mol with the formation of 2 hydrogen bonds. Conclusion: From the result, it could be concluded that the P. bicolor leaves contain various bioactive compounds which are considered as a good anti-diabetic drug.

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.

scholarly journals Effect of Azadirachta indica Bio-Compounds against KpsM Protein of Acinetobacter baumannii

2021 ◽  
pp. 773-780
Author(s):  
V. Thiru Kumaran ◽  
A. S. Smiline Girija ◽  
P. P. Sankar Ganesh ◽  
J. Vijayashree Priyadharshini
Keyword(s):  
Binding Energy ◽  
Acinetobacter Baumannii ◽  
Azadirachta Indica ◽  
Nosocomial Infections ◽  
In Silico ◽  
Experimental Studies ◽  
Docking Simulation ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Selection Of

Background: Acinetobacter baumannii was considered as a low priority pathogen earlier, and is been now reported as a priority pathogen causing nosocomial infections. Selection of natural compounds to target the organism is the need of the hour. Aim: This study is aimed to target the KpsM protein of A. baumannii with the bio-compounds from Azadirachta indica using in-silico docking analysis. Materials and Methods: KpsM protein was retrieved and optimisation of protein was done. After that optimization and ligand preparation was carried out. It was continued by molinspiration assessment of the molecular properties of selected compounds. It was followed by docking simulation and docking visualisation. Results: Out of the 7 compounds of Azadirachta indica, dihydro diisoeugenol is the best compound to act on the KpsM protein of Acinetobacter baumannii and a binding energy of -6.83Kcal/Mol. Conclusion: The findings of the study reports isoeugenol with more binding energy than other compounds towards the selected protein KpsM of Acinetobacter baumannii. However it requires further experimental studies to understand the mechanism of its actions and safety.

Hetero-Tricyclic Lead Scaffold as Novel PDE5A Inhibitor for Antihypertensive Activity: In Silico Docking Studies

2019 ◽  
Vol 15 (4) ◽  
pp. 318-333
Author(s):  
Dipak P. Mali ◽  
Neela M. Bhatia
Keyword(s):  
In Silico ◽  
Docking Study ◽  
Docking Studies ◽  
Antihypertensive Activity ◽  
In Silico Docking ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Nitrogen Heteroatom ◽  
Inhibitory Potential ◽  
Vlife Mds

Objective:To screen the phytochemicals for phosphodiesterase 5A (PDE5A) inhibitory potential and identify lead scaffolds of antihypertensive phytochemicals using in silico docking studies.Methods:In this perspective, reported 269 antihypertensive phytochemicals were selected. Sildenafil, a PDE5A inhibitor was used as the standard. In silico docking study was carried out to screen and identify the inhibiting potential of the selected phytochemicals against PDE5A enzyme using vLife MDS 4.4 software.Results:Based on docking score, π-stacking, H-bond and ionic interactions, 237 out of 269 molecules were selected which have shown one or more interactions. Protein residue Gln817A was involved in H-boding whereas Val782A, Phe820A and Leu804A were involved in π-stacking interaction with ligand. The selected 237 phytochemicals were structurally diverse, therefore 82 out of 237 molecules with one or more tricycles were filtered out for further analysis. Amongst tricyclic molecules, 14 molecules containing nitrogen heteroatom were selected for lead scaffold identification which finally resulted in three different basic chemical backbones like pyridoindole, tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline as lead scaffolds.Conclusion:In silico docking studies revealed that nitrogen-containing tetrahydro-pyridonaphthyridine and dihydro-pyridoquinazoline tricyclic lead scaffolds have emerged as novel PDE5A inhibitors for antihypertensive activity. The identified lead scaffolds may provide antihypertensive lead molecules after its optimization.

scholarly journals In vitro toxicity and in silico docking analysis of two novel selective AH-receptor modulators

2018 ◽  
Vol 52 ◽  
pp. 178-188 ◽  
Author(s):  
Selma Mahiout ◽  
Sara Giani Tagliabue ◽  
Atefeh Nasri ◽  
Iyekhoetin Matthew Omoruyi ◽  
Lars Pettersson ◽  
...  
Keyword(s):  
In Silico ◽  
In Vitro Toxicity ◽  
Ah Receptor ◽  
Docking Analysis ◽  
In Silico Docking ◽  
Receptor Modulators

scholarly journals MOLECULAR DOCKING TERPINEN-4-OL SEBAGAI ANTIINFLAMASI PADA ATEROSKLEROSIS SECARA IN SILICO

Jurnal Kimia ◽  
2019 ◽  
pp. 221
Author(s):  
N. M. P. Susanti ◽  
N. P. L. Laksmiani ◽  
N. K. M. Noviyanti ◽  
K. M. Arianti ◽  
I K. Duantara
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Endothelial Dysfunction ◽  
Hydrogen Bonds ◽  
In Silico ◽  
Inflammatory Process ◽  
Mapk Pathway ◽  
Chronic Inflammatory Disease ◽  
Mitogen Activated Protein Kinase ◽  
Mitogen Activated Protein

Atherosclerosis is a chronic inflammatory disease that begins with endothelial dysfunction, it caused fat accumulation and plaque growth in the inner arteries walls. Endothelial dysfunction will activate the Mitogen Activated Protein Kinase (MAPK) pathway involving ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, as well as the Nuclear Factor Kappa B (NF-kB) pathway involving IKK proteins. Terpinen-4-ol is constituent found in the bangle rhizome. The purpose of this study were to determine the affinity and mechanisms of terpinen-4-ol against ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins as anti-inflammatory in atherosclerosis performed using molecular docking method. The study was conducted exploratively with several steps such as preparation and optimization of terpinen-4-ol structure, preparation of 3D ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins, validation method of molecular docking, and docking terpinen-4-ol in these proteins. The docking result are assessed from the binding energy and hydrogen bonds formed between terpinen-4-ol and proteins. The smaller value of binding energy terpinen-4-ol with target proteins showed the complex that form more stable. The result showed that terpinen-4-ol and has activity in inhibiting the inflammatory process because it is able to disturb ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins with respective bond energy values -5,12; -5,24; -5,08; -5,88; and -4,99 Kcal/mol. The molecular mechanism in inhibiting the activity of ERK1, ERK2, JNK1, JNK2, and p38MAPK proteins is through the formation of hydrogen bonds in these proteins. These results show that terpinen-4-ol have the potential to inhibit inflammatory process and the formation of atherosclerotic plaque can be obstructed. Keywords : atherosclerosis, terpinen-4-ol, molecular docking, in silico

scholarly journals Novel Binding Mechanisms of Fusion Broad Range Anti-Infective Protein Ricin A Chain Mutant-Pokeweed Antiviral Protein 1 (RTAM-PAP1) against SARS-CoV-2 Key Proteins in Silico

Toxins ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 602
Author(s):  
Yasser Hassan ◽  
Sherry Ogg ◽  
Hui Ge
Keyword(s):  
In Silico ◽  
Protein Structures ◽  
Ligand Docking ◽  
Pokeweed Antiviral Protein ◽  
Antiviral Protein ◽  
Ricin A Chain ◽  
In Silico Docking ◽  
A Chain ◽  
Binding Mechanisms ◽  
Ricin A

The deadly pandemic named COVID-19, caused by a new coronavirus (SARS-CoV-2), emerged in 2019 and is still spreading globally at a dangerous pace. As of today, there are no proven vaccines, therapies, or even strategies to fight off this virus. Here, we describe the in silico docking results of a novel broad range anti-infective fusion protein RTAM-PAP1 against the various key proteins of SARS-CoV-2 using the latest protein-ligand docking software. RTAM-PAP1 was compared against the SARS-CoV-2 B38 antibody, ricin A chain, a pokeweed antiviral protein from leaves, and the lectin griffithsin using the special CoDockPP COVID-19 version. These experiments revealed novel binding mechanisms of RTAM-PAP1 with a high affinity to numerous SARS-CoV-2 key proteins. RTAM-PAP1 was further characterized in a preliminary toxicity study in mice and was found to be a potential therapeutic candidate. These findings might lead to the discovery of novel SARS-CoV-2 targets and therapeutic protein structures with outstanding functions.

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